Suchergebnisse

iTRAQ labeling of peptides is widely used for quantitative comparison of biological samples using mass spectrometry. However, iTRAQ determined protein ratios have varying credibility depending on the number and quality of the peptide ratios used to generate them, and accounting for this becomes problematic particularly in the multirun scenario needed for larger scale biological studies. One approach to this problem relies on the use of sophisticated statistical global models using peptide ratios rather than working directly with the protein ratios, but these yield complex models whose solution relies on computational approaches such as stage-wise regression, which are nontrivial to run and verify. Here we evaluate an alternative pragmatic approach to finding differentially expressed proteins based on combining protein ratio p-values across experiments in a fashion similar to running a meta-analysis across different iTRAQ runs. Our approach uses the well-established Stouffer's Z-transform for combining p-values, alongside a ratio trend consistency measure, which we introduce. We evaluate this method with data from two iTRAQ experiments using plant and animal models. We show that in the specific context of iTRAQ data analysis this method has advantages of simplicity, high tolerance of run variability, low false discovery rate, and emphasis on proteins identified with high confidence. ; This work was supported through access to facilities managed by Bioplatforms Australia and funded by the Australian Government National Collaborative Research Infrastructure Strategy and Education Investment Fund Super Science Initiative.

iTRAQ labeling of peptides is widely used for quantitative comparison of biological samples using mass spectrometry. However, iTRAQ determined protein ratios have varying credibility depending on the number and quality of the peptide ratios used to generate them, and accounting for this becomes problematic particularly in the multirun scenario needed for larger scale biological studies. One approach to this problem relies on the use of sophisticated statistical global models using peptide ratios rather than working directly with the protein ratios, but these yield complex models whose solution relies on computational approaches such as stage-wise regression, which are nontrivial to run and verify. Here we evaluate an alternative pragmatic approach to finding differentially expressed proteins based on combining protein ratio p-values across experiments in a fashion similar to running a meta-analysis across different iTRAQ runs. Our approach uses the well-established Stouffer's Z-transform for combining p-values, alongside a ratio trend consistency measure, which we introduce. We evaluate this method with data from two iTRAQ experiments using plant and animal models. We show that in the specific context of iTRAQ data analysis this method has advantages of simplicity, high tolerance of run variability, low false discovery rate, and emphasis on proteins identified with high confidence. ; This work was supported through access to facilities managed by Bioplatforms Australia and funded by the Australian Government National Collaborative Research Infrastructure Strategy and Education Investment Fund Super Science Initiative.

Abstract
Neuropeptide Y (NPY), an endogenous peptide composed of 36 amino acids, has been investigated as a potential therapeutic agent for neurodegenerative diseases due to its neuroprotective attributes. This study investigated the neuroprotective effects of NPY in a mouse model of glaucoma characterized by elevated intraocular pressure (IOP) and progressive retinal ganglion cell degeneration. Elevated IOP in mice was induced through intracameral microbead injections, accompanied by intravitreal administration of NPY peptide. The results demonstrated that NPY treatment preserved both the structural and functional integrity of the inner retina and mitigated axonal damage and degenerative changes in the optic nerve under high IOP conditions. Further, NPY treatment effectively reduced inflammatory glial cell activation, as evidenced by decreased expression of glial fibrillary acidic protein and Iba-1. Notably, endogenous NPY expression and its receptors (NPY-Y1R and NPY-Y4R) levels were negatively affected in the retina under elevated IOP conditions. NPY treatment restored these changes to a significant extent. Molecular analysis revealed that NPY mediates its protective effects through the mitogen-activated protein kinase (MAPK) and PI3K/Akt signaling pathways. These findings highlight the therapeutic potential of NPY in glaucoma treatment, underscoring its capacity to preserve retinal health, modulate receptor expression under stress, reduce neuroinflammation, and impart protection against axonal impairment.