The Dynamic Landscapes of Circular RNAs in Axolotl, a Regenerative Medicine Model, with Implications for Early Phase of Limb Regeneration.

Circular RNAs (circRNAs) are of relevance to regenerative medicine and play crucial roles in post-transcriptional and translational regulation of biological processes. circRNAs are a class of RNA molecules that are formed through a unique splicing process, resulting in a covalently closed-loop structure. Recent advancements in RNA sequencing technologies and specialized computational tools have facilitated the identification and functional characterization of circRNAs.

Data mining and molecular dynamics analysis to detect HIV-1 reverse transcriptase RNase H activity inhibitor.

HIV-1 is a deadly virus that affects millions of people worldwide. In this study, we aimed to inhibit viral replication by targeting one of the HIV-1 proteins and identifying a new drug candidate. We used data mining and molecular dynamics methods on HIV-1 genomes.

Machine Learning Methods for Virus-Host Protein-Protein Interaction Prediction.

The attachment of a virion to a respective cellular receptor on the host organism occurring through the virus-host protein-protein interactions (PPIs) is a decisive step for viral pathogenicity and infectivity. Therefore, a vast number of wet-lab experimental techniques are used to study virus-host PPIs. Taking the great number and enormous variety of virus-host PPIs and the cost as well as labor of laboratory work, however, computational approaches toward analyzing the available interaction data and predicting previously unidentified interactions have been on the rise.

A correlation coefficient-based feature selection approach for virus-host protein-protein interaction prediction.

Prediction of virus-host protein-protein interactions (PPI) is a broad research area where various machine-learning-based classifiers are developed. Transforming biological data into machine-usable features is a preliminary step in constructing these virus-host PPI prediction tools. In this study, we have adopted a virus-host PPI dataset and a reduced amino acids alphabet to create tripeptide features and introduced a correlation coefficient-based feature selection.

First case with RANBP2 biallelic mutation and severe acute necrotizing encephalopathy phenotype.

Familial acute necrotizing encephalopathy (ANE) is a rapidly progressive encephalopathy that can occur after common viral infections at different stages of life. The clinical findings of 2 siblings diagnosed with ANE were shared and the whole-exome-sequencing study of the index case was performed. It was confirmed by the Sanger method.

ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor.

Adenoviruses (AdVs) constitute a diverse family with many pathogenic types that infect a broad range of hosts. Understanding the pathogenesis of adenoviral infections is not only clinically relevant but also important to elucidate the potential use of AdVs as vectors in therapeutic applications. For an adenoviral infection to occur, attachment of the viral ligand to a cellular receptor on the host organism is a prerequisite and, in this sense, it is a criterion to decide whether an adenoviral infection can potentially happen.

Preclinical Molecular Signatures of Spinal Cord Functional Restoration: Optimizing the Metamorphic Axolotl () Model in Regenerative Medicine.

Regenerative medicine offers hope for patients with diseases of the central and peripheral nervous system. Urodele amphibians such as axolotl display an exceptional regenerative capacity and are considered as essential preclinical model organisms in neurology and regenerative medicine research. Earlier studies have suggested that the limb regeneration ability of this salamander notably decreases with induction of metamorphosis by thyroid hormones.

In Silico Analysis of a Highly Mutated Gene in Cancer Provides Insight into Abnormal mRNA Splicing: Splicing Factor 3B Subunit 1 Mutant.

Cancer is the second leading cause of death worldwide. The etiology of the disease has remained elusive, but mutations causing aberrant RNA splicing have been considered one of the significant factors in various cancer types. The association of aberrant RNA splicing with drug/therapy resistance further increases the importance of these mutations.

Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl.

The axolotl (Ambystoma mexicanum) salamander, a urodele amphibian, has an exceptional regenerative capacity to fully restore an amputated limb throughout the life-long lasting neoteny. By contrast, when axolotls are experimentally induced to metamorphosis, attenuation of the limb's regenerative competence is noticeable. Here, we sought to discern the proteomic profiles of the early stages of blastema formation of neotenic and metamorphic axolotls after limb amputation by employing LC-MS/MS technology.