Search Results (1,472)

Transposable elements (TEs) are major components of plant genomes and play crucial roles in adaptive genome evolution and stress tolerance. Under abiotic stress, activated TEs can generate abundant genetic variation and regulate the expression of stress-responsive genes. As a pioneer species in desert and saline–alkali environments, Tamarix chinensis L. has been little studied with respect to the abundance and evolutionary relationships of its LTR retrotransposons, particularly their activation patterns under salt and alkali stresses. This study aimed to investigate the characteristics of the reverse transcriptase (RT) domain of LTR retrotransposons in T. chinensis and to determine their patterns of activation in response to salt and alkali stresses. A total of 629 Ty1-copia and 607 Ty3-gypsy RT nucleotide sequences, which displayed high AT/GC ratios and evidence of stop codon insertions, were identified in T. chinensis by amplicon sequencing. Among these, 211 Ty1-copia and 117 Ty3-gypsy RT sequences with potential transpositional activity each contained distinct domains, suggesting a high degree of conservation. Phylogenetic analysis revealed that the RT sequences of T. chinensis are closely related to those of mangrove, wild potato, and Ipomoea, and may have undergone horizontal transfer. Expression analysis showed that 634 and 181 RT sequences were activated under salt and alkali stresses, respectively, with the majority belonging to salt-induced Ty1-copia families. Compared with the control group, under salt and alkali stresses, the cTy1-copia elements (Ty1-copia with amplificated from cDNA of T. chinensis, the same below) with dominant abundance were mainly concentrated in the Angela subfamily, while the cTy3-gypsy elements induced by alkali stress were primarily distributed in the Tekay and Reina subfamilies. Furthermore, four cTy1-copia and five cTy3-gypsy were identified as candidate key LTR retrotransposons responsive to salt and alkali stresses. Overall, this study provides new insights into the epigenetic mechanisms underlying the adaptation of T. chinensis to saline and alkali stresses and offers a theoretical basis for its potential applications in saline–alkali land reclamation. Full article

The SARS-CoV-2 Omicron variant caused a global surge in COVID-19 cases following its emergence in November 2021, rapidly diversifying in the subsequent months. Although many studies have documented Omicron’s diversification, few have explored its impact on pediatric populations or the seasonality of other respiratory viruses in children. This study aims to investigate the diversity and circulation patterns of SARS-CoV-2 Omicron sublineages in pediatric patients in São Paulo, Brazil, and assess their co-circulation with other respiratory pathogens. Respiratory samples collected from patients under 18 years old across five hospitals between January 2022 and April 2023 were tested for different respiratory viruses using real-time RT-PCR. Whole-genome sequencing was performed on SARS-CoV-2-positive samples. Among the 7868 pediatric respiratory samples tested, 3902 were positive for viral pathogens. Respiratory Syncytial Virus accounted for the highest number of positive cases (n = 1248), exhibiting an atypical off-season peak in November 2022. SARS-CoV-2 was detected in 297 samples, of which 103 were sequenced. BA.1 and BA.5 sublineages had predominant genomic diversity and circulation time. These findings highlight the Omicron variant’s significant impact on the epidemiology and seasonal distribution of respiratory viruses in children, emphasizing the ongoing need for vaccination and robust surveillance efforts in pediatric populations. Full article

Background: Goji berry, known as a “superfood”, is widely distributed in northwest China and possesses significant medicinal and health value. The CER gene family serves as a key regulator of cuticular wax synthesis, which plays important roles in enhancing plant drought resistance and disease tolerance. However, genome-wide identification of the goji CER gene family and its expression analysis across different varieties and organs have not been reported. Methods: Based on SEM observations and wax load measurements, this study identified CER gene family members using whole genome data of the goji berry. Representative genes were selected and their expression patterns in different varieties and organs were validated by qRT‒PCR. Results: The stem wax load was significantly higher than that in other organs, while the leaf wax load of ‘Ningqi I’ goji was significantly higher than that in other varieties, consistent with SEM observations. A total of 113 CER gene family members were identified in goji berry, which were unevenly distributed on 12 chromosomes. The goji CER proteins mainly localized in the cell membrane, cytoplasm, chloroplast, and nucleus and clustered into five subfamilies. Ten conserved motifs were identified in CER proteins, with Motif5 and Motif7 being the most widely distributed. The LbaCER10-1 gene contained the highest number of exons (39). Cis-acting elements related to light-responsiveness, MeJA-responsiveness, and ABA-responsiveness showed high frequencies. Goji berry shared more homologous CER genes with tomato, potato, and tobacco than with Arabidopsis, with chr3 and chr9 being most conserved while chr7 showed greater variation. Conclusions: Integrating SEM, wax load, and qRT‒PCR results, LbaCER1-1 was identified as a candidate gene responsible for the higher wax load on goji stems, while LbaCER2-5 and LbaCER3-12 were candidate genes for greater wax load on ‘Ningqi I’ leaves. Full article

Aluminum (Al) is solubilized as phytotoxic Al³⁺ in acidic soils, rapidly inhibiting root elongation. To detoxify Al, plant roots secrete organic acids that chelate the ion. The transcription factor SENSITIVE-TO-PROTON-RHIZOTOXICITY1 (STOP1) regulates the export, distribution and metabolism of organic acids, which is crucial for Al resistance. Plant DICARBOXYLATE-CARRIERs (DICs) located in the inner mitochondrial membrane are presumed to exchange the dicarboxylates. However, whether Al or STOP1 modulates DIC expression to coordinate the organic acid shuttle remains unclear. Here, in the model legume Medicago truncatula, we identified three DIC genes and twelve in tetraploid Medicago sativa. Phylogenetic analysis places all Medicago DICs in a clade with Arabidopsis AtDIC1 and AtDIC2, whereas AtDIC3 lacks an ortholog in M. truncatula. Mining RNA-seq datasets followed by qRT-PCR validation showed that MtDIC2 is upregulated by Al in roots in a MtSTOP1-dependent manner. Consistently, STOP1-binding motifs exist in the MtDIC2 promoter, and MtSTOP1 binds to the MtDIC2 promoter in yeast. Furthermore, MsDIC2.4 shows an increase under Al treatment. Our study provides a genome-wide characterization of Medicago DICs and identifies MtDIC2 as a candidate target of MtSTOP1, whose Al-responsive induction may enhance organic acid flux across the mitochondrial membrane. Full article

Radiotherapy (RT) is a standard treatment for cervical cancer, but its efficacy is often limited by tumor hypoxia and low radiosensitivity. Radiosensitizers that enhance RT without dose escalation are therefore of clinical interest. Alpha-mangostin (AM), a xanthone from Garcinia mangostana, exhibits anticancer and ROS-inducing properties. This study evaluated whether AM enhances radiosensitivity in vitro. Cytotoxicity (0–35 µM) was assessed by the MTT assay, and radiation sensitivity (0–6 Gy) was assessed by clonogenic survival. γ-H2AX immunofluorescence, cell cycle distribution, apoptosis induction, and clonogenic survival assessments were used to investigate the radiosensitization effect. AM showed dose-dependent cytotoxicity in HeLa cells at an inhibitory concentration 20 (IC20) of 13.67 µM while sparing fibroblasts. The radiation lethal dose 20 (LD20) was 1.4 Gy. However, combination treatment used AM at 12 µM (IC14) combined with 2 Gy (LD30) irradiation to avoid 50% cell death. AM enhanced G2/M arrest by 21.10% (p < 0.01) versus controls. In combination treatment, AM significantly increased γ-H2AX-positive cells to 48.2% (p < 0.0001), elevated apoptosis to 39.48% (p < 0.0001), and decreased clonogenic survival to 28% (p < 0.0001) compared with control. A combination index of about 0.9 indicated synergism. Therefore, AM effectively radiosensitized HeLa cells via increased DNA double-strand breaks and G2/M arrest. Full article

Background: PAL genes are crucial for plant growth and stress response, yet studies on the PAL gene family in Camellia nitidissima are sparse. Methods: The PAL gene family was screened from the entire genome of C. nitidissima, and their physicochemical properties, chromosomal locations, intraspecific and interspecific collinearity, conserved motifs, phylogenetic trees, cis-acting elements, and gene structures were analyzed. The expression patterns of the CnPAL genes were compared across different tissues, and the highly expressed CnPAL1 gene was expressed in prokaryotes, and its enzyme activity was validated using UPLC-MS technology. Results: The results revealed that six CnPALs were identified in the C. nitidissima genome, distributed unevenly across six chromosomes. The CnPAL proteins shared similar physicochemical properties, with highly conserved motifs and gene structures. Promoter analysis showed multiple cis-acting elements in the CnPALs genes. Intra-species collinearity analysis revealed that all CnPALs were collinear with multiple PAL genes in C. nitidissima, while inter-species collinearity analysis indicated that CnPALs were collinear with the PAL genes in Camellia oleifera and Camellia sinensis. Furthermore, the transcriptomic data of C. nitidissima demonstrated tissue-specific expression of the CnPALs, although qRT-PCR validation showed some discrepancies with the sequencing result. The qRT-PCR revealed varied expression patterns among the six CnPALs, with the CnPAL1 gene showing relatively higher expression levels. Subsequently, cloning, prokaryotic expression, and enzyme activity analysis confirmed the effective catalytic activity of the CnPAL1 protein. Conclusions: This study lays the foundation for understanding the functions of CnPAL genes and offers insights for genetic improvement of C. nitidissima. Full article

Background: Cryptochromes (CRYs) are not only blue-light receptors in plants but also participate in abiotic stress responses, making them essential for plant growth and development. Methods: In this study, the CRY gene family in potato (StCRY) was identified and analyzed using bioinformatics approaches, and the expression patterns of StCRY genes under different abiotic stresses were validated through transcriptome datasets and RT-qPCR analysis. Results: A total of 7 StCRY genes were identified, unevenly distributed across 4 chromosomes. The StCRY genes exhibit conserved structures, with predicted subcellular localization primarily in the nucleus, cytoplasm, and plastids. Promoter region analysis revealed the significant presence of cis-acting elements related to light, plant growth and development, hormones, and stress responses. Phylogenetic analysis classified the CRY gene family into three subgroups and identified one pair of collinear genes. StCRY genes show a closer evolutionary relationship with tomato, followed by Arabidopsis thaliana, and are least related to rice. Transcriptome and RT-qPCR analyses under cold, drought, and salt stresses revealed differential expression among StCRY genes: StCRY3 and StCRY7 respond positively to cold stress, StCRY1 and StCRY5 are upregulated under drought and salt stresses, and StCRY7 expression is positively correlated with salt stress. Conclusions: Collectively, this study provides a preliminary characterization of the CRY gene family in potato and establishes a theoretical foundation for further investigations into the molecular mechanisms of blue-light receptors in abiotic stress responses. Full article

Thaumatin-like proteins (TLPs), a subfamily of pathogenesis-related (PR) proteins, play a vital role in plant defense against pathogens. In this study, 23 CsTLP genes were identified in the Citrus sinensis genome. These genes encode proteins ranging from 203 to 512 amino acids, with molecular weights between 21.88 and 53.75 kDa, classifying them as small molecular weight proteins. The CsTLP genes are unevenly distributed across eight chromosomes, with chromosome 3 containing the highest number (6 genes). Subcellular localization predictions indicate that most CsTLPs are located in the extracellular space. Phylogenetic analysis with Arabidopsis thaliana TLPs classified the CsTLPs into 10 clades, with clade 5 being the largest. Three segmentally duplicated gene pairs were identified, suggesting a mechanism for the expansion of this gene family. Expression profiling revealed tissue-specific patterns, with the highest expression levels observed in roots and leaves. Under biotic stress, qRT-PCR analysis of 12 selected CsTLPs demonstrated pathogen-specific responses: CsTLP9 and CsTLP22 were strongly upregulated during Huanglongbing (HLB, bacterial) infection, by 21.70-fold and 9.47-fold, respectively. Multiple genes, including CsTLP5/13/18/21/23, exhibited over 10-fold upregulation following Citrus Anthracnose (CA, fungal) infection; however, most genes showed only weak responses to Citrus tristeza virus (CTV, viral). These findings underscore the regulatory significance of CsTLPs in pathogen responses and provide an important theoretical foundation for enhancing molecular disease-resistance breeding in Citrus sinensis. Full article

Lipid transfer proteins (LTPs) play crucial regulatory roles in plant growth, development, and abiotic stress responses. Stipagrostis pennata is a species of grass widely distributed in arid and semi-arid regions, particularly adapted to desert and steppe environments. Under extreme drought conditions, it exhibits a variety of physiological and morphological adaptation mechanisms, making it an important species for studying plant drought tolerance. Recently, LTPs have been found to exhibit upregulated expression under drought stress in plants such as wheat and tobacco, enhancing their drought tolerance. However, the functional role of LTPs in S. pennata remains unexplored. In this study, the SpLTP1 gene was isolated from S. pennata via molecular cloning, encoding a 116-amino acid protein. Phylogenetic analysis revealed that this protein contains a highly conserved nsLTP1 (cd01960) domain and has high sequence similarity with LTPs of Setaria viridis, Setaria italica, Musa acuminata and Phragmites australis. qRT-PCR revealed that SpLTP1 was highly expressed and dynamically regulated under drought, suggesting its potential role in root rhizosheath formation and drought tolerance. To investigate SpLTP1 function, SpLTP1-overexpressing (SpLTP1-OE) and complementation (SpLTP1-atltp) Arabidopsis lines were generated using the floral dip method, in comparison with the existing wild-type (WT) and the LTP-deficient mutant (atltp). Drought stress phenotyping and physiological assays indicated that SpLTP1 likely enhances drought tolerance by elevating antioxidant enzyme activities and osmolyte accumulation. Comparative transcriptome analysis of SpLTP1-OE and WT plants further suggested that SpLTP1 modulates critical pathways, including phenylpropanoid biosynthesis, zeatin biosynthesis, and plant hormone signal transduction, thereby influencing plant growth and stress adaptation. These findings not only provide novel insights into the molecular mechanisms by which SpLTP1 regulates rhizosheath development in S. pennata but also establish a foundation for deciphering its role in extreme drought adaptation. Full article

(1) Background: The BMP/GDF (Bone Morphogenetic Protein/Growth Differentiation Factor) subfamily (Decapentaplegic-Vg1-related, DVR) within the transforming growth factor beta (TGF-β) superfamily plays critical roles in governing biological developmental processes and physiological functions. (2) Methods: In this study, we systematically investigated the DVR gene family in hexaploid Qihe gibel carp (Carassius gibelio var. Qihe) through comprehensive genomic identification, phylogenetic analysis, chromosome mapping, and cis-regulatory element prediction. The experimental design for gene expression analysis involved collecting samples from multiple tissues (brain, muscle, liver, kidney, etc.) and different developmental stages (20, 45, and 60 days post hatching, dph) to examine the expression patterns of four GDF8 genes using quantitative real-time PCR (qRT-PCR). (3) Results: We identified 50 DVR members in Qihe gibel carp. Phylogenetic analysis classified the 50 DVR family members into 20 distinct protein types, with 29 BMPs (Bone Morphogenetic Proteins) and 21 GDFs (Growth Differentiation Factors) identified. All 50 DVR proteins of Qihe gibel carp have similar TGF-β domains except for four BMP1 proteins. Chromosomal localization revealed widespread distribution of DVR members across 36 chromosomes, a pattern potentially linked to the hexaploid genome of Qihe gibel carp. Genes within the same subgroup exhibited conserved intron–exon architectures and similar intron numbers; syntenic conservation within subgroups may reflect functional constraints after polyploidization, implying evolutionary pressure to maintain functional domains. Through spatiotemporal expression profiling, we uncovered functional divergence among four GDF8 (myostatin) paralogs: GDF8-1 and GDF8-2 were predominantly expressed in brain and muscle tissues (dorsal and caudal), while GDF8-3 and GDF8-4 showed hepatic, cerebral, and renal specificity. Intriguingly, all paralogs exhibited a gradual upregulation during late development (20–60 days post hatching, dph), with peak expression staggered between 45 dph (GDF8-1/2) and 60 dph (GDF8-3/4). (4) Conclusions: These findings suggest that GDF8 plays a critical regulatory role in the growth and development of Qihe gibel carp. Collectively, these results provide a foundation for further investigations into the functional roles of the DVR gene family during the ontogenetic development of this species. Full article

Background/Objectives: Breast cancer remains one of the leading causes of cancer-related mortality in women worldwide, highlighting the urgent need for effective and less toxic therapeutic strategies. Thymoquinone (TQ), a bioactive phytochemical derived from Nigella sativa, possesses antioxidant and anticancer activities. Methotrexate (MTX), a widely used folate antagonist, is an established chemotherapeutic agent but is limited by toxicity and resistance. This study aimed to investigate the potential synergistic effects of TQ and MTX in estrogen receptor-positive MCF-7 breast cancer cells. Methods: MCF-7 cells were exposed to TQ (0–100 μM), MTX (0–10 μM), and their combinations for 24–72 h. Cell viability was assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, and drug interactions were evaluated using the Chou–Talalay method. Apoptosis was quantified by Annexin V/Propidium Iodide (PI) flow cytometry, and cell cycle distribution was analyzed by PI staining. Intracellular reactive oxygen species (ROS) generation was measured using a 2′,7′-Dichlorofluorescin diacetate (DCFH-DA) assay, while antioxidant enzyme (superoxide dismutase (SOD), catalase (CAT)) activities were quantified spectrophotometrically. Gene expression of Bax, Bcl-2, NF-κB, MMP-2, and MMP-9 was determined by Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). Results: TQ and MTX each reduced cell viability in a dose- and time-dependent manner, while combination treatment significantly enhanced cytotoxicity compared with single agents (p < 0.01). Combination Index (CI) values < 1 confirmed a synergistic interaction, particularly at 50 μM TQ + 5 μM MTX and 100 μM TQ + 10 μM MTX. Combination therapy increased total apoptosis up to 83.6%, markedly elevated the Bax/Bcl-2 ratio, and enhanced caspase-3 activation. Cell cycle analysis revealed pronounced G2/M arrest. ROS levels increased approximately six-fold, accompanied by significant suppression of SOD and CAT activities. qRT-PCR results demonstrated upregulation of pro-apoptotic Bax and downregulation of anti-apoptotic B-cell lymphoma 2 (Bcl-2), nuclear factor kappa B (NF-κB), matrix metalloproteinase (MMP)-2, and MMP-9. Conclusions: TQ potentiates the anticancer activity of MTX in MCF-7 breast cancer cells by synergistically inducing apoptosis, oxidative stress, and cell cycle arrest while suppressing metastasis-related genes. This combination may represent a promising therapeutic strategy for breast cancer, warranting further validation in in vivo and clinical studies. Full article

Amaranthus palmeri is an aggressive, highly invasive weed that thrives across a wide range of adverse environments worldwide; nevertheless, the mechanisms underlying its rapid expansion remain largely unstudied. Glutathione peroxidase (GPX) is a crucial enzyme within the antioxidant defense system, belonging to the phylogenetic conserved family of oxidoreductases present in all living organisms. Despite its significance, the role of GPX in A. palmeri has not been reported. This study identified eight GPX genes (ApGPXs) in A. palmeri through comprehensive bioinformatics and gene expression analyses. The research examined the characteristics, evolutionary relationships, chromosomal mapping, gene structure, subcellular localization, conserved motifs, and cis-acting elements of these genes, as well as their evolutionary conserved functions in relation to Arabidopsis thaliana GPXs and RT-qPCR analysis under various stress conditions. The ApGPXs were distributed across scaffolds (2, 4, and 12) of the A. palmeri genome. Phylogenetic analysis grouped GPX genes into four subgroups, and conserved motifs were found within certain phylogenetic subgroups. We identified Actin8 as the most stable internal reference gene for A. palmeri under diverse stress conditions. Gene expression analysis revealed that ApGPXs participate in both early and late regulatory responses to oxidative stress induced by NaCl, high temperature, osmotic pressure, and glufosinate ammonium. The Arabidopsis GPX mutant (AT4G31870) exhibited a stronger flg22-induced oxidative burst than the wild type, and qPCR confirmed that AtGPXs contribute significantly to glufosinate ammonium stress responses. Evolutionary analysis found high sequence similarity between ApGPX4 and AT1G63460, as well as ApGPX3 and AT4G11600. Also, ApGPX3 and AT4G11600 shared similar expression patterns under glufosinate ammonium stress. This research presents the first gene family study in A. palmeri and provides foundational insights for future studies in this economically critical species. Our findings establish a framework for mitigating A. palmeri’s impact on crop production and exploring ApGPXs in developing herbicide- and stress-tolerant cultivars. Full article

In traditional scheduling operations, dispatchers mainly rely on SCADA/EMS systems or personal experience. However, with access to a large number of new energy sources, the scale of the distribution network continues to expand, and its topology becomes increasingly complex, leading to potential security risks in scheduling operations. Therefore, it is very important to carry out risk assessments before scheduling operations. In this paper, risk theory is introduced into the field of distribution network scheduling operations, and a new risk assessment method is proposed considering various uncertain factors in the distribution network. In order to comprehensively analyze the influence of uncertainty factors in the operational process of a new distribution network, the output probability models of wind power, photovoltaic power, and load are first constructed in this study. Then, the improved Latin hypercube sampling method is used to extract the operating state of the distribution network system from the probability model, and the node voltage over-limit and line power flow overload are used as indicators to measure the severity of the consequences so as to establish a quantitative scheduling operation risk assessment system and analyze its framework in detail. Finally, simulation analysis is carried out in the improved IEEE-RTS79 test system: taking 15–25 lines from the operation state to the maintenance state as an example, this paper analyzes the influence of different locations and capacities of wind and solar access on the scheduling operation risk of distribution networks. The results can provide a reference for dispatchers to prevent risks before operation. Full article

Pepper (Capsicum spp.) is an economically valuable crop worldwide including in the United States due to its nutritional benefits in human health and widespread use as a spice or vegetable. Although numerous viruses have been reported infecting peppers in the USA, little is known about the diversity and distribution of pepper-infecting viruses in Oklahoma. To address this knowledge gap, we conducted a comprehensive pepper virome study to identify viruses infecting pepper and their incidence across six different counties in Oklahoma. A total of 310 plant samples including pepper and other potential hosts were collected during the 2021 and 2022 growing seasons. Samples were analyzed using high-throughput sequencing (HTS) and/or reverse transcription-polymerase chain reaction (RT-PCR) assays. Viral contigs identified via HTS were further validated through RT-PCR or PCR assays followed by Sanger sequencing. In total, 17 distinct viruses were detected, including 15 RNA and two DNA viruses, with several representing putatively novel findings. The most prevalent virus was beet curly top virus (BCTV), followed by tomato yellow leaf curl virus (TYLCV), potato yellow dwarf virus/constricta yellow dwarf virus (PYDV/CYDV), and pepper mild mottle virus (PMMoV). Virus incidence varied by season and location, with some surveys showing infection rates exceeding 80%. This study provides the first in-depth characterization of the pepper virome in Oklahoma and valuable insights into the prevalence and distribution of pepper-infecting viruses. These findings will support the development of informed, targeted strategies for virus detection and management in pepper production systems. Full article

Dermatan sulfate (DS) is an animal glycosaminoglycan with significant structural heterogeneity and a high, but variable density of negative electric charge. Owing to these characteristics DS displays a high degree of biological reactivity that is subject to regulation. We previously demonstrated that structural variants of DS rapidly induce moderate necroptosis in luminal breast cancer cells. In the present study, we investigated the intracellular molecular mechanism(s) that may underlie this effect, focusing on the expression of key regulators of intrinsic (BCL-2A1) and extrinsic (cFLIP) apoptosis, autophagy (Beclin-1), and oxidative stress protection (heme oxygenase-1 (HO-1)). Using RT-qPCR, Western blotting, immunofluorescence, and pharmacological inhibition, we have shown for the first time that DS, depending on its structure and the cancer cell line, can rapidly, albeit transiently, upregulate either the long or short cFLIP splicing variant and also reduce the level of HO-1. These effects are mediated via DS-triggered PI3K and/or NFκB signaling. Moreover, DS can also influence the intracellular distribution of these proteins. In contrast, this glycan did not affect the expression of BCL-2A1 and BECN1. These findings indicate that DS induces coordinated molecular remodeling in luminal breast cancer cells that creates an intracellular environment favorable for necroptosis induction. Full article