Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Pharmacokinetic changes induced by focused ultrasound in glioma-bearing rats using dynamic contrast-enhanced MRI measurement

It has been shown that focused ultrasound (FUS) can be effectively used for brain tumor therapy, and as a noninvasive, targeted drug delivery technique combined with microbubbles. In this study, magnetic resonance imaging (MRI) was used to measure the kinetics of Gadolinium diethylenetriamine Penta acetic acid (Gd-DTPA) in glioma-bearing rats. Ten glioma-bearing rats (9-12 weeks, 290-340 g weight) were used in the study. After the use of dynamic contrast enhancement (DCE)-MRI, the spatial permeability of FUS-induced blood-brain barrier disruption (BBB-D) was evaluated, and the kinetic parameters by the general kinetic model (GKM) were calculated. The results show that mean trans K of the contralateral tumor was significantly lower than the mean trans K of sonicated tumor. Moreover, the transfer constant trans K in ultrasound tumors was closely related to tissue extravasation (R = 0.95), suggesting that DCE-MRI can determine drug accumulation in the brain. Except for a few small red blood cell extravasations, there was no macroscopic damage according to the histologic analysis. The study showed that the DCE-MRI can be a valuable tool in quantifying BBB permeability in tumors and monitor the kinetics of FUS-induced BBB-D processes.