Biology subjects

Wang, B.

Publications and source records attributed to Wang, B..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Structural Basis for Iterative Methylation by a Cobalamin-dependent Radical S-Adenosylmethionine Enzyme in Cystobactamids Biosynthesis

Cystobactamids are non-ribosomal peptide natural products that function as DNA gyrase inhibitors, exhibiting significant antibacterial activity. They are isolated from Cystobacter sp. Cbv34 and contain various alkoxy groups on para-aminobenzoic acid moieties, which are believed to play a crucial role in antibacterial functions. The alkoxy groups are generated by iterative methylations on a methoxy group by the cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) enzyme CysS. CysS catalyzes up to three methylations to give ethoxy, isopropoxy, sec-butoxy, and tert-butoxy groups. For each methylation, CysS uses a ping-pong mechanism in which two molecules of SAM are consumed. One SAM is used to methylate cob(I)alamin, while another generates a 5'-deoxyadenosyl 5'-radical to initiate substrate methylation. However, little is known about how the enzyme promotes both Cbl methylation and iterative substrate methylation, which occur by polar SN2 and radical processes, respectively. Here, we report three X-ray crystal structures of a homolog of CysS from Corallococcus sp. CA054B. Two were determined in the presence of methoxy- and ethoxy-containing substrates, showing how CysS accommodates substrates and products during iterative methylation. The third structure, determined in the absence of a substrate, exhibits structural changes that reorient the SAMs conformation to allow for the methylation of cob(I)alamin.

biochemistry↗

bioRxiv2025

Identification of short peptides that correlate with cytoplasmic retention of human proteins

One group of human proteins found in the cytoplasm, but not in the nucleus is characterized by the presence of short (6-9aa), specific amino acid sequences thought to be involved in retaining proteins in the cytoplasm (cytoplasmic retention sequences). While strong evidence supports the ability of some peptides to act in this way, the number of such supported cases is small. We have taken the view that the situation would be improved by enhancing the methods available to identify cytoplasmic retention (CR) peptides. Here we describe an appropriate bioinformatic method to identify CR peptides using information about their location at the ends of cytoplasmic proteins. The method was then used to link seven different human cytoplasmic proteins with peptides suggested to have cytoplasmic retention activity. Further analysis was carried out with isoforms of the cytoplasmic proteins identified. Amino acid sequence information showed that while the proposed CR amino acid sequences can be the same or distinct in different protein isoforms, they are always located at the same site in the protein. For instance, while the proposed retention sequence of CCDC57 isoform X18 is MLARLVSNS, in isoform 7 it is SEPALNEL yet the two sequences are each located between amino acids 5 and 13 in the CCDC57 sequence. The results support the view that protein isoform is involved in determining the location of the CR sequence in a protein while the peptide sequence itself affects other variables such as the sub-region of the cytoplasm the protein needs to occupy. Overall, the study yielded identification of 15 candidate CR peptides in which 10 of the 15 have un-related amino acid sequences.

cell biology↗

bioRxiv2025

Tuning Mitotic Recombination with Patterned DNA Nicks for Precision Mosaic Analysis

CRISPR/Cas9-based mosaic analysis is a powerful tool for in vivo genetics but is limited by cytotoxicity and mutagenesis associated with DNA double-strand breaks (DSBs). Here, we establish Cas9-derived nickases as safer and more reliable alternatives for inducing mitotic recombination in Drosophila. We demonstrate that single-strand nicks are sufficient to generate mosaic clones and systematically dissect the parameters governing this process. We find that clone frequency can be controlled by the gRNA nicking pattern, with two distant nicks on the same DNA strand synergistically enhancing recombination by over nine-fold compared to a single nick. Based on these findings, we propose a mechanistic model for nick-induced crossover and provide a versatile toolkit for generating tissue-specific nickases. This work establishes nickase-based MAGIC as a superior method for high-fidelity clonal analysis, enabling more precise investigation of gene function in development and disease. SIGNIFICANCE STATEMENTThe CRISPR/Cas9-based mosaic technique, MAGIC, is a versatile tool for in vivo biological investigations. However, its reliance on DNA double-strand breaks (DSBs) can cause significant, unintended cell damage. Here we establish that Cas9-derived nickases, which create gentler single-strand nicks, are a superior alternative. We show that nickases safely induce genetic mosaics in Drosophila by avoiding this cellular toxicity. By systematically dissecting the process, we discovered principles of gRNA design that allow clone frequencies to be tuned for different experimental needs. This work provides a new mechanistic model for nick-induced genetic exchange, a high-fidelity "nickase-MAGIC" method, and a versatile toolkit for precision clonal analysis.

developmental biology↗

bioRxiv2025

DNACSE: Enhancing Genomic LLMs with Contrastive Learning for DNA Barcode Identification

DNA barcoding is a powerful tool for exploring biodiversity, and DNA language models have significantly facilitated its construction and identification. However, since DNA barcodes come from a specific region of mitochondrial DNA and there are structural differences between DNA barcodes and reference genomes used to train existing DNA language models, it is difficult to directly apply the existing DNA language models to the DNA barcoding task. To address this, this paper introduce DNACSE (DNA Contrastive Learning for Sequence Embeddings), an unsupervised noise contrastive learning framework designed to fine-tune the DNA language foundation model while enhancing the distribution of the embedding space. The results demonstrate that DNACSE outperforms direct usage of DNA language models in DNA barcoding-related tasks. Specifically, in fine-tuning and linear probe tasks, it achieves accuracy rates of 99.17% and 98.31%, respectively, surpassing the current state-of-the-art BarcodeBERT by 6.44% and 6.44%. In zero-shot clustering tasks, it raises the Adjusted Mutual Information (AMI) score to 92.25%, an improvement of 8.36%. In addition, zero-shot benchmarking and genomic benchmarking tests are evaluated, indicating that DNACSE enhances the performance of DNA language models in generalized genomic tasks. In summary, DNACSE has demonstrated excellent performance in DNA barcode species classification by making full use of multi-species information and DNA barcode information, providing a feasible way to further explore and protect biodiversity. The code repository is available at https://github.com/Kavicy/DNACSE.

bioinformatics↗

bioRxiv2025

Differentially acetylated chitosan oligosaccharides as plant defense elicitors against spider mites

The increasing challenges of pesticide resistance and environmental degradation in modern agriculture require sustainable pest management strategies. This study investigates the efficacy of a specific type of hetero-chitooligosaccharide called DACOS, as a plant defense inducer against the two-spotted spider mite, Tetranychus urticae Koch. DACOS is characterized with 85% deacetylation and an average molecular weight of 1 kDa. In planta bioassays revealed a dose-dependent suppression of mite performance on DACOS-treated leaves of kidney bean seedlings, with peak efficacy occurring at 80 ppm. This concentration reduced mite survival by 30% and fecundity by 59% after six days. In addition to the local effects, mite survival and fecundity were also reduced on untreated leaves of the same seedlings, confirming that the effect of DACOS on plant defense is systemic. Behavioral choice assays revealed that DACOS-treated leaves induced 73% mite repellency. No direct acaricidal effects were observed, which confirms the role of DACOS as a plant defense elicitor. Metabolic profiling revealed enriched pathways (e.g., monoterpenoid biosynthesis and -linolenic acid metabolism) that produce volatile organic compounds with repellent properties. These findings suggest that DACOS is an environmentally friendly biostimulant that can enhance plant defense, bypass pesticide resistance, and promote the sustainability of crop production.

physiology↗

bioRxiv2025

Distinct and compensatory roles of Stag1 and Stag2 in post-mitotic genome refolding

The three-dimensional architecture of the eukaryotic genome is largely shaped by the cohesin complex, which contains either Stag1 or Stag2 subunits. Although both subunits contribute to chromatin organization, their specific functions in de novo loop formation during post-mitotic genome refolding remain elusive. Here, we leverage the mitosis-to-G1 transition to dissect their individual roles. We found that Stag1 depletion has a negligible impact on post-mitotic genome restructuring or transcription reactivation. In contrast, Stag2 orchestrates chromatin remodeling in a manner that is both cell cycle stage-specific and chromatin context-dependent. During early-G1, Stag2 preferentially associates with euchromatin, where it drives the rapid formation of small chromatin loops. This facilitates prompt promoter-enhancer (P-E) contact formation and enables efficient transcription activation. As the nuclear concentration of Stag2 increases by late-G1, it progressively suppresses large loops, likely due to its shorter chromatin residence time and its potential to competitively displace the more extrusion-capable Stag1-associated cohesin. Mechanistically, Stag2-mediated loop extrusion is constrained by CTCF-bound barriers, rather than by genomic travel distance. Although Stag2 associates rapidly with euchromatin in early-G1, its recruitment to heterochromatin is delayed until late-G1. Simultaneous depletion of both Stag proteins results in a synergistic loss of virtually all structural loops and a more severe disruption of transcription than that caused by individual deletions. Together, these results establish Stag2 as the principal regulator of post-mitotic genome reorganization among Stag paralogs, mediating spatiotemporal control of chromatin architecture, while Stag1 provides compensatory support to ensure functional robustness.

molecular biology↗

bioRxiv2025

On-The-Fly Live-Cell Intrinsic Morphological Drug and Genetic Screens by Gigapixel-per-second Spinning Arrayed Disk Imaging

Next-generation drug discovery and functional genomics require rapid, unbiased single-cell profiling at scale--demands that exceed the limited speed, throughput, and labor-intensive labeling constraints of conventional high-content image-based screening. We introduce spinning arrayed disk (SpAD), a high-throughput, label-free imaging platform for live-cell imaging that integrates continuous circular scanning, ultrafast quantitative phase imaging (QPI), and a novel circular array of 96 culture chambers. SpAD achieves an order-of-magnitude reduction in imaging time compared to traditional fluorescence-based workflows, while remaining compatible with standard cell culture workflows. By extracting rich biophysical features using intrinsic morphological (InMorph) profiling and machine learning, SpAD enables sensitive, large-scale screening of drug responses and CRISPR gene knockouts without labeling. Critically, label-free biophysical readouts from SpAD reveal mechanism-linked changes in mass, refractive index, subcellular textures, and light scattering that fluorescent labels often obscure. SpAD thereby resolves subtle phenotypes and heterogeneous subpopulations with high reproducibility, providing a robust, scalable foundation for precision cellular morphological assays.

bioengineering↗

bioRxiv2025

Elevated activity of the mesolimbic dopamine system promotes feeding during pregnancy in mice

The pregnancy period is accompanied by increased feeding behavior to accommodate the elevated energy demands associated with fetal growth and development. However, the underlying neural circuitry and molecular mechanisms mediating increased feeding during pregnancy are largely unknown. Here, we utilize a combination of fiber photometry, chemogenetics, and mouse behavioral assays to characterize altered feeding behavior during pregnancy in mice. We uncover that pregnancy increases the activity of the mesolimbic dopamine system during both homeostatic and hedonic feeding behavior in mice. VTA dopamine neurons are ultimately required for promoting increased hedonic feeding during pregnancy as inhibition of these cells selectively reduces acute high fat diet intake in pregnant mice. Further, pregnant mice exhibit increased sensitivity to food deprivation, an effect which requires activity of the mesolimbic dopamine system. Together, these findings provide a circuit basis mediating altered hedonic feeding behavior and sensitivity to negative energy balance during pregnancy in mice. HighlightsO_LIVTA dopamine neurons show enhanced responsivity to palatable food during pregnancy C_LIO_LIVTA dopamine neurons show enhanced responsivity to negative energy balance during pregnancy C_LIO_LINucleus accumbens dopamine is increased during homeostatic and hedonic feeding in pregnant mice C_LIO_LIVTA dopamine neuron activity regulates hedonic eating and fast-induced refeeding in pregnant mice C_LI

neuroscience↗

bioRxiv2025

High-Power Dual-Channel Chamber for High-Frequency Magnetic Neuromodulation

ObjectiveSeveral novel methods, including magnetogenetics and magnetoelectric stimulation, use high frequency alternating magnetic fields to precisely manipulate neural activity. To quantify the behavioral effects of such interventions in a freely moving mouse, we developed a dual-channel magnetic chamber, specifically designed for rate-sensitive magnetothermal-genetic stimulation, and adaptable for other uses of alternating magnetic fields. ApproachThrough an optimized coil design, the system allows independent control of two spatially orthogonal uniform magnetic fields delivered at different frequencies within a 10 x 10 x 6 cm3 chamber suitable for mouse studies. The two channels have nominal frequencies of 50 and 550 kHz with peak magnetic field strengths of 88 and 12.5 mT, achieved with resonant coil drives having peak voltages of 1.6 and 1.8 kV and currents of 1.0 and 0.26 kA, respectively. Additionally, a liquid cooling system enables magnetic field generation for second-level durations, and an observation port and camera allow video capture of the animals behavior within the chamber. Main ResultsThe system generates high-amplitude magnetic fields across two widely separated frequency channels with negligible interference (< 1%). Relatively uniform magnetic field distribution ({+/-}10% across 94% of the chamber volume) is maintained throughout the chamber, and temperature increase of the inner side of the coil enclosure during the operation is limited to < 0.35 {degrees}C/s to ensure in vivo safety. Using cobalt-doped and undoped iron oxide nanoparticles, we demonstrate channel-specific heating rates of 3.5 {degrees}C/s and 1.5 {degrees}C/s, respectively, validating frequency-selectivity. Both channels can run continuously for 4 seconds stably. SignificanceWe present a novel magnetic stimulation platform that combines high-frequency, high-power capability with two independently-controlled channels generating different frequencies, along with a real-time behavioral observation system for freely moving animals. The system supports frequency-multiplexed stimulation strategies for precise modulation of neural activity, making it a versatile tool for advancing magnetogenetics, neural circuit interrogation, and noninvasive stimulation approaches in neuroscience and bioengineering.

bioengineering↗

bioRxiv2025

Deep Learning-Based Genetic Perturbation Models Do Outperform Uninformative Baselines on Well-Calibrated Metrics

Single cell genetic perturbation modeling involves predicting the effects of unobserved genetic manipulations, enabling scalable in silico screens for target discovery. Recent reports have claimed that deep learning-based perturbation models fail to outperform uninformative baselines, raising doubts about their utility. Here, we show that these conclusions largely stem from limitations of benchmarking metrics, not from the models themselves. We introduce a framework for evaluating bench-mark metric calibration using positive and negative controls, including a new positive control baseline (the interpolated duplicate) and a quantitative calibration measure (the dynamic range fraction). Across 14 perturbation datasets and 13 evaluation metrics, we find that conventional metrics such as mean squared error (MSE) and control-referenced delta correlation (Pearson({Delta}ctrl)) are often poorly calibrated, whereas weighted and rank-based alternatives exhibit consistent calibration. Under well-calibrated metrics, deep learning models outperform mean, control, and linear baselines, and in some cases even surpass the additive baseline in combination-prediction tasks. Calibrated evaluation thus explains prior reports of model underperformance, revealing that deep learning models do outperform uninformative baselines.

bioinformatics↗

bioRxiv2025

Elevated Temperatures Representing Heatwave Conditions Shift Active Nitrifying Communities and Their Viruses in Tidal Flats and Agricultural Soils

Global heatwave intensification associated with climate change will impact the nitrogen cycle, yet its effect on specific nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable isotope probing (SIP) coupled with metagenomics, we show that elevated temperatures associated with heatwave conditions restructure active nitrifying communities and their viruses in Yangtze River estuary tidal flats and adjacent agricultural soils. In tidal flats, high temperatures shifted active ammonia-oxidizing archaea and bacteria (AOA and AOB), and nitrite-oxidizing bacteria (NOB) from marine to terrestrial ecotypes. In contrast, heatwave conditions stimulated terrestrial ecotypes of AOA but suppressed AOB in agricultural soils. 13C-labeled nitrifier-infecting viruses also showed temperature-driven shifts in activity, lifestyle, and auxiliary metabolic genes in concert with hosts. Notably, AOA viruses carried the plastocyanin gene, potentially augmenting host metabolism. These findings demonstrate heatwaves drive complex shifts in nitrifier communities and their interactions with viruses, impacting global nutrient cycling under climate extremes.

microbiology↗

bioRxiv2025

Single-particle multi-parametric microscopy reveals structural, size, and payload heterogeneity in mRNA-loaded lipid nanoparticles

Deciphering the heterogeneity of mRNA-containing lipid nanoparticles (LNPs) is essential for understanding the relationship between their microscopic properties and therapeutic function. Here, by combining alternating laser excitation (ALEX) with Convex Lens-induced Confinement (CLiC) microscopy, we simultaneously measure size, multi-color fluorescence, mRNA payload, and Forster resonance energy transfer (FRET) of individual suspended LNPs containing labeled lipid and mRNA molecules. By varying formulation parameters, including ionizable lipids, formulation buffers, and molecular ratios, we investigated and correlated key microscopic properties for relevant vaccine formulations. While the per-particle lipid fluorescence was lower for empty versus mRNA-loaded particles for all formulations, the relative size of empty versus mRNA-loaded particles depended upon the formulation and intraparticle structure. When comparing CLiC-ALEX to cryogenic transmission electron microscopy measurements (Cryo-TEM), for the LNP formulations that display blebs, the fraction of bleb LNPs is in close agreement with the fraction of mRNA-containing LNPs. CLiC-ALEX also enabled quantification of the per-particle mRNA fluorescence and FRET signals, and thus the heterogeneity in the mRNA copy number and mRNA-LNP structural arrangements, where the results were compared with biophysical estimates based on the LNP formulations. These rigorous biophysical insights are critical to inform our understanding of structure-activity relationships and inform rational design of nanomedicines.

biophysics↗

bioRxiv2025

Single-Cell RNA and ATAC Sequencing Reveal Cellular Heterogeneity and Chromatin Accessibility Dynamics in Young Chinese Breast Cancer Patients across Pre- and Post-Neoadjuvant Therapy

Young breast cancer (YBC) patients (age [≤] 40) exhibit aggressive features and poor prognosis, while facing complex needs including breast-conserving surgery and fertility preservation. Neoadjuvant therapy (NAT) is important for tumor downstaging and breast-conserving surgery in YBC treatment, but the NAT response mechanisms in YBC patients remain unelucidated. Here, we analyzed pre- and post-NAT samples from Chinese YBC patients using scRNA-seq and scATAC-seq. We found that NAT reshaped cellular heterogeneity in the tumor microenvironment (TME), reducing epithelial and T cells while increasing endothelial cells and fibroblasts. Residual cancer cells showed enriched epithelial-mesenchymal transition (EMT) and stromal remodeling programs. NAT responders had fewer luminal-like cells and retained basal-like cells in an early hybrid EMT state, whereas non-responders maintained both populations with late hybrid EMT. We identified therapy-resistant genes and motifs (e.g., VTCN1, PROM1, MZB1, Fox family) and linked CXCL13 upregulation to poor NAT response and tumor-specific T-cell expansion. Cell-cell communication analysis revealed NAT reprograms the TME by suppressing VEGF and TNF signaling in basal cells, while residual luminal cells transmit EGFR and CD47-SIRPA signals.

cancer biology↗

bioRxiv2025

ARHGEF17 Deficiency Induces Endothelial Dysfunction and Intracranial Aneurysm Formation via RhoA/ROCK2/MLC Signaling Pathway

BACKGROUNDGenetic susceptibility is a major determinant in intracranial aneurysm (IA) formation and rupture, yet the underlying mechanisms linking genetic variation to vascular dysfunction remain largely unknown. We have identified mutations in ARHGEF17, a guanine nucleotide exchange factor that regulates RhoA activation and cytoskeletal organization, as potential risk variants for IA. Given ARHGEF17s regulatory role in endothelial barrier integrity and actin remodeling, we hypothesized that ARHGEF17 deficiency promotes IA pathogenesis through dysregulation of the RhoA/ROCK2/MLC signaling axis, leading to endothelial dysfunction and vascular wall instability. METHODSCRISPR-Cas9-mediated ARHGEF17 knockout (ARHGEF17-/-) mice and morpholino-based ARHGEF17-deficient zebrafish were established to assess the in vivo vascular effects of ARHGEF17 loss. An intracranial aneurysm model combining elastase injection and deoxycorticosterone acetate (DOCA)-induced hypertension was used to evaluate aneurysm incidence, rupture rate, and survival. Structural remodeling of the Circle of Willis (CoW) was assessed by Victoria Blue, EVG, and Picrosirius Red staining, as well as immunofluorescence for -SMA, OPN, CD31, and inflammatory markers. Complementary in vitro studies were performed in HUVECs using lentiviral ARHGEF17 silencing (three shRNAs of varying efficiency) to examine endothelial proliferation, migration, tube formation, and barrier function (TEER). Activation of RhoA/ROCK2/MLC signaling was quantified by G-LISA and Western blotting. The ROCK inhibitor Y-27632 (10 M) was applied to determine pathway dependence. RESULTSARHGEF17-/- mice exhibited a significantly higher incidence and rupture rate of intracranial aneurysms, accompanied by fragmentation of elastic fibers, loss of collagen organization, vascular smooth muscle cell dedifferentiation, and robust inflammatory activation in the CoW. Zebrafish lacking ARHGEF17 showed frequent intracranial hemorrhage and compromised vascular wall integrity, further confirming ARHGEF17s role in cerebrovascular stability. In ECs, ARHGEF17 knockdown impaired proliferation, migration, tube formation, and barrier integrity in a silencing-efficiency-dependent manner. Mechanistically, ARHGEF17 deficiency activated the RhoA/ROCK2/MLC pathway, leading to increased phosphorylation of MLC and MYPT1 and disorganization of F-actin and junctional proteins. Pharmacological inhibition with Y-27632 restored endothelial function, normalized cytoskeletal structure, and re-established junctional continuity, indicating a ROCK2-dependent mechanism. CONCLUSIONSOur findings establish ARHGEF17 as a critical regulator of cerebrovascular integrity and identify RhoA/ROCK2/MLC mediated cytoskeletal remodeling as the mechanistic link between ARHGEF17 deficiency and aneurysm pathogenesis. Loss of ARHGEF17 compromises endothelial barrier function, triggers vascular inflammation, and promotes aneurysm formation and rupture. Importantly, ROCK inhibition rescues endothelial dysfunction, highlighting the RhoA/ROCK2/MLC axis as a promising therapeutic target for ARHGEF17 mutation-associated intracranial aneurysms.

neuroscience↗

bioRxiv2025

Evaluation of antibiotic and peptide vaccine strategies for mirror bacterial infections

Recent advances in synthetic biology have raised concerns that the creation of bacteria composed completely of mirror-image biomolecules may be possible in the coming decades. Such "mirror bacteria" could pose an unprecedented biosecurity risk, as they are predicted to be highly virulent pathogens resulting from severe immune evasion. Pharmaceutical interventions, including antibiotics and vaccines, could likely provide some limited protection in the event of a mirror bacterial outbreak. Understanding the feasibility of specific pharmaceutical antimirror strategies may help inform the appropriate measures to confront the risks of mirror bacteria. Here, we experimentally evaluated the prospects of previously proposed antimirror antibiotic and vaccine strategies. First, we assessed the expected efficacy of existing antibiotics chloramphenicol, linezolid, tedizolid, and aztreonam against mirror bacteria by characterizing the antibacterial activities of their enantiomers against natural-chirality bacteria. We found that ent-chloramphenicol, ent-linezolid, ent-tedizolid, and ent-aztreonam exhibited minimal antibiotic activity, suggesting that their parent antibiotics would be ineffective against mirror bacterial infections. Second, to explore whether the enantiomers of existing antibiotics could be suitable as antimirror antibiotics, we evaluated the acute toxicities of ent-chloramphenicol, ent-linezolid, ent-tedizolid, and ent-aztreonam in mice, finding that these compounds have favorable acute toxicity profiles compatible with their continued development. Finally, we investigated D-peptide-based approaches to antimirror vaccines, finding that three bacterially-derived D-peptides induced robust D-peptide-specific antibody responses in mice when conjugated to a carrier protein and adjuvanted. Our results support previous suggestions that the enantiomers of existing antibiotics and D-peptide conjugate vaccines represent feasible pharmaceutical strategies against mirror bacterial infections. IMPORTANCETechnologies enabling the creation of mirror bacteria--bacteria constructed of molecules that are mirror images of those found in nature--may be on the horizon. If created, mirror bacteria would likely pose an unprecedented risk to life on earth given their evasion of natural immune responses. Although they would not protect against widespread environmental damage, antibiotics and vaccines could provide some limited protection to human populations in the event of a mirror bacterial outbreak. We experimentally assessed the prospects of three antimirror strategies: repurposing existing antibiotics, developing mirror versions of existing antibiotics, and developing vaccines based on mirror-image peptides. We broadly conclude that many existing antibiotics are unlikely to be effective against mirror bacteria, while the mirror images of existing antibiotics and mirror-image peptides could serve as foundations for antimirror antibiotics and vaccines, respectively. Our findings may help inform discussions on the proper role of medical countermeasures to defend against mirror bacteria.

microbiology↗

bioRxiv2025

Pharmacological Induction of Irreversible Senescence in Drug-Tolerant Persister Cells Prevents Tumor Relapse

Despite substantial advances in targeted therapies, most patients with advanced cancers ultimately relapse. This relapse is frequently seeded by drug-tolerant persister cells (DTPs), which persist as minimal residual disease (MRD) by adopting a reversible quiescent state and later reacquire proliferative capacity under ongoing treatment. To address this, we sought to convert quiescent DTPs into an irreversible, non-proliferative state by pharmacologically inducing senescence. Through large-scale chemical screening and combination optimization, we identified SAHA plus tilorone dihydrochloride (SIC) as a regimen that robustly induces senescence in melanoma DTPs and abolishes their proliferative potential in vitro. Mechanistically, SAHA relieves HDAC1-mediated repression of HMGA2, a key senescence driver, while tilorone synergistically inhibits autophagy to promote a fully senescent state. In a melanoma xenograft mouse model receiving MAPK-targeted therapy, SIC treatment significantly suppressed MRD progression. Importantly, SIC also induced robust senescence across diverse DTP models irrespective of tumor origin, mutational background, or prior treatment. Collectively, these findings provide proof-of-concept that converting DTPs from reversible quiescence to permanent senescence represents an effective strategy to prevent relapse under targeted therapy and position SIC as a broadly applicable pharmacological approach for durable control of residual disease in advanced cancers.

cancer biology↗

bioRxiv2025

A Na+-selective High-salt Taste Receptor Mediates State-Dependent Sodium Aversion

Sodium is an essential ion, but harmful in excess. Animals must suppress sodium aversion during deficiency, yet a cation-nonselective override would expose them to other harmful salts. Whether and how the sensory periphery regulates high-salt taste to achieve Na+-specific tuning remains unknown. Here we identify a Na+-selective, state-tunable high-salt detection mechanism in Drosophila. IR11a and IR25a function in bitter gustatory receptor neurons (GRNs) and are required for aversion specifically to high Na+. Loss of IR11a abolishes responses to Na+ and Li+ while sparing detection of K+, Ca2+, and bitter compounds. Heterologous expression confirms that IR11a and IR25a together confer Na+ responsiveness. During sodium deprivation, Na+ sensitivity in IR11a-expressing neurons is decreased and restored upon satiety, allowing flies to attenuate Na+ aversion specifically. The IR7c-dependent nonselective mechanism remains insensitive to sodium deprivation, thereby preserving aversion to other noxious cations even during sodium deficiency. The IR11a-mediated response is amiloride-sensitive, a functional signature reminiscent of mammalian ENaC despite the absence of sequence homology. This work reveals that peripheral high-salt taste combines a fixed, cation-nonselective defense with a sodium-selective, physiologically tunable mechanisms, offering a candidate logic for aversive high-salt taste in vertebrates, where the molecular basis remains poorly defined.

neuroscience↗

bioRxiv2025

Core Clock Protein Subcellular Dynamics Coordinate Local and Global Circadian Control in Syncytia.

Circadian rhythms are pervasive among eukaryotes, and the underlying clocks share a common regulatory architecture - a negative feedback loop. A wealth of genetic and biochemical data underpin current perceptions of circadian oscillators but aspects of their cell biology remain cryptic, especially in syncytial systems. We employed novel microfluidic systems and a blind mutant that retains circadian function to simultaneously track multiple clock components in vivo across circadian cycles, revealing remarkable subcellular and subnuclear dynamics of clock proteins and providing insights into spatiotemporal regulation in a multinucleated system. Despite heterogeneity of clock gene (frq) expression, we find robust cycles in FRQ nuclear localization among all nuclei and document free diffusion of multiple clock components among nuclei. Within nuclei, clock components form distinct, small, highly dynamic nuclear bodies that persist throughout the cycle, occasionally co-localizing for circadian regulatory functions. This rich context of in vivo spatiotemporal information illustrates how separate nuclear clocks ensure synchronous regulation of cellular activities across a macroscopic syncytium.

cell biology↗