Biology subjects

Ho, H.

Publications and source records attributed to Ho, H..

13 recordsLinked to original sources

bioRxiv2026

Suspension-Based Human Esophagoids Recapitulate WNT2B-Dependent Regulation of Esophageal Basal Progenitors

Background & AimsThe human esophagus undergoes a tightly regulated developmental program, transitioning from a simple columnar epithelium in early development to a mature stratified squamous tissue essential for adult barrier function. Here, we constructed a developmental cell atlas spanning early development to adulthood and leveraged it to generate physiologically relevant in vitro models. MethodsWe utilized single-cell RNA sequencing and spatial multiplex proteomics of human esophageal tissue from early development through adulthood. We established a feeder-supported 2D culture system and a Matrigel-free, suspension-based 3D esophagoid model in a 96-well format. To interrogate WNT2B function, we analyzed patient tissue harboring WNT2B loss-of-function mutations and performed WNT inhibition in esophagoids. ResultsSequencing profiling identified stage-specific epithelial populations: multiciliated and GPC3 basal cells were unique to early development; KRT14 basal and CRNN luminal cells were adult-specific; and COL17A1, LY6D, and KRT4 populations were shared across stages. Spatially organized WNT2B, KIT, and VWC2 mesenchymal subtypes were identified. The 2D system preserved both epithelial and mesenchymal compartments with transcriptional fidelity. Esophagoids exhibited basal-to-luminal stratification, mesenchymal compartmentalization, and required stromal interactions for formation. WNT2B repressed self-renewal of TP63 basal progenitors and inhibited proliferation, confirmed by pharmacologic inhibition of WNT in the in vitro esophagoids. ConclusionsWe present a stage-resolved atlas of human esophageal development and a scalable esophagoid platform recapitulating esophageal architecture. WNT2B regulates progenitor dynamics by restraining basal cell self-renewal. Esophagoids provide a physiologically relevant system for modeling esophageal development and disease. Visual Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/733451v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1af5743org.highwire.dtl.DTLVardef@8a061dorg.highwire.dtl.DTLVardef@1975c3forg.highwire.dtl.DTLVardef@292ce9_HPS_FORMAT_FIGEXP M_FIG C_FIG Key Findings and ImplicationsO_LIDevelopmental Atlas: The study presents a comprehensive transcriptional and structural atlas of the human esophageal epithelium, identifying conserved and stage-specific epithelial populations from early development to adulthood. Notably, stage-specific gene expression of multiciliated and GPC3 basal cells were unique to early development, while KRT14 basal and CRNN luminal cells were adult specific, with COL17A1+ (basal), LY6D+ (epibasal), and KRT4+ (middle), shared at all stages. C_LIO_LIMesenchymal Diversity: Spatial and transcriptional profiling revealed distinct mesenchymal subtypes, including WNT2B, KIT, and VWC2 populations, which are spatially organized and contribute to epithelial-mesenchymal signaling. These findings reinforce the role of stromal-epithelial interactions in esophageal development. C_LIO_LI2D Esophagus Cell Culture System: A feeder-supported 2D cell culture system was developed that retains both epithelial and mesenchymal populations, preserving transcriptional fidelity and enabling long-term expansion for mechanistic studies. C_LIO_LI3D Esophagoid Model: A suspension-based 3D organoid system was optimized using a 96-well format, enabling high-throughput generation of esophagoids with robust epithelial stratification and mesenchymal compartmentalization. These organoids recapitulate key features of the human esophagus, including basal-to-luminal organization, and require stromal interactions for formation. C_LIO_LIFunctional Role of WNT2B in esophagus development: Both in vivo and in vitro analyses demonstrated that WNT2B regulates epithelial progenitor dynamics and tissue architecture by repressing self-renewal of basally localized TP63+ cells and inhibiting proliferation. Loss-of-function models and WNT pathway modulation confirmed its role in epithelial-mesenchymal crosstalk and organoid integrity. C_LI

developmental biology↗

bioRxiv2026

Hippocampal brain-machine interface-based navigation reveals CA1 representations of intended actions

The hippocampus integrates external cues and self-motion to construct cognitive maps. Activating these maps independently of immediate sensory and motor signals can support navigation by predicting future locations. The neural basis of such internally driven activation remains poorly understood. To address this, we had mice use a brain-machine interface (BMI) to directly control navigation from real-time hippocampal activity. In this condition, CA1 responses encoding running movement were not navigationally relevant, and place codes rapidly reconfigured to form new representations that discarded locomotion-related signals. By comparing neural representations across BMI-controlled navigation, locomotion-controlled navigation, and passive playback of predetermined routes, we found evidence of response patterns that were specific to conditions in which neural activity could causally influence an animals travel. This suggests the existence of CA1 responses that are not tied to external stimuli or self-motion, and that are suppressed when animals are merely passive observers.

neuroscience↗

bioRxiv2025

Dissecting novel object exploration: a fully automated homecage-based novel object recognition test

The novel object recognition test is a frequently used memory test in rodents. Due to its ethological nature, cross-species relevance, and specificity to testing hippocampal and parahippocampal function, it has been widely applied in basic and translational research. However, its implementation proves challenging due to multiple uncontrolled factors. Here, we describe a fully automated homecage-based novel object recognition test for assessing long-term object memory in mice. We present an empirically guided computational model to show the robustness of this approach despite ambiguity in defining exploratory behaviours. We show that mice preferentially explored novel compared to familiar objects after 24-hour and 7-day retention periods, starting to discern them while still a distance away. The findings were replicated across two facilities. Furthermore, the ability to recognise the novel object depends on the mouses prior interactions with the replaced object after 24 hours, but not after 7 days. Finally, we showed that external factors may introduce undesired exploration biases, which can be addressed using relative instead of absolute discrimination measures. The fully automated homecage-based object recognition test will improve standardisation, rigour, and reproducibility, as well as expand our understanding of the factors influencing object exploratory behaviours and object memory. MotivationRecognition of objects as novel or familiar is an important cognitive memory function with cross-species relevance. Extensive work has provided a good understanding of the brain regions involved. Despite the apparent simplicity of novel object recognition (NOR) tests, they remain challenging due to their sensitivity to various uncontrolled experimental factors and differences in study design. Here, we report a fully automated standardised NOR test carried out in a mouses homecage, which minimises previously reported variability in NOR tests. HighlightsO_LIFully automated novel object recognition test for assessing long-term object memory in the mouses homecage C_LIO_LIA robust analysis pipeline described C_LIO_LITest replicated in two facilities with comparable results C_LIO_LIAn empirically guided computational model pointing to the robustness of this approach introduced C_LIO_LIMajor factors affecting the ability to discriminate novel from familiar objects, including object exploration bias, are described C_LI

neuroscience↗

bioRxiv2025

Phage intervention improves colitis and response to corticosteroids by attenuating virulence of Crohn's disease-associated bacteria

Adherent-invasive Escherichia coli (AIEC) exhibit proinflammatory properties and have been implicated in the pathogenesis of Crohns disease (CD), a form of inflammatory bowel disease (IBD). Antibiotic use in CD lacks specificity and may worsen microbiome disruption, prompting interest in bacteriophages (phages) for targeted microbiome editing. Here, we identified HER259, a phage active against the clinical AIEC strain NRG857c. Using gnotobiotic models of AIEC-driven colitis, we show that HER259 attenuates AIEC virulence, including suppression of the FimH adhesin through inversion of the fimS promoter to its off orientation. Withdrawal of HER259 treatment leads to reversion of the fimS promoter and reactivated colitis in mice. HER259 phage also enhances the therapeutic effect of sub-therapeutic budesonide, independent of microbial drug metabolism. These findings support targeted phage therapy as an adjunct treatment approach in IBD, demonstrating modulation of bacterial virulence and improved response to conventional treatments which may reduce drug-related side effects. One Sentence SummaryBacteriophage HER259 improves colitis severity mediated by Crohns disease Escherichia coli NRG857c, and increases efficacy of budesonide.

microbiology↗

bioRxiv2025

GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies

Functional genomic sequences occupy an infinitesimal fraction of the astronomically large DNA sequence space, implying that evolution explores a low-dimensional manifold shaped by universal biochemical and evolutionary constraints. To investigate this underexplored Genomic Manifold Hypothesis using scalable, data-driven evidence, we developed GenomeOcean, a 4-billion-parameter generative model trained on 219 TB of diverse, co-assembled global environmental metagenomic data using an optimized transformer. The model captures both universal phylogenetic syntax and protein-coding fidelity. Furthermore, we validate the embeddings intrinsic low dimensionality. Crucially, comparisons with the independently trained Evo 2 model demonstrate a strong linear correspondence between their embedding spaces and convergent generative behaviors. These results suggest that the genomic manifold represents a fundamental biological principle, offering a unified framework for understanding evolutionary constraints and guiding synthetic biology.

bioinformatics↗

bioRxiv2024

Thrombolysis exacerbates cerebrovascular injury after ischemic stroke via a VEGF-B dependent effect on adipose lipolysis

Cerebrovascular injuries leading to edema and hemorrhage after ischemic stroke are common. The mechanisms underlying these events and how they are connected to known risk factors for poor outcome, like obesity and diabetes, is relatively unknown. Herein we demonstrate that increased adipose tissue lipolysis is a dominating risk factor for the development of a compromised cerebrovasculature in ischemic stroke. Reducing adipose lipolysis by VEGF-B antagonism improved vascular integrity by reducing ectopic cerebrovascular lipid deposition. Thrombolytic therapy in ischemic stroke using tissue plasminogen activator (tPA) leads to increased risk of hemorrhagic complications, substantially limiting the use of thrombolytic therapy. We provide evidence that thrombolysis with tPA promotes adipose tissue lipolysis, leading to a rise in plasma fatty acids and lipid accumulation in the ischemic cerebrovasculature after stroke. VEGF-B blockade improved the efficacy and safety of thrombolysis suggesting the potential use of anti-VEGF-B therapy to extend the therapeutic window for stroke management.

neuroscience↗

bioRxiv2024

Zebrafish Foxl2l suppresses stemness and directs feminization of germline progenitors

Zebrafish is an important organism for genetic studies, but its germ cell types and the mechanism of sex differentiation remain elusive. Here, we conducted a single-cell transcriptomic profiling and charted a developmental trajectory going from germline stem cells, through early, committed, and late progenitors, to pre-meiotic and meiotic cells. A transcription factor, Foxl2l, is expressed in the progenitors committed to the ovary fate. CRISPR-Cas9-mediated mutation of foxl2l produced 100% male fish with normal fertility. Another single-cell profiling of foxl2l-/- germ cells reveals the arrest of early progenitors. Concomitantly the expression of nanos2 (stem cell marker) and id1 (transcription repressor in stem cells) was elevated together with an increase of nanos2+ germ cell in foxl2l mutants, indicating the reversion to the stem cell state. Thus, we have identified developmental stages of germ cells in juvenile zebrafish and demonstrated that Foxl2l drives zebrafish germ cell progenitors toward feminization and prevents them from reverting back to the stem cell state.

developmental biology↗

bioRxiv2022

A novel fully-automated system for lifelong continuous phenotyping of mouse cognition and behaviour

Comprehensive ethologically-relevant behavioural phenotyping in rodent experiments is essential for deciphering the neural basis of animal cognition. Automated home-cage monitoring systems present a valuable tool to fulfil this need. However, they often involve complex animal training routines, water or food deprivation, and probe a limited range of behaviours. Here, we present a new fully automated AI-driven home-cage system for cognitive and behavioural phenotyping in mice. The system incorporates spontaneous alternation T-maze, novel-object recognition and object-in-place recognition tests combined with monitoring of an animals position, water consumption, quiescence and locomotion patterns, all carried out continuously and simultaneously in an unsupervised fashion over long periods of time. Mice learnt the tasks rapidly without any need for water or food restrictions. We applied ethomics approach to show that combined statistical properties of multiple behaviours can be used to discriminate between mice with hippocampal, medial entorhinal and sham lesions and accurately predict genotype of Alzheimers disease mouse models on an individual animal level, surpassing the performance of several gold standard cognitive tests. This technology could enable large-scale behavioural screening for genes and neural circuits underlying spatial memory and other cognitive processes.

neuroscience↗

bioRxiv2022

Persistent Memory as an Effective Alternative to Random Access Memory in Metagenome Assembly

The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is a process that is memory intensive and time consuming. Multi-terabyte sequences can become too large to be assembled on a single computer node, and there is no reliable method to predict the memory requirement due to data-specific memory consumption pattern. Currently, out-ofmemory (OOM) is one of the most prevalent factors that accounts for metagenome assembly failures. In this study, we explored the possibility of using Persistent Memory (PMem) as a less expensive substitute for dynamic random access memory (DRAM) to reduce OOM and increase the scalability of metagenome assemblers. We evaluated the execution time and memory usage of three popular metagenome assemblers (MetaSPAdes, MEGAHIT, and MetaHipMer2) in datasets up to one terabase. We found that PMem can enable metagenome assemblers on terabyte-sized datasets by partially or fully substituting DRAM at a cost of longer running times. In addition, different assemblers displayed distinct memory/speed trade-offs in the same hardware/software environment. Because PMem was provided directly without any application-specific code modification, these findings are likely to be generalized to other memory-intensive bioinformatics applications.

bioinformatics↗

bioRxiv2020

An inhalation anaesthesia approach for neonatal mice allowing streamlined stereotactic injection in the brain

Investigating brain function requires tools and techniques to visualise, modify and manipulate neuronal tissue. One powerful and popular method is intracerebral injection of customised viruses, allowing expression of exogenous transgenes. This technique is a standard procedure for adult mice, and is used by laboratories worldwide. Use of neonatal animals in scientific research allows investigation of developing tissues, and enables long-term study of cell populations. However, procedures on neonatal mice are more challenging, due to the lack of reliable methods and apparatus for anaesthesia of these animals. Here, we report an inhalation-based protocol for anaesthesia of neonatal (P0-2) mice, and present a custom 3D-printed apparatus for maintenance of anaesthesia during surgical procedures. This approach significantly enhances animal welfare and facilitates wider and simpler use of neonatal rodents in scientific research. Our optimised method of anaesthesia enables a rapid method of stereotactic injection in neonatal mice for transduction of brain tissue. We demonstrate this procedure for targeted labelling of specific brain regions, and in vivo modification of tissue prior to organotypic culture. This anaesthetic approach can be readily employed by any laboratory, and will enable safer use of neonatal rodents across a diverse spectrum of scientific disciplines. HighlightsO_LIDevelopment of inhalation-based anaesthesia for early postnatal (P0-2) mice C_LIO_LI3D-printed mould allows anaesthetic maintenance for neonatal surgery C_LIO_LIImproved mouse welfare through reliable neonatal inhalation anaesthesia C_LIO_LIRapid procedure for brain transduction of mouse litter in under 2 hours C_LI

neuroscience↗

bioRxiv2019

A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome

Current supervised phylogeny-based methods fall short on recognizing species assembled from metagenomic datasets from under-investigated habitats, as they are often incomplete or lack closely known relatives. Here, we report an efficient software suite, \"Genome Constellation\", that estimates similarities between genomes based on their k-mer matches, and subsequently uses these similarities for classification, clustering, and visualization. The clusters of reference genomes formed by Genome Constellation closely resemble known phylogenetic relationships while simultaneously revealing unexpected connections. In a dataset containing 1,693 draft genomes assembled from the Antarctic lake communities where only 40% could be placed in a phylogenetic tree, Genome Constellation improves taxa assignment to 61%. It revealed six clusters derived from new bacterial phyla and 63 new giant viruses, 3 of which missed by the traditional marker-based approach. In summary, we demonstrate that Genome Constellation can tackle the computational and algorithmic challenges in large-scale taxonomy analyses in metagenomics.

bioinformatics↗

bioRxiv2018

Using Google Trends to Examine the Spatio-Temporal Incidence and Behavioral Patterns of Dengue Disease: A Case Study in Metropolitan Manila, Philippines

Dengue is a major public health concern and an economic burden in the Philippines. Despite the countrys improved dengue surveillance, it still suffers from various setbacks and therefore needs to be complemented with alternative approaches. Previous studies have demonstrated the potential of internet-based surveillance such as Google Dengue Trends (GDT) in supplementing current epidemiological methods for predicting future dengue outbreaks and patterns. With this, our study aims to assess the temporal relationship of GDT and dengue incidence in Metropolitan Manila from previous years and examine web search behavior of the population towards the disease. The study collated and organized the population statistics and reported dengue cases in Metropolitan Manila from respective government agencies to calculate the spatial and temporal dengue incidence. The relative search volume of the term dengue and top dengue-related search queries in Metropolitan Manila were obtained and organized from the Google trends platform. Data processing of GDT and dengue incidence was performed by conducting an adjustment procedure and subsequently used for correlation and cross-correlation analyses. Moreover, a thematic analysis was employed on the top dengue-related search queries. Results revealed a high temporal relationship between GDT and dengue incidence when either one of the variables is adjusted. Cross-correlation showed that there is delayed effect (1-2 weeks) of GDT to dengue incidence, demonstrating its potential in predicting future dengue outbreaks and patterns in Metropolitan Manila. Thematic analysis of dengue-related search queries indicated 5 categories namely; (a) dengue, (b) sign and symptoms of dengue, (c) treatment and prevention, (d) mosquito and (e) other diseases where the majority of the search queries was signs and symptoms which indicate the health-seeking behavior of the population towards the disease.

epidemiology↗

bioRxiv2018

Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF

BackgroundOrganohalide-respiring bacteria (OHRB) play an important role in the global halogen cycle and bioremediation of industrial sites contaminated with chlorinated organics. One notable OHRB is Dehalobacter restrictus strain CF, which is capable of respiring chloroform to dichloromethane. Improved bioremediation strategies could be employed with a greater understanding of D. restrictus metabolism in isolate and community cultures. To this end, we reconstructed the genome-scale metabolic network of D. restrictus to study its metabolism in future studies using flux balance analysis.\n\nMethodThe RAST annotation server and Model SEED framework were used to obtain a draft metabolic network reconstruction. Additional curation was required for its acetyl-CoA sources, the Wood-Ljungdahl pathway, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes.\n\nResultsiHH623 is the first curated genome-scale metabolic model in the Peptococcaceae family. It spans 1087 reactions and 983 metabolites, covering 623 genes (21% of all ORFs). Its potential sources of acetyl-CoA are pyruvate ferredoxin oxidoreductase, pyruvate formate lyase, acetyl-CoA synthetase, phosphate acetyltransferase, and CO-methylating acetyl-CoA synthase. NADPH may be regenerated by isocitrate dehydrogenase, malic enzyme, NADP-reducing hydrogenase, cytosolic formate dehydrogenase, ferredoxin-dependent bifurcating transhydrogenase, 5-methyltetrahydrofolate dehydrogenase, and 5-10-methylenetetrahydrofolate. Additional reactions that were added or removed to the D. restrictus reconstruction are discussed.\n\nConclusionsWe reconstructed the genome-scale metabolic network of D. restricus by obtaining an initial draft with the RAST server and Model SEED framework. Curation was required for D. restricus acetyl-CoA sources, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes. This metabolic model can be used to decipher D. restrictus metabolism in isolate and community cultures in future studies, or as a template to reconstruct the metabolic network of other Peptococcaceae species. The extensive curation of the draft metabolic network reconstruction highlights the need to be cautious of automated metabolic network reconstruction.

systems biology↗