Biology subjects

Tan, N.

Publications and source records attributed to Tan, N..

10 recordsLinked to original sources

bioRxiv2026

Proton FLASH preserves neurocognition across delivery techniques: implications for clinical translation in pediatric brain tumors

BackgroundRadiation therapy is integral to the curative treatment of childhood brain tumors but contributes to late neurocognitive impairment in survivors. FLASH (ultra-high dose rate, >40Gy/s) reduces normal-tissue toxicity in preclinical models, and proton-FLASH is currently the only modality capable of delivering ultra-high dose rates to the deep targets, such as pediatric brain tumors. However, two questions remain unresolved before clinical translation: (1) whether the FLASH effect can be achieved on synchrotron-based proton systems, which deliver protons in discrete spills that may be insufficient to cover a clinical target within a single delivery, and (2) which dose-rate metric, among the multiple definitions currently used in the field, best predicts the biological FLASH effect. MethodsC57BL/6 mice (7-8 weeks) received 10 Gy whole-brain RT via a clinical Hitachi ProBEAT synchrotron with CBCT-guided delivery, using three transmission-beam techniques: single-spill pencil beam scanning (SS PBS), multi-spill PBS with [~]2-second inter-spot delay (MS PBS), and passive scatter (PS), compared to conventional (CONV) delivery and unirradiated controls (n=24-28/group, equal sex distribution). Dose rate was quantified using three frameworks: field dose rate (FDR), PBS dose rate (PBSDR), and dose-averaged dose rate (DADR). Recognition memory was assessed by novel object recognition (NOR) at 6 weeks post-RT, and cognitive flexibility was assessed via touchscreen visual discrimination and reversal learning at 14 weeks. Hippocampal neuroinflammation was evaluated by immunofluorescence and immunohistochemistry for Iba1, NeuN, and GFAP. ResultsFLASH conditions were met by SS PBS and PS under all three dose-rate definitions, but MS PBS qualified as FLASH only by DADR. Despite this, neuroprotection was preserved across all three FLASH techniques: discrimination index was significantly higher for SS PBS (P=0.021), MS PBS (P=0.008), and PS (P<0.001) versus CONV, with no significant difference between FLASH techniques. On touchscreen testing, FLASH-treated females demonstrated preserved cognitive flexibility (P=0.047 vs. CONV on reversal learning correct trials). Iba1+ microglia were reduced in FLASH compared to CONV mice, with morphology suggestive of preserved homeostatic state. ConclusionsSynchrotron-based proton FLASH preserves neurocognitive function across all delivery techniques, including under multi-spill delivery essential for treating clinical-scale pediatric brain tumors. Critically, this neuroprotection was observed even for deliveries that qualified as FLASH only by DADR, identifying DADR as the dose-rate metric most relevant to the biological FLASH effect with direct implications for clinical trial design and dose-rate reporting standards.

cancer biology↗

bioRxiv2026

Advancing ab initio genome annotation with OrionGeno

The rapid expansion of eukaryotic genome sequencing has created an urgent demand for accurate and scalable genome annotation. Existing ab initio methods often struggle to reconstruct complex gene architectures and generalize across distant lineages, limiting their use for large-scale annotation. Here we present OrionGeno, a phylogeny-aware deep learning model for end-to-end eukaryotic genome annotation. OrionGeno integrates phylogenetic context, long-range sequence modeling and joint prediction of gene structures and repetitive elements to annotate exons, introns, untranslated regions and repeats directly from genomic sequences. Applied to chromosome-level eukaryotic genomes from NCBI that lack annotations, OrionGeno generates annotations for more than 5,300 genomes, substantially expanding public annotation resources. Across diverse eukaryotic lineages, OrionGeno outperforms state-of-the-art methods at the exon, gene, protein-sequence, and protein-structural levels. It also identifies candidate protein-coding loci absent from reference protein-coding annotations in well-curated genomes. Together with a web platform and integrated annotation database, OrionGeno provides a scalable and accessible framework for translating genome assemblies into functional biological resources and supporting large-scale biodiversity initiatives such as the Earth BioGenome Project.

bioinformatics↗

bioRxiv2026

Behavior evolves as a correlated response to selection on cuticle color in Drosophila melanogaster and D. simulans

To predict adaptive evolution, we need to understand the degree to which selection on one trait can constrain or redirect evolutionary responses in other traits. We used artificial selection on cuticle color in Drosophila melanogaster and D. simulans to investigate whether color and behavior evolve in tandem. We selected for light and dark thoracic colors for 16 generations in two populations per species and measured correlated responses in aggression, basal activity, total activity, sleep, and geotaxis. Dark selected individuals consistently showed higher aggression and basal activity than light selected or control flies across both species and sexes, pointing to a modest but repeatable correlated response. In contrast, patterns for geotaxis, sleep, and total activity evolved unpredictably, often varying across species and populations, and showed no clear association with color. Within-population phenotypic correlations between color and aggression were significant but weak (rho = -0.035, rho{superscript 2} = 0.001), suggesting that color is a poor predictor of individual aggressive behavior. Populations evolving higher aggression also tended to evolve higher basal activity (rho = 0.52, p = 0.004), suggesting activity may have evolved as a correlated response rather than through a direct color-activity link. The persistence of correlated responses in aggression and basal activity in response to selection on color is consistent with a conserved genetic basis, such as pleiotropy or linkage disequilibrium, although our data do not distinguish between these mechanisms. Identifying the loci underlying variation in both color and behavior, and testing their effects experimentally, will clarify how multivariate genetic covariance shapes the direction and pace of adaptive evolution.

evolutionary biology↗

bioRxiv2025

HerbComb: an integrated database for the discovery of novel combinational therapies from herbal medicines

Drug combinations have gained increasing interest due to their potential for optimal efficacy and the ability to overcome drug resistance. Herbal medicine is a complex system with multiple ingredients and has illustrated apparent therapeutic effects through thousands of years of clinical experience, offering a rich resource for combinational therapies. However, the underlying mechanism of their synergistic therapeutic effects for disease treatment remains obscure for most herbal medicines. To fill this gap, we developed an integrated database named HerbComb (https://herbcomb.com/) to discover combinatorial therapies in herbal medicine, featuring three unique functions: drug prepositioning, customized combinatorial analysis, and biological and pharmacological features. Additionally, transcriptional gene signatures and ADMET properties were also interrogated as interactive functionalities to facilitate combinational analysis. Using Tongxinluo for Stroke as a case study, we identified and validated Oleanolic acid and Ferulic acid as synergistic ingredients. In summary, HerbComb is a versatile data exploration platform designed to characterize synergistic interactions among herbal medicines, enhancing the understanding of synergistic mechanisms and facilitating the discovery of effective drug combinations.

pharmacology and toxicology↗

bioRxiv2024

Multisensory gamma stimulation enhances adult neurogenesis and improves cognitive function in a mouse model of Down syndrome

Down syndrome (DS) has been linked with deficits in hippocampal dependent cognitive tasks and adult neurogenesis, yet treatment options are still very limited. We and others previously showed that a non-invasive multisensory gamma stimulation using light and sound at 40 Hz ameliorated Alzheimers disease pathology and symptoms in mouse models. In this study, we tested the effects of 40 Hz multisensory stimulation in the Ts65Dn mice, a mouse model of DS. For three weeks, mice were exposed daily to one hour of stimulation or one hour of ambient light and sound. Mice receiving the stimulation showed improved object recognition and spatial working memory. Using single nuclei RNA-seq and experimental validations in mouse hippocampal samples, we identified underlying expression changes in gene regulatory networks and demonstrated increased adult neurogenesis and reorganization of synapses as potential mechanisms for these improved cognitive phenotypes. Together, our data reveal a novel effect of multisensory gamma stimulation on adult neurogenesis and beneficial effects of 40 Hz treatment on cognitive function in DS model mice. Significance StatementWe present strong evidence, using a well-characterized mouse model, that the cognitive and neurogenesis deficits in Down syndrome can be improved through non-invasive multi-sensory gamma stimulation. Employing a systems biology approach, we provide extensive hippocampal single-cell resolution gene expression signatures and changes in gene regulatory networks in response to sensory gamma stimulation.

neuroscience↗

bioRxiv2023

Scalable Mesenchymal Stem Cells Enrichment from Bone Marrow Aspirate using Deterministic Lateral Displacement (DLD) Microfluidics Sorting

The growing interest in regenerative medicine has opened new avenues for novel cell therapies using stem cells. Bone Marrow Aspirate (BMA) is an important source of stromal mesenchymal stem cells (MSCs). Conventional MSC harvesting from BMA relies on archaic centrifugation methods, often leading to poor yield due to osmotic stress, high centrifugation force, convoluted workflow, and long experimental time ([~] 2 - 3 hours). To address these issues, we have developed a scalable microfluidic technology based on Deterministic Lateral Displacement (DLD) for MSC isolation. This passive, label-free cell sorting method capitalizes on the morphological differences between MSCs and blood cells (leukocytes and RBCs) for effective separation using an inverted L-shaped pillar array. To improve throughput, we developed a novel portable multiplexed DLD system that can process 2.5 mL of raw BMA in 20 {+/-} 5 minutes, achieving a 2-fold increase in MSC recovery compared to centrifugation methods. Taken together, we envision the developed DLD platform will enable fast and efficient isolation of MSCs from BMA for effective downstream cell therapy in clinical settings.

bioengineering↗

bioRxiv2022

Functional imaging and quantification of multi-neuronal olfactory responses in C. elegans

Many animals perceive odorant molecules by collecting information from ensembles of olfactory neurons. Each neuron employs receptors that are tuned to recognize certain odorant molecules by chemical binding affinity. Olfactory systems are able, in principle, to detect and discriminate diverse odorants by using combinatorial coding strategies. Multineuronal imaging with high-throughput stimulus delivery allows comprehensive measurement of ensemble-level sensory representations. We have used microfluidics and multineuronal imaging to study ensemble-level olfactory representations at the sensory periphery of the nematode C. elegans. The collective activity of nematode chemosensory neurons reveals high-dimensional representations of olfactory information across a broad space of odorant molecules. We reveal diverse tuning properties and dose-response curves across chemosensory neurons and across odorants. We describe the unique contribution of each sensory neuron to an ensemble-level code for volatile odorants. We also show how natural stimuli, a set of nematode pheromones, are encoded by the sensory periphery. The integrated activity of the C. elegans chemosensory neurons contains sufficient information to robustly encode the intensity and identity of diverse chemical stimuli.

neuroscience↗

bioRxiv2022

Mutations of SARS-CoV-2 variants of concern escaping Spike-specific T cells

The amino acid (AA) mutations that characterise the different variants of concern (VOCs), which replaced the ancestral SARS-CoV-2 Wuhan-Hu-1 isolate worldwide, provide biological advantages such as increased infectivity and partial escape from humoral immunity. Here we analysed the impact of these mutations on vaccination- and infection-induced Spike-specific T cells. We confirmed that, in the majority of infected or vaccinated individuals, different mutations present in a single VOC (Delta) or a combined mosaic of more than 30 AA substitutions and deletions found in Alpha, Beta, Gamma, Delta and Omicron VOCs cause modest alteration in the global Spike-specific T cell response. However, distinct numerically dominant Spike-specific CD4 and CD8 T cells preferentially targeted regions affected by AA mutations and do not recognise the mutated peptides. Importantly, some of these mutations, such as N501Y (present in Alpha, Beta, Gamma, and Omicron) and L452R (present in Delta), known to provide biological advantage to SARS-CoV-2 in terms of infectivity also abolished CD8 T cell recognition. Taken together, our data show that while global mRNA vaccine- and infection-induced Spike-specific T cells largely tolerate the diverse mutations present in VOCs, single Spike-specific T cells might contribute to the natural selection of SARS-CoV-2 variants.

immunology↗

bioRxiv2021

Rapid determination of the wide dynamic range of SARS-CoV-2 Spike T cell responses in whole blood of vaccinated and naturally infected

BackgroundAntibodies and T cells cooperate to control virus infections. The definition of the correlates of protection necessary to manage the COVID-19 pandemic, require both immune parameters but the complexity of traditional tests limits virus-specific T cell measurements. MethodsWe test the sensitivity and performance of a simple and rapid SARS-CoV-2 Spike-specific T cell test based on stimulation of whole blood with peptides covering the SARS-CoV-2 Spike protein followed by cytokine (IFN-{gamma}, IL-2) measurement in different cohorts including BNT162b2 vaccinated (n=112; 201 samples), convalescent asymptomatic (n=62; 62 samples) and symptomatic (n=68; 115 samples) COVID-19 patients and SARS-CoV-1 convalescent individuals (n=12; 12 samples). ResultsThe sensitivity of the rapid cytokine whole blood test equates traditional methods of T cell analysis (ELISPOT, Activation Induced Markers). Utilizing this test we observed that Spike-specific T cells in vaccinated preferentially target the S2 region of Spike and that their mean magnitude is similar between them and SARS-CoV-2 convalescents at 3 months after vaccine or virus priming respectively. However, a wide heterogeneity of Spike-specific T cell magnitude characterizes the individual responses irrespective of the time of analysis. No correlation between neutralizing antibody levels and Spike-specific T cell magnitude were found. ConclusionsRapid measurement of cytokine production in whole blood after peptide activation revealed a wide dynamic range of Spike-specific T cell response after vaccination that cannot be predicted from neutralizing antibody quantities. Both Spike-specific humoral and cellular immunity should be tested after vaccination to define the correlates of protection necessary to evaluate current vaccine strategies.

immunology↗

bioRxiv2020

Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals

Memory T cells induced by previous infections can influence the course of new viral infections. Little is known about the pattern of SARS-CoV-2 specific pre-existing memory T cells in human. Here, we first studied T cell responses to structural (nucleocapsid protein, NP) and non-structural (NSP-7 and NSP13 of ORF1) regions of SARS-CoV-2 in convalescent from COVID-19 (n=24). In all of them we demonstrated the presence of CD4 and CD8 T cells recognizing multiple regions of the NP protein. We then show that SARS-recovered patients (n=23), 17 years after the 2003 outbreak, still possess long-lasting memory T cells reactive to SARS-NP, which displayed robust cross-reactivity to SARS-CoV-2 NP. Surprisingly, we observed a differential pattern of SARS-CoV-2 specific T cell immunodominance in individuals with no history of SARS, COVID-19 or contact with SARS/COVID-19 patients (n=18). Half of them (9/18) possess T cells targeting the ORF-1 coded proteins NSP7 and 13, which were rarely detected in COVID-19- and SARS-recovered patients. Epitope characterization of NSP7-specific T cells showed recognition of protein fragments with low homology to "common cold" human coronaviruses but conserved among animal betacoranaviruses. Thus, infection with betacoronaviruses induces strong and long-lasting T cell immunity to the structural protein NP. Understanding how pre-existing ORF-1-specific T cells present in the general population impact susceptibility and pathogenesis of SARS-CoV-2 infection is of paramount importance for the management of the current COVID-19 pandemic.

immunology↗