Assessing the Expression of Long INterspersed Elements (LINEs) via Long-Read Sequencing in Diverse Human Tissues and Cell Lines.

Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. LINEs replicate using an RNA intermediate followed by reverse transcription and are typically a few kilobases in length. LINE activity creates genomic structural variants in human populations and leads to somatic alterations in cancer genomes. Long-read RNA sequencing technologies, including Oxford Nanopore and PacBio, can directly sequence relatively long transcripts, thus providing the opportunity to examine full-length LINE transcripts. This study focuses on the development of a new bioinformatics pipeline for the identification and quantification of active, full-length LINE transcripts in diverse human tissues and cell lines. In our pipeline, we utilized RepeatMasker to identify LINE-1 (L1) transcripts from long-read transcriptome data and incorporated several criteria, such as transcript start position, divergence, and length, to remove likely false positives. Comparisons between cancerous and normal cell lines, as well as human tissue samples, revealed elevated expression levels of young LINEs in cancer, particularly at intact L1 loci. By employing bioinformatics methodologies on long-read transcriptome data, this study demonstrates the landscape of L1 expression in tissues and cell lines.

Structural and Morphological Properties of Wool Keratin and Cellulose Biocomposites Fabricated Using Ionic Liquids.

In this study, the structural, thermal, and morphological properties of biocomposite films composed of wool keratin mixed with cellulose and regenerated with ionic liquids and various coagulation agents were characterized and explored. These blended films exhibit different physical and thermal properties based on the polymer ratio and coagulation agent type in the fabrication process. Thus, understanding their structure and molecular interaction will enable an understanding of how the crystallinity of cellulose can be modified in order to understand the formation of protein secondary structures. The thermal, morphological, and physiochemical properties of the biocomposites were investigated by Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), and X-ray scattering. Analysis of the results suggests that both the wool keratin and the cellulose structures can be manipulated during dissolution and regeneration. Specifically, the ß-sheet content in wool keratin increases with the increase of the ethanol solution concentration during the coagulation process; likewise, the cellulose crystallinity increases with the increase of the hydrogen peroxide concentration via coagulation. These findings suggest that the different molecular interactions in a biocomposite can be tuned systematically. This can lead to developments in biomaterial research including advances in natural based electrolyte batteries, as well as implantable bionics for medical research.

The Impact of Composition and Morphology on Ionic Conductivity of Silk/Cellulose Bio-Composites Fabricated from Ionic Liquid and Varying Percentages of Coagulation Agents.

Blended biocomposites created from the electrostatic and hydrophobic interactions between polysaccharides and structural proteins exhibit useful and unique properties. However, engineering these biopolymers into applicable forms is challenging due to the coupling of the material's physicochemical properties to its morphology, and the undertaking that comes with controlling this. In this particular study, numerous properties of the Bombyx mori silk and microcrystalline cellulose biocomposites blended using ionic liquid and regenerated with various coagulation agents were investigated. Specifically, the relationship between the composition of polysaccharide-protein bio-electrolyte membranes and the resulting morphology and ionic conductivity is explored using numerous characterization techniques, including scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray scattering, atomic force microscopy (AFM) based nanoindentation, and dielectric relaxation spectroscopy (DRS). The results revealed that when silk is the dominating component in the biocomposite, the ionic conductivity is higher, which also correlates with higher ß-sheet content. However, when cellulose becomes the dominating component in the biocomposite, this relationship is not observed; instead, cellulose semicrystallinity and mechanical properties dominate the ionic conduction.

Facile treatment to fine-tune cellulose crystals in cellulose-silk biocomposites through hydrogen peroxide.

The modulation of structural fibrous protein and polysaccharide biopolymers for the design of biomaterials is still relatively challenging due to the non-trivial nature of the transformation from a biopolymer's native state to a more usable form. To gain insight into the nature of the molecular interaction between silk and cellulose chains, we characterized the structural, thermal and morphological properties of silk-cellulose biocomposites regenerated from the ionic liquid, 1-ethyl-3-methylimidazolium acetate (EMIMAc), as a function of increasing coagulation agent concentrations. We found that the cellulose crystallinity and crystal size are dependent on the coagulation agent, hydrogen peroxide solution. The interpretation of our results suggests that the selection of a proper coagulator is a critical step for controlling the physicochemical properties of protein-polysaccharide biocomposite materials.