Biology subjects

Yan, J.

Publications and source records attributed to Yan, J..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

A Multi-lensed Comparative Analysis of Select Secondary Metabolites Produced by Kale, Brassica oleracea, in Simulated Microgravity Versus Gravity Conditions

Extended journeys through space are a goal of NASA. Yet, astronauts will face elevated health risks from microgravity and radiation as journeys continue for longer time periods. Approaches to combatting these health risks consist of growing fresh super foods in space for astronaut consumption while in flight. However, while a great deal is known about the effects of microgravity of humans, little is known about its effects on the nutrient profiles of plants. Endeavors towards understanding more about these effects are currently funded by NASA grants. Kale, a metabolite and specifically a flavonoid-rich crop, stands as a promising candidate for growth on space flights. We observed the effects of simulated microgravity broadly on the F1 cultivar, Starbor Kale metabolomics, and further focused on flavonoid content, using a 2-D clinostat. Extracts of kale were analyzed by proton nuclear magnetic resonance (1H NMR), and high-performance thin layer chromatography (HPTLC). 1H NMR spectra of clinostat-grown kale showed that samples from simulated microgravity conditions had an increased number of peaks in the aromatic region (6.5 to 8.5 ppm) when compared with gravity grown kale. HPTLC confirmed greater banding in medium- and high-polarity solvent systems, while low-polarity extracts showed no differences. Overall, we noted that the microgravity grown kale had greater amounts of bands present. These results signal that microgravity stressors may be connected to the increased secondary metabolite production in kale. Our findings underscore kale to be a prospective crop to be grown in space flight to combat effects of microgravity.

plant biology↗

bioRxiv2025

Dual-mode intramolecular agonist-dependent mechanoactivation of the adhesion GPCR ADGRG1/GPR56

Mechanical stimuli instruct cardinal cellular decisions pertaining to cell fate, proliferation, morphology, and movement1,2. How adhesion G protein-coupled receptors (aGPCRs), a large family of mechanosensors with more than 30 members in humans3-5, transduce mechanical cues into metabotropic commands has been a matter of debate due to the lack of suitable approaches to analyze receptor activation during mechanotransduction in live cells6. A central question is whether aGPCR activation strictly requires mechanical dissociation of the autoproteolyzed N- and C-terminal fragment (NTF and CTF) complex to expose the tethered intramolecular agonist (TIA; 'Stachel'). Here, we investigated human ADGRG1/GPR56 (G1), an aGPCR with roles in brain development7, skeletal muscle8, and platelet function9, to study the events during aGPCR mechanotransduction by monitoring receptor dissociation and G protein recruitment in real time during cell migration and substrate deformation. Magnetic-tweezer measurements at a physiologically relevant loading rate showed that isolated G1 GAIN domains can partially unfold and refold at forces below those required for NTF-CTF dissociation. In cells, G1 dissociation occurred at retracting fibers during cell migration10 over an adhesive substrate through its native extracellular matrix ligand, tissue transglutaminase 2 (TG2), and was enhanced by cell stretching. Simultaneous live recording of G protein recruitment and pharmacological assays during mechanical stimulation of G1 reveal a dual-mode activation mechanism: mechanical force elicits robust metabotropic signaling without requiring NTF dissociation and generates an intracellular response commensurate with the fully dissociated receptor. Both signaling modes depend on an intact Stachel element11,12 of the receptor under our experimental conditions. Our findings determine mechanotransduction principles governing aGPCR activation at the cell-ECM interface. We reveal that G1 does not function as a simple binary switch, but rather as a highly sophisticated mechanosensor that dynamically encodes localized extracellular tension into distinct, highly scalable metabotropic outputs.

cell biology↗

bioRxiv2025

Modification of RNAs in natural rG4 (MoRNiNG), A Database of RNA Modification Sites Associated with the Dynamics of RNA Secondary Structures

RNA structures are essential building blocks of functional RNA molecules. Profiling secondary structures in vivo and in real-time remains challenging because RNAs exhibit dynamic structures and complex conformations. Besides the stem-loop canonical secondary structure, the non-canonical structure RNA G-quadruplex (rG4) is of great interest for its potential as a drug target. Early studies have demonstrated that RNAs can form distinct secondary structures. However, it is not well understood how distinct RNA structures, formed from the same RNA sequences, function within the transcriptome. The factors driving and regulating structure transitions remain poorly investigated. Inspired by a segment in the HOXB9 mRNA capable of forming multiple structures, we found that many RNA segments across the transcriptome exhibit multi-faceted structure-forming potential. For the HOXB9 case, we demonstrated that RNA modification influences RNA structure and binding with RNA binding proteins. Therefore, we collected RNA modification sites naturally occurring in the putative G-quadruplex-forming sequences (PQSs) of transcripts and developed MoRNiNG, a freely accessible database at https://www.cityu.edu.hk/bms/morning. The database is designed and organized by reliability tiers determined by the resolution of RNA modification sites and capable of including various large datasets. We experimentally validated the influence of m6A, m5C, and A-to-I editing on rG4-forming sequences and provided evidence to support the modification switch concept. The diversity and transition of secondary structures from the same RNA segment offers valuable insights into the regulation of RNA structure dynamics.

systems biology↗

bioRxiv2025

Resolving the estrogen paradox in hereditary retinal degeneration: Esr1 activation suppresses Tnf-α signaling as a photoreceptor self-protection mechanism

Retinitis pigmentosa (RP) is an inherited retinal degenerative disorder characterized by progressive photoreceptor loss and irreversible blindness. Increasing evidence implicates neuroinflammation as a contributor to photoreceptor degeneration extending beyond the initial genetic insult. Although estrogen has been reported to exert anti-inflammatory effects in the central nervous system, its role in RP remains controversial, with some studies suggesting a paradoxical exacerbation of retinal pathology. To address this discrepancy, we identify estrogen receptor alpha (Esr1) as a central immunoregulatory hub in RP. Transcriptomic analyses of rd1 and rd10 revealed upregulation of estrogen-responsive and inflammatory pathways, with Esr1 expression markedly elevated during degeneration. TUNEL assays demonstrated that systemic estradiol (E2) exerted divergent effects, protective in rd1 yet deleterious in rd10, whereas selective pharmacological activation of Esr1 with propyl pyrazole triol (PPT) consistently reduced photoreceptor death, preserved dark-adapted ERG responses, and downregulated inflammatory mediators including Tnf-, Cx3cl1/Cx3cr1, Cd68, and Iba1. Mechanistically, Esr1 activation repressed microglial Tnf transcription and disrupted a self-sustaining Cx3cl1/Cx3cr1-Tnf- signaling loop driving microglial recruitment, activation and neurotoxicity in the outer nuclear layer (ONL). Targeted interventions confirmed tumor necrosis factor receptor 1 (Tnfr1) as the principal mediator of Tnf-induced photoreceptor death: selective inhibition with R7050 conferred superior protection compared with broad-spectrum Tnf- inhibitors (etanercept, infliximab). Cx3cr1 blockade likewise suppressed microglial activation and improved visual outcomes. Collectively, our findings establish Esr1 activation as not merely an external intervention but the amplification of an intrinsic self-protective program, positioning Esr1, Tnfr1, and Cx3cr1 as actionable therapeutic targets to suppress neuroinflammation and preserve vision in RP and related retinal disorders.

neuroscience↗

bioRxiv2025

Cross-species optimization of nuclei isolation in plants

Single-cell technologies are transforming plant biology, yet broadly transferable nuclei isolation remains a key bottleneck for snRNA-seq. We developed a reproducible, Percoll-based workflow that is applicable to multiple maize tissues and eight additional plant species. In maize, nuclei from root, stem, leaf, and embryo consistently concentrated at the 80% Percoll interface and exhibited high integrity, with typical recoveries > 50,000 nuclei per sample. For other species, gradient compositions were tuned according to genome size to achieve efficient enrichment and clean suspensions, and yields ranged from 20,000 to 50,000 nuclei per sample. Downstream validation showed that nuclei from special interest maize and Tripsacum generated high-quality 10x Genomics snRNA-seq libraries, as supported by cDNA quality profiles. These results demonstrate the versatility and robustness of the method across species and tissues.

plant biology↗

bioRxiv2025

Fast Multi-objective RNA Optimization with Autoregressive Reinforcement Learning

Codon optimization is essential in mRNA vaccine development, while existing tools face limitations in the computational efficiency, sequence diversity and universality. To address these challenges, we develop RNAJog (RNA Joint Optimization with autoregressive Generative model), a framework integrating autoregressive generation with reinforcement learning to optimize codon sequences for minimum free energy (MFE), codon adaptation index (CAI) and GC content, even enabling sequence design without requiring annotated training data. Evaluations in both in silico and wet-lab experiments have confirmed RNAJogs effectiveness and efficiency, with two orders of magnitude faster than traditional algorithm (LinearDesign) for long RNA sequence and about a 10-fold increase in antibody titer compared to the wild-type mRNA for Influenza virus hemagglutinin (HA) mRNA vaccine design in mouse. RNAJog also supports biological constraints for sequence optimization. Using this feature, we minimized m6A modification motifs in Bmp2 coding sequence for enhancing the translational efficiency and RNA stability, which are validated in cell-based experiments.

bioinformatics↗

bioRxiv2025

Vibrio cholerae adhesin-derived peptide mediates strong pull-off forces in aqueous high ionic strength environments

In this letter, the pull-off forces of adsorbed films of four Bap1-inspired peptides in various solvents were investigated on negatively charged mica substrates using the surface forces apparatus (SFA), complemented with dynamic light scattering (DLS) for characterizing the aggregation behavior of peptides in solution. Bap1-inspired peptides consisted of the 57 amino acid wild-type sequence (WT); a scrambled version of the WT used to investigate the impact of the primary amino acid sequence in pull-off forces (Scr); a ten amino acid sequence rich in hydrophobic content (CP) of the WT sequence, and an eight amino acid sequence (Sh1) that corresponds to the pseudo-repeating sequence in the 57 AA. SFA results showed remarkable pull-off forces for CP, particularly in the presence of salts: measured pull-off forces were 26.0 {+/-} 7.0 mN/m for no dwell-time and up to 42.0 {+/-} 8.8 mN/m when surfaces were left in contact for 30 minutes. DLS observations indicate that salts favor large peptide aggregation for all constructs (Hz > 1 {micro}m), as compared to milliQ (Hz {approx} 100-500 nm) water and DMSO (Hz {approx} 100 nm), resulting in heterogeneous peptide film thicknesses. This letter concludes with a comparison to the pull-off forces of mussel foot protein-inspired peptides reported in the literature.

biophysics↗

bioRxiv2025

A Transient Immunostimulatory Niche Synergizes Adoptive and Endogenous Immunity for Enhanced Tumor Control

Adoptive Cell Therapy (ACT) has achieved curative responses in hematological malignancies, yet its translation to solid tumors remains limited by manufacturing bottlenecks, systemic toxicities, and poor T-cell infiltration and persistence within the immunosuppressive tumor microenvironment (TME). Here, we report the development and mechanism of ACTIVATE (Adoptive Cell Therapy and Immunostimulatory Vehicle for Anti-Tumor Efficacy), which leverages an injectable hydrogel depot technology that forms a transient inflammatory niche for localized co-delivery of adoptive T cells and native cytokines. By tuning cytokine identity, ACTIVATE enables precise modulation of T-cell expansion, effector function, and interaction with endogenous immune networks. We found that enhancing T-cell proliferation alone is insufficient to drive robust tumor control; instead, coordinated engagement of both adoptive and endogenous immune responses is critical for durable anti-tumor efficacy. In vivo, this orchestration via ACTIVATE led to enhanced infiltration and cytotoxicity of both adoptive and host-derived immune effectors, while driving robust recruitment and activation of T cells, B cells, dendritic cells, and macrophages in the tumor-draining lymph nodes. This local immune activation can further reshape the TME, promoting antigen presentation and suppressing immunoregulatory populations, thus enhancing anti-tumor efficacy in murine melanoma and lymphoma models. These findings establish ACTIVATE as a modular platform for orchestrating coordinated immune responses to improve ACT outcomes in solid tumors.

immunology↗

bioRxiv2025

Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation

Precise regulation of transcription factor (TF) expression is critical for maintaining cell identity, but studies on how graded expression levels affect cellular phenotypes are limited. To address this gap, we employed human embryonic stem cells (hESCs) as a dynamic model to study gene dosage effects and systematically titrated key TFs NANOG and OCT4 expression using CRISPR interference (CRISPRi). We then profiled transcriptomic changes in hESCs under self-renewal and differentiation conditions using single-cell RNA-seq (scRNA-seq). Quantitative modeling of these Perturb-seq datasets uncovers distinct response patterns for different types of genes, including a striking non-monotonic response of lineage-specific genes during differentiation, indicating that mild perturbations of hESC TFs promote differentiation while strong perturbations compromise it. These discoveries suggest that fine-tuning the dosage of stem cell TFs can enhance differentiation efficiency and underscore the importance of characterizing TF function across a gradient of expression levels.

developmental biology↗

bioRxiv2025

Regulatory Plasticity and Metabolic Trade-offs Drive Adaptive Evolution of Alternative Flagellar Configurations in Pseudomonas aeruginosa

Evolutionary constraints governing flagellar number in bacterial pathogens remain poorly understood. While related Pseudomonas species are hyperflagellated, P. aeruginosa maintains strict monoflagellation through the FleQ-FleN regulatory circuit. Here, we demonstrate that FleN dosage is essential for maintaining monoflagellation and bacterial fitness. Wild-type P. aeruginosa consistently displayed unipolar monoflagellation, while {Delta}fleN mutants developed over two-to-five flagella per cell in uni- or bipolar arrangements. Hyperflagellated {Delta}fleN cells exhibited severe fitness defects including reduced growth rates, attenuated virulence in nematode infection models, and competitive disadvantages in co-culture experiments. Remarkably, {Delta}fleN cells rapidly evolved suppressor mutations in fleQ that partially restored growth and motility without always restoring monoflagellation. Five independent suppressor alleles mapped to critical FleQ functional domains (four in the AAA+ ATPase domain, one in the DNA-binding domain), suggesting reduced protein activity that rebalances the disrupted regulatory circuit. Single-cell motility analysis revealed that suppressor strains exhibit heterogeneous swimming dynamics, with subpopulations achieving wild-type speeds despite carrying multiple flagella. Proteomic analysis demonstrated that hyperflagellation triggers extensive cellular reprogramming beyond flagellar components, affecting metabolic pathways, stress responses, and signaling networks. While hyperflagellated cells suffered complete loss of pathogenicity in animal infection models, environmental selection under viscous conditions could drive wild-type cells to evolve enhanced motility through specific fleN mutations. These findings suggest that bacterial flagellar regulatory circuits function as evolutionary capacitors, normally constraining phenotypic variation but enabling rapid adaptation to alternative motility configurations when environmental pressures exceed the performance limits of standard monotrichous flagellation. SIGNIFICANCE STATEMENTBacterial flagella are extracellular appendages that rotate to propel the cell and enable swimming motility. While some bacteria have multiple flagella, many pathogenic species like Pseudomonas aeruginosa have just one. Surprisingly, mutants of P. aeruginosa with multiple flagella performed worse, i.e., they grew more slowly, were less infectious in laboratory animals, and were outcompeted by wild-type bacteria. Even when some mutant bacteria evolved compensatory changes, they still struggled compared to single-flagellum bacteria. This reveals an important evolutionary trade-off: while multiple flagella might seem advantageous for movement, having just one flagellum allows bacteria to grow faster and cause more severe infections. This plasticity likely explains why P. aeruginosa is so successful both in the environment and as a human pathogen.

microbiology↗

bioRxiv2025

Conformations and sequence determinants in the lipid binding of an adhesive peptide derived from Vibrio cholerae biofilm

Surface adhesion is critical to the survival of pathogenic bacteria both in natural niches and during infections, often via forming matrix-embedded communities called biofilms. We previously identified a 57-amino acid peptide (Bap1-57aa) as a key contributor to biofilm adhesion of the pandemic pathogen Vibrio cholerae to various surfaces including lipid membranes. Here, we combine biophysical, computational, and genetic approaches to elucidate the molecular mechanism. A central aromatic-rich motif anchors the peptide to lipid bilayers while peripheral pseudo repeats enhance binding through avidity. Surprisingly, the core motif undergoes a lipid-induced conformational transition into a {beta}-hairpin, enabling robust membrane insertion. Moreover, the biofilm-derived peptide, conserved in several other Vibrio species, can adhere to model host surfaces and is sensitive to membrane curvature. Our results provide molecular insight into biofilm adhesion and may lead to new strategies for targeted biofilm removal and the design of bioinspired underwater adhesives. TeaserA short peptide from Vibrio cholerae binds lipids using a unique {beta}-hairpin motif and contributes to host colonization.

microbiology↗

bioRxiv2025

Integrated Systems Vaccinology Reveals Distinct Metabolic Responses to SARS-CoV-2 Infection and DNA-Based Vaccines in Ferrets

Understanding systemic effects of vaccination and infection is central to defining correlates of protection against SARS-CoV-2. We used untargeted serum metabolomics to profile the immunometabolic landscape of ferrets after SARS-CoV-2 infection and DNA-/protein-based vaccination. Ferrets were vaccinated with either a multigenic DNA vaccine encoding SARS-CoV-2 RBD, M, and N (OC2), an N-only DNA vaccine (OC12), a recombinant spike protein with QS-21 adjuvant (S+QS21), or a hepatitis B/D control construct (Hep-B/D), and subsequently challenged with SARS-CoV-2. Serum was analyzed longitudinally at baseline, post-vaccination, and post-challenge. SARS-CoV-2 infection induced broad metabolic reprogramming, involving TCA cycle, glutathione metabolism, and nucleotide turnover, reflecting inflammation and cellular activation. OC2 vaccination induced strong metabolic shifts in amino acid and mitochondrial pathways despite low pre-challenge anti-S antibodies. Post-challenge, these shifts extended to redox and nucleotide pathways, correlating with robust anti-S and very strong anti-N antibody responses and complete viral clearance in BAL, but with marked airway pathology, consistent with T cell-mediated clearance of infected cells. S+QS21 and OC12 induced distinct, immunogen-specific signatures with partial protection, while Hep-B/D showed minimal systemic engagement. Metabolite-antibody correlations revealed vaccine-specific associations, highlighting lipid and amino acid pathways as potential immunogenicity biomarkers. Overlap and heatmap analyses showed that metabolic trajectories reflect both the magnitude and quality of immune training. These findings underscore the value of systems vaccinology in resolving mechanistic differences in vaccine responses and support metabolic profiling as a tool for evaluating immune efficacy in preclinical vaccine studies.

immunology↗

bioRxiv2025

SMCHD1 compacts DNA directly in an ATP-regulated manner

Structural maintenance of chromosome (SMC) complexes play crucial roles in genome organization by DNA loop extrusion. SMCHD1 is a non-canonical SMC protein important for X-inactivation, imprinting and the silencing of specific autosomal genes. While it is known to be a repressor, little is known about its structure or mechanism of action. Here, we show that the SMCHD1 homodimer is flexible and dynamic in solution. This flexibility is conferred by its yet uncharacterized linker domain, which can alter its length by dynamically switching between compact and extended conformations. Interestingly, we observed that SMCHD1 can directly bridge and compact DNA, independently of other proteins, forming large protein-DNA clusters. SMCHD1 contains a GHKL ATPase domain and SMC hinge domain, however each domain alone is insufficient for DNA compaction. DNA compaction rate decreases when the linker domain is removed. The coiled-coil domain does not affect compaction rate but facilitates interaction with a partner protein LRIF1. Surprisingly, DNA compaction by SMCHD1 does not require ATP and paradoxically, compaction rate is reduced with the addition of ATP. Similarly, SMCHD1 forms clusters with reconstituted nucleosome arrays in the absence of ATP, and the addition of ATP results in a reduction in cluster sizes. Our data provides biophysical and mechanistic insights into the role of SMCHD1 in gene silencing and genome organization.

molecular biology↗

bioRxiv2025

Long-acting hydrogel-based depot formulations of tirzepatide and semaglutide for the management of type 2 diabetes and weight

Several incretin hormone therapies have been clinically approved and have revolutionized the treatment of diabetes and obesity. Promising therapeutics include semaglutide (Ozempic(R) and Wegovy(R)), an agonist for glucagon-like peptide-1 (GLP-1) receptor, and tirzepatide (Mounjaro(R)), a dual agonist for GLP-1 and glucose-dependent insulinotropic polypeptide (GIP) receptors. These molecules help to regulate blood glucose levels, enhance insulin secretion and sensitivity, and reduce appetite. Currently, these treatments require weekly injections, which can be challenging for patients to adhere to. We recently reported the development of an injectable hydrogel depot technology enabling months-long release of semaglutide (Sema). Here, we further develop this technology for improved prolonged release of both Sema and tirzepatide (TZP). In a rat model of diabetes, we show a single administration of hydrogel-based formulations of either Sema or TZP maintained relevant drug levels for over 6 weeks. In these studies, single administrations of long-acting hydrogel-based therapies of Sema or TZP were similarly effective at regulating blood glucose and weight compared to daily injections of either Sema or TZP in standard aqueous vehicles. This hydrogel depot technology is easy to manufacture, injectable, and exhibits excellent biocompatibility, enabling months-long-acting treatments with the potential to improve management of diabetes and weight.

bioengineering↗

bioRxiv2025

Reversible Sandwich-Based Particle Nanoswitch for Continuous Protein Monitoring at Picomolar Concentrations with Automated Calibration

Continuous monitoring of specific proteins is essential for understanding the dynamics of biological systems and for enabling real-time measurement-and-control strategies in bioprocesses. Ideally, sensors for continuous monitoring should be intrinsically reversible and able to perform accurate measurements over long time spans. Here, we present a particle nanoswitch sensor containing two different antibody fragments that bind reversibly to a protein of interest and thus form transient sandwich complexes. The antibody fragments are incorporated into the sensor using site-specific conjugation strategies to achieve optimal antibody orientation. Short-lived sandwich complexes are detected with single-molecule resolution, by tracking the motion of tethered particles. The sensing concept is demonstrated for lactoferrin, an iron-binding and immune-modulating protein. We show continuous measurements of picomolar concentrations with a response time of [~]10 min over periods of 12-15 h. Automated calibration strategies are described that result in a mean absolute relative difference below 10% compared to reference measurements. These results demonstrate how continuous fast protein sensing at picomolar concentrations can be achieved using reversible sandwich-based particle nanoswitches, enabling long-term monitoring of dynamic bioprocesses.

bioengineering↗

bioRxiv2025

Neurodevelopmental Impact of Bipolar Disorder Genetic Risk on Cortical Thickness and Network Topology in Adolescents

Bipolar disorder (BD) is a highly heritable psychiatric condition characterized by recurrent mood episodes that commonly manifest during adolescence. Although polygenic risk scores (PRS) effectively quantify genetic susceptibility to BD, the neurobiological correlates of this genetic risk during adolescent brain development remain unclear. Using normative modeling and longitudinal neuroimaging data from the Adolescent Brain Cognitive Development (ABCD) cohort (N = 4519), we examined cortical thickness (CT) deviations and structural covariance network (SCN) alterations in adolescents stratified into high and low BD genetic risk groups based on PRS. Adolescents with high PRS for bipolar disorder exhibited greater cortical thickening in the inferior frontal gyrus and primary visual cortex, whereas those with low PRS demonstrated greater thickening in the posterior cingulate cortex and middle precentral gyrus. These patterns suggest PRS-related variations in cortical maturation, potentially reflecting distinct neurodevelopmental trajectories associated with genetic susceptibility to bipolar disorder. Furthermore, high PRS individuals displayed altered SCN topology, characterized by decreased local clustering and enhanced global network efficiency. Longitudinal data show that these abnormal regions exhibit atypical developmental trajectories, accompanied by a global reorganization of network topology. Additionally, high genetic risk was associated with lifestyle factors, especially correlated with increased positive expectancies toward substance use. Eventually, we found three potential BD risk genes during adolescence, including PLEKHA2, ZSCAN31 and ANK3, encoding the function of the postsynaptic membrane and synaptic membrane. These findings elucidate early neurodevelopmental deviations linked to genetic risk for BD, highlighting potential biomarkers for early identification and targeted interventions.

neuroscience↗

bioRxiv2025

Single-cell imaging reveals spontaneous phenotypic sorting and bet-hedging in developing biofilms

How phenotypic heterogeneity shapes biofilm architecture and development remains poorly understood. Motivated by this, we developed imaging tools to track intracellular levels of c-di-GMP, a key second messenger that controls the motile-to-sessile transition, in developing Vibrio cholerae biofilms at single-cell resolution. We show that c-di-GMP levels spontaneously bifurcate into a bimodal distribution that forms a spatially sorted pattern: High-c-di-GMP cells dominate the biofilm core while low-c-di-GMP cells localize to the periphery. Combining single-lineage tracing, mutant analysis, and agent-based modeling, we reveal that this pattern arises from differential viscosity and surface friction mediated by matrix-dependent interactions between cells and their microenvironments. We demonstrate that this heterogeneity and phenotypic sorting enable continuous emergence and shedding of planktonic cells, enhancing fitness in fluctuating environments. Our findings uncover a differential drag mechanism for pattern formation in multicellular systems, and expand the classical picture of biofilm lifecycle by highlighting the functional significance of phenotypic heterogeneity.

biophysics↗

bioRxiv2025

The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for desiccation tolerance. Here, we present a chromosome-level, haplotype-resolved reference genome for M. flabellifolia alongside transcriptomic profiling across a natural dehydration-rehydration cycle. The 1.28 Gb genome exhibits unusually consistent chromatin architecture with putative holocentric chromosome organization across highly divergent haplotypes. We identified an XY sexual system with a small sex-determining region on chromosome 8. Transcriptomic changes during dehydration varied with the severity of water loss and pointed to early suppression of growth, progressive activation of protective mechanisms, and reversible changes in transcript abundance upon rehydration. Co-expression networks and targeted gene family analyses revealed dynamic regulation of LEA and ELIP genes, with evidence of transcriptome "priming" in hydrated plants, with transcript abundance shifting toward highly disordered proteins during desiccation. Enrichment of ABA and light-responsive cis-regulatory elements in key genes support the existence of conserved stress response pathways. M. flabellifolias rich profile of phenolics and antioxidant genes highlight the overlap between desiccation tolerance and medicinal potential. Together, this study provides foundational resources for understanding the genomic architecture and reproductive biology of M. flabellifolia while offering new insights into the mechanisms of desiccation tolerance.

plant biology↗