Search Results (362)

The WRKY gene family comprises important transcription factors widely distributed in plants and plays significant roles in the growth and development, diverse (biotic and abiotic) stress responses, and various biological processes. In the current study, 96 identified HvLWRKY genes were classified into three groups and seven subgroups. Among these, 89 genes possessed the conserved domain WRKYGQK. A total of ten motifs were harbored in HvLWRKY genes with two to four introns. Fragmental duplication was suggested to be the prime force that drove the evolution of HvLWRKY genes. A high degree of collinearity was observed between barley and Triticum spelta. Cis-elements of HvLWRKYs were closely associated with abiotic stress, light response, and hormone response; however, there were differences in the numbers among groups. HvLWRKY genes, even the paralogous gene pairs, from different clades were differentially regulated under cold treatments in two landraces. HvLWRKY33, 43, 44, 57, 65, and 77 were homologous with the relative AtWRKY genes in Arabidopsis thaliana. They are suggested to regulate abiotic and pathogen resistance of two barley landraces via SA and JA pathways. Meanwhile, some genes (for example, HvLWRKY1 and HvLWRKY32) were specifically expressed in either cold-tolerant or cold-sensitive landraces. Under cold stress, different cold-responsive patterns occurred in different barley landraces. These findings provide a foundation for further studies on cold resistance in barley landraces and offer new insights for application of WRKY genes in barley breeding. Full article

Calcium-dependent protein kinases (CDPKs) are crucial regulators in calcium-mediated signal transduction pathways, playing a pivotal role in plant response to abiotic stresses. However, there is still limited knowledge regarding the genes of the Populus tomentosa CDPK family and their underlying functions in response to arsenic (As) stress and arbuscular mycorrhizal fungi (AMF) colonization. In our study, 20 PtCDPKs were identified in the P. tomentosa genome. Phylogenetic analysis categorized these PtCDPK genes into four subgroups based on sequence homology. Motif analysis revealed that PtCDPK genes within the same group share a similar exon–intron structure, conserved domains, and composition. The promoters of PtCDPK genes were found to contain a multitude of cis-acting elements, including light-response elements, phytohormone-response elements, and stress-response elements. The analysis of genes provided insights into the evolutionary dynamics and expansion of the PtCDPK gene family within P. tomentosa. The PtCDPK genes exhibited a strong collinear relationship with the CDPK genes of two model plants, namely, Arabidopsis thaliana and Oryza sativa L. Specifically, 10 gene pairs showed collinearity with Arabidopsis; in contrast, 14 gene pairs were collinear with rice. Transcriptome analysis of gene expression levels in P. tomentosa roots under both As stress and arbuscular mycorrhizal fungi (AMF) colonization conditions revealed that 20 PtCDPK genes had differential expression patterns. Under As stress, AMF inoculation led to the upregulation of 11 PtCDPK genes (PtCDPKSK5, X2, 1-3, 20-1, 24, 26-X1-1, 26-X1-2, 29-1, 29-2, 32, and 32-X1) and the downregulation of 8 PtCDPK genes, including PtCDPK1-1, 1-2, 8-X1, 10-X4, 13, 20-2, 26-X2, and 26-X3. The RT-qPCR results for 10 PtCDPK genes were consistent with the transcriptome data, indicating that AMF symbiosis plays a regulatory role in modulating the expression of PtCDPK genes in response to As stress. The principal findings of this study were that PtCDPK genes showed differential expression patterns under As stress and AMF colonization, with AMF regulating PtCDPK gene expression in response to As stress. Our study contributes to developing a deeper understanding of the function of PtCDPKs in the Ca²⁺ signaling pathway of P. tomentosa under As stress and AMF inoculation, which is pivotal for elucidating the molecular mechanisms underlying As tolerance in AMF-inoculated P. tomentosa. Full article

Caffeic acid-O-methyltransferase (COMT) is a key enzyme in lignin synthesis and secondary metabolism in plants, and it participates in the regulation of plant growth and development as well as plants’ stress response. To further investigate the function of COMT in grapevine, a total of 124 COMT family genes were identified from three Vitis species in this study, namely Pinot noir (Vitis vinifera L.), Vitis amurensis, and Vitis riparia. The amino acid sequence encoded by these genes ranged from 55 to 1422 aa, and their molecular mass ranged from 6640.82 to 77,034.43 Da. Subcellular localization prediction inferred that they were mainly located in the plasma membrane and cytoplasm. The prediction of secondary structures showed that α-helix and irregular coiled-coil were primary structural elements. These genes were unevenly distributed across 10 different chromosomes, respectively. Phylogenetic tree analysis of the amino acid sequences of VvCOMT, VaCOMT, VrCOMT, and AtCOMT proteins showed that they were closely related and were divided into four subgroups. The motif distribution was similar among the cluster genes, and the gene sequence was notably conserved. The 124 members of the COMT gene family possessed a variable number of exons, ranging from 2 to 13. The promoter region of all of these COMTs genes contained multiple cis-acting elements related to hormones (e.g., ABA, IAA, MeJA, GA, and SA), growth and development (e.g., endosperm, circadian, meristem, light response), and various stress responses (e.g., drought, low temperature, wounding, anaerobic, defense, and stress). The intraspecies collinearity analysis suggested that there were one pair, three pairs, and six pairs of collinear genes in Va, Pinot noir, and Vr, respectively, and that tandem duplication contributed more to the expansion of these gene family members. In addition, interspecific collinearity revealed that the VvCOMTs had the strongest homology with the VaCOMTs, followed by the VrCOMTs, and the weakest homology with the AtCOMTs. The expression patterns of different tissues and organs at different developmental stages indicated that the VvCOMT genes had obvious tissue expression specificity. The majority of VvCOMT genes were only expressed at higher levels in certain tissues. Furthermore, we screened 13 VvCOMT genes to conduct qRT-PCR verification according to the transcriptome data of VvCOMTs under abiotic stresses (NaCl, PEG, and cold). The results confirmed that these genes were involved in the responses to NaCl, PEG, and cold stress. This study lays a foundation for the exploration of the function of the COMT genes, and is of great importance for the genetic improvement of abiotic stress resistance in grapes. Full article

This study addresses the long-standing difficulty of predicting the remaining useful life (RUL) of rolling bearings from highly non-stationary vibration signals by proposing WaveAtten, a symmetry-aware deep learning framework. First, mirror-symmetric and bi-orthogonal Daubechies wavelet filters are applied to decompose each raw signal into multi-scale approximation/detail pairs, explicitly preserving the left–right symmetry that characterizes periodic mechanical responses while isolating asymmetric transient faults. Next, a bidirectional sparse-attention module reinforces this structural symmetry by selecting query–key pairs in a forward/backward balanced fashion, allowing the network to weight homologous spectral patterns and suppress non-symmetric noise. Finally, the symmetry-enhanced features—augmented with temperature and other auxiliary sensor data—are fed into a long short-term memory (LSTM) network that models the symmetric progression of degradation over time. Experiments on the IEEE PHM2012 bearing dataset showed that WaveAtten achieved superior mean squared error, mean absolute error, and R² scores compared with both classical signal-processing pipelines and state-of-the-art deep models, while ablation revealed a 6–8% performance drop when the symmetry-oriented components were removed. By systematically exploiting the intrinsic symmetry of vibration phenomena, WaveAtten offers a robust and efficient route to RUL prediction, paving the way for intelligent, condition-based maintenance of industrial machinery. Full article

C2H2 zinc finger proteins (C2H2-ZFPs) constitute one of the largest transcription factor families in plants, playing crucial roles in growth, development, and stress responses. Here, we performed a comprehensive genome-wide analysis of C2H2-ZFPs in foxtail millet (Setaria italica v2.0), identifying 67 members that were unevenly distributed across all nine chromosomes. Most SiC2H2 proteins were predicted to be alkaline, stable, and nuclear-localized, with the exception of SiC2H2-11 and SiC2H2-66, which were chloroplast-targeted. Phylogenetic analysis with Arabidopsis thaliana and Oryza sativa (rice) homologs classified these genes into seven distinct subfamilies, each containing the characteristic motif1 domain. Evolutionary studies revealed 14 segmental duplication events and strong syntenic conservation with Triticum aestivum (wheat, 163 orthologous pairs), suggesting conserved functions during evolution. Promoter analysis identified multiple cis-acting elements associated with light responsiveness, hormone signaling, and stress adaptation. Transcriptome profiling and qPCR validation in the YuGu 56 cultivar identified several stress-responsive candidates, including SiC2H2-35 and SiC2H2-58 (salt tolerance), as well as SiC2H2-23 (5.19-fold induction under salt stress) and SiC2H2-32 (5.47-fold induction under drought). This study provides some valuable insights into the C2H2-ZFP family in foxtail millet and highlights potential genetic markers for improving stress resilience through molecular breeding approaches. Full article

Background: The Human Papillomavirus (HPV) vaccine generates high antibody titers against targeted HPV types. This study investigated vaccine-induced anti-HPV18 immunoglobulin (IgG) antibody titers and subsequent HPV18/45 infections. Methods: We performed a nested matched case-control study leveraging a prospective longitudinal cohort of adolescent and young adult women (AYW) vaccinated with the quadrivalent HPV vaccine (4vHPV) attending the Mount Sinai Adolescent Health Center (MSAHC) in Manhattan, NY. The case individuals included AYW who had an incident detection of cervical HPV18 (n = 3) or HPV45 (n = 34) DNA after vaccination and were compared to two vaccinated control individuals (HPV18/45-negative); one random control (RC, n = 37) and one high-risk control (HRC, n = 37) selected from the upper quartile of a sexual risk behavior score. Serological titers against HPV18 were measured by end-point dilution and enzyme-linked immunosorbent assay (ELISA) in serum collected before the incident detection of HPV. Matching was performed based on age at first dose, follow-up time, and sexual risk behavior score. Conditional logistic regression was used to assess the association between case-control status and anti-HPV antibody titers, consistent with the matched-pair design. Results: Antibody titers for HPV18 were most different between AYW who developed an HPV18/45 infection compared to high-risk controls OR = 1.66, 95% CI: 0.96–2.85 (p = 0.1629). Analyses of pooled data from vaccinated recipients including who developed HPV16/31 or HPV18/45 infections demonstrated that the odds of a one-log unit increase in anti-HPV16 or 18 antibody titers, respectively, were 40% higher in the combined control groups (RC + HRC, n = 160) (OR = 1.40, 95% CI: 1.09–1.79, p = 0.0135) and 73% higher in the HRC (n = 80) (OR 1.73, 95% CI: 1.34, 2.52, p = 0.0117) compared to HPV16/18/31/45 cases (n = 80). Conclusions: Overall, these findings suggest that higher IgG antibodies to HPV16/18 after vaccination represent an increased likelihood of protection from homologous and cross-reactive HPV types (HPV16/18/31/45). These results show that differences in antibody titers are associated with breakthrough infection after vaccination, suggesting that further study of long-term antibody titers and infection should be pursued. Full article

The yellow flower lotus (Nelumbo lutea) is the sister species of the sacred lotus (N. nucifera). The evolution of gene expression patterns across multiple tissues during the species divergence of these two lotuses remains unexplored. The WUSCHEL-related homeobox (WOX) family, a plant-specific transcription factor family, plays a crucial role in tissue development and stress responses. In this study, utilizing a chromosome-level reference genome and a transcriptome database covering multiple tissues, we identified and categorized 11 NlWOX genes into three subfamilies. We identified seven syntenic gene pairs between NnWOXs and NlWOXs that originated from whole-genome duplications. Through conserved motif analysis, we found subfamily-specific motifs in the protein sequences of NnWOXs and NlWOXs. Variations in the three-dimensional conformations of homologous WOX genes indicate function divergences between the two lotus species. The gene expression matrix of NlWOX across tissues reveals expression divergences within N. lutea and between the two lotus species. By employing a weight gene co-expression network analysis pipeline, we developed eight NlWOX co-expression networks that differed from the co-expression networks of their syntenic genes. Overall, our findings suggest that genomic variations in the WOX orthologs contribute to the distinct expression patterns and regulatory networks observed during the evolution of these two lotuses. Full article

Spinach (Spinacia oleracea L.) is an important leafy vegetable but is vulnerable to viral infections that significantly affect its quality and yield. In this study, we identified virus-infected spinach exhibiting typical symptoms with yellowing, wrinkling, and mottling in Beijing. But conventional RT-PCR screening for twelve common plant viruses yielded negative results. Then, using transcriptome sequencing along with a de novo assembly approach, we obtained the complete viral genome, which consists of RNA1 (5916 nucleotides) and RNA2 (3576 nucleotides). BLASTN analysis against the NCBI viral genome database revealed high homology with broad bean wilt virus 2 (BBWV2), leading us to designate this isolate as BBWV2-SP (GenBank accession numbers PV102464 and PV102465). Phylogenetic analysis indicated that BBWV2-SP shares 96.69% nucleotide sequence identity with a Liaoning isolate from Chenopodium album MN786955 and clusters within the Chinese evolutionary lineage. We developed primers targeting the conserved region of the RNA2 coat protein, amplifying a 478-base-pair product. All symptomatic spinach samples tested positive, while asymptomatic controls remained negative, confirming the causal relationship between BBWV2-SP and the observed disease symptoms. This study provides the complete genome assembly of the spinach isolate BBWV2-SP and establishes a molecular detection protocol for BBWV2 in spinach. These findings offer essential technical support for field monitoring, epidemiological surveillance, and disease control strategies, while also enhancing our understanding of BBWV2′s genetic diversity and mechanisms of pathogenicity. Full article

Influenza A virus (IAV) is a highly diverse pathogen with genetic variability primarily driven by mutation and reassortment. Using next-generation sequencing (NGS), we characterised defective viral genomes (DVGs) generated during the serial passaging of influenza A/Puerto Rico/8/1934 (H1N1) virus in embryonated chicken eggs. Deletions were the most abundant DVG type, predominantly accumulating in the polymerase-encoding segments. Notably, we identified and validated a novel class of multisegment DVGs arising from intersegment recombination events, providing evidence that the IAV RNA polymerase can detach from one genomic template and resume synthesis on another. Multisegment recombination primarily involved segments 1–3 but also occurred between other segment pairings. In specific lineages, certain multisegment DVGs reached high frequencies and persisted through multiple passages, suggesting they are not transient by-products of recombination but may possess features that support stable maintenance. Furthermore, multisegment DVGs were shown to be encapsidated within virions, similar to deletion DVGs. The observation of recombination between segments with limited sequence homology underscores the potential for complex recombination to expand IAV genetic diversity. These findings suggest recombination-driven DVGs represent a previously underappreciated mechanism in influenza virus evolution. Full article

Tieguanyin tea, celebrated as one of China’s top ten famous teas, is highly regarded for its unique flavor and taste. However, recent intensification of global warming has escalated the occurrence of abiotic stresses, posing significant threats to the growth, development, yield, and quality of Tieguanyin tea plants. DOF (DNA-binding one zinc finger protein), a plant-specific transcription factor, plays a critical role in plant development and stress response. In this study, we identified and analyzed 58 CsDOF genes across the whole genome, which were found to be randomly and unevenly distributed across 15 chromosomes. A phylogenetic tree was constructed using DOF genes from Arabidopsis thaliana and Tieguanyin, categorizing these genes into 10 subgroups. Collinearity analysis revealed homologous gene pairs between CsDOF and OsDOF(19 pairs), StDOF (101 pairs), and ZmDOF (24 pairs). Cis-acting element analysis indicated that CsDOF genes contain elements related to both stress and hormone responses. Heat map analysis demonstrated that subfamily C2 predominantly regulates the growth and development of roots, stems, and leaves in Tieguanyin. Tertiary structure analysis of CsDOF proteins revealed diverse structures, underscoring the functional variability within the CsDOF gene family. Furthermore, qRT-PCR analysis was employed to assess the expression profiles of 13 CsDOF genes under high-temperature and drought conditions. Notably, CsDOF51 and CsDOF12 exhibited significant expression changes under drought and high-temperature stress, respectively, while CsDOF44 showed significant changes under both conditions. This study provides foundational knowledge of the CsDOF gene family and offers novel insights for enhancing the drought and heat tolerance of Tieguanyin tea. Full article

Hepatitis C virus (HCV) infection remains a significant global health burden, driven by the emergence of drug-resistant strains and the limited efficacy of current antiviral therapies. A promising strategy for therapeutic intervention involves targeting the NS3 protease, a viral enzyme essential for replication. In this study, we present the first computational model specifically designed to identify NS3 protease inhibitory peptides (NS3IPs). Using amino acid composition (AAC) and K-spaced amino acid pair composition (CKSAAP) features, we developed machine learning classifiers based on support vector machine (SVM) and random forest (RF), achieving accuracies of 98.85% and 97.83%, respectively, validated through 5-fold cross-validation and independent testing. To support the accessibility of the strategy, we implemented a web-based tool, iDNS3IP, which enables real-time prediction of NS3IPs. In addition, we performed feature space analyses using PCA, t-SNE, and LDA based on AAindex descriptors. The resulting visualizations showed a distinguishable clustering between NS3IPs and non-inhibitory peptides, suggesting that inhibitory activity may correlate with characteristic physicochemical patterns. This study provides a reliable and interpretable platform to assist in the discovery of therapeutic peptides and supports continued research into peptide-based antiviral strategies for drug-resistant HCV. To enhance its flexibility, the iDNS3IP web tool also incorporates a BLAST-based similarity search function, enabling users to evaluate inhibitory candidates from both predictive and homology-based perspectives. Full article

Drosophila subobscura is a Palearctic species that colonized the west coast of South and North America in the last quarter of the 20th century. This species stands out for its large chromosomal inversion polymorphism that affects its five long chromosomes. Studies of natural populations revealed that the inversion polymorphism has an adaptive character and while the arrangement U_st was classified as adapted to cold, other arrangements, such as U₁₊₂₊₆ and U₁₊₈₊₂, were considered warm adapted. Characterization of the inversion breakpoints will allow a first approach to the genes included in the inversions and to find candidates to be affected by selection. In this work, we take advantage of the existence of a reference genomic sequence carrying the U₁₊₂ arrangement to locate the breakpoints of the U₆ and U₈ inversions, mapping paired-end Illumina reads from two homokaryotypic strains to U₁₊₂₊₆ and U₁₊₈₊₂, respectively. To date, most of the characterized inversion breakpoints in D. subobscura have been generated by non-homologous end-joining. In contrast, the U₆ and U₈ inversions seem to have originated by transposons, and, at the distal breakpoint of inversion U₈, we describe a new fold-back-like element characteristic of the suboscura species group that we have named Ziga-Zaga. Full article

This study aimed to clarify the sequence characteristics and spatiotemporal expression patterns of the insulin-like growth factor 1 receptor (IGF1R) gene in Alopex lagopus (Arctic fox), thereby addressing the existing knowledge gap regarding IGF1R-mediated growth regulation in this species. The findings establish a crucial foundation for subsequent investigations into the correlation between this gene and Arctic fox growth traits. Specific primers were designed based on the cDNA sequence of the canine IGF1R gene (Accession No. XM_545828). The full-length coding sequence (CDS) of the Arctic fox IGF1R gene (1617 bp, encoding 538 amino acids) was successfully cloned via RT-PCR. Phylogenetic analysis using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithm revealed a 99% sequence homology in the IGF1R gene between the Arctic fox and canine, confirmed their closest evolutionary relationship. Protein characterization showed that the IGF1R protein has a molecular weight of 60.62 kDa (theoretical isoelectric point pI = 5.15), containing one fibronectin type-III domain and one tyrosine kinase domain, classifying it as an acidic hydrophilic transmembrane protein. Phosphorylation site prediction identified 27 phosphorylation sites, with secondary structures dominated by α-helices (26.39%) and random coils (52.79%). The IGF1R gene displayed significant tissue-specific expression variations across 12 examined tissues in Arctic foxes: highest expression levels in testis, minimal expression in stomach, and no detectable expression in duodenum. Spatiotemporal expression analysis revealed that in 2-, 4-, and 6-month-old individuals, hepatic IGF1R exhibited a progressive increase, testicular expression reached peak levels at 6 months, and skeletal muscle demonstrated transient upregulation peaking at 4 months. These spatiotemporal expression patterns suggest that IGF1R may participate in metabolism and organ developmental processes during critical growth stages of Arctic foxes through tissue-specific regulation. Full article

Immunotherapy has become one of the primary forms of cancer treatment. The inhibition of immune checkpoint molecules, including indoleamine 2,3-dioxygenase (IDO), is a promising approach for immunotherapy. Phosphatase and tensin homolog (PTEN) is well known as a tumor suppressor that antagonizes oncogenic signaling molecules/pathways and plays a key role in the prognosis and (immuno)therapy of the disease. In this study, twenty healthy and tumorous renal tissue pairs were investigated, and the mRNA (RT-qPCR) and protein (Western blot) expression of IDO and PTEN were analyzed. In two cancer cell lines (CAKI-2; A-498), the protein of IDO and PTEN was measured followed by IDO induction with interferon alpha-2 (IFN-α2). According to our results, a significantly higher mRNA expression of IDO and PTEN was found in tumorous tissues compared to the adjacent healthy kidney specimens. The mRNA expression of IDO and PTEN showed a positive correlation in 80% of the sample pairs. Western blot results confirmed the protein expression of both IDO and PTEN. In the cell lines, immunocytochemistry showed that IDO is inducible with IFN-α2. In summary, our results suggest that IDO expression may play a role in the development of renal cancer, and IDO as well as PTEN might be potential biomarkers for patients with RCC. Full article

The Mildew Resistance Locus (Mlo) gene family is reported in various species as regulators of powdery mildew (PM) resistance. However, the Mlo genes in cucurbit crops remain limited. In this study, a genome-wide investigation of Mlo genes was conducted in eight Cucurbitaceae species and in rice, maize, arabidopsis, and barley, and a total of 202 Mlo genes were identified. The phylogenetic analysis showed that 202 Mlo genes can be classified into six clades, and the Mlo genes from clades I and III are likely pivotal in regulating PM resistance in dicotyledonous and monocotyledonous plants, respectively. The Ka/Ks ratios for these homologous Mlo gene pairs ranged from 0 to 0.6, revealing that they underwent substantial purifying selection during evolution. Among 12 crops, there were the most Mlo genes (22 Cm-mlo) in melon. An expression analysis revealed that six Cm-mlo genes showed expression responses to PM infection in which Cm-mlo38 and Cm-mlo44 were phylogenetically close to Mlo genes that regulated PM resistance. Using the VIGS system for silencing, Cm-mlo38 and Cm-mlo44 enhanced resistance to PM in susceptible material. A protein interaction analysis indicated that Cm-mlo38 might regulate PM resistance through interactions with PR5 and CML proteins. These results provide a comprehensive understanding of the Mlo family in Cucurbitaceae and pave the way for future functional analysis and genetic improvement for improving PM resistance in Cucurbitaceae. Full article