DNA, Volume 5, Issue 2 (June 2025) – 4 articles

Background/Objectives: Branch dieback and canker diseases caused by Cytospora species adversely impact the health of woody plants worldwide. Results: During this survey, 59 Cytospora isolates were obtained from symptomatic trees and shrubs growing in southwest Ontario and Saskatchewan, Canada. A DNA barcoding approach combined with morphological characterization identified 15 known species of Cytospora associated with these diseases: C. chrysosperma, C. curvata, C. euonymina, C. hoffmannii, C. kantschavelii, C. leucosperma, C. leucostoma, C. nitschkeana, C. piceae, C. populina, C. pruinopsis, C. pruinosa, C. ribis, C. schulzeri, and C. sorbina. The most common species isolated from multiple hosts were C. sorbina (10), C. chrysosperma (8), C. nitschkeana (6), and C. pruinosa (6). A wide range of host associations, including non-conifer species, was observed for C. piceae. Conclusions: The obtained results contribute to the study of diversity, host affiliation, geographical distribution, and pathogenicity of Cytospora species occurring on woody plants in both natural habitats and agricultural systems. The findings support the effectiveness of using DNA barcodes in fungal taxonomy and plant pathology studies. Full article

DNA damage and repair have been central themes in cellular biology research. Broadly, DNA damage is understood as modifications to canonical nucleotides that disrupt their function during transcription and replication. A deeper biochemical understanding of DNA damage is essential, as the genome governs all cellular processes. We can classify DNA damage according to whether the modifications to the nucleic acid scaffold are chemically or enzymatically initiated. This distinction is important because chemical modifications are often irreversible, sometimes sparse, and difficult to detect or control spatially and replicate systematically. This can result in genomic damage or modifications to nucleotides in the nucleotide pool, which is less commonly studied. In contrast, enzymatic modifications are typically induced by the cell for specific purposes and are under strong regulatory control. Enzymatic DNA modifications also present a degree of sequence specificity and are often reversible. However, both types of DNA modifications contribute to cellular aging when poorly repaired and, as a result, remain incompletely understood. This review hopes to gather less studied mechanisms in nucleotide modifications and show research gaps in our current understanding of nucleotide biology. By examining the implications of these mechanisms on DNA modifications, in the nucleotide pool and genome, we may gain insights into innovative strategies for mitigating the effects of cellular aging. Full article

Background/Objectives: Thyroid hormones are key regulators in hepatic metabolic pathways. Although they regulate various hepatic genes, only a few are known to be under direct transcriptional regulation through thyroid hormone receptors. To better understand the roles of thyroid hormones in the liver, it is critical to identify thyroid hormone-responsive genes at the cellular level. Methods: A cDNA microarray analysis was applied to primary cultures of rat hepatic cells treated with triiodothyronine (T3) at 10⁻⁹ M for 24 h to identify the differentially expressed genes. The identified gene expressions were further examined in vivo using F344 rats. The reporter gene assay was performed to investigate the transcriptional activity of the upstream region of the gene. Results: A limited number of genes were listed, and only three of them, pyridoxal kinase (Pdxk), phosphoenolpyruvate carboxykinase 1 (Pck1), and solute carrier family 17 member 2 (Slc17a2), were confirmed to be upregulated by quantitative RT-PCR. The mRNA expression of these genes increased in the livers of F344 rats after T3 injection, suggesting the physiological relevance in vivo. There are two partially conserved thyroid hormone-responsive elements (TREs) in the upstream region of the rat Pdxk gene. The reporter gene assay indicated that an imperfect TRE (5′-gGGTCAxxxxAGGaCt-3′) located at −2146 was sufficient for the thyroid hormone-induced transcription of the gene. Conclusions: The present study identified novel T3-responsive genes, pdxk and Slc17a2. Promoter analyses showed that a single TRE in the pdxk gene accounts for the transcriptional regulation by T3. Full article

Cancers that arise from germline mutations of breast cancer associated gene 1 (BRCA1), which is a crucial player in homologous recombination (HR) DNA repair, are vulnerable to DNA-damaging agents such as platinum and PARP inhibitors (PARPis). Increasing evidence suggests that BRCA1 is an essential driver of all phases of the cell cycle, thereby maintaining orderly steps during cell cycle progression. Specifically, loss of BRCA1 activity causes the S-phase, G₂/M, spindle checkpoints, and centrosome duplication to be dysregulated, thereby blocking cell proliferation and inducing apoptosis. In vertebrates, loss of HR genes such as BRCA1 and/or BRCA2 is lethal, since HR is a prerequisite for genome integrity. Thus, cancer cells utilize alternative DNA repair pathways such as non-homologous end joining (NHEJ) to cope with the loss of BRCA1 function. In this review, we attempt to update and discuss how these novel components are crucial for regulating DNA damage repair (DDR) in BRCA1-deficient cancers. Full article