Biology subjects

Khan, A.

Publications and source records attributed to Khan, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Whole genome duplication uncouples cell volume scaling from mitochondrial homeostasis

Whole genome duplication, or polyploidy, increases cell size and nuclear volume, yet how cells maintain cytonuclear balance and metabolic fitness following ploidy expansion remains unclear. Using isogenic series of Saccharomyces cerevisiae strains ranging from haploid (1N) to tetraploid (4N), and isogenic human diploid and tetraploid cell lines, we investigated the impact of polyploidy on mitochondrial homeostasis and metabolic adaptation. Quantitative proteomics uncovered a sub-linear scaling of mitochondrial proteins with increasing ploidy, with pronounced depletion of respiratory chain components, mitochondrial DNA maintenance factors, and redox homeostasis proteins. These changes were highly conserved, indicating a conserved consequence of genome expansion. Impaired mitochondrial scaling reduced respiratory growth, membrane potential and oxygen consumption, and elevated oxidative stress. In budding yeast, the mitochondrial dysfunction triggered reactive oxygen species (ROS) accumulation and an unconventional activation of stress-responsive signaling pathways, including the Hog1 and cell integrity MAPK networks, which converged on Rtg2-dependent retrograde signaling to promote mitochondrial metabolism despite chronic dysfunction. Our findings identify defective mitochondrial scaling as a key consequence of polyploidy and establish ROS- and stress signaling-dependent retrograde response as a key adaptive mechanism linking genome duplication to mitochondrial homeostasis and cellular fitness.

cell biology↗

bioRxiv2026

Aneuploidy profiling among different types of brain metastases reveals a colon cancer-specific chromosomal signature

Brain metastasis is a significant cause of patient morbidity and mortality. There is increasing evidence that genomic instability features such as aneuploidy are associated with metastases to the brain and other organs. We analyzed the genomic instability of brain metastases among different cancer types. This included brain metastases from non-small cell lung, breast, melanoma and colorectal cancer. Our study identified a significantly higher degree of genomic instability in colorectal brain metastases compared to the other types of brain metastases. Nex, we examined the brain metastases for the types of aneuploidy events, namely chromosomal arm imbalances that involved gains or losses. Colorectal cancer brain metastases had specific chromosomal arm imbalance profiles that included gains of 13q and 20q which were significantly more frequent compared to the other cancer types. We examined other colorectal cancer metastatic sites in the lung, liver, lymph nodes and the primary colon. Examining colorectal cancer metastases more closely, aneuploidy gains across either arms for chromosomes 7 and 16 were also higher among brain metastases compared to liver, lung and lymph node metastases. Overall, this study shows that colorectal cancer brain metastasis has specific aneuploidy profiles different than other cancer types as well as being different among other metastatic organ sites.

cancer biology↗

bioRxiv2026

Molecular control of replication licensing speed by c-MYC

A critical prerequisite for DNA replication is genome-wide origin licensing, a process tightly restricted to the G1 cell cycle phase. This restriction means that short G1 cells must license quickly or risk incomplete replication and genome instability, but mechanisms to increase licensing speed are largely unknown. Using quantitative single cell approaches, we identify here a non-canonical role for c-MYC as a potent origin licensing accelerator. Importantly, a point mutation separates c-MYC-induced rapid licensing from the well-known c-MYC gene expression function. c-MYC accelerates licensing through the TRRAP lysine acetyltransferase adapter and GCN5 acetyltransferase. In addition c-MYC has the unexpected ability to induce widespread linker histone H1 eviction. Moreover, directly reducing chromatin-bound histone H1 is sufficient to accelerate licensing. In addition, c-MYC stimulates licensing in heterochromatin, a typically slow-licensing genome compartment. We suggest that global chromatin opening promotes rapid licensing when G1 phase is short such as during early development, rapid progenitor cell proliferation, and adaptation to oncogene activation.

molecular biology↗

bioRxiv2026

Membrane Filtration Removes Lipids and Compromises the Acoustic Stability of Nanobubbles

Nanobubbles (NBs) have been widely investigated as ultrasound contrast and therapeutic agents, yet whether submicron gas bubbles can directly generate measurable ultrasound signals remains controversial. Because acoustic scattering scales with bubble size, several studies have recently attributed nanobubble echogenicity primarily to larger bubbles. A recent Science Advances publication, attributed the loss of ultrasound signal after filtration to the removal of residual larger bubbles [1]. This interpretation assumes that filtration acts solely as a size-selection process. Here, we show that filtration also alters the shell properties and stability of lipid-coated NBs, independent of size. Filtered NBs (F-NBs) show significant lipid loss and accumulation on the filters themselves, resulting in decreased bubble stability and greater susceptibility to destruction under acoustic excitation. To decouple size from processing effects, we generated NB populations size-matched to filtered samples using increased centrifugation (IC-NBs), a comparatively gentler separation method. Despite comparable size distributions, IC-NBs retained sustained ultrasound scattering, whereas filtered NBs showed significantly reduced acoustic persistence. Filtration through 5 m pores, ~5-fold larger than the largest bubbles, preserved acoustic persistence but still reduced bubble concentration by ~30%, suggesting that membrane contact may contribute to bubble loss beyond size exclusion. Complementary lipid and gas-content assays provided further evidence of filtration-induced changes. The 0.45 m filtration removed substantially more total lipid than could be attributed to free-lipid removal alone, while the lipid associated with the larger bubbles removed during filtration accounted for only ~5% of the additional lipid loss. Encapsulated gas content remained comparable to that of size-matched centrifuged controls, suggesting that the reduced acoustic stability of filtered NBs is more closely associated with changes in lipid content than with loss of the gas core. These results indicate that membrane filtration is not a purely size-selective process: it removes substantially more lipid than size exclusion predicts and yields bubbles that are less stable under ultrasound, most likely through changes in shell lipid content or in the surrounding lipid reservoir, underscoring the importance of processing-induced effects in interpreting nanobubble echogenicity.

biophysics↗

bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗

bioRxiv2026

Graph-based pangenome of Venturia inaequalis, the apple scab fungus, reveals structural variants associated with population differentiation

Plant pathogen genomes adapt across coding and non-coding regions in response to their hosts, environments, and disease management practices. Venturia inaequalis, the causal agent of apple scab, has evolved alongside its Malus host throughout apple domestication. We generated 17 high-quality genome assemblies, including the first chromosome-scale assembly of V. inaequalis, to define the species' complete gene content and investigate the role of structural variation in genome evolution. Together with a previously published scaffold-level reference, these assemblies were used to construct a gene-based pangenome containing 215,301 predicted protein-coding genes clustered into 13,240 orthogroups, 88.11% of which were core (73.86%) or soft-core (14.25%), 11.88% shell (present in 2-16 isolates), and 0.1% private, indicating a highly conserved gene repertoire. Virulence-associated effectors were significantly enriched in the soft-core and shell components, and accessory apoplastic effectors displayed elevated nucleotide diversity and nonsynonymous-to-synonymous substitution ratios (Ka/Ks) relative to core effectors, consistent with diversification. We further identified a putative accessory chromosome of variable size (23-132.6 kb) in European and U.S. isolates encoding genes with virulence function. A graph-based pangenome identified 38,799 non-redundant structural variants (SVs), largely driven by Gypsy LTR retrotransposons. We used the graph-based pangenome to genotype 136 globally distributed V. inaequalis isolates and identified variants differentiating populations associated with domesticated apple (Malus domestica) from those associated with its Central Asian wild progenitor, M. sieversii. Together, these resources establish a foundation for future studies of diversity, host adaptation, and genome evolution in V. inaequalis.

genomics↗

bioRxiv2026

Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq

Plasmid construction underpins molecular biology and synthetic biology, yet validation is often limited to the inserted fragment rather than the whole plasmid, and around a third of laboratory-made plasmids carry sequence errors that can affect function. Sanger sequencing scales poorly across whole plasmids, while short-read approaches cannot resolve the repeated DNA parts, such as promoters, that are common in synthetic constructs. We present PICARD-seq, a rapid nanopore-based protocol that uses off-the-shelf Tn5 rapid barcoding reagents and a MinION to sequence pools of whole plasmids in under a day, and we systematically benchmark the computational pipelines available for analysing the resulting data. Using a curated set of 25 plasmids of known sequence spanning 3.0-20.6 kbp, including various dilution series and repetitive multi-part constructs, we ran five independent replicates of each pipeline. The ONT EPI2ME Clone Validation workflow was fast (13-18 min) but stochastic, varying between replicates for both plasmids assembled and what sequence was returned; Canu outperformed the default Flye assembler, and reducing the minimum coverage parameter from 60x to 20x substantially improved assembly of large, repetitive, and dilute samples. The ensemble assembler Autocycler was slower (81-111 min) but gave the highest and most consistent rate of recovering the expected sequence. Complementary read mapping with minimap2 distinguished genuine sequence differences from assembly artefacts. Applying PICARD-seq to problematic plasmids revealed backbone concatemers, a misincorporated promoter part, and a mixed population of rearranged molecules in a repetitive construct. PICARD-seq makes routine whole-plasmid validation practical and affordable for individual laboratories.

bioinformatics↗

bioRxiv2026

BiofilmQ-HT: An integrated browser-based workflow for standardized analysis of high-throughput crystal violet-based biofilm assays

The crystal violet (CV) microtiter plate assay is widely used to compare microbial biofilm formation because it is inexpensive, simple, and readily adapted to 96-well formats. Its high-throughput design enables multiple strains, growth conditions, and treatments to be tested in parallel, but increasing experimental complexity can make downstream data handling difficult. Plate layouts, absorbance measurements, blank correction, replicate analysis, and visualization are often managed using separate spreadsheets or software, requiring repeated transfer and organization of experimental information. This can compromise consistency in linking measurements with their corresponding conditions and controls. We developed BiofilmQ-HT, a standalone, browser-based workflow that integrates plate annotation with direct import of plate-reader data, condition-specific blank correction, replicate summarization, growth-normalized specific biofilm formation (SBF) analysis, percentage-inhibition analysis, visualization, and data export. The workflow was applied to three representative datasets: a comparison of biofilm formation in 25% and 100% media, an analysis of bacteriophage- and antibiotic-associated antibiofilm activity, and a screening of biofilm formation among natural microbial isolates. These applications demonstrate a common analytical framework for comparative biofilm analysis, antibiofilm screening, and high-throughput isolate screening while retaining experimental conditions and controls. By linking plate organization to quantitative analysis and reporting, BiofilmQ-HT provides a reproducible and traceable approach for processing condition-rich CV assay datasets and facilitates consistent comparisons across experimental groups. The utility therefore improves consistency in data handling without altering the underlying experimental assay or requiring changes to the established assay.

microbiology↗

bioRxiv2026

Sequence-Derived Representations versus Pfam-Domain Content for Biosynthetic Gene Cluster Retrieval

Retrieving BGCs related to those of a known producer can be regarded as a representation-learning objective. We hypothesize that ESM-2 sequence-derived representations of BGCs can improve retrieval beyond the Pfam-domain content metric. Our toolkit is the following: group-disjoint train, validation, and test assignments, validation-frozen model selection, [fi]ve seeds, and family-level paired inference. Of 6,953 atlas BGCs from 182 deduplicated Streptomyces griseus genome accessions, 5,325 silver-labeled BGCs are split into 98 training, 21 validation, and 21 test reference groups. Of the test reference groups, 16 are eligible for retrieval diagnostics. Pfam Jaccard scored Recall@50 of 0.8788, while Pfam-augmented BGC-SetNet scored 0.8472. The combination of ESM and Pfam-augmented BGC-SetNet scored 0.8769. A weighted Pfam Jaccard obtained a slightly higher score of 0.8789, which has a negligible difference compared to unweighted Pfam accard. Our results do not support the claim that sequence-derived representations can recover alternative biosynthetic pathways on this benchmark. Instead, explicit Pfam remains the major signal for this objective. Our results de[fi]ne the curation and pathway-level validation processes that are necessary for a more robust biological test.

bioinformatics↗

bioRxiv2026

PRELIMINARY IN VITRO EVALUATION OF NARINGIN AND QUERCETIN FOR POTENTIAL BIOENHANCEMENT OF ANDROGRAPHOLIDE USING PLASMA PROTEIN BINDING AND HEPATIC MICROSOMAL STABILITY ASSAYS

Several potentially potent anticancer drugs have been identified by in vitro evaluation, such as Andrographolide. These compounds show strong anticancer activity in vitro, but struggle to reach effective concentrations in the bloodstream when taken orally because they dissolve poorly in water or break down rapidly in the body. Bioenhancers, which are compounds that have potential to improve drug stability in the body, offer an alternative solution to overcome this limitation. Naringin and Quercetin have been identified as candidate bioenhancers, and have been hypothesized to potentially slow rapid first pass metabolism of poorly bioavailable drugs. Our work focuses on testing Naringin and Quercetin because they are flavonoids with therapeutic potential, due to their anti-inflammatory and antioxidant properties. Data from the hepatic microsomal assays performed on Naringin and Quercetin suggest moderate to proficient periods of stability in the body, with Naringin having 91.86% remaining, while Quercetin had 74.84% remaining. When administered alongside Andrographolide, a drug known to rapidly degrade in the body, Naringin raised its metabolic stability from 38.93% to 80.77% and on the other hand, Quercetin raised Andrographolide metabolic stability from 38.93% to 86.70%. In addition, plasma protein binding assays show the percentage of compounds available at the target site where Naringin was observed to be 49.32% bound and Quercetin found to be 50.14% bound, implying 50.68% of Naringin, and 49.86% of Quercetin available at the target site, respectively. This preliminary study explores whether Quercetin and Naringin could act as bioenhancers by remaining stable and available in plasma and by slowing the metabolism of poorly bioavailable drugs such as Andrographolide.

pharmacology and toxicology↗

bioRxiv2026

Spatial remodeling of the thymic stroma with age disrupts niches for T cell selection and tolerance

Age-associated thymic involution is a major driver of immunosenescence, yet the cellular and spatial mechanisms coordinating age-related thymic remodeling remain incompletely understood. Combining single-cell transcriptomics, chromatin accessibility profiling, and spatial transcriptomics, we generated a spatially resolved multi-omic atlas of the aging mouse thymus. We show that thymic aging is not simply a process of epithelial loss, but a spatial reorganization of the stroma into new microenvironments, including age-associated epithelial states, a fibroblast-supported epithelial progenitor niche, and tertiary lymphoid structures. This remodeling displaces niches supporting positive and negative thymocyte selection and coincides with an intrinsic decline in cortical thymic epithelial cell function. Ligand-receptor mapping identifies medullary fibroblasts as a signaling hub sustaining epithelial progenitors and promoting tertiary lymphoid structure neogenesis, linking these hallmarks of thymic aging. Together, our findings reframe thymic involution as spatial stromal reorganization that links stromal remodeling to impaired thymopoiesis, central tolerance, and immune aging.

immunology↗

bioRxiv2026

PWO1 and TRB proteins coordinate chromatin regulation to prevent premature differentiation and ectopic lignin deposition in Arabidopsis

The Arabidopsis PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) and Telomere Repeat-Binding Proteins 1-3 (TRB1-3, TRBs) associate with distinct and shared protein complexes involved in epigenetic regulation, yet their cooperative roles in chromatin control and plant development remain largely unexplored. Here, we show that the interaction between PWO1 and TRBs is evolutionarily conserved. Both PWO1 and TRBs associate with plant telomeres, interact at these regions, and are co-enriched at subsets of interspersed telo-box motifs across regulatory regions genome-wide. TRBs facilitate PWO1 binding at shared genomic regions, including telo-box motifs. PWO1 and TRBs share a substantial number of genomic targets and preferentially bind chromatin regions associated with transcriptionally active states, whereas TRBs alone associate with repressive marks at thousands of loci. Genetic analyses show that the pwo1 trb1 trb3 triple mutant displays severe developmental defects, including main stem arrest and early maturation associated with aberrant lignin deposition in interfascicular tissues. In the triple mutant, key enzymes in the lignin biosynthesis pathway are upregulated, indicating that PWO1, TRB1, and TRB3 cooperatively regulate secondary cell wall formation. Together, our findings provide new insights into how PWO1 and TRBs cooperate to regulate chromatin states and orchestrate plant development, highlighting their central role in controlling gene expression programs. Significance statementThis study shows that PWO1 and TRB proteins co-occupy telomeres, including interspersed telo-box motifs, to regulate chromatin organization and plant development, particularly ectopic lignin deposition. Our findings reveal how these nuclear protein factors coordinate epigenetic states in Arabidopsis thaliana, providing a framework for understanding the control of developmental programs. O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/740627v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1a3d544org.highwire.dtl.DTLVardef@1067082org.highwire.dtl.DTLVardef@1c49163org.highwire.dtl.DTLVardef@252171_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Evolutionarily conserved PWO-TRB interactions and their shared roles in chromatin regulation and plant development. Created with BioRender.com. C_FIG

plant biology↗

bioRxiv2026

Chronic Polystyrene Nanoplastics Exposure Reprograms Gene Expression, Alternative Splicing, and Disrupts Host Microbiome Metabolic Networks to Promote Atherosclerosis in LDLr- Knockout Mice

Although micro- and nanoplastics have been detected in human atherosclerotic plaques, their mechanistic contribution to disease pathogenesis remains poorly defined. Most experimental studies have used microplastics (particles > 1 m) in non-atherosclerotic animal models or the ApoE-/- mouse, relying on short-term exposure or single-pathway analyses, whereas the chronic cardiovascular effects of nanoplastics (< 100 nm) remain exceedingly scarce--despite their higher biological reactivity and greater tissue penetrance. To address this gap, this study employs a multi-omics approach to investigate the chronic (12-week) oral exposure to 80 nm polystyrene nanoplastics in LDLr-/- mice. We uniquely integrate aortic plaque quantification, hepatic transcriptomics with global alternative splicing profiling, gut microbiome 16S sequencing, and liver untargeted metabolomics to construct a unified host-microbiome-metabolite network. Nanoplastic exposure significantly exacerbates aortic lipid deposition, suppresses hepatic detoxification and anti-atherogenic lipid pathways primarily through transcriptional and post-transcriptional level changes driven by alternative splicing events (e.g., intron retention and isoform switching), and induces gut dysbiosis marked by a reduction in SCFA-producing commensals and enrichment of pro-atherogenic pathobionts--perturbations that correlate with specific hepatic functional modules. Metabolomic changes, including decreased levels of the glutathione precursor {gamma}-glutamylcysteine and the choline-derived metabolite neurine, implicate oxidative stress and TMAO-related pathways. Cross-species validation using human atherosclerotic transcriptomic and metagenomic datasets supports the clinical translatability. By integrating multi-level biological responses, this work establishes nanoplastics as an environmental cardiovascular risk factor and uncovers novel regulatory mechanisms involving splicing-associated transcriptional reprogramming and gut-liver crosstalk, offering potential early-warning biomarkers and therapeutic targets for nanoplastic-associated cardiovascular disease. HighlightsO_LIExposure to polystyrene nanoplastics (80 nm) increases aortic lipid burden in LDLr-/- mice. C_LIO_LIAlternative splicing and isoform switching were identified as novel hepatic responses. C_LIO_LISCFA-producing gut commensals are depleted, and pathobionts are enriched in response to nanoplastics. C_LIO_LIA gut-liver network links suppressed detoxification to gut microbial dysbiosis. C_LIO_LIMouse transcriptomics and metagenomics overlap with human atherosclerosis omics datasets. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/736446v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@196ad0eorg.highwire.dtl.DTLVardef@13b95d3org.highwire.dtl.DTLVardef@e963c4org.highwire.dtl.DTLVardef@94f60c_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

molecular biology↗

bioRxiv2026

Polystyrene microplastics uptake drives Inflammatory, Epitranscriptomic, and Metabolic Reprogramming in Human aortic endothelial cells

Microplastics (MPLs) are pervasive environmental pollutants increasingly linked to adverse human health outcomes, including atherosclerosis. However, the underlying mechanisms remain poorly understood. Human aortic endothelial cells (HAECs), which line the inner surface of blood vessels, play a critical role in maintaining vascular homeostasis and in the development of atherosclerosis. This study demonstrates that polystyrene microplastics enter HAECs through clathrin-mediated endocytosis and macropinocytosis and subsequently co-localize with mitochondria and lysosomes. Exposure to MPLs induced coordinated transcriptional, epitranscriptomic, and metabolomic reprogramming in HAECs. Transcriptomic analysis revealed disruption of mitochondrial genes and activation of inflammatory pathways with the response of the NF-{kappa}B pathway being particularly prominent. Mass spectrometry analysis of RNA modification further identified significant remodeling of the epitranscriptomic landscape, highlighted by increased 1-methyladenosine (m1A) modification and reciprocal regulation of its associated enzymes (TRMT61A upregulation and ALKBH3 suppression), along with alterations in other RNA modifications such as m3C, pseudouridine ({Psi}), m5C, and m7G. Comparative analysis of transcriptomic profiles from human atherosclerotic plaques revealed shared dysregulated pathways in vascular regulation and cellular signaling. Metabolomic profiling further showed extensive remodeling of lipid metabolic networks associated with oxidative stress and inflammation. Together, these findings suggest that MPLs exposure may disrupt endothelial function and pose a potential risk to human cardiovascular health. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/737624v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@2ad601org.highwire.dtl.DTLVardef@47f041org.highwire.dtl.DTLVardef@ee45cdorg.highwire.dtl.DTLVardef@128d6d5_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers

Despite the importance of population descriptors in human genomics research, many scientists struggle to translate evolving ethical guidelines into their computational workflows. To characterize this gap between recommendations and implementation, we conducted a mixed-methods survey of early-career researchers to assess how they understand and implement the landmark 2023 NASEM report on the use of population descriptors in human genetics research. We show that while exposure to the report fosters ethical awareness, fundamental misconceptions about race and ancestry persist across academic disciplines, and trainees face structural bottlenecks, including legacy data constraints and a lack of technical confidence. To address this gap, we offer actionable, stakeholder-specific recommendations across the research lifecycle ranging from decision-support tools to "bring-your-own-data" workshops to leadership from academic journals, scientific societies, and trainee mentors. Ultimately, we argue that to promote scientific rigor and reduce bias in genetic discoveries, the scientific ecosystem must invest in the infrastructure necessary to empower the next generation of researchers.

genetics↗

bioRxiv2026

Determining Reliable Neural Targets for enhancing Motor Sequence Learning: A preparatory study for focal tDCS

BackgroundMotor sequence learning (MSL) underlies the acquisition of everyday skilled movements, and transcranial direct current stimulation (tDCS) has shown promise for enhancing it, although reported effects vary considerably. Before such interventions can be applied and interpreted reliably, the behavioural and neural signatures of the underlying task should be shown to be robust. This study therefore characterised an fMRI-based Serial Reaction Time Task (SRTT) protocol and evaluated the consistency of its behavioural and fMRI-based neural signatures in repeated measurements to identify potential network targets for tDCS. MethodsTwenty healthy young- to middle-aged adults (10 females; mean age 24, SD 4) performed the SRTT during 3T fMRI in two sessions about one week apart, each using one of two matched, non-overlapping task versions in counterbalanced order. We examined block-wise behaviour, task-related and sequence-specific brain activation (general task activation relative to baseline and the SEQ > RND contrast), and functional connectivity using two complementary approaches: the task and temporal dynamics of seed-based connectivity (SBC) within an a priori-defined motor network (M1, SMA, PMC, putamen, and cerebellum), and whole-brain generalised psychophysiological interaction (gPPI) for the SEQ > RND contrast. ResultsReaction time decreased steadily across sequence blocks and returned toward baseline during random blocks, confirming implicit sequence learning; this pattern was consistent across both sessions and both task versions. Test-retest reliability was excellent for random-block reaction time (ICC {approx} .80 - .85), and modest for sequence blocks (ICC {approx} .29 - .53). General task activation (sequence and random performance relative to baseline) engaged the expected sensorimotor network, including the primary motor cortex (M1), premotor cortex, and SMA, with M1 more strongly engaged during sequence than random blocks. The sequence-specific contrast (SEQ > RND) additionally revealed six clusters spanning the left superior parietal cortex, bilateral supplementary and cingulate motor areas, bilateral secondary somatosensory cortex, and left ventral visual cortex together with cerebellar Crus I. The a priori defined motor network was engaged across all task phases and was anchored throughout by strong M1-SMA coupling, with overall network coupling following a non-monotonic course across the session, consistent with successive stages of resource allocation, consolidation, and automatisation. The gPPI analysis identified four sequence-specific connectivity clusters, dominated by a right-lateralised visuomotor network and a somatosensory-visual integration channel. ConclusionsTogether, these findings indicate a two-component architecture for SRTT performance: a left hemispheric cortico-striato-cerebellar network that supports performance and acquisition of the sequence, and a right hemispheric network associated with monitoring its predictable structure. Within this protocol, the SRTT produced robust and stable group-level signatures of implicit motor learning, yielding well-defined network targets for future tDCS interventions..

neuroscience↗

bioRxiv2026

Life-cycle trajectory inference links temperature-gated progenitors to reproductive fate

Temperature shapes reproductive strategies across animals, yet how individuals switch between sexual and asexual reproduction remains unknown. We establish the planarian Phagocata morgani as a model for temperature-dependent reproductive plasticity and adapt multiplexed single-cell transcriptomics to profile >1 million nuclei from >300 animals across body sizes and temperatures. Leveraging individual variation in cell composition, we reconstruct an organism-wide trajectory that bifurcates toward alternative reproductive fates. Temperature extremes constrain worms to one fate, whereas intermediate conditions permit probabilistic commitment to either. At the bifurcation, temperature gates a stem cell pool: warmth suppresses differentiation and promotes progenitor accumulation, whereas cold transcriptionally activates this pool for de novo sexual organogenesis. These findings reveal how environmental inputs act on stem cells to couple body size, temperature, and reproductive fate.

Developmental Biology↗

bioRxiv2026

Decoding Chromosome Radiosensitivity in G0-Phase PBMCs: Genomic Determinants, Age, Sex effects, and Implications in Radiation Dose Assessment

Low-dose ionizing radiation from natural and anthropogenic sources is typically not of significant concern under normal conditions. However, in case of radiological incidents, it becomes an important environmental hazard, raising concern for public health and necessitating reliable biological indicators of exposure. Chromosomal aberrations are most reliable markers of radiation exposure and are more or less universally assessed in metaphases. Recently, rapid assessment of aberrations in G-phase lymphocytes using G-PCC-FISH has gained attention and is recognized as the most suitable method for dose assessment in cases of high-dose or partial-body exposure. This is first study in G-phase at such scale to establish baseline and radiation induced aberrations in peripheral blood mononuclear cells (PBMCs) from 24 healthy human donors (12 males, 12 females, 21-60 Y). Using whole chromosome painting (WCP) of Chromosomes 1, 2 & 4 and scoring across >8500 cells post 0, 2, and 4 Gy {gamma}-radiation exposure, we quantified 5586 aberrations and investigated their relationship with underlying genomic features. Our findings includeNo significant effect of age or sex on chromosomal radiosensitivity, supporting the robustness of pooled biodosimetric calibration curves for dose assessment within the studied age range of 21-60 years. Chromosome-specific radiosensitivity does not appear to be solely dependent on chromosome size and shows a potential association with gene density and total transcript length. From public health point of view the present data provides reference values for interphase chromosomal damage as well as radiation induced reference values for two important dose points across age groups and sexes. This approach enhances emergency preparedness for radiological events by enabling rapid biodosimetry, especially critical when metaphase cells are unavailable as in cases of accidental high-dose or partial exposures. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/728688v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@4f8a68org.highwire.dtl.DTLVardef@7ed80org.highwire.dtl.DTLVardef@7977bforg.highwire.dtl.DTLVardef@a4c0be_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO A 24-donor study to assess baseline and radiation response age and sex. Additionally substantial data analysed to assess radiosensitivity of chromosomes and its genomic determinants. C_FIG

genomics↗