Biology subjects

Krivoy, A.

Publications and source records attributed to Krivoy, A..

3 recordsLinked to original sources

bioRxiv2026

IPF AT2 cells are stuck in transition and biophysically dysfunctional

Idiopathic Pulmonary Fibrosis (IPF) is an incurable disease with extensive molecular, cellular, and organ level dysfunction. A major gap in IPF research is the lack of understanding of how short-term cellular behavior causes long-term tissue remodeling. By optimizing lung slices from explanted human lungs, we discovered foci of migratory non-canonical alveolar type 2 (AT2) cells in regions of established lung fibrosis and found that these cells are trapped in states of cellular transition that are driven by persistent developmental repair programs. Consistent with these biophysical behaviors, pharmacological activation of {beta}-catenin reproduced persistent migration, whereas YAP activation restrained it. We conclude that imbalanced developmental programs drive AT2 cell motility and lesion heterogeneity, providing a mechanistic link between short-term cellular dynamics and slowly progressive fibrosis of IPF.

cell biology↗

bioRxiv2022

Residual DNA in enzymes may pose a challenge for DIY RNA sequencing protocols: how to deal

High-throughput RNA sequencing (RNA-seq) is widely employed for gene expression profiling. This report on do-it-yourself RNA-Seq library preparation pitfalls, highlighting their correct identification and successful overcoming, may be helpful to research groups commencing a DIY RNA-Seq workflow and facing similar problems.

genomics↗

bioRxiv2021

SYSTEM ANALYSIS OF THE SEQUENCING QUALITY OF HUMAN WHOLE EXOME SAMPLES ON BGI NGS PLATFORM

Human whole exome sequencing (WES) is now the standard for most medical genetics applications worldwide. The leaders are manufacturers of enrichment kits that base their protocols on a hybridization approach using cRNA or cDNA biotinylated samples specific to regions of interest in the genome. Recently, platforms from the Chinese company MGI Tech have been successfully promoted in the markets of many countries in Europe and Asia. There is no longer any question about their reliability and the quality of the data obtained. However, very few task-specific kits for WES, in particular, are presented for these sequencers. We have developed our solution for library pre-capture pooling and exome enrichment using Agilent probes. In this work, we demonstrate on a set of standard benchmark samples from the Platinum Genome Collection that our protocol, called "RSMU_exome", is superior to the kit from MGI Tech in qualitative and quantitative terms. It allows detecting more SNVs and CNVs with superior sensitivity and specificity values, generates fewer PCR duplicates, allows more samples to be pooled in a single enrichment, and requires less raw data to produce results comparable to the MGI Tech solution. Also, our protocol is significantly cheaper than the kit from the Chinese manufacturer.

genomics↗