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Rajendra Babu, K.

Publications and source records attributed to Rajendra Babu, K..

2 recordsLinked to original sources

Systematic optimization of Caenorhabditis elegans cryopreservation

Caenorhabditis elegans (C. elegans) is a non-parasitic roundworm widely utilized as a versatile model organism for studying fundamental biological processes. Despite the availability of multiple cryopreservation methods, variations in the selection of developmental stage, cryoprotectant composition, and storage conditions may sometimes cause inconsistencies and uncertainty among researchers. In this study, we followed a step-by-step approach to optimize the C. elegans cryopreservation process. Firstly, different larval stages (L1-gravid adult) of C. elegans were cryopreserved using a fixed concentration of trehalose-DMSO and glycerol, followed by the post-thaw survival rate assessment. We found that the starved L1 larvae has the highest survival rate among other developmental stages. Subsequently, the starved L1 larvae was cryopreserved using different concentrations (5%, 10%, and 15%) of DMSO and glycerol and found that 5% DMSO has the most effective cryoprotection. Finally, the impact of storage conditions on worm viability was evaluated by placing cryogenic vials in different storage boxes, including standard cardboard cryogenic boxes, Styrofoam boxes, and isopropanol-based freezing containers, and found that standard cardboard cryogenic boxes provided higher worm viability. The finalized protocol was then validated across multiple mutant and transgenic strains to confirm its reproducibility and broad suitability. Taken together, our results demonstrate that starved L1 larvae cryopreserved with 5% DMSO using a standard cardboard cryogenic box provided the highest survival rate (>90%) across wild-type, mutant, and transgenic strains. Here we propose a simple, reproducible, and strain-independent protocol for cryopreservation of C. elegans. The proposed protocol can be easily adopted in C. elegans research laboratories and stock centers globally.

genetics↗

Pan-cancer analysis of RNA binding proteins (RBPs) reveals the involvement of the core pre-mRNA splicing and translation machinery in tumorigenesis

RNA binding proteins (RBPs) are key regulators of posttranscriptional processes such as RNA maturation, transport, localization, turnover and translation. Despite their dysregulation in various diseases including cancer, the landscape of RBP expression and regulatory mechanisms in human cancer has not been well characterized. Here, we analyzed mRNA expression of 1487 RBPs in ~6700 clinical samples across 16 human cancer types and found that there were significantly more upregulated RBPs than downregulated ones in tumors when compared to their adjacent normal tissues. Across almost all of the 16 cancer types, 109 RBPs were consistently upregulated (cuRBPs) while only 41 RBPs were consistently downregulated (cdRBPs). Integrating expression with the copy number and DNA methylation data, we found that the overexpression of cuRBPs is largely associated with the amplification of copy number, whereas the downregulation of cdRBPs may be a result of epigenetic silencing mediated by DNA methylation. Furthermore, our results indicated that cuRBPs could work together to promote cancer progression potentially through the involvement of splicing and translation machinery, while cdRBPs might function independently to suppress tumorigenesis. Additionally, we focused on colon cancer and identified several novel potential oncogenic RBPs, such as PABPC1L which might promote cancer development via regulating the core splicing machinery. In summary, we showed distinct expression landscapes, regulatory mechanisms and characteristics of cuRBPs and cdRBPs and implicated several novel RBPs in cancer pathogenesis. Moreover, our results suggest that the involvement of the core pre-mRNA splicing and translation machinery could be critical in tumorigenesis.

systems biology↗