Zakharova, M. | Search bioRxiv

bioRxiv2024

Switching to external flows: perturbations of developing vasculature within chicken chorioallantoic membrane

The impact of fluid flow shear stresses, generated by the movement of blood through vasculature, on the organization and maturation of vessels is widely recognized. Nevertheless, it remains uncertain whether external fluid flows outside of the vasculature in the surrounding tissue can similarly play a role in governing these processes. In this research, we introduce an innovative technique called superfusion-induced vascular steering (SIVS). SIVS involves the controlled imposition of external fluid flow patterns onto the vascularized chick chorioallantoic membrane (CAM), allowing us to observe how this impacts the organization of vascular networks. To investigate the concept of SIVS, we conducted superfusion experiments on the intact chick CAM cultured within engineered eggshell system, using phosphate buffered saline (PBS). To capture and analyze the effects of superfusion, we employed a custom-built microscopy setup, enabling us to image both superfused and non-superfused regions within the developing CAM. This study provides valuable insights into the practical application of fluid superfusion within an in vivo context, shedding light on its significance for understanding tissue development and manipulation in an engineering setting.

bioengineering↗

bioRxiv2022

Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules

The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide after N211 deletion, L212I substitution and EPE 212-214 insertion. The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.

immunology↗