Biology subjects

Ng, K. H.

Publications and source records attributed to Ng, K. H..

10 recordsLinked to original sources

bioRxiv2026

Modular gene tagging in C. elegans

Tagging a gene endogenously can identify when the gene is expressed and where the protein is localized. CRISPR is the primary tool for generating tags of endogenous genes, but it is error-prone and requires unique reagents for each gene and tag. Recombinases can insert DNA in an error-free and modular manner. Here, we tested eight recombinases for germline function in the nematode C. elegans, and introduce PhIT, a recombinase-based method for protein tagging. First, a short 39bp PhiC31 attB landing pad is inserted into the locus by CRISPR. This strain is a resource which can be used to insert a variety of modular tags. Second, tags are inserted by the integrase PhiC31, and in tandem, extraneous backbone sequences are removed by a tyrosine recombinase. Current modular tags include seven different fluorescent proteins, FLP-regulated cell-specific expression constructs, and degron tags. Importantly, tags can be inserted by genetic crosses instead of by microinjection.

genomics↗

bioRxiv2025

Learning Invariant Graph Representations for Cox Survival Modeling under Distribution Shifts

Survival prediction from high-dimensional biomedical data is frequently compromised by distribution shifts across multi-center cohorts, where models trained on specific populations often rely on spurious correlations that fail to generalize to new environments. While recent independence-driven reweighting techniques attempt to mitigate this, they typically treat patients as isolated instances, neglecting the intrinsic topological structures and biological pathways shared within patient populations. To address this limitation, we propose InvGraphCox (Invariant Graph Cox), a novel framework that integrates graph-structured representation learning with robust survival modeling. InvGraphCox constructs a k-nearest-neighbor patient graph to capture local manifold structures and employs a Variational Graph Autoencoder (VGAE) combined with a cohort-wise alignment mechanism to learn low-dimensional patient embeddings that are invariant to site-specific biases. We comprehensively evaluate the framework across three distinct experimental settings: the Curated Top-100 Gene Benchmark for stable biomarker identification, large-scale, high-dimensional transcriptomic datasets (Ovarian and Breast Cancer) for unsupervised representation learning, and clinical datasets (Breast and Lung Cancer) involving mixed-type covariates. Experimental results demonstrate that InvGraphCox consistently outperforms state-of-the-art baselines in terms of discrimination, calibration, and risk stratification, confirming its ability to extract robust, biologically meaningful representations in heterogeneous healthcare settings.

bioinformatics↗

bioRxiv2025

The serotonin 1B receptor modulates striatal activity differentially based on behavioral context

The dorsomedial striatum (DMS) is critical for goal-directed behavior and has been implicated in both motivating and inhibiting behavioral responses. The DMS circuitry is complex as it integrates multiple inputs from the cortex, thalamus, and other subcortical structures including midbrain dopamine neurons. Though less studied, serotonin neurons from the dorsal raphe nucleus also richly innervate the DMS, which expresses the majority of the 14 receptor subtypes for serotonin. In particular, slice electrophysiology shows that the serotonin 1B receptor (5-HT1BR) impacts DMS physiology and plasticity, and behavioral experiments show that 5-HT1BR expression modulates impulsivity and other DMS-dependent reward-related behaviors. In these studies, our goal was to investigate the effects of 5-HT1BR on the DMS in vivo during goal-directed behavior in mice. Using a genetic 5-HT1BR loss-of-function model, we examined the calcium activity of individual medium spiny neurons (MSNs) in the DMS during operant tasks of responding and waiting. We found that knockout of 5-HT1BRs resulted in a significant reduction of excitatory calcium responses and an increase in the proportion of cells with inhibitory calcium responses following receipt of a reward. This suggests that serotonin may recruit MSN activity in response to reward via actions at 5-HT1BRs. On the other hand, in a behavioral paradigm designed to test impulsivity, we found that serotonin may inhibit DMS calcium activity through 5-HT1BRs. Specifically, mice lacking 5-HT1BR expression had a larger proportion of cells showing increased calcium responses during the waiting period of the trial, compared to controls. These results point to the importance of in vivo studies to understand the functional role of DMS serotonin in reward-related behavior. Overall our results demonstrate that serotonin can modulate the DMS in a behavioral state-specific manner, potentially providing a mechanism for how serotonin effects on behavior are context-dependent.

neuroscience↗

bioRxiv2025

Predicting Early Transitions in Respiratory Virus Infections via Critical Transient Gene Interactions

Early detection of respiratory virus infections, such as influenza A (H3N2), is critical for timely intervention and disease management. Conventional biomarkers often overlook the complex and dynamic nature of gene regulatory changes, while existing predictive models frequently lack automation and robust external validation. Thus, we present CRISGI (Critical tran-Sient Gene Interaction), a computational framework that detects early-warning signals of infection by identifying dynamic changes in gene-gene interactions--termed critical transient interactions--from bulk RNA-seq data. CRISGI leverages critical transition (CT) theory to capture a GRNs unstable intermediate state, known as the CT stage, before irreversible phenotypic shifts. Applied to a human challenge study with H3N2, CRISGI identified 128 critical transition edges (128-TER). These were used to train predictive models capable of forecasting symptom status and onset timing. 128-TER was then validated across six temporal transcriptomic datasets involving three respiratory viruses (H3N2, H1N1, HRV). The 128-TER consistently distinguished symptomatic individuals, predicted infection onset, and revealed phenotype-specific enrichment patterns. Notably, CRISGI captured immune-related transitions involving interferon-stimulated genes (e.g., IFIT1, CXCL10), underscoring their role in early host defense. CRISGI advances early-warning biomarker discovery by integrating interaction-level dynamics and predictive modeling. Its reproducibility across viruses highlights shared immune activation pathways, supporting its utility in both research and clinical contexts.

bioinformatics↗

bioRxiv2024

Improving Mannanase Production in Bacillus subtilis for Fibre Hydrolysis during Solid-State Fermentation of Palm Kernel Meal

The primary challenge in utilizing palm kernel meal (PKM, an agricultural by-product) as non- ruminant livestock feed is its high fibre content, predominantly in the form of mannan. Microbial fermentation offers an economically favourable alternative to enzyme supplementation for breaking down fibre in lignocellulosic biomass. In a recent study, we have isolated and characterized an undomesticated strain (Bacillus subtilis F6) that is able to secrete mannanase. In this work, the mannanase production was substantially improved by optimizing multiple regulatory elements controlling the mannanase expression. Mannanase GmuG, sourced from B. subtilis F6 and verified for its hydrolytic activity on PKM fibre, was expressed using a replicative plasmid (pBE-S). The recombinant strain of B. subtilis F6 exhibited 1.9-fold increase in the mannanase activity during solid-state fermentation. Optimization of signal peptide and ribosome binding site further enhanced mannanase activity by 3.1-fold. Subsequently, promoter screening based on highly transcribed genes in B. subtilis F6 resulted in a significant 5.4-fold improvement in mannanase activity under the nprE promoter. The nprE promoter was further refined by eliminating specific transcription factor binding sites, enhancing the mannanase activity further by 1.8-fold. Notably, a substantial 35-40% reduction in PKM fibre content was observed after 30 h of fermentation using the recombinant strains. Lastly, the highest mannanase-producing strain was examined for scaled-up fermentation. The impacts of fermentation on fibre and protein contents, as well as the surface morphology of PKM, were analysed. The outcomes of this study offer an efficient method for robust mannanase expression in B. subtilis and its potential application in the biotransformation of PKM and other mannan-rich bioresources for improved feed utilization. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/602432v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@10fbb9corg.highwire.dtl.DTLVardef@1e619fborg.highwire.dtl.DTLVardef@1b3bc0corg.highwire.dtl.DTLVardef@fec816_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Hydrolysis of palm kernel meal fibre using a newly isolated Bacillus subtilis F6 with high mannanase activity

High fibre content is the main limitation of using mannan-rich palm kernel meal (PKM) in feeding non-ruminant livestock. Microbial fermentation stands out as a cost-effective and environmentally friendly approach for hydrolysing fibre in lignocellulosic biomass. In this study, a Bacillus subtilis strain F6 with high mannanase secretion capability was isolated from an environmental source. Fermentation of PKM using strain F6 resulted in at least a 10% reduction in its neutral detergent fibre content. Notably, the strain exhibited a rapid response to PKM, with significant mannanase activity detected as early as 6 h, enabling fibre hydrolysis within a short fermentation period. Subsequent transcriptome analysis uncovered potential enzymes involved in PKM fibre degradation, and the purified recombinant enzymes were generated to assess their activity on PKM fibre degradation. {beta}-mannanase GmuG demonstrated strong hydrolysis activity of PKM fibre, and its biochemical properties were determined. Overall, the study reported the isolation of a B. subtilis strain suitable for fibre hydrolysis of mannan-rich biomass, followed by an investigation to identify and characterize the enzyme responsible for fibre degradation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/599806v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@50b8c8org.highwire.dtl.DTLVardef@1937688org.highwire.dtl.DTLVardef@4b0ab6org.highwire.dtl.DTLVardef@ac727a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Does What You Eat Affect How You Mate? Disentangling the Interactions Between Diet-Induced Phenotypic Plasticity and Adult Reproductive Strategies in Black Soldier Flies.

Phenotypic plasticity enables organisms to response to environmental variations by generating a range of phenotypes from a single genotype. In holometabolous insects, traits that influence larval plasticity may hold relevance for adult life history strategies. We present a comprehensive investigation into phenotypic plasticity in black soldier flies, a species known for its efficient waste-to-biomass conversion in the larval stage. Here, we document adult sex-specific plastic responses and reproductive strategies shaped by larval diets. We examined traits including adult body size, reproductive organ development, sperm length, mating behaviours, egg production and other life history parameters across different treatments. Our findings reveal notable sex-specific differences in phenotypic plasticity, with females showing increased plasticity in reproductive investment. Furthermore, males and females differed starkly in allometric growth and weight ratio of reproductive organs. Diets that facilitated longer male lifespans also prompted earlier male emergence suggesting an interplay between lifespan and degree of protandry. This maximizes the overlap of male and female lifespans, thereby enhancing mating success in diverse environmental conditions. Our results reveal plastic responses in mating behaviours, where diets producing smaller adults, smaller reproductive organs, and shorter sperm correlated with significantly enhanced mating effort and performance. This study highlights the complex interactions between nutrition, development, and reproductive strategies, and has significant implications for the insect bioconversion industries.

evolutionary biology↗

bioRxiv2021

Organ-specific microbiota enhances the terrestrial lifestyle of a brachyuran crab

Brachyuran crabs originated in the oceans and evolved specific morphological and physiological adaptations to live in freshwater, intertidal and even terrestrial habitats but the role of a selection mechanism involving symbiotic microorganisms long these colonization processes are not known. In this work we investigated the associated microbiota of three populations of a terrestrial brachyuran crab, Chiromantes haematocheir, to find evidence of a conserved crab-specific microbiome unrelated to the population of origin and dissimilar from environmental microbial assemblages. Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs and environmental matrices to profile microbial communities. In spite of the presence of truly marine larval stages and no gregarious behaviour, favouring microbiota exchanges, we found common, organ-specific microbiota, associated to the gut and the gills of the crabs (with more than 15% of the genera detected specifically enriched only in one organ). Our results suggest an early establishment of a new common, stable microbiota in the transition from water to land.

zoology↗

bioRxiv2018

Sex differences in fear regulation and reward seeking behaviors in a fear-safety-reward discrimination task

Reward availability and the potential for danger or safety potently regulates emotion. Despite women being more likely than men to develop emotion dysregulation disorders, there are comparatively few studies investigating fear, safety and reward regulation in females. Here, we show that female Long Evans rats do not suppress conditioned freezing in the presence of a safety cue, nor do they extinguish their freezing response, whereas males do both. Females were also more reward responsive during the reward cue until the first footshock exposure, at which point there were no sex differences in reward seeking to the reward cue. Darting analyses indicate females might be able to regulate this behavior in response to the safety cue, suggesting they might be able to discriminate between fear and safety cues but do not demonstrate this with conditioned suppression of the freezing behavior. However, levels of darting in this study were too low to make any clear conclusions. In summary, females showed a significantly different behavioral profile than males in a task that tests the ability to discriminate among fear, safety and reward cues. This paradigm offers a great opportunity to test for mechanisms that are generating these behavioral sex differences in learned safety and reward seeking.

neuroscience↗

bioRxiv2018

Establishment of signaling interactions with cellular resolution for every cell cycle of embryogenesis

Intercellular signaling interaction plays a key role in breaking fate symmetry during animal development. Identification of the signaling interaction at cellular resolution is technically challenging, especially in a developing embryo. Here we develop a platform that allows automated inference and validation of signaling interaction for every cell cycle of C. elegans embryogenesis. This is achieved by generation of a systems-level cell contact map that consists of 1,114 highly confident intercellular contacts by modeling analysis and is validated through cell membrane labeling coupled with cell lineage analysis. We apply the map to identify cell pairs between which a Notch signaling interaction takes place. By generating expression patterns for two ligands and two receptors of Notch signaling pathway with cellular resolution using automated expression profiling technique, we are able to refine existing and identify novel Notch interactions during C. elegans embryogenesis. Targeted cell ablation followed by cell lineage analysis demonstrates the roles of signaling interactions over cell division in breaking fate symmetry. We finally develop a website that allows online access to the cell-cell contact map for mapping of other signaling interaction in the community. The platform can be adapted to establish cellular interaction from any other signaling pathways.

cell biology↗