Biology subjects

Pham, V. T.

Publications and source records attributed to Pham, V. T..

4 recordsLinked to original sources

bioRxiv2025

MLT-11 is necessary for C. elegans embryogenesis and conserved sequences play distinct roles in cuticle structure

Apical extracellular matrices (aECMs) are associated with many epithelia and many form a protective layer against biotic and abiotic threats in the environment. Despite their importance, we lack a deep understanding of their structure and dynamics in development and disease. C. elegans molting offers a powerful entry point to understanding developmentally programmed aECM remodeling. Here, we show that the poorly characterized putative protease inhibitor gene, mlt-11, is directly regulated by the NHR-23 transcription factor. We identify key cis-regulatory elements required for robust mlt-11 expression. An internal MLT-11::mNeonGreen translational fusion transiently localized to the aECM in the cuticle and embryo. MLT-11::mNeonGreen was also detected in lining openings to the exterior (vulva, rectum, mouth). mlt-11 is necessary to pattern all layers of the adult cuticle, and reduction of MLT-11 levels disrupted the barrier function of the cuticle. Deletion of conserved Kunitz protease inhibitor domains or intervening sequences produced a range of defects including either left or right rollers, and small separations of the cuticle along the length of the animal (microblisters). MLT-11 is processed into at least two fragments and internal and C-terminal mNeonGreen knock-ins display distinct localization patterns. Predicted mlt-11 null mutations caused fully penetrant embryonic lethality and elongation defects. Together, this work suggests that MLT-11 localizes similarly to pre-cuticle components and conserved sequences play distinct roles in promoting proper assembly of the aECM.

developmental biology↗

bioRxiv2024

LightMed: A Light-weight and Robust FFT-Based Model for Adversarially Resilient Medical Image Segmentation

Accurate and reliable medical image segmentation is essential for computer-aided diagnosis and formulating appropriate treatment plans. However, real-world challenges such as suboptimal image quality and computational resource constraints hinder the effective deployment of deep learning-based segmentation models. To address these issues, we propose LightMed, a novel efficient neural architecture based on Fast Fourier Transform (FFT). Different from prior works, our model directly learns on the frequency domain, harnessing its resilience to noise and un-even brightness, which common artifacts found in medical images. By focusing on low-frequency image components, we significantly reduce computational complexity while preserving essential image features. Our deep learning architecture extracts discriminative features directly from the Fourier domain, leading to improved segmentation accuracy and robustness compared to traditional spatial domain methods. Additionally, we propose a new benchmark incorporating various levels of Gaussian noise to assess susceptibility to noise attacks. The experimental results demonstrate that LightMed not only effectively eliminates noise and consistently achieves accurate image segmentation but also shows robust resistance to imperceptible adversarial attacks compared to other baseline models. Our new benchmark datasets and source code are publicly available at https://github.com/HySonLab/LightMed.

bioinformatics↗

bioRxiv2024

MLT-11 is a transient apical extracellular matrix component required for cuticle patterning and function

C. elegans molting offers a powerful entry point to understanding developmentally programmed apical extracellular matrix remodeling. However, the gene regulatory network controlling this process remains poorly understood. Focusing on targets of NHR-23, a key transcription factor that drives molting, we confirmed the Kunitz family protease inhibitor gene mlt-11 as an NHR-23 target. Through reporter assays, we identified NHR-23-binding sites that are necessary and sufficient for epithelial expression. We generated a translational fusion and demonstrated that MLT-11 is localized to the cuticle and lined openings to the exterior (vulva, rectum, mouth). We created a set of strains expressing varied levels of MLT-11 by deleting endogenous cis-regulatory element sequences. Combined deletion of two cis-regulatory elements caused developmental delay, motility defects, and failure of the cuticle barrier. Inactivation of mlt-11 by RNAi produced even more pronounced defects. mlt-11 is necessary to pattern every layer of the adult cuticle, suggesting a broad patterning role prior to the formation of the mature cuticle. Together these studies provide an entry point into understanding how individual cis-regulatory elements function to coordinate expression of oscillating genes involved in molting and how MLT-11 ensures proper cuticle assembly.

developmental biology↗

bioRxiv2020

Detecting Insulitis in Type 1 Diabetes with Ultrasound Phase-change Contrast Agents

Type 1 diabetes (T1D) results from immune infiltration and destruction of insulin-producing {beta}-cells within the pancreatic islets of Langerhans (insulitis), resulting in loss of glucose homeostasis. Early diagnosis during pre-symptomatic T1D would allow for therapeutic intervention prior to substantial loss of {beta}-cell mass at T1D onset. There are limited methods to track the progression of insulitis and {beta}-cell mass decline in pre-symptomatic T1D. During insulitis, the islet microvasculature increases permeability, such that sub-micron sized particles can extravasate and accumulate within the islet microenvironment. Ultrasound is a widely deployable and cost-effective clinical imaging modality. However, conventional microbubble contrast agents are restricted to the vasculature. Sub-micron sized nanodroplet (ND) phasechange agents can be vaporized into micron-sized bubbles; serving as a circulating microbubble precursor. We tested if NDs extravasate into the immune-infiltrated islet microenvironment. We performed ultrasound contrast-imaging following ND infusion in NOD mice and NOD;Rag1ko controls, and tracked diabetes development. We measured the biodistribution of fluorescently labeled NDs, with histological analysis of insulitis. Ultrasound contrast signal was elevated in the pancreas of 10w NOD mice following ND infusion and vaporization, but was absent in both the non-infiltrated kidney of NOD mice and pancreas of Rag1ko controls. High contrast elevation also correlated with rapid diabetes onset. In pancreata of NOD mice, infiltrated islets and nearby exocrine tissue were selectively labeled with fluorescent NDs. Thus, contrast ultrasound imaging with ND phase-change agents can detect insulitis prior to diabetes onset. This will be important for monitoring disease progression to guide and assess preventative therapeutic interventions for T1D. SignificanceThere is a need for imaging methods to detect type1 diabetes (T1D) progression prior to clinical diagnosis. T1D is a chronic disease that results from autoreactive T cells infiltrating the islet of Langerhans and destroying insulin-producing {beta}-cells. Overt disease takes years to present and is only diagnosed after significant {beta}-cells loss. As such, the possibility of therapeutic intervention to preserve {beta}-cell mass is hampered by an inability to follow pre-symptomatic T1D progression. There are immunotherapies that can delay T1D development. However identifying at risk individuals, and tracking whether therapeutic interventions are impacting disease progression, prior to T1D onset, is lacking. A method to detect insulitis and {beta}-cell mass decline would present an opportunity to guide therapeutic treatments to prevent T1D.

bioengineering↗