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The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

BackgroundThe accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues.ResultsA total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated genes. A median of two 5' untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as noncoding genes in fetal tissues but as protein-coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available quantitative trait loci data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network.ConclusionsThese validated results show significant improvement over current bovine genome annotations.

Purpose: This study aims to analyze the clinicopathological characteristics and survival outcomes of tongue cancer in the pediatric population, a topic with limited existing data, using a population‐based cohort. Methods: Pediatric patients diagnosed with tongue cancer from 1975 to 2018 were identified from the Surveillance, Epidemiology, and End Results (SEER) database. Survival rates were assessed using Kaplan–Meier analysis. Univariate survival analysis was conducted with the log‐rank test, while multivariate analysis involved Cox proportional‐hazards regression to identify factors influencing overall survival (OS). A predictive nomogram was developed based on Cox regression findings. Results: In total, 97 pediatric patients with tongue cancer were identified, with a median age at diagnosis of 15 years (range: 1–19 years). Tumors were classified as squamous cell carcinoma (45.4%), rhabdomyosarcoma (RMS) (13.4%), and others (41.2%). Of the patients, squamous cell carcinoma was more common in older children, whereas rhabdomyosarcoma was more common in younger children. The Cox proportional hazard regression revealed that histology and surgery were significant independent predictors of overall survival. The chance of death increased with no surgery. Moreover, patients with squamous cell carcinoma or rhabdomyosarcoma have a poorer survival percentage than patients with other subtypes. Conclusions: Tongue cancer in children is rare and associated with poor survival outcomes. This study highlights the significance of tumor histology and surgical intervention in determining overall survival, offering valuable insights for clinical decision‐making in pediatric tongue cancer. [ABSTRACT FROM AUTHOR]

This study focused on utilizing cellulose nanocrystal (CNC)–polyvinyl alcohol (PVA) composite in optical sensor applications to detect high humidity conditions and determine water concentration in ethanol. We focused on the composite's effectiveness in moisture absorption to demonstrate visual color change. We demonstrated that the different molecular weights of PVA significantly affect CNC's chiral nematic structure and moisture absorption capability. PVA with molecular weight 88 k–97 k exhibited the disintegration of its chiral nematic structure at 30 wt%, whereas low molecular weight PVA (n~1750) showed no structural disintegration even at 100 wt% concentration when analyzed through UV-Vis spectroscopy. Further, the thermal crosslinking of the CNC-PVA composite showed no significant loss of moisture sensitivity for all molecular weights of the PVA. We observed that the addition of PVA to the sulfated CNC obtained from sulfuric acid hydrolysis did not facilitate moisture absorption significantly. A CNC-PVA sensor was developed which can detect high humidity with 2 h. of exposure time. 2,2,6,6-tetramethylpiperidin-1-piperidinyloxy oxidized CNC (TEMPO-CNC) having carboxylic functionality was also used to prepare the CNC-PVA composite films for comparing the effect of functional groups on moisture sensitivity. Finally, we demonstrated a facile method for utilizing the composite as an optical sensor to detect water concentration in ethanol efficiently; thus, it can be used in polar organic solvent dehydration applications. [ABSTRACT FROM AUTHOR]

Background: Thoracic aortic dissection (TAD) is a silent killer. Approximately two-thirds of the cases occur in the ascending aorta (i.e. type A dissection) and majority of them are unrelated to genetic mutations. However, animal models of spontaneous type A dissection are not widely available. In the present study, a novel mouse TAD model was created. Further, the role of gasdermin D (GSDMD) in TAD development was evaluated., Methods: TADs were created by treating ascending aorta of adult mice (C57BL/6J) with active elastase (40.0 U/ml) and β-aminopropionitrile (Act E+BAPN). The temporal progress of the TAD pathology was rigorously characterized by histological evaluation and scanning electron microscopy, while potential mechanisms explored with bulk RNA sequencing of specimens collected at multiple timepoints. With this novel TAD model, further experiments were performed with Gsdmd -/- mice to evaluate its impact on TAD formation., Results: The ascending aorta challenged with Act E+BAPN developed pathology characterized by an early onset of intimomedial tears (complete penetration) and intramural hematoma, followed by progressive medial loss and aortic dilation. Ingenuity Pathway Analysis and functional annotation of differentially expressed genes suggested that a unique inflammatory micro-environment, rather than general inflammation, promoted the onset of TADs by specifically recruiting neutrophils to the aortic wall, while the pathology at the advanced stage was driven by T-cell mediated immune injury. Gsdmd -/- attenuated medial loss, adventitial fibrosis, and dilation of TADs. This protective effect was associated with a reduced number of TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) positive cells and T-cells in TADs., Conclusions: A novel mouse TAD model was created in the ascending aorta. It produces a unique microenvironment to activate different immune cell subsets, promoting onset and subsequent remodeling of TADs. Consistently, Gsdmd -/- attenuates TAD development, with modulation of cell death and T-cell response likely acting as the underlying mechanism.

Disruption of sleep and circadian rhythms are a comorbid feature of many pathologies, and can negatively influence many health conditions, including neurodegenerative disease, metabolic illness, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. The interaction between sleep and/or circadian rhythms with the use of Alternative Polyadenylation (APA) has been largely undescribed, particularly in the context of other disorders. APA is a process that generates various transcript isoforms of the same gene affecting its mRNA translation, stability, localization, and subsequent function. Here we identified unique APAs expressed in rat brain over time-of-day, immediately following sleep deprivation, and the subsequent recovery period. From these data, we performed a secondary analysis of these sleep- or time-of-day associated PASs with recently described APA-linked human brain disorder susceptibility genes., Competing Interests: Competing Interests J.G. is the founder of Blood Brain Biotechnology, LLC and a member of its scientific advisory board. Jon Davis is a principal scientist at Integrated Physiology Research, Novo Nordisk. All other authors declare no competing interests.