Biology subjects

Pham, T. K.

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

3 recordsLinked to original sources

bioRxiv2025

Proteomic characterisation of Japanese quails unique seminal foam

Male Japanese quail (Coturnix japonica) produce a unique proctodeal foam upon ejaculation which is thought to enhance fertilisation success. However, the precise function and proteomic characterisation of this foam remain largely unexplored. Using high throughput LC-MS/MS proteomics analysis, we characterised the proteome of the quail seminal foam for the first time. Our analysis confidently identified 224 proteins in the foam using 32 pooled samples from 96 males. 96.4% of proteins had orthologs in the closely related (diverged 35 million years ago) chicken (Gallus gallus) which generated 40 Gene Ontology terms. Further interrogation revealed proteins involved in sperm motility, maturation and DNA protection, suggesting the foam plays a role in fertilisation success. Proteins linked to immune defence and inflammation modulation were identified, indicating the foam may protect sperm from antigens and reduce female immunogenic responses. This work advances our understanding of the function and evolution of Japanese quail unique seminal foam and directs future experiments to investigate the role of key seminal foam proteins in post-copulatory sexual selection. Significance of the StudySeminal fluid plays an important role in fertilisation success, yet the molecular components of seminal fluid and their function remain poorly understood in most species. This study provides the first comprehensive proteomic characterisation of a unique seminal foam produced by the Japanese quail (Coturnix japonica), revealing its potential mechanistic function in sperm regulation, sperm motility, immune protection, and fertilisation success. By identifying key proteins associated with energy production, membrane fluidity, and sperm maturation, our findings suggest the foam may influence post-ejaculatory sperm function. Additionally, the identification of immunity proteins indicates a role in sperm protection and modulation of female immune responses. This study advances our understanding of avian reproductive biology and opens new avenues for investigating the specific role of seminal foam proteins in fertilisation dynamics and post-copulatory sexual selection.

evolutionary biology↗

bioRxiv2024

Glutathione Oxidation in Cerebrospinal Fluid as a Biomarker of Oxidative Stress in Amyotrophic Lateral Sclerosis

BackgroundOxidative stress is a key feature of several neurodegenerative diseases, including Amyotrophic Lateral Sclerosis (ALS). Identification of reliable biomarkers of oxidative stress would be beneficial for drug-target engagement studies. MethodsWe performed unbiased quantitative mass spectrometry (MS)-based analysis to measure changes in protein abundance and oxidation in cerebrospinal fluid (CSF) from a cohort of ALS patients and healthy controls at two time points (approximately four months apart) to capture disease progression. In addition, we developed a sensitive and targeted quantitative MS method to measure glutathione oxidation state in the same sets of CSF samples. ResultsProteomic analysis of CSF revealed statistically significant changes in the abundance of several proteins, including CHIT1, CHI3L1, CHI3L2 and COL18A1 in ALS patients compared to healthy controls at both time points. Several sites of protein oxidation were significantly altered in ALS compared to healthy controls, and total levels of reversible protein oxidation were elevated in ALS patients. Given that glutathione oxidation could be a useful biomarker of oxidative stress, we also measured glutathione and its oxidation state in CSF in the same cohorts of samples. Total GSH (tGSH), GSSG levels and the GSSG/GSH ratio were significantly higher in the ALS than in the healthy control group for both time points. For the first visit, fold changes of tGSH, GSSG, and GSSG/GSH ratio in ALS compared to HC were 1.33 (p = 0.0215), 1.54 (p = 0.0041) and 1.80 (p = 0.0454), respectively. For the second visit, these values were 1.50 (p = 0.0143), 2.00 (p = 0.0018) and 2.14 (p = 0.0120), respectively. Furthermore, we found positive correlations between disease duration until the first visit and total glutathione (tGSH), GSSG and GSSG/GSH ratio. Finally, there was a strong positive correlation between the total intensity of reversibly oxidised proteins and the ratio of GSSG/GSH in ALS patients at both visits. ConclusionWe propose that measuring levels of glutathione oxidation in CSF could act as a stratification biomarker to select ALS patients for antioxidant therapy and an approach to monitor the treatment response to therapeutic agents targeting oxidative stress.

neuroscience↗

bioRxiv2024

Rapid degradation of Histone Deacetylase 1 (HDAC1) reveals essential roles in both gene repression and active transcription

Histone Deacetylase 1 (HDAC1) removes acetyl groups from lysine residues on the core histones, a critical step in the regulation of chromatin accessibility. Despite histone deacetylation being an apparently repressive activity, suppression of HDACs causes both up- and down-regulation of gene expression. Here we exploited the degradation tag (dTAG) system to rapidly degrade HDAC1 in embryonic stem cells (ESCs) lacking its paralog, HDAC2. Unlike HDAC inhibitors that lack isoform specificity, the dTAG system allowed specific degradation and removal of HDAC1 in <1 hour (100x faster than genetic knockouts). This rapid degradation caused increased histone acetylation in as little as 2 hours, with H2BK5 and H2BK11 being the most sensitive. The majority of differentially expressed genes following 2 hours of HDAC1 degradation were upregulated (275 genes up vs 15 down) with increased proportions of downregulated genes observed at 6 (1,153 up vs 443 down) and 24 hours (1,146 up vs 967 down) respectively. Upregulated genes showed increased H2BK5ac and H3K27ac around their transcriptional start site (TSS). In contrast, decreased acetylation of super-enhancers (SEs) was linked to the most strongly downregulated genes. These findings suggest a paradoxical role for HDAC1 in the maintenance of histone acetylation levels at critical enhancer regions required for the pluripotency-associated gene network.

molecular biology↗