Search Results (10,296)

HCT116 is a colorectal cancer cell line frequently used in anti-tumor drug development experiments as well as in studies of the molecular machinery of eukaryotic cells. It is well characterized by the presence of several single-nucleotide and short mutations in multiple oncogenes and tumor suppressor genes, including KRAS, PIK3CA, MLH1, CTNNB1, CDKN2A, TGFBR2, and BRCA2. However, its landscape of large genomic rearrangements (LGRs) and copy number variants (CNVs) is still far from being fully understood. Therefore, the aim of this study was to identify LGRs and CNVs in several HCT116 cell line samples using Oxford Nanopore sequencing technology, including three samples from the SRA NCBI database, and to compare common and unique variants across all samples. Using the recently developed eLaRodON tool, we identified 22,666 common LGRs, among which more than 70% of tandem duplications and deletions larger than 80 kb were confirmed by CNV analysis. Among LGRs affecting protein-coding sequences, two in-frame rearrangements were identified: a deletion of exons 4–6 and a duplication of exon 10 in the CCSER1 gene, which encodes a cell division regulator protein. Given its high rearrangement rate in various tumors and the clinical significance of its overexpression, this finding may be potentially useful in future research on this cell line. Regarding differences between samples, we found that LGRs in the laboratory sample and in one of the three SRA NCBI samples occurred more frequently via ALR/Alpha repeats than via Alu repeats, in contrast to common LGRs and those unique to the other samples, a finding that may indicate the presence of unique mechanisms of genomic instability. Thus, this study reveals a broad spectrum of large genomic rearrangements and copy number variants that can be identified in the HCT116 cell line using Oxford Nanopore sequencing, including rearrangements specific to distinct cell line samples. Full article

Background/Objectives: Outer membrane vesicles (OMVs) are membrane-encapsulated spherical structures ~120 nm in diameter derived from Gram-negative bacterial cell envelopes. OMVs are primarily generated by outer membrane blebbing but contain proteins, DNA, and RNAs at concentrations distinct from that of the intracellular complement. OMVs have been associated with a number of different cellular functions including intercellular communication and resistance to phage. Methods: As bacterial small RNAs (sRNAs) also participate in bacteriophage defense and are specifically delivered to and enriched in OMVs, we recently elected to examine the effects of P22 infection on Salmonella cytosolic and OMV sRNA abundance by employing RNA sequencing. Results: We find that P22 infection triggers a global reduction in sRNAs (with Salmonella sRNA expression levels averaging only 15.6% those observed in noninfected cells) coupled with a reciprocal 72.7% global increase in Salmonella tRNA expression levels. Additionally, of note, while OMV small noncoding RNA (sncRNA) abundance is normally ~1/10 that found in the cytosol, we find that P22 infection triggers active OMV encapsulation and secretion of: (1) a subset of sRNAs, (2) all Salmonella tRNAs including one highly complementary to the P22 genome, and, much to our surprise, (3) ten distinct sRNAs expressed from P22. Conclusions: In summary, the work presented here identifies several Salmonella sncRNA cytosolic and/or OMV abundances significantly altered during P22 infection, and to our knowledge, this constitutes the first reported characterization of bacteriophage-encoded sRNAs being actively secreted within host OMVs. Full article

Poxviruses are large double-stranded DNA (dsDNA) viruses that cause important human and animal diseases, including smallpox and mpox. Poxviruses have also been identified in diverse bat populations; however, their potential for zoonotic transmission and adaptation to other mammalian hosts remains poorly understood. Poxviruses encode numerous immunomodulatory proteins that contribute to virulence, immune evasion, and host range. In this study, we performed a comparative genomic analysis of two bat-associated poxviruses belonging to the genus Vespertilionpoxvirus: hypsugopox virus (HYPV) and eptesipox virus (EPTV). Our analyses revealed 24 novel putative ORFs in HYPV and three in EPTV, thereby substantially expanding the inferred coding capacity of these viruses. Comparative analyses further revealed gene duplication and fragmentation events affecting several virulence and host range factors, as well as other unusual genomic features, including the presence of two divergent E3L homologs in EPTV. Together, our findings provide new insights into the genome evolution and potential host adaptation of bat-associated poxviruses and establish a foundation for future functional studies of Vespertilionpoxvirus biology, host–virus interactions, and zoonotic potential. Full article

Heat stress has emerged as one of the major environmental factors constraining rice growth. In our previous studies, OsPUP1, a member of the purine transporter protein family in rice, has been verified to be involved in the transport of cytokinin (CK). Unfortunately, the role of the OsPUP1 gene in the heat stress response has not been fully elucidated to date. In this study, we show that overexpression of OsPUP1, encoding a purine permease in rice, leads to severe growth inhibition and oxidative damage under heat stress. OsPUP1 overexpression lines exhibited increased accumulation of peroxides and malondialdehyde (MDA), along with significantly reduced activities of superoxide dismutase (SOD) and peroxidase (POD). Together with previous findings, these results suggest that OsPUP1 modulates CK transport, thereby influencing the spatial distribution of CK within the plant, which in turn regulates antioxidant defense mechanisms and heat stress response. This study uncovers a key role for OsPUP1 in controlling thermotolerance in rice and highlights the importance of CK distribution in plant adaptation to heat stress. Full article

A comprehensive analysis of the microcin J25 (MccJ25) biosynthetic gene cluster revealed a previously uncharacterized 96-base pair overlapping gene, designated mcjX. This gene features a +1 reading frame shift relative to the primary sequence and encodes a 31-amino acid peptide. Notably, 53 nucleotides overlap with the 3′ terminus of the structural gene mcjA. Such significant overlaps are rare features in the Escherichia coli genome, highlighting the hidden complexity of microbial operon architectures. In this study, we demonstrate that mcjX is actively translated. Functional assays, including green fluorescent protein reporter systems, suggest that McjX acts as a negative regulator of the mcjA promoter, modulating MccJ25 expression. This discovery represents the first report of a regulatory mechanism mediated by an overlapping gene within a lasso peptide operon, providing new perspectives on how microbial genomes fine-tune the production of antimicrobial peptides through compact genetic organization. Full article

p53 tumor suppressor evolved as a critical player in navigating the response to environmental stresses such as DNA or oxidative damage and drives cell fate by governing life and death decisions. The p53 protein is encoded by the most commonly mutated gene in human cancers. TP53 gene mutations are associated with worse prognosis and refractory and relapsed disease. The most prevalent mutations are of the missense type and often result in disruption of the DNA-binding capacity and transcription activity. In healthy cells, p53 protein is tightly regulated by its E3 ubiquitin ligase, MDM2 (HDM2), its own transcription target. Mutant p53, therefore, escapes the regulation by the negative feedback loop and is often found upregulated in cancer cells. The efforts to exploit wild-type and mutant p53 for precision oncology have been ongoing in the last two decades yet have not been successful. A recently reported strategy to target TP53-mutant cancers leverages induced proximity, utilizing the high cellular abundance of mutant p53 as a scaffold to concentrate a small-molecule inhibitor against an essential survival protein. This strategy relies on the Regulated Induced Proximity TArgeting Chimera (RIPTAC). Given the recent FDA approval of the first chimeric drug, vepdegestrant, killing by proximity might turn out to be a promising medical advancement for precision oncology. Full article

Background: Lychee fruits are sweet and juicy, yet mitochondrial genomic data for this species remains scarce, limiting in-depth studies of its genetic and evolutionary characteristics. To address this gap, in this study, the abortive-seeded cultivar ‘Xianjinfeng’ (XJF) and the large-seeded cultivar ‘Xinqiumili’ (XQML) were selected for analysis. Using third-generation sequencing technology, we sequenced, assembled, and annotated their mitochondrial genomes, and compared their structural characteristics and evolutionary relationships. Results: Assembly revealed mitochondrial genome sizes of 579,270 bp for XJF and 579,261 bp for XQML, both with 45.41% GC content. The mitogenomes contain 396 repetitive sequences, including 47 tandem repeats and 165 dispersed repeats, with SSR loci primarily 10–14 bp in length. Each genome encoded 62 genes, comprising 22 tRNAs, 3 rRNAs, and 35 protein-coding genes. Further analysis revealed 15 homologous sequences originating from chloroplasts in both mitochondrial genomes, totaling 12,194 bp (2.11% of the mitochondrial genome). These included 9 tRNA genes, 4 rRNA genes, and partial protein-coding sequences. Additionally, 184 simple sequence repeats (SSRs) were identified in both cultivars, whereas 564 and 563 potential RNA editing sites were predicted by computational tools in XJF and XQML, respectively, indicating subtle genetic differences between the cultivars. This study also analyzed codon usage preferences, nucleotide diversity, and chloroplast-to-mitochondria gene transfer events. Collinearity and comparative genomics results indicate that lychee is closely related to Nephelium lappaceum L. and Xanthoceras sorbifolium Bunge within the Sapindaceae family. Conclusions: In this study, two high-quality lychee mitochondrial genomes were successfully assembled and annotated, enriching the mitochondrial genome resources of Sapindaceae plants and laying a foundation for future lychee phylogenetic and evolutionary studies of closely related species. Full article

Background/Objectives: Autophagy is a key degradative pathway involved in orthodontic tooth movement. DNA damage-regulated autophagy modulator 1 (DRAM1), a protein that plays a central role in the degradation of autophagic cargo, exhibits differential regulation in human periodontal ligament (hPDL) fibroblasts under compressive force. Single-nucleotide polymorphisms (SNPs) may influence force-induced gene expression. Therefore, this study investigated the impact of DRAM1 SNPs on its expression in hPDL fibroblasts under compression force. Methods: The hPDL sample comprised cells of 59 patients. A physiological compressive strain of 2 g/cm³ was used to simulate orthodontic tooth movement. Total RNA from hPDL fibroblasts was isolated to determine DRAM1 relative gene expression under loaded conditions and in a physiological control. Furthermore, a genotyping analysis of six SNPs within the DRAM1 gene (rs756534 (G/T), rs2138257 (C/T), rs2176092 (C/T), rs4622329 (A/G), rs10860812 (A/G), and rs4764657 (A/G)) was performed using real-time polymerase chain reaction. DRAM1 expression was com-pared among genotypes of each SNP using an alpha of 5%. Linear regression analysis was then employed to evaluate SNP-SNP interaction. Results: The relative DRAM1 gene expression was not statistically significantly different (p > 0.05) according to the geno-types. The SNP-SNP interaction did not demonstrate any statistically significant associ-ation either. Conclusions: DRAM1 gene expression in hPDL fibroblasts under orthodontic compression may not be regulated by the studied intronic SNPs in the gene encoding DRAM1. Full article

Background/Objectives: The genes encoding HSPA1A, HSPA1B, and HSPA1L, located in the MHC class III region at 6p21.3–22.1, a region implicated in susceptibility to schizophrenia, are critical regulators of neurodevelopmental processes and contribute to synaptic neuroprotection. This study investigated whether the HSPA1A, HSPA1B, and HSPA1L genes are associated with schizophrenia. Methods: We sequenced the coding regions of HSPA1A, HSPA1B, and HSPA1L from 100 patients with schizophrenia to identify genetic variants. Further, we conducted a genetic association analysis of three SNPs (rs9469057, rs142416335, and rs2075800) in the HSPA1L gene in 519 patients with schizophrenia and 1492 healthy controls from the Taiwan Biobank. We analyzed the function of the HSPA1L protein via immunoblotting. Results: We identified 17 coding variants, including 8 missense and 9 synonymous mutations, in 100 patients with schizophrenia. Three variants (HSPA1L^p.Ala8Pro, HSPA1L^p.Ala8Thr, and HSPA1L^p.Glu602Lys) in the HSPA1L gene did not exhibit any significant differences in allele or genotype frequencies between patients and control subjects. Notably, one ultra-rare missense mutation, HSPA1L^p.Val262Met, was not documented in the control sample in Taiwan BioBank. Immunoblotting revealed HSPA1L^p.Val262Met mutant with decreased protein expression in SH-SY5Y cells compared with the wild type. Conclusions: While common variants in the HSPA1A, HSPA1B, and HSPA1L genes do not seem to be significant genetic risk factors for schizophrenia in this cohort, the ultra-rare mutation, HSPA1L^p.Val262Met, significantly reduces protein expression. These preliminary findings suggest that a potential loss-of-function or reduced expression of the HSPA1L gene may be a predisposing factor contributing to schizophrenia vulnerability in certain individuals. However, the finding should be replicated in other independent samples. The in vitro and in vivo impacts of the associated mutation at the HSPA1L gene on the pathophysiology of schizophrenia are worthy of future investigation. Full article

The oral pathogen Filifactor alocis encodes a repeats-in-toxin (RTX) protein, FtxA, that is encoded by the ftxA gene; it is present in approximately 50% of known isolated strains from various infected oral sites, including periodontitis, peri-implantitis, and root canal infections. It has been determined from PCR assessment of periodontally diseased cohorts in Ghana and Australia. Based on current knowledge, ftxA appears to be associated with both the progress and severity of periodontitis. This finding could potentially be linked to enhanced levels of ftxA-positive F. alocis, relative to ftxA-negative strain, and/or, in addition, a synergy between ftxA-positive strains and other periodontal pathogens. The exact mechanism remains unclear but may depend on an FtxA-mediated shifting of the host cell response toward immunosuppression. The main objective of the present work was to evaluate the prevalence and loads of F. alocis and the presence of ftxA in subgingival plaque in patients recruited for periodontal treatment in Sweden. This observational study included all samples that were received from external clinics over one full year (n = 71 patients). Our findings revealed that F. alocis was carried by 49 (69%) of the individuals, with the prevalence of ftxA amounting to 42.9% (n = 21). In 32 of the 71 samples, F. alocis could be quantitatively assessed. In this sub-population of F. alocis-positive patients, high loads of the bacterium were not related to age, and high loads were more frequently observed upon carriage of ftxA. The presence of, and co-colonization with, F. alocis with four additional periodontal pathogens was also evaluated. F. alocis was notable in that it co-colonized with all of the other species. Moreover, it was detected alongside two and even three of the other species within the same sample. Full article

Fruit color is a key quality indicator for apples and directly influences their market value. The process of fruit ripening encompasses various physiological and biochemical changes, such as the breakdown of chlorophyll and the buildup of anthocyanins and carotenoids. This study investigated the mechanism of chlorophyll degradation in apple peels using ‘Granny Smith’ varieties. The experiments involving the treatment with methyl jasmonate (MeJA) indicated that a concentration of 10 µM MeJA led to a reduction in chlorophyll degradation, while a higher concentration of 1500 µM MeJA enhanced this degradation, which aligned with the variations observed in the expression of genes associated with chlorophyll degradation. The key chlorophyll degradation gene MdSGR1 was cloned and found to be induced by methyl jasmonate. MdSGR1 encodes a 283-amino-acid protein belonging to the stay-green superfamily. The promoter possesses inducible cis-acting elements that respond to methyl jasmonate, low temperature and light, while the protein is localized to chloroplasts. Overexpression and silencing vectors were constructed. Overexpression of MdSGR1 induced chlorosis in tobacco leaves and ‘Granny Smith’ apple peels, decreased chlorophyll content, and upregulated related gene expression. Conversely, silencing MdSGR1 produced opposite effects. Arabidopsis thaliana plants overexpressing MdSGR1 exhibited low chlorophyll content, reduced photosynthetic rate, upregulated expression of genes associated with chlorophyll degradation. The results of yeast one-hybrid and dual-luciferase reporter assays indicated that the MdMYC2 transcription factor interacts with the promoter region of MdSGR1. In conclusion, MdSGR1 is crucial for the degradation of chlorophyll in apple peel, and it is regulated both by the MdMYC2 transcription factor and different concentrations of MeJA. This study preliminarily elucidated the regulatory mechanism of methyl jasmonate on chlorophyll degradation in fruit peel, and these findings provide an important theoretical basis for controlling degreening and color quality in apple fruit. Full article

Herpes simplex virus 1 (HSV-1) is a rare cause of acute hepatitis, especially in patients with chronic immunosuppression. We performed whole-genome HSV-1 sequencing with a metagenomics approach on peripheral blood samples from an Italian case of fatal acute liver failure with high circulating HSV-1 (1,129,900,000 copies/mL), followed by phylogenetic analysis. After multiple sequence alignment, a final dataset of 182 whole-genome sequences was selected. The sequenced HSV-1 strain belonged to a phylogenetic clade isolated in Florida in 2002 (OQ724868.1). A characterization of single nucleotide polymorphisms and indels was performed to determine their effects on the viral genome: only one variant, classified as an indel, was detected with a high impact effect (c.905_906insGTTTT) in the UL49A gene, which is known to encode a membrane protein regulating virion morphogenesis, replication and assembly. In addition, this study also detected variants in other genes involved in crucial steps of the HSV-1 life cycle, like alpha-regulation (US7), capsid transport (UL36) and viral polymerase function (UL30). In conclusion, the results of this variant analysis confirmed that in HSV-1 hepatitis, some viral regions may be hotspots for adaptive mutations with a substantial impact on viral replication or immune evasion. Full article

Drought stress is one of the most prevalent abiotic stressors and severely impairs plant growth and productivity. Therefore, identifying functional genes associated with drought tolerance is essential for the molecular breeding of drought-resistant crops. The RD22 (Responsive to Desiccation 22) gene family encodes conserved BURP domain-containing proteins that participate in plant responses to drought stress. In this study, two RD22 homologs, DsRD22a and DsRD22b, were isolated and characterized from the drought-tolerant ornamental species Dianthus spiculifolius. Sequence analysis showed that both proteins contain a conserved BURP domain and are typical members of the RD22 family. Tissue-specific expression analysis revealed that both genes were predominantly expressed in leaves and stems. Abiotic stress assays demonstrated that the expression levels of DsRD22a and DsRD22b were significantly induced by abscisic acid (ABA), osmotic stress, and salt stress, whereas their transcriptional responses to relatively low-temperature and oxidative stress were relatively weak. Subcellular localization analysis indicated that DsRD22a and DsRD22b proteins are localized in the cytoplasm. Heterologous overexpression assays showed that transgenic Arabidopsis thaliana lines overexpressing DsRD22a or DsRD22b exhibited significantly enhanced tolerance to salt and osmotic stresses compared with wild-type (WT) plants. Soil drought assays further confirmed that the transgenic lines had higher soluble protein contents and improved drought tolerance than WT plants. These findings suggest that DsRD22a and DsRD22b positively regulate plant responses to drought stress, potentially by promoting soluble protein accumulation. Collectively, DsRD22a and DsRD22b represent valuable candidate genes for the genetic improvement of drought tolerance in plants. Full article

Immunohistochemistry (IHC) is a widely used method for detecting specific proteins in tissue samples, helping diagnose diseases such as cancer. Traditional analysis methods rely heavily on human interpretation, which can lead to inconsistencies. In this study, we propose DeepFlare, a weakly supervised deep learning framework for cross-modality translation and segmentation of immunofluorescence and immunohistochemistry images. The proposed method utilizes multiplex immunofluorescence (mpIF) and co-registered IHC images, combined with preprocessing techniques such as affine transformation, stain normalization, noise reduction, and artifact removal. Multiple imaging channels, including hematoxylin, DAPI, Lap2, and nuclear envelope signals, are leveraged to generate segmentation masks using a U-Net++ architecture. The final segmentation mask is obtained through weighted fusion of modality-specific outputs. A generative adversarial network (GAN) is employed to measure translation fidelity between generated and real images. Weakly supervised learning techniques, including image-level supervision and consistency constraints, are applied to enhance performance under limited annotation scenarios. Pretrained pathology foundation encoders such as UNI and Virchow are integrated to extract multi-scale morphological and contextual features. Explainable AI techniques are incorporated to highlight critical regions and refine model attention. Experimental results demonstrate strong performance, achieving an SSIM of 0.7077 for image translation and a Dice score of 0.7424 for segmentation. The integration of the UNI encoder provides marginal improvement over the baseline (0.72 Dice score), indicating limited domain adaptation without fine-tuning on the dataset of 1264 training samples. Full article

1-Deoxy-D-xylulose-5-phosphate synthase (DXS) serves as the initial rate-limiting enzyme in the methylerythritol phosphate (MEP) pathway, governing the biosynthesis of precursors for photosynthetic pigments and terpenoids. In this study, the LaDXS2-2 gene was cloned and functionally characterized in lavender (Lavandula angustifolia). The full-length coding sequence (CDS) of LaDXS2-2 spans 2178 base pairs, encoding a protein of 725 amino acids. Phylogenetic analysis revealed that LaDXS2-2 is most closely related to the DXS from Salvia miltiorrhiza. Expression profiling demonstrated that LaDXS2-2 was highly expressed in flower buds, and its transcript levels were significantly upregulated (p < 0.05) in response to ethephon, high light intensity, and low temperature, while exhibiting tissue-specific responses to gibberellin application. Subcellular localization assays confirmed LaDXS2-2 is targeted to the chloroplast. Heterologous overexpression of LaDXS2-2 in tobacco resulted in a marked increase in photosynthetic pigment content, enhanced the actual photochemical efficiency of photosystem II [Y(II)], and reduced non-photochemical quenching (NPQ). Integrated transcriptomic and metabolomic analyses further revealed that LaDXS2-2 overexpression activated the diterpenoid biosynthesis pathway and upregulated amino acid metabolism as well as the TCA cycle, while competitively suppressing phenylpropanoid and flavonoid biosynthesis pathways. These findings indicate that LaDXS2-2 not only enhances photosynthetic efficiency by promoting the synthesis of photosynthetic pigments but also suggests a potential role in influencing primary carbon and nitrogen metabolism, as inferred from transcriptomic and metabolomic data. This functionality may ultimately influence plant growth and metabolic homeostasis. Overall, this study provides a theoretical foundation for the synergistic improvement of photosynthetic efficiency and secondary metabolism in crops. Full article