SEARCH · bioRxiv Science

Results for “Preprint”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

500 records · Page 22Linked to original sources

bioRxiv2026

A Computational Re-evaluation of Spatial Trials for Zoonotic Tuberculosis Control: Model Misspecification, Diagnostic Miss-classification, and the Illusion of Wildlife Culling Efficacy

1. Wildlife reservoir management frequently relies on the Randomised Badger Culling Trial's (RBCT) trade-off hypothesis, which posits that reductions in cattle herd infections are offset by a perturbation effect driven by disrupted host dispersal. This paper evaluates the computational and epidemiological robustness of this historical trial, which serves as the foundational empirical experiment guiding zoonotic tuberculosis (Mycobacterium bovis) control policies. 2. Using generalized linear mixed models with a generalized Poisson error distribution to explicitly address historical data overdispersion, this study contrasts traditional parametric inference against exact cluster-constrained permutation tests across distinct operational definitions of disease incidence. 3. Non-parametric diagnostics reveal that previously reported treatment and perturbation effects render as statistical artifacts under exact non-parametric permutation. Inside culling zones, parametric significance fails to withstand exact permutation verification due to extreme data leverage in localized cluster blocks. 4. Crucially, when diagnostic misclassification biases are eliminated by analysing total reactor datasets, all apparent culling effects disappear, and information criteria overwhelmingly favour nested null architectures. Unconfirmed reactors likely represent true biological infections missed by low-sensitivity post-mortem macro-necropsy, proving that host removal tracks observation noise rather than genuine zoonotic transmission pathways. 5. Finally, empirical scaling conducted in this study identifies a novel mathematical saturation effect, demonstrating that this sub-linear scaling is an operational artifact of unmodelled herd-level disease recurrence over time. 6. Policy implications. Because current zoonotic tuberculosis intervention frameworks are built upon a structurally misspecified statistical model, they have driven large-scale veterinary policies resulting in substantial, unevidenced ecological and economic interventions while failing to provide genuine public health, animal health, or disease control benefits.

ecology↗

bioRxiv2026

A conserved cysteine-histidine-glutamate metal site identifies DUF501 (Rv1025), an essential uncharacterised protein family of Mycobacterium tuberculosis, as a candidate metalloenzyme and drug target

A substantial fraction of the Mycobacterium tuberculosis proteome remains functionally uncharacterised. Rv1025, a 155-residue protein carrying the domain of unknown function DUF501 (Pfam PF04417), is essential by transposon mutagenesis and vulnerable by CRISPR interference, an attractive but neglected drug target, yet has never been functionally described. The family (4,370 proteins, no Gene Ontology term, no solved structure) is uncharacterised across all organisms and essential in three Actinobacterial genera. A Foldseek search of the AlphaFold model against complete structural databases finds no significant homolog, indicating a novel fold. The operon eno-divIC-Rv1025-ppx2 is conserved across the Actinobacteria phylum, yet AlphaFold-Multimer finds no direct complex between Rv1025 and its neighbour DivIC. Instead, conservation across 8,700 homologous sequences reveals a near-invariant Cys113-His115-Glu59 cluster forming a pocket. Holo AlphaFold3 predictions with Zn, Fe and Mn confidently place a divalent metal on this triad at 2.25-2.47 A; mutating the triad relocates the metal, and an independent backbone-geometry predictor recovers the same site, confirming specificity. The triad is universal across the family: present in all 1,472 near-complete bacterial sequences of the Pfam alignment, with no non-conservative substitution among the 2,228 sequences examined, a defining feature of bacterial DUF501 rather than a mycobacterial peculiarity. We propose that DUF501 is a metal-binding protein and candidate metalloenzyme, the first functional hypothesis for this family, whose conserved, essential metal pocket is a promising drug target. As the predictions build on a conservation-defined site within a fully computational study, they are supportive rather than proof of metal occupancy and warrant experimental validation.

microbiology↗

bioRxiv2026

Glutaminase contributes to MYC-induced cell-autonomous autophagy and to RasV12-dependent non-autonomous autophagy in the Drosophila wing disc epithelium

MYC-driven metabolic reprogramming supports rapid cell growth but also creates metabolic demands that require adaptive mechanisms to maintain cellular homeostasis. Here, combining clonal analysis in Drosophila wing imaginal discs with studies in Schneider S2 cells, we identify glutamine metabolism as a component of Myc-induced autophagy. Myc increased the expression of genes involved in glutamine utilization, including glutaminase (GLS), and enhanced ammonia production, a metabolic by-product of glutaminolysis. Genetic depletion of GLS in clones suppressed the accumulation of Myc-induced Atg8a-positive structures and reduced autophagic flux, demonstrating that glutaminase contributes to the autophagic response elicited by Myc. Exogenous NHCl was sufficient to induce Atg8a-positive structures and partially restored their accumulation following GLS depletion, supporting ammonia as a downstream contributor to this response. Mechanistically, Myc-induced autophagy in clones required the core autophagy factor Atg5 but was not suppressed by depletion of Rheb or Atg1, consistent with an autophagic program that can operate independently of canonical TOR-Atg1 signaling. We further found that Myc activity is required for RasV12-driven epithelial overgrowth and that RasV12 cells induce a pronounced non-cell-autonomous accumulation of Atg8a-positive structures in wild-type cells surrounding RasV12 clones. Depletion of either Myc or GLS in RasV12 cells strongly reduced this neighboring autophagic response, linking Myc-dependent glutamine metabolism in transformed cells to autophagy in the surrounding tissue. Together, our findings identify GLS-dependent glutamine metabolism as a previously unrecognized component of Myc-induced autophagy and extend this relationship to Ras-transformed epithelia, where Myc and Gls contribute to non-cell-autonomous autophagic responses in neighboring cells.

cell biology↗

bioRxiv2026

Rapid phase resetting of Aedes aegypti circadian rhythms by transient alterations in light exposure

Circadian clocks enable mosquitoes to anticipate recurring environmental variations and coordinate behaviors critical for survival and disease transmission, such as locomotion, reproduction, host-seeking, and blood-feeding, with times of day when performance is maximal. In Aedes aegypti, locomotor activity follows a robust diurnal rhythm shaped by endogenous circadian clocks and environmental cues, among which light has been shown to be the primary source of temporal information. While early studies established the role of light in regulating locomotor activity, behavior, oviposition and pupation, it remains unclear which features of a light cycle drive changes in circadian rhythms. This question is increasingly relevant as Ae. aegypti is frequently exposed to artificial and dynamic lighting conditions in urban environments. Here, we investigated how transient changes in light schedules influence circadian rhythms in locomotor activity by systematically manipulating the timing, duration, and direction of light exposure. Using a high-throughput assay, we tested over 1900 individuals, including wild-type and timeless knockout mutants, and showed that a single day of al tered lighting is sufficient to induce robust phase shifts, with no evidence of masking effects. A 6-hour light pulse was sufficient to re-entrain mosquitoes regardless of the timing of the pulse, and phase shifts were primarily driven by the offset time of the light pulse, indicating that light-offset acts as a major zeitgeber. Together, these findings challenge conventional assumptions about the timescale of circadian synchronization and highlight the remarkable plasticity of mosquito behavior in response to anthropogenic light. Eventually, these effects could explain the rapid adaptation of the species to urban environments and have potential consequences for disease transmission dynamics.

animal behavior and cognition↗

bioRxiv2026

PGM3 inhibition rewires RUVBL2-dependent DNA repair and induces a BRCAness-like state in pancreatic cancer cells

Pancreatic ductal adenocarcinoma (PDAC) exhibits profound metabolic rewiring and strong resistance to DNA-damaging therapies, yet how metabolic pathways regulate genome maintenance remains poorly understood. The hexosamine biosynthetic pathway (HBP) integrates nutrient availability with protein glycosylation through production of UDP-GlcNAc, but its role in DNA damage response (DDR) regulation is unclear. Here we show that inhibition of the HBP enzyme phosphoglucomutase-3 (PGM3) reduces DNA repair capacity in pancreatic cancer cells. Transcriptomic and functional analyses reveal that the selective PGM3 inhibitor FR054 amplifies gemcitabine-induced replication stress, disrupts ATR-CHK1 and ATM-CHK2 checkpoint signaling, and selectively impairs homologous recombination. Glycoproteomic profiling identifies the AAA+ ATPase RUVBL2 as a key metabolic-DDR node. Gemcitabine increases RUVBL2 O-GlcNAcylation, with Thr81 identified as a modified residue within the Walker A nucleotide-binding motif. Structural modelling predicts that Thr81 O-GlcNAcylation stabilizes the RUVBL1-RUVBL2 complex without compromising ATP-Mg engagement. PGM3 inhibition and Thr81 mutation similarly reduced ATR and ATM abundance and promoted persistent DNA damage, supporting a role for RUVBL2 Thr81 O-GlcNAcylation in sustaining checkpoint signalling and genome stability. Consequently, PGM3 inhibition induces a BRCAness-like state that sensitizes pancreatic cancer cells to PARP inhibition, both in vitro and in vivo, as well as to ionizing radiation. These findings reveal a nutrient-sensitive mechanism linking protein glycosylation to genome maintenance and identify HBP-dependent DNA repair as a potentially actionable vulnerability in pancreatic cancer.

cancer biology↗

bioRxiv2026

Data-driven spectroscopic dictionaries and detector-calibrated inference for photon-limited Raman hyperspectral imaging of living cells

Label-free Raman imaging of living cells is photon limited: at exposures compatible with cellular dynamics, single-pixel spectra carry about one count per channel on a dominant smooth background. We present an unmixing framework in which the decoder of a physics-constrained autoencoder is restricted to a data-driven spectroscopic dictionary: band centers,widths, and pseudo-Voigt shapes are measured from the dataset and fixed, and the network learns only nonnegative band amplitudes, a smooth B-spline background, and a per-pixel gain.First, on slit-scanning images of HeLa cells (532 nm) the dictionary yields spike-free component spectra that read as band tables, including a resonance-enhanced cytochrome-c-associated component matching literature spectra, and the most stable decomposition against the component number. Second, the dictionary and initialization calibrated at 1 s exposure perline transfer to 100 ms per line (12 s sweeps): cytochrome-c spectral identity survives a single sweep (correlation 0.92) while its map remains photon limited; the dictionary provides spectral physicality, and the transferred initialization prevents a structural collapse that global map correlations miss; in a measurement-derived phantom the dictionary estimator holds thecytochrome-c spectrum to 17-19{degrees} spectral angle at 100 ms, where classical factorizations and free decoders lose it (55-64{degrees}). Estimation on the count-equivalent detector output uses a calibrated shifted-Poisson quasi-likelihood. Third, evaluation must be time matched:correlation against a separately acquired reference saturates through slow specimen drift and acquisition mismatch rather than photon noise, and the self-consistency of learned denoisers is inflated by shared bias; time-matched self-consistency and independent cross-checks areproposed.

cell biology↗

bioRxiv2026

Linking continuous behavior to aesthetic enjoyment in a walkable virtual-reality museum tour: effects of agency and a painting-level analysis framework

Museum visits typically follow curator-defined routes that constrain how visitors shape their own experience, yet choice is widely held to heighten engagement, autonomy, and enjoyment. Virtual reality (VR) offers a setting in which to study these processes because it combines ecological immersion with precise, continuous behavioral measurement. We investigated (i) whether VR- derived behavioral signals are associated with self-reported enjoyment during a virtual museum tour, and (ii) whether the level of agency afforded to visitors influences enjoyment. Forty-eight adults completed a room-scale, life-size VR tour (8 * 4 m) of seven paintings from the Tel Aviv Museum of Art, each accompanied by a synchronized audio guide. Synchronized gaze and head- position streams were logged continuously (50 Hz) and segmented into painting-level viewing episodes using a trial-and-tile pipeline that intersects each painting's trial interval with an empirically defined spatial window in front of the canvas. Participants were randomly assigned to one of three agency conditions, Active (choice before every artwork), Semi-Active (choice for the first three), or Passive (fixed route),while the artwork sequence was held identical. Self- reported enjoyment at the tour and painting levels did not differ reliably across agency conditions. Among VR-derived measures, gaze engagement during the audio guide showed the clearest (though modest) association with painting-level liking, whereas locomotion and pacing measures were weak and inconsistent predictors. Agency nonetheless reliably modulated several gaze- and time-based viewing measures. The findings reveal a dissociation between subjective enjoyment and the micro-structure of viewing, and establish a reusable framework for full-tour, painting-level behavioral analysis in immersive settings.

neuroscience↗

bioRxiv2026

Zebrafish larval nitrogen excretion is flexible and resilient to loss of rhesus glycoproteins

Nitrogenous waste excretion is essential for all developmental stages of fish. Embryonic fish excrete urea, transitioning to cutaneous and later branchial ammonia excretion. In zebrafish, ammonia excretion involves rhesus glycoproteins Rhbg and Rhcgb in keratinocytes and ionocytes, but the developmental moment they appear in the gill remains unclear. Potential redundancy between Rhbg and Rhcgb in ammonia excretion is also not fully investigated, nor is the difference in response to low pH. We hypothesized that rhesus glycoproteins are partially redundant, and that they differ in their response to low pH as ammonia excretion enables ionocytes to exchange Na+ and H+ (Rh-NHE-metabolon). We predicted that a loss of rhbg or rhcgb induces compensatory responses. We characterized the transition from urea to branchial ammonia excretion from 0 to 8 days-post fertilization (dpf) and the response to pH 5.0 on the expression and localization of rhesus glycoproteins in control zebrafish and rhbg or rhcgb-crispants. Effects of high external ammonia (HEA, 500 M NH4Cl) and 10 mM HEPES-buffering were further characterized in rhcgb-crispants. Rhag and Rhbg appeared in the gill at 5 dpf, while Rhcgb appeared at 6 dpf. A loss of rhbg or rhcgb did not impact baseline N-excretion, illustrating that zebrafish can maintain ammonia excretion without the full complement of rhesus glycoproteins. We observed no compensatory increase in rhesus glycoproteins, but expression of the transporter hippocampus-abundant transcript 1b increased. HEA-exposed rhcgb-crispants switched to urea as primary nitrogen waste. Together, these findings underline the plasticity of the larval in dealing with nitrogenous waste.

physiology↗

bioRxiv2026

Tendon-derived injectable bio-instructive gel augments tenogenic differentiation of iMSC-SCX cells and extracellular matrix remodeling

In the US, 33 million musculoskeletal injuries have been reported per year, with 50% involving tendons and ligaments in both athletic and aging populations. Tendon repair often results in the formation of biomechanically inferior scar tissue rather than functional regeneration. Local cell therapy is garnering significant interest in tendon repair because it provides a targeted means to repopulate defects with potent therapeutic cells. Here, we developed a porcine tendon-derived thermoresponsive extracellular matrix hydrogel (TG) as an injectable, bio-instructive carrier for scleraxis-overexpressing induced mesenchymal stem cell derived tenocytes (iTenocytes), with the goal of improving cell retention and overall transplantation success. TG was compositionally distinct from purified collagen (PC, from rat tail type 1 collagen) and exhibited favorable material properties for a minimally invasive percutaneous strategy, including thermoresponsive gelation, shear-thinning injectability, retention at the injection site, and controlled biodegradation. In vitro, TG supported three-dimensional cell residence, promoted cell interconnectivity and redistribution at the matrix interface, and increased collagen type I release from iTenocytes compared to those embedded in PC. Transcriptomic and proteomic analyses further showed that TG enhanced programs associated with tenogenic maturation, extracellular matrix assembly, focal adhesion, mechano-transduction, and remodeling. In a rat Achilles tendon partial defect model, both optical imaging and histological analyses demonstrated retention of iTenocytes at the injection site. Additionally, confocal imaging demonstrated retention of iTenocytes within the defect site for up to 10 days. Together, these findings identify TG as a biofunctional injectable carrier that supports the tenogenic characteristics of iTenocytes and enhances their local persistence after transplantation.

cell biology↗

bioRxiv2026

Single-Cell Analytics for Dose Response (SCADR) discriminates PTEN missense variants by lipid and protein phosphatase dysfunction

The proliferation of sequencing efforts has revealed a vast and expanding catalog of single nucleotide gene variants, many associated to, but with unclear roles in disease. Fully charactering variant impacts and linking specific protein dysfunctions to disease are challenging due to the multi-functional nature of many proteins and varying degree of variant effects on these functions. Lagging are sensitive approaches to empirically assess the impact of missense variant-induced single amino acid changes on a wide range of protein functions. To address these issues, we have developed an open-source computational analysis tool called SCADR (Single-Cell Analytics for Dose Response) for simultaneously measuring and comparing impacts of exogenously-expressed variants on multiple signaling pathways using multiplex phospho-antibody spectral flow cytometry in human cell lines. SCADR retains and correlates single-cell measures of signal protein activity states along with expression levels of exogenously-expressed variants, providing rich characterization of multiple protein functions, signaling protein interactions, and enhanced discrimination of variant impacts on different signaling pathways, highlighting each variants unique dysfunction profile. Here, we apply SCADR for analyses of the impact of 6 variants of the tumor-suppressor protein PTEN (P38H, C124S, G129E, Y138L, D268E, 4A) expressed in HEK293 cells on the phosphorylation states of the canonical and noncanonical downstream signaling proteins Akt, S6, CREB, ERK, and p38 detected with fluorophore-conjugated phospho-antibodies, along with an antibody detecting an N-terminal HA tag on PTEN variants allowing measures of dose-response effects of each variants expression on signaling cascades. Results identify variant-specific impacts on downstream signaling cascades.

genomics↗

bioRxiv2026

Chronic opioid-associated immune dysregulation among people living with HIV

Objectives: Persistent immune dysregulation contributes to chronic disease among people living with HIV (PWH), even after viral suppression with antiretroviral therapy (ART). Although chronic opioid exposure is associated with adverse clinical outcomes, its impact on immune homeostasis during ART remains incompletely understood. We investigated whether opioid use disorder (OUD) is associated with persistent systemic and cellular immune dysregulation despite ART-mediated reductions in HIV viral load (VL). Methods: Peripheral blood was collected longitudinally from PWH with OUD (PWH/OUD+) and detectable HIV VL during 6 months of optimized ART (months 0, 3, and 6). A reference cohort of PWH without OUD (PWH/OUD-) and suppressed HIV VL provided a single blood sample. Immune profiling included plasma inflammatory biomarkers, multiplex cytokine analyses, spectral flow cytometry, and assessment of monocyte cytokine responses following lipopolysaccharide (LPS) stimulation. Mixed-effects models adjusted for HIV VL and VL-stratified analyses were performed. Results: PWH/OUD+ exhibited persistent immune dysregulation despite reductions in HIV VL. Plasma sCD163, sCD14, fractalkine, and I-TAC remained elevated, whereas TGF-{beta}1 was reduced. OUD was associated with expansion of CD16 monocytes and altered expression of CCR2, CD38, and CD11b. CD4 and CD8 T cells, NK cells, and B cells also exhibited persistent alterations in markers of activation, metabolism, and trafficking. Monocytes from PWH/OUD+ displayed attenuated cytokine responses following LPS stimulation. Conclusions: OUD is associated with persistent systemic and cellular immune dysfunction in PWH despite ART-mediated viral suppression, supporting opioid exposure as an independent contributor to chronic immune dysregulation that may promote inflammation, immune dysfunction, and long-term HIV-associated comorbidities. Keywords: HIV, Opioid-use disorder, innate immunity, cytokine

immunology↗

bioRxiv2026

N6-methyladenosine regulates Influenza A virus mRNA stability yet is rarely found on genomic RNA

Previous studies have found widespread N6-methyladenosine (m6A methylation) on all forms of Influenza A virus (IAV) RNA, with m6A found critical for viral replication, pathogenicity as well as viral RNA packaging. Here we applied the latest quantitative technologies to revisit the methylation landscape on the anti-sense genomic RNA of IAV. Unexpectedly, upon Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS) analysis of IAV virion -extracted genomic RNA, we detected very little m6A regardless of production from human cells or chicken eggs. Concordantly, Nanopore direct RNA sequencing also detected an overall low occurrence and stoichiometry (generally <5%) of m6A across all viral genomic RNA segments, compared with abundant m6A sites on viral mRNAs at ~20-30% m6A. Cross validation with glyoxal- and nitrite-mediated deamination of unmethylated adenosines (GLORI) confirmed multiple m6A sites on viral mRNA yet very few m6A on the genomic RNA. This paucity of m6A on genomic RNA makes it unlikely that m6A contributes to viral RNA packaging. Knockdown or pharmacological inhibition of the m6A methyltransferase METTL3 as well as the reader protein YTHDF2 both reduced viral mRNA levels and infectious viral particle production, with YTHDF2 promoting viral mRNA stability. Thus, the presence of m6A on IAV transcripts is indeed proviral, yet it is the mRNAs instead of genomic RNAs that are methylated at functionally relevant levels. Lastly, we provide proof of concept that a METTL3 small molecule inhibitor can be antiviral, and propose that m6A-targeted antivirals would mainly impact the intracellular gene expression phase of IAV replication.

microbiology↗

bioRxiv2026

Loss of ELM1B impairs mitochondrial fission, matrix redox state and stress tolerance in Physcomitrium patens

Mitochondria are endosymbiont-derived organelles that play a central role in cellular metabolism, energy production and stress responses. While single mitochondria represent functional units, they continuously exchange their contents through fusion and fission, facing stress conditions as a dynamic population. To date, it remains largely unknown how stress alters mitochondrial dynamics in plants and how altered dynamics affect mitochondrial properties and plant stress resilience. Here, we investigate mitochondrial dynamics in response to oxidative stress in the non vascular model plant Physcomitrium patens. By creating mutants with impaired mitochondrial fission in different reporter lines for mitochondrial parameters, we additionally analyse effects of chronic changes to mitochondrial population dynamics. We found that Mito-Paraquat (MtPQ) treatment increased the glutathione redox potential EGSH in mitochondria, the cytosol and chloroplasts, as monitored via roGFP2-based genetically encoded biosensors. Mitochondria elongated within hours and showed a concomitant and heterogenous increase of matrix EOSred, that we propose as a marker for matrix protein damage. Mitochondrial fission mutants lacking PpELM1B (ELONGATED MITOCHONDRIA) displayed distinct changes of mitochondrial morphology parameters as determined by automated 3D-segmentation and feature mapping (MorphoMapper) of confocal z-stacks. Elongated mitochondria in Ppelm1bge lines showed an oxidative matrix EGSH shift and increased matrix EOSred while matrix mixing still occurred, albeit at the same slow rate as in wildtype, within days. Macroscopically, Ppelm1bge lines displayed reduced growth, decreased respiration, and a higher sensitivity to oxidative stress. Our results show that plant mitochondrial morphology and physiological parameters specifically shift in response to stress and impaired fission. Mitochondrial fission is vital to maintain a healthy mitochondrial population that sustains plant oxidative stress tolerance.

plant biology↗

bioRxiv2026

A multiscale analysis of liver lobule fibrosis and its impact on drug propagation and metabolism - a DLA approach

Employing DLA methods, this paper explores the self-assembly of collagen fibers and resulting fibrosis at three scales up to the scale of regular lobule models. This allows a mechanistic exploration of the effects of collagen on drug transport (flow and diffusion) and metabolism. In addition, this method permits an analysis of fiber growth characteristics. First, variations of the DLA method of Parkinson et al (1994) will be used to generate multiple explicit collagen microfibril self-assembly using DLA particles in one dimension using cubic grid blocks of (4 mm)3 in a 240 x 20 x 20 grid model. The second stage will be to assess the consequences of various densities of these fibers in three dimensions on flow reductions at a higher scale. Here we utilize DLA methods in cubic grid blocks of (80 nm)3 to mimic 3D collagen self-assembly of fibrils. We then apply a pressure gradient or specified flow rates across a spatially gridded version of these models to quantify flow effects. This region represents a local zone of liver tissue affected by fibrosis. Analytic models of fibrotic effects on flow are employed for comparison. A third stage explores the implications of fibrosis in a liver lobule model using multiple grid blocks of size 3200 mm to represent the lobule tissue. Here, a continuum model of fiber density is employed, based on the previous two scales. The model also includes the effects of additional grid blocks representing sinusoidal flow paths found in the lobule. We contrast and quantify drug propagation and metabolism of molecular dissolved versus nanoparticle delivery vehicles in fibrotic media, achieved by upscaling explicit collagen distributions to appropriate average values.

physiology↗

bioRxiv2026

Melanophilin, a Myosin Va Adapter Protein, Biases Track Selection of Myosin Va-and Kinesin-1-Transported Liposomes at Actin-Microtubule Intersections In Vitro

Secretory vesicle transport from the Golgi to the cell membrane involves kinesin and myosin Va motors on the vesicle surface cooperatively navigating their shared cargo through numerous actin-microtubule (MT) intersections. How the track on which the cargo exits the intersection is selected so that vesicles are delivered to their destination with spatial and temporal fidelity remains unclear. Here we hypothesized that melanophilin -- the adapter that links myosin Va to pigmented melanosomes and can bind to both actin and MTs -- acts as a phosphorylation-dependent switch to bias track preference at actin-MT intersections. To test this, we modeled melanosome transport in vitro using 350-nm liposomes with ~5 surface-bound molecules each of constitutively active myosin Va, kinesin-1, and full-length melanophilin with varying phosphorylation levels. Liposomes were then challenged with actin-MT intersections. Regardless of the track the liposomes entered the intersection on, liposomes with phosphorylated melanophilin were biased towards exiting the intersection on actin filaments while those with dephosphorylated melanophilin were biased to exit on MTs. Consistent with this, phosphorylated melanophilin showed a 2-fold preference to bind actin over MTs, and slowed liposome transport by myosin Va along actin filaments by ~40% by effectively acting as an anchor. Conversely, dephosphorylated melanophilin preferentially bound (2-fold) MTs over actin and, by acting as a tether, increased the kinesin-1 liposome transport distance on MTs. Therefore, melanophilin, based on its phosphorylation state, can bias track selection of cargo transported by kinesin-1 and myosin Va through the cell's complex cytoskeletal network with its numerous actin-MT intersections.

biophysics↗

bioRxiv2026

Ribosomal proteins are major substrates of starvation-induced endosomal microautophagy in Drosophila.

Maintenance of cellular homeostasis requires tight coordination between protein synthesis and degradation, particularly at old age and under conditions of stress including starvation. Autophagy contributes to sustain this balance by degrading cytoplasmic proteins and organelles. It thus is essential to prevent the accumulation of damaged proteins and organelles and to recycle nutrients. Of the three forms of autophagy, macroautophagy, chaperone mediated autophagy, and (endosomal) microautophagy (e-MI), the latter remains the least well understood. During e-MI, cytosolic substrate proteins are captured into late endosomes via ESCRT-dependent multivesicular body formation and then degraded in late endosomes or lysosomes. e-MI is thought to contribute to protein quality control under basal conditions and under stress. Importantly, very little is known about the endogenous substrates of e-MI in flies and thus about its physiological role. Performing integrative multi-omic analyses in Drosophila larval fat body that has functions similar to mammalian liver and adipose tissue, we identified 153 high-confidence endogenous e-MI substrates with the degradation of ribosomal proteins by e-MI being the most strongly affected functional category. Generally, we found that starvation caused the depletion of proteins involved in translation, aminoacyl-tRNA synthesis, and ribosomal biogenesis, without affecting their level of transcripts. Importantly, we observe a striking specificity between e-MI and macroautophagy, as the two pathways largely target distinct protein sets including different subsets of ribosomal proteins. Our metabolomic analysis further shows that genetic inhibition of e-MI reverses the reduced levels of amino acid caused by starvation. Together, our findings reveal ribosome turnover as a central physiological function of Drosophila e-MI and establish e-MI as a pathway driving metabolic adaptation during starvation.

cell biology↗

bioRxiv2026

Constructing microbiome co-occurrence networks with confidence: A conditional, nonparametric, inference-based approach

Constructing microbial association networks is a common strategy for exploring relationships among taxa in microbiome studies. Although marginal correlation methods are easy to implement and allow formal inference, they can produce spurious edges driven by indirect associations through other taxa. Conditional graphical-modeling methods aim to recover direct associations, but many rely on Gaussian or linear assumptions and often provide limited uncertainty quantification. We propose a conditional, nonparametric approach based on the scaled expected conditional covariance (SEcov). SEcov measures population-level conditional association by residualizing each taxon with respect to the remaining taxa and scaling the resulting expected conditional covariance. The resulting estimator can incorporate flexible machine-learning methods for conditional-mean estimation and admits asymptotic normal inference, enabling p-values and confidence intervals for taxon-pair associations. We demonstrate through simulation studies that our proposed approach improves network recovery relative to other methods, and we illustrate the new method via construction of a co-occurrence network for the vaginal microbiome during pregnancy. IMPORTANCEHigh-throughput sequencing has made it possible to characterize microbial communities at large scale, and network analysis is widely used to summarize relationships among taxa. However, networks based on marginal correlations may include indirect associations, whereas many conditional graphical models rely on assumptions that may be difficult to justify for sparse, zero-inflated, compositional microbiome data. SEcov offers a practical alternative by estimating conditional associations nonparametrically and attaching inferential uncertainty to individual edges. This allows investigators to construct microbiome networks using statistically interpretable evidence for taxon-pair associations, rather than relying solely on arbitrary correlation cutoffs or regularization tuning parameters.

bioinformatics↗

bioRxiv2026

spatialMET: an open and scalable framework for spatial metabolomics analysis

Mass spectrometry imaging (MSI) enables spatially resolved metabolomics in intact tissue sections, but analysis remains challenging at scale. Existing MSI workflows often require users to combine multiple software tools, while others rely on proprietary vendor software that limits interoperability and reproducibility. To address these challenges, we developed spatialMET, an open-source framework that provides an end-to-end workflow for MSI analysis. spatialMET provides a unified platform for preprocessing, spatial domain detection, and visualization. Downstream analyses include differential abundance testing, spatial autocorrelation and gradient analysis, dimensionality reduction, and correlation network analysis. Spatial domain detection uses hcdist, a C-based hierarchical clustering implementation that substantially reduces runtime and memory use relative to existing R-based approaches. spatialMET can be run through an interactive R Shiny application or as a standalone command-line workflow for larger datasets or high-performance computing environments. Applied to mouse small cell lung cancer MALDI-MSI data containing 284,673 pixels, spatialMET identified tumor-associated, stromal, and adjacent lung spatial domains that aligned with matched histology. Differential abundance analysis identified 117 m/z features that differed between tumor and stromal regions, while spatial autocorrelation analyses revealed spatially structured abundance patterns. Applying spatialMET to mouse lung adenocarcinoma data from an entire lung lobe containing 338,477 pixels further demonstrated scalability and captured spatial heterogeneity across tumor and surrounding lung tissue. In summary, spatialMET provides a scalable, open-source framework for end-to-end spatial metabolomics analysis, and it is distributed as a Docker container for reproducible deployment. Source code and installation instructions are available at https://github.com/biodatalab/spatialMET.

bioinformatics↗