Biology subjects

Hwang, H. J.

Publications and source records attributed to Hwang, H. J..

6 recordsLinked to original sources

bioRxiv2025

Feeding Drosophila highly radioresistant fungi improves survival and gut morphology following acute gamma radiation exposure

Diverse fungi have been historically vital reservoirs of drug discovery, providing life-saving pharmaceuticals. Many species of fungi, yeasts in particular, are highly resistant to radiation, with their cellular contents potentially conferring dietary radioresistance. We developed a Drosophila model to test whether feeding two highly radioresistant fungi, Aureobasidium pullulans and Rhodotorula taiwanensis, could improve fly lifespan and gut morphology after acute irradiation. We constructed a dosimetry curve for the lifespan response of males and females to irradiation and found dose-dependent and sex-specific effects on lifespan. We also determined that the sex-specific response to irradiation correlated with nuclear morphology defects in the gut, with the more radiosensitive males displaying increased midgut cellular holes and aberrant nuclear morphology. To determine if feeding Aureobasidium pullulans and Rhodotorula taiwanensis before irradiation could improve survival and gut morphology, we first exclusively fed males and females each fungus and observed that they tolerated the diet well. Using these methods, we found that only two days of prefeeding Aureobasidium pullulans increased male lifespan, but not female, after irradiation, and improved nuclear morphology in the gut. However, dietary Rhodotorula taiwanensis was not protective. Overall, this study identified a highly radioresistant dietary fungus, Aureobasidium pullulans, as effective for extending male Drosophila lifespan and improving gut morphology following irradiation. Since the gut is particularly sensitive to the effects of irradiation, this fungus indicates a potential therapeutic for patients undergoing radiotherapy. Furthermore, this method could identify additional radioresistant fungi that protect the gut from radiation injury.

cell biology↗

bioRxiv2024

Drosophila Clueless ribonucleoprotein particles display novel dynamics that rely on the availability of functional protein and polysome equilibrium

The cytoplasm is populated with many ribonucleoprotein (RNP) particles that post-transcriptionally regulate mRNAs. These membraneless organelles assemble and disassemble in response to stress, performing functions such as sequestering stalled translation pre-initiation complexes or mRNA storage, repression and decay. Drosophila Clueless (Clu) is a conserved multi-domain ribonucleoprotein essential for mitochondrial function that forms dynamic particles within the cytoplasm. Unlike well-known RNP particles, stress granules and Processing bodies, Clu particles completely disassemble under nutritional or oxidative stress. However, it is poorly understood how disrupting protein synthesis affects Clu particle dynamics, especially since Clu binds mRNA and ribosomes. Here, we capitalize on ex vivo and in vivo imaging of Drosophila female germ cells to determine what domains of Clu are necessary for Clu particle assembly, how manipulating translation using translation inhibitors affects particle dynamics, and how Clu particle movement relates to mitochondrial association. Using Clu deletion analysis and live and fixed imaging, we identified three protein domains in Clu, which are essential for particle assembly. In addition, we demonstrated that overexpressing functional Clu disassembled particles, while overexpression of deletion constructs did not. To examine how decreasing translation affects particle dynamics, we inhibited translation in Drosophila germ cells using cycloheximide and puromycin. In contrast to stress granules and Processing bodies, cycloheximide treatment did not disassemble Clu particles yet puromycin treatment did. Surprisingly, cycloheximide stabilized particles in the presence of oxidative and nutritional stress. These findings demonstrate that Clu particles have novel dynamics in response to altered ribosome activity compared to stress granules and Processing bodies and support a model where they function as hubs of translation whose assembly heavily depends on the dynamic availability of polysomes.

cell biology↗

bioRxiv2024

Feeding a rich diet supplemented with the translation inhibitor cycloheximide decreases lifespan and ovary size in Drosophila

Drosophila oogenesis has long been an important model for understanding myriad cellular processes controlling development, RNA biology, and patterning. Flies are easily fed drugs to disrupt various molecular pathways. However, this is often done under poor nutrient conditions that adversely affect oogenesis, thus making analysis challenging. Cycloheximide is a widely used compound that binds to and stalls the ribosome, therefore reducing protein synthesis. Since egg production is a highly nutrient-dependent process, we developed a method to feed female Drosophila a rich diet of yeast paste supplemented with cycloheximide to better determine the effect of cycloheximide treatment on oogenesis. We find flies readily consume cycloheximide-supplemented yeast paste. Males and females have reduced lifespans when maintained on cycloheximide, with males exhibiting a dose-dependent decrease. While females did not exhibit decreased egg-laying, their ovaries were smaller and the number of progeny reduced, indicating substandard egg quality. Finally, females fed cycloheximide have disrupted oogenesis, with smaller ovaries, missing ovariole stages, and an increase in apoptotic follicles. Together, these data support that reduced protein synthesis adversely affects oogenesis with a rich diet that provides optimal nutrient conditions. In addition, this method could be used more broadly to test the effect of other drugs on Drosophila oogenesis without the confounding effects caused by poor nutrition.

developmental biology↗

bioRxiv2023

Density Physics-Informed Neural Network reveals sources of cell heterogeneity in signal transduction

The transduction time between signal initiation and final response provides valuable information on the underlying signaling pathway, including its speed and precision. Furthermore, multimodality in transduction-time distribution informs that the response is regulated by multiple pathways with different transduction speeds. Here, we developed Density physics-informed neural network (Density-PINN) to infer the transduction-time distribution, challenging to measure, from measurable final stress response time traces. We applied Density-PINN to single-cell gene expression data from 16 promoters regulated by unknown pathways in response to antibiotic stresses. We found that promoters with slower signaling initiation and transduction exhibit larger cell-to-cell heterogeneity in response intensity. However, this heterogeneity was greatly reduced when the response was regulated by slow and fast pathways together. This suggests a strategy for identifying effective signaling pathways for consistent cellular responses to disease treatments. Density-PINN can also be applied to understand various time delay systems, including infectious diseases.

systems biology↗

bioRxiv2020

The role of Ca2+ and protein scaffolding in the formation in nature's water oxidizing complex

The photosystem II (PSII) complex catalyzing the H2O-oxidation reaction of photosynthesis is highly prone to photodamage. Nature has evolved synthesis and repair mechanisms that include the photooxidative self-assembly, termed photoactivation, of the Mn4CaO5 metal cluster responsible for H2O-oxidation. Assembly is a multi-step light-driven process that proceeds with low quantum yield, involves a critical molecular rearrangement between light-activated steps, and is prone to photoinactivation and mis-assembly. A sensitive polarographic technique was used to track the assembly process under flash illumination as a function of the constituent Mn2+ and Ca2+ ions in genetically engineered samples to elucidate the action of Ca2+ and peripheral proteins. We show that the protein scaffolding that organizes this process is modulated allosterically by the assembly protein Psb27, which together with Ca2+, stabilizes the intermediates of photoactivation, a feature especially evident at long intervals between photoactivating flashes. Besides stabilizing intermediates, the Ca2+ ion is also critical to prevent photoinactivation due to inappropriate binding of Mn2+. Overexpression of Psb27, deletion of extrinsic protein PsbO, and excess Ca2+ characteristically modify these processes and retard the dark rearrangement. The results suggest the involvement of three metal binding sites, two Mn and one Ca with occupation of the Ca site by Ca2+ critical for the suppression of inactivation and the long-observed competition between Mn2+ and Ca2+ occurring at the second Mn site necessary for trapping the first stable assembly intermediates. Significance StatementThe oxidation of water by the photosystem II is the foundation of bioproductivity on Earth and represents a blueprint for sustainable, carbon neutral technologies. Water oxidation is catalyzed by a metal cluster containing of 4 Mn and 1 Ca atoms linked via oxo bridges. The initial assembly is a complex sequential reaction harnessing the photochemical reaction center to photooxidatively incorporate Mn2+ and Ca2+ ions into the catalytic unit embedded in the protein matrix. This photoassembly is crucial for both de novo biosynthesis and as part of the self-healing mechanism to cope with incessant photodamage that photosynthetic organisms experience. The results have implications for the natural mechanism as well as the highly desirable biomimetic devices currently envisioned for solar energy production.

biophysics↗

bioRxiv2019

Pan-genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia

The Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and Elizabethkingia meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84 respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75 and 0.54 respectively.

bioinformatics↗