Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae
We report the first draft genome assembly for Prochilodus magdalenae, the leading representative species of the Prochilodontidae family in Colombia. This 1.2-Gb assembly, with a GC content of 42.0% and a repetitive content of around 31.0%, is in the range of previously reported characid species genomes. Annotation identified 34,725 nuclear genes, and BUSCO completeness value was 94.9%. Gene ontology and primary metabolic pathway annotations indicate similar gene profiles for P. magdalenae and the closest species with annotated genomes: blind cave fish (Astyanax mexicanus) and red piranha (Pygocentrus nattereri). A comparat...
Source: Frontiers in Genetics - January 19, 2023 Category: Genetics & Stem Cells Source Type: research

Editorial: Epigenetics of metabolism, immunology and aging
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 18, 2023 Category: Genetics & Stem Cells Source Type: research

Editorial: The functional role of non-coding RNAs in tumor microenvironment and metastasis of genitourinary tumor and its potential application as tumor molecular biomarkers
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 18, 2023 Category: Genetics & Stem Cells Source Type: research

Construction and validation of an aging-related gene signature predicting the prognosis of pancreatic cancer
Conclusion: In conclusion, we identified an aging-related signature and nomogram with high prediction performance of survival and immune cell infiltration for pancreatic cancer. This signature might potentially help in providing personalized immunotherapy for patients with pancreatic cancer. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 18, 2023 Category: Genetics & Stem Cells Source Type: research

Whole-genome DNA methylome analysis of different developmental stages of the entomopathogenic fungus Beauveria bassiana NCHU-157 by nanopore sequencing
The entomopathogenic fungus (EPF), Beauveria bassiana, is an important and commonly used EPF for microbial control. However, the role of DNA methylation has not been thoroughly studied. Therefore, the whole genomic DNA methylome of one promising EPF isolate, B. bassiana NCHU-157 (Bb-NCHU-157), was investigated by Oxford Nanopore Technologies (ONT). First, the whole genome of Bb-NCHU-157 was sequenced by next-generation sequencing (NGS) and ONT. The genome of Bb-NCHU-157 contains 16 contigs with 34.19 Mb and 50% GC content, which are composed of 10,848 putative protein-coding genes. Two putative DNA methyltransferases (DNM...
Source: Frontiers in Genetics - January 18, 2023 Category: Genetics & Stem Cells Source Type: research

Promoting patient engagement in cancer genomics research programs: An environmental scan
Conclusion: Programs studying cancer genomics are deeply committed to increasing research participation among diverse populations through patient engagement. Yet, the field needs to reach a consensus on the meaning of patient engagement, develop a taxonomy of patient engagement measures in cancer genomics research, and identify optimal strategies to engage patients in cancer genomics. Addressing these needs could enable patient engagement to fulfill its potential and accelerate the pace of cancer genomic discoveries. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 18, 2023 Category: Genetics & Stem Cells Source Type: research

High-expression of the innate-immune related gene UNC93B1 predicts inferior outcomes in acute myeloid leukemia
Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy with dismal prognosis. Identification of better biomarkers remained a priority to improve established stratification and guide therapeutic decisions. Therefore, we extracted the RNA sequence data and clinical characteristics of AML from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression database (GTEx) to identify the key factors for prognosis. We found UNC93B1 was highly expressed in AML patients and significantly linked to poor clinical features (p < 0.05). We further validated the high expression of UNC93B1 in another independent AML ...
Source: Frontiers in Genetics - January 18, 2023 Category: Genetics & Stem Cells Source Type: research

RNA modification writers pattern in relation to tumor microenvironment and prognosis in prostate cancer
Conclusion: This work is a comprehensive analysis of modified writers in prostate cancer and identified them to have a role in chemotherapy and immunotherapy. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 18, 2023 Category: Genetics & Stem Cells Source Type: research

Case report: A novel de novo loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia
Conclusion: This study has not only expanded the mutation spectrum in the gene TBX2 but also facilitated the diagnosis and genetic counseling of related features in affected families. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 17, 2023 Category: Genetics & Stem Cells Source Type: research

Biochemical exploration of β-lactamase inhibitors
This study discusses recent advances in our knowledge of the biochemistry behind β-lactam breakdown, with special emphasis on the mechanism of inhibitors for β-lactam complexes with β-lactamase. The study also focuses on the pharmacokinetic and pharmacodynamic properties of all inhibitors and then applies them in clinical settings. Our analysis and discussion of the challenges that exist in designing inhibitors might help pharmaceutical researchers address root issues and develop more effective inhibitors. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 17, 2023 Category: Genetics & Stem Cells Source Type: research

A shortest path-based approach for copy number variation detection from next-generation sequencing data
Copy number variation (CNV) is one of the main structural variations in the human genome and accounts for a considerable proportion of variations. As CNVs can directly or indirectly cause cancer, mental illness, and genetic disease in humans, their effective detection in humans is of great interest in the fields of oncogene discovery, clinical decision-making, bioinformatics, and drug discovery. The advent of next-generation sequencing data makes CNV detection possible, and a large number of CNV detection tools are based on next-generation sequencing data. Due to the complexity (e.g., bias, noise, alignment errors) of next...
Source: Frontiers in Genetics - January 17, 2023 Category: Genetics & Stem Cells Source Type: research

Preclinical species gene expression database: Development and meta-analysis
The evaluation of toxicity in preclinical species is important for identifying potential safety liabilities of experimental medicines. Toxicology studies provide translational insight into potential adverse clinical findings, but data interpretation may be limited due to our understanding of cross-species biological differences. With the recent technological advances in sequencing and analyzing omics data, gene expression data can be used to predict cross species biological differences and improve experimental design and toxicology data interpretation. However, interpreting the translational significance of toxicogenomics ...
Source: Frontiers in Genetics - January 17, 2023 Category: Genetics & Stem Cells Source Type: research

Identification of immune signatures in Parkinson ’s disease based on co-expression networks
In this study, the protein-protein interaction networks (PPI) data, 2747 human immune-related genes (HIRGs), 2078 PD-related genes (PDRGs), and PD-related datasets (GSE49036 and GSE20292) were downloaded from the Human Protein Reference Database (HPRD), Amigo 2, DisGeNET, and Gene Expression Omnibus (GEO) databases, respectively. An immune- or PD-directed neighbor co-expressed network construction (IOPDNC) was drawn based on the GSE49036 dataset and HPRD database. Furthermore, a PD-directed neighbor co-expressed network was constructed. Modular clustering analysis was performed on the genes of the gene interaction network ...
Source: Frontiers in Genetics - January 17, 2023 Category: Genetics & Stem Cells Source Type: research

Clinical and functional analyses of the novel STAR c.558C > A in a patient with classic lipoid congenital adrenal hyperplasia
Conclusion: Our findings reveal the molecular mechanisms underlying LCAH pathogenesis, further expanding the genotype and clinical spectrum of LCAH. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 17, 2023 Category: Genetics & Stem Cells Source Type: research

Employing machine learning using ferroptosis-related genes to construct a prognosis model for patients with osteosarcoma
Identifying effective biomarkers in osteosarcoma (OS) is important for predicting prognosis. We investigated the prognostic value of ferroptosis-related genes (FRGs) in OS. Transcriptome and clinical data were obtained from The Cancer Genome Atlas and Gene Expression Omnibus. FRGs were obtained from the ferroptosis database. Univariate COX regression and LASSO regression screening were performed and an FRG-based prognostic model was constructed, which was validated using the Gene Expression Omnibus cohort. The predictive power of the model was assessed via a subgroup analysis. A nomogram was constructed using clinical mark...
Source: Frontiers in Genetics - January 17, 2023 Category: Genetics & Stem Cells Source Type: research