Search Results (11,628)

Flowering promoting factor 1 (FPF1) is a key regulator of plant flowering time. While the functions of the FPF family have been characterized in species such as Arabidopsis and rice, systematic studies on the tomato FPF family remain limited. In this study, we comprehensively analyzed the FPF family in tomato (Solanum lycopersicum L.), identifying five SlFPF members in the tomato genome. Phylogenetic analysis classified these genes into five distinct subgroups, and chromosome mapping revealed their distribution across three chromosomes, with the highest density on chromosome 1. Promoter analysis identified a range of putative cis-acting elements related to abiotic stress and hormonal responses. Differential expression analysis of various tissues showed that the five SlFPF genes exhibit varying expression levels, where SlFPF1 had a significantly higher expression compared to the others. Following treatments with abiotic stresses (NaCl, PEG, dark, and low light) and phytohormones (GA, MeJA, ABA, and SA), SlFPF1 expression is notably higher under GA treatment than under other conditions. Based on these findings, SlFPF1 and GA treatments were selected for further functional analysis. The results show that GA treatment significantly promotes multiple morphological traits, including root length, stem diameter, leaf area, plant height, dry weight, and fresh weight. However, silencing SlFPF1 expression led to a reduction in all these traits. Moreover, in SlFPF1-silenced plants, GA treatment failed to enhance root length, leaf area, fresh weight, and dry weight, indicating that GA-dependent growth promotion in tomato plants relies on SlFPF1. This study provides a theoretical foundation for understanding the SlFPF gene family and its role in plant growth and stress responses. Full article

Tomato (Solanum lycopersicum L.) is an important horticultural crop. Carotenoid cyclase dioxygenase (CCD) is an enzyme responsible for cleaving carotenoids, which is involved in regulating plant growth and response to abiotic stresses. However, the role of SlCCDs in tomato stress resistance remains unclear. This study used the tomato variety ‘Micro-Tom’ as the material to investigate the function of SlCCDs in stress responses. Through whole-genome analysis, a total of 12 SlCCDs members (SlCCD1–SlCCD12) were identified. Systematic evolutionary analysis classified them into four branches, and members within the same branch maintained a conserved structure. The promoter analysis revealed that SlCCDs contain multiple hormones and stress response elements. The qRT-PCR analysis revealed that SlCCD11 was the most highly expressed gene in the leaves. In addition, multiple SlCCDs showed significant responses to abscisic acid (ABA), methyl jasmonate (MeJA), light, and sodium chloride (NaCl) treatments. Among them, the expression of SlCCD11 significantly increased under salt stress. By silencing SlCCD11 using virus-induced gene silencing (VIGS) technology, it was found that the chlorophyll content, antioxidant enzyme activity, and ABA-related gene expression in the TRV:SlCCD11 plants under salt stress were all lower than the control samples, while the carotenoid content and ROS accumulation were higher. This indicates that SlCCD11 is a positive regulatory factor for salt stress. In conclusion, this study systematically analyzed the SlCCD gene family and revealed the positive role of SlCCD11 in tomato response to salt stress, providing a candidate gene for genetic improvement of crop stress resistance. Full article

Squamosa promoter binding protein (SBP) plays a vital role in plant growth, development, and responses to abiotic stresses. The genus Notopterygium is an endangered perennial herbaceous plant mainly distributed in the high-altitude Qinghai–Tibet Plateau and adjacent areas, which possibly occurred the adaptive evolution to the extreme environmental conditions. In this study, we firstly determined the genome-wide structural characteristics, evolutionary history, and expression profiles of the SBP family genes in Notopterygium species by using genome, transcriptome, and DNA resequencing data. We have also investigated the response patterns of SBPs of N. franchetii to the drought and high-temperature stresses. The 21, 18, and 18 SBP family genes of three Notopterygium species, N. incisum, N. franchetii, and N. forrestii, were, respectively, identified and classified into eight subfamilies, with four subfamily members regulated by miR156. The structure analysis showed that the members of the same SBP subfamily had similar structures and conserved motif composition. Cis-element analysis suggested that those SBP genes may have been essential to the growth and environmental adaptation of Notopterygium. The expansion of the SBP gene family was mainly caused by the whole genome duplication/segmental duplication and transposable element duplication. Evolutionary analysis showed the SBP gene family experienced severe contraction events and most of the gene copies underwent purification selection. Population genetics analysis based on SBPs variations suggested that the genus Notopterygium species have obvious genetic structure and interspecific differentiation. RNA-seq and qRT-PCR experiments demonstrated that the expressions of SBPs genes in Notopterygium were not species-specific, but tissue-specific. NinSBP08 and NinSBP10/12 may have played the key roles in heat tolerance and drought resistance, respectively. These results provided novel insights into the evolutionary history of the SBP gene family in the endangered herb Notopterygium species in the high-altitude Qinghai–Tibet Plateau and adjacent areas. Full article

PIN-LIKES (PILS) auxin transport genes play key roles in plant development, but their functions and molecular mechanism in soybean yield remain unclear. Here, we characterized the 44-member soybean GmPILS genes via comprehensive analyses. Phylogenetic analysis classified GmPILS into three subfamilies, with most proteins being hydrophobic, stable, and membrane-localized. Chromosomal distribution showed random scattering across 17 chromosomes, with gene duplication driving family expansion. Expression profiling identified GmPILS36 and GmPILS40 as seed-specific and differentially expressed between cultivated Suinong14 (SN14) and wild ZYD00006 (ZYD06) soybeans. Population genetic analyses revealed GmPILS40 experienced a domestication bottleneck without yield-related superior haplotypes, while GmPILS36 underwent selection during landrace-to-improved variety domestication. A coding region CC/TT natural variation in GmPILS36 (S/A substitution) was significantly associated with seed weight per plant and 100-seed weight, with the TT genotype conferring superior traits. This study provides insights into GmPILS genes’ evolution and identifies GmPILS36 as an important candidate gene for further functional study and investigation of the molecular mechanisms regulating soybean yield. Full article

Liver cancer, also known as hepatocellular carcinoma (HCC), remains a major global health concern, with high mortality driven by late-stage diagnosis, limited treatment efficacy, and frequent therapeutic resistance. Matrix metalloproteinases (MMPs), a large family of zinc-dependent endopeptidases, are central to the biological processes that drive liver tumor initiation and progression. By degrading and reorganizing extracellular matrix components, MMPs facilitate tumor expansion, tissue invasion, and metastatic dissemination. In addition, these enzymes regulate the availability of growth factors, cytokines, and chemokines, thereby influencing angiogenesis, inflammation, immune cell recruitment, and the development of an immunosuppressive tumor microenvironment. Aberrant expression or activity of multiple MMP family members is consistently associated with aggressive clinicopathologic features, including vascular invasion, increased metastatic potential, and reduced patient survival, highlighting their promise as prognostic markers and actionable therapeutic targets. Past attempts to modulate MMP activity were hindered by broad inhibition profiles and dose-limiting toxicities, underscoring the need for improved specificity and delivery strategies. Recent advances in molecular design, biologics engineering, and nanotechnology have revitalized interest in MMP targeting by enabling more selective, context-dependent modulation of proteolytic activity. Preclinical studies demonstrate that carefully tuned MMP inhibition can limit tumor invasion, enhance anti-angiogenic responses, and potentially improve the efficacy of existing systemic therapies, including immuno-oncology agents. This review synthesizes current knowledge on the multifaceted roles of MMPs in HCC pathobiology and evaluates emerging therapeutic strategies that may finally unlock the clinical potential of targeting these proteases. Full article

Previous studies have shown that miR-5110 regulates pigmentation by cotargeting melanophilin (MLPH) and WNT family member 1 (WNT1). In order to find the possible molecular mechanism for pigmentation, we examined the mRNA expression profiles in melanocytes of alpaca transfected with miR-5110, inhibitor or negative control (NC) plasmids using high-throughput RNA sequencing. The results showed that a total of 91,976 unigenes were assembled from the reads, among which 13,262 had sequence sizes greater than 2000 nucleotides. According to the KEGG pathway analysis, four pathways related to melanogenesis, the MAPK signaling pathway, Wnt signaling pathway, and cAMP signaling pathway were identified. Compared to the NC, 162 gene were upregulated and 41 genes were downregulated in melanocytes over expressed by miR-5110. The differential expressions of mRNAs Dickkopf 3 (DKK3), premelanosome protein (Pmel), insulin-like growth factor 1 receptor (IGF1R), cyclin-dependent kinase 5 (CDK5), endothelin receptor type B (Ednrb), kit ligand (Kitl), Myc, and S100 were verified using qRT-PCR, which agreed with the results of RNA sequencing. We also verified the differential expressions of mRNAs of some genes in the MAPK signaling pathway using qRT-PCR, which agreed with the results of RNA sequencing. Interestingly, several genes were screened as candidates for the melanogenesis regulated by miR-5110, including Kitl and MAPK-activated protein kinase 3 (MAPKAPK3). These findings provide new insights for further molecular studies on the effects of miR-5110 on the melanogenesis and pigmentation. Full article

Seventy 28-day-old weaned barrow piglets (Duroc × Landrace × Large White; 7.2 ± 0.20 kg) were used to determine the effects of 25-hydroxyvitamin D₃ (25-OH-VD₃) combined with phytase and probiotics on calcium and phosphorus metabolism and bone development. Five dietary groups were tested: basal diet + 50 µg/kg 25-OH-VD₃ (CON); basal diet with 17% reduced calcium and phosphorus + 50 µg/kg 25-OH-VD₃ (LCP); LCP + 50 mg/kg phytase (LH); LCP + 10 mg/kg probiotics (LC); LCP + 50 mg/kg phytase + 10 mg/kg probiotics (LHC). The experiment lasted for 31 days, including 3 days adaptation period. Apparent phosphorus digestibility was higher in the LH and LHC groups than in the CON group (p < 0.05). Bone mineral density and calcium content in metacarpal and rib bones were also higher in the LHC group compared with the CON, LCP, LC, and LH groups (p < 0.05). The jejunal mRNA expression of solute carrier family 34 members (SLC34A1, SLC34A2, and SLC34A3) members was higher in the LHC group than the CON, LCP, LC, and LH groups (p < 0.05), while the relative protein expression of the calcium-sensing receptor in the kidneys was lower in the CON group than in the LCP, LH, LC, and LHC groups (p < 0.05). Additionally, supplementation with 25-OH-VD₃, either alone or in combination with phytase and probiotics, was associated with an increased abundance of beneficial gut bacteria. Overall, combined supplementation of 25-OH-VD₃, phytase and probiotics enhanced bone development in weaned piglets fed a low-calcium, low-phosphorus diet by improving calcium and phosphorus utilization and calcium–phosphorus metabolic regulation. Full article

The basic/helix-loop-helix (bHLH) transcription factors are crucial regulators of plant development and stress responses. In this study, we conducted a genome-wide analysis of the bHLH family in Rosa roxburghii, an economically important fruit crop. A total of 89 non-redundant RrbHLHs were identified and unevenly distributed across the seven chromosomes. Phylogenetic analysis classified them into 23 subfamilies and 7 Arabidopsis subfamilies were absent, indicating lineage-specific evolutionary trajectories. Conserved motif and gene structure analyses showed that members within the same subfamily generally shared similar architectures, yet subfamily-specific variations were evident, suggesting potential functional diversification. Notably, key residues involved in DNA-binding and dimerization were highly conserved within the bHLH domain. Promoter analysis identified multiple cis-acting elements related to hormone response, stress adaptation, and tissue-specific regulation, hinting at broad regulatory roles. Expression profiling across fruit developmental stages and in response to GA₃ treatment revealed dynamic expression patterns. Furthermore, 21 duplicated gene pairs (17 segmental and 4 tandem duplicated pairs) were identified, with most evolving under purifying selection. Detailed analysis of these pairs revealed that segmental duplication, coupled with structural variations such as exon indels, dissolution/joining, and exonization/pseudoexonization, substantially contributed to their functional divergence during evolution. Our results provide a basis for understanding the evolution and potential functions of the RrbHLHs. Full article

Background: The zinc finger-homeodomain (ZF-HD) transcription factor family exerts pivotal regulatory functions in plant development and stress responses, yet a systematic genome-wide survey is lacking for Rosa chinensis. Methods: In this study, we performed a comprehensive genome-wide identification and analysis of RcZF-HD genes in R. chinensis using bioinformatics approaches. Nine RcZF-HD loci were mined from the rose genome and comprehensively profiled for physicochemical parameters, phylogenetic affiliations, chromosomal positions, exon–intron architectures, conserved motifs, and spatiotemporal expression landscapes. Results: The results showed that RcZF-HD genes were unevenly distributed across four chromosomes (Chr2, Chr4, Chr6, and Chr7), with tandem duplication events detected on chromosomes 2 and 7, suggesting their contribution to gene family expansion. Maximum-likelihood phylogeny placed RcZF-HD proteins within nine well-supported sub-clades alongside Arabidopsis orthologs, implying both evolutionary conservation and lineage-specific divergence. All members retain canonical zinc-finger domains, yet acquire unique motif signatures predictive of functional specialization. Gene structure analysis revealed considerable diversity in exon–intron organization. Expression profiling across six different tissues (root, stem, leaf, bud, flower, and fruit) demonstrated remarkable tissue-specific expression patterns. Notably, RchiOBHm_Chr2g0168531 exhibited extremely high expression in stem tissue, while RchiOBHm_Chr7g0181371 showed preferential expression in flower tissue, suggesting specialized roles in stem development and floral organ formation, respectively. The cold-stress challenge of ‘Old Blush’ petals further disclosed pronounced up-regulation of seven RcZF-HD genes, attesting to their critical contribution to low-temperature tolerance. Conclusions: Integrative analyses furnish a multidimensional blueprint of the rose RcZF-HD repertoire, providing molecular landmarks for future functional dissection and ornamental trait engineering. Full article

Background: Osteosarcoma (OSA) is the most common type of bone cancer in canines. Novel therapies are required to prevent the growth, survival, and metastatic progression of this cancer, to increase life expectancy of patients. Immunohistochemical (IHC) studies and RNA sequencing help us gain a deeper understanding into the molecular mechanisms of the disease. Methods: We previously compared canine OSA tissues with patient matched non-tumour tissues, revealing 442 overexpressed genes within the samples. The present research used IHC staining for four of these genes in OSA tissues: G protein-coupled receptor 64 (GPR64), TOX High Mobility Group Box Family Member 3 (TOX3), Matrix Metallopeptidase 12 (MMP-12), and Forkhead Box F1 (FOXF1). H-scoring was performed to quantitatively assess protein expression and qualitatively contextualise staining locations. Additional analyses addressed whether gender or anatomical location of lesions (axial or appendicular tumours) affected protein expression. cBioPortal was employed to analyse expression and genetic alterations in patients. Results: GPR64, TOX3, MMP-12, and FOXF1 showed high mRNA expression and genetic alterations in people with OSA. GPR64, TOX3, MMP-12, and FOXF1 were all expressed in canine OSA with novel findings regarding cellular expression. Additionally, differential sex expression was revealed for GPR64 and TOX3. Potential biomarkers or therapeutic targets were identified. Conclusions: These studies, and subsequent analysis, have provided insights into the molecular mechanisms associated with OSA progression and revealed potential biomarkers for diagnostic and prognostic purposes. A deeper understanding of genetic and protein interactions will support and progress novel pathways towards diagnostic, prognostic, and treatment interventions for OSA in both veterinary and human medicine. Full article

Hylocereus undatus growth is limited by long-term heat stress, and heat shock protein 70 (Hsp70) is crucial in the plant’s heat stress (HS) response. In a previous study, transcriptomic data revealed that Hsp70 family members in pitaya seedlings respond to temperature changes. This study identified 27 HuHsp70 genes in pitaya, analyzed their physicochemical properties (such as molecular weight and isoelectric point), and divided them into five subfamilies with conserved gene structures, motifs (short conserved sequence patterns), and cis-acting elements (regulatory DNA sequences). The Ks value (synonymous substitution rate) ranged from 0.93~3.54, and gene duplication events occurred between 71.17 and 272.19 million years ago (Mya). Under HS, eight and nine differentially expressed genes (DEGs) were detected at 24 h and 48 h, respectively. Quantitative real-time PCR (qRT-PCR, a method for measuring gene expression) verified the expression trends, with HuHsp70-11 expression increasing with heat shock duration, indicating that HuHsp70-11 is a key candidate. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that HuHsp70s, especially HuHsp70-11, play key roles in responding to high temperatures (HT) in H. undatus seedlings. A potential model by which HuHsp70-11 removes excess reactive oxygen species (ROS) and enhances cell membrane permeability was constructed. These results provide new perspectives for exploring the HS response mechanisms and adaptability of H. undatus plants to heat stress. Full article

Tumor tissue is surrounded by mast cells (MCs), which participate in the inflammatory immune response by producing cytokines, proteases, and other molecules. MCs are involved in both innate and acquired immunity and are associated with the IgE response through the FcεRI receptor. MCs mediate inflammation in several immune reactions, including acute hyperreactivity, leukocyte recruitment, acute tissue swelling, anaphylaxis, and pro-inflammatory cytokine production. They not only function as pro-inflammatory effector cells but may also contribute to the regulation of the acquired immune response in tumor tissue. Therefore, MCs may mediate immunity in breast cancer by promoting remodelling and counteracting cancer growth. They also produce anti-inflammatory substances, such as histamine, transforming growth factor-β (TGF-β)1, IL-10, and IL-4, which inhibit the acquired immune response and reduce the inflammatory state. IL-37 and IL-38 are novel natural regulators of inflammation and are anti-inflammatory members of the IL-1 family. IL-1, generated by immune cells such as macrophages and lymphocytes, is released downstream of oncogenes in breast cancer, triggering an inflammatory response by stimulating other pro-inflammatory cytokines such as IL-6, tumor necrosis factor (TNF), and IL-33 (an early warning cytokine). Therefore, blocking IL-1 with IL-37 or IL-38 could represent a novel therapeutic strategy that, when combined with other treatments, could be beneficial in breast cancer. This review focuses on the new discoveries and insights into the role of MCs in breast cancer. We also analyzed molecules that can promote tumor growth and those that can inhibit cancer development and metastasis. This review aims to study the role of MCs accumulated in the stroma of breast adenocarcinoma in relation to secreted anti-inflammatory cytokines, such as IL-37 and IL-38. Full article

Procypris rabaudi, a member of the Cyprinidae family and genus Procypris, has been designated as a national second-class protected wildlife species in China due to a significant decline in its wild populations. Understanding its genomic characteristics and mitochondrial genome structure is crucial for germplasm conservation and systematic classification. In this study, we utilized high-throughput sequencing to investigate the genome of P. rabaudi. The genome size was 1.5 Gb, with a heterozygosity rate of 0.44% and 61.47% of repetitive sequences. We identified 1,151,980 simple sequence repeats (SSRs), with mononucleotide repeats being the most abundant at 55.34%. The complete mitochondrial genome was assembled with 16,595 bp length. A phylogenetic tree constructed from 13 mitochondrial protein-coding genes indicated that genus Procypris was most closely related to genus Luciocyprinus and formed a monophyletic group with Cyprinus, Carassioides, and Carassius. Pairwise Sequentially Markovian Coalescent (PSMC) analysis revealed a rapid population expansion prior to the Last Interglacial Period, followed by a decline after reaching its peak during Last Glacial Period. Notably, P. rabaudi exhibited a two-peak demographic pattern during both the Last Glacial Period. These genomic data provide valuable resources for the conservation of P. rabaudi germplasm and for future studies on cyprinid classification and evolution. Full article

This study comprehensively characterizes the PEBP gene family in Cymbidium sinense, an orchid with a prolonged vegetative phase that limits its industrial production. Genome-wide analysis identified six CsPEBPs, classified into FT-like, TFL1-like, and MFT-like subfamilies. Evolutionary, gene structure, and collinearity analyses revealed both conservation and lineage-specific diversification of these genes. CsFTL3, a distinctive FT-like member, displayed notably high expression during the bud undifferentiated stage, followed by a sharp downregulation upon floral initiation. Functional studies identified CsFTL3 as a key floral repressor. Heterologous overexpression in Arabidopsis delayed flowering time from 32.0 days (wild-type) to 63.0–75.3 days (transgenic) and increased rosette leaf number from 12.6 to 33.0–34.5, while its knockdown via virus-induced gene silencing (VIGS) in C. sinense accelerated floral bud development and upregulated flowering-promoter genes. Phylogenetically, CsFTL3 falls within the flowering repressor FT-I clade, and multiple sequence alignment identified critical amino acid substitutions (Y134S, W138L, Q140E) that likely underpin its functional divergence from typical flowering promoters. Furthermore, promoter analysis revealed an enrichment of light-, hormone-, and stress-responsive cis-elements, and its expression was modulated by gibberellin (GA), abscisic acid (ABA), and low-temperature treatments. Predicted protein–protein interaction and transcriptional regulatory networks provide preliminary insights into its complex regulation. We conclude that CsFTL3 acts as a crucial floral inhibitor, integrating environmental and endogenous cues to repress flowering. These findings offer fundamental insights into the molecular mechanisms of flowering in orchids and provide a valuable genetic resource for molecular breeding programs aimed at achieving precise flowering time control. Full article

In mammals, CD22 is a member of the Siglec family and plays essential roles in B-cell activation, signal transduction, and immune regulation. However, its functions in teleost fish remain largely unclear. In this study, a CD22 homolog designated On-CD22 was identified and cloned from Nile tilapia (Oreochromis niloticus). On-CD22 transcripts were highly expressed in the head kidney and peripheral blood of healthy fish and showed significant expression changes following infection with Streptococcus agalactiae, Aeromonas hydrophila, or stimulation with poly(I:C). Subcellular localization analysis indicated that On-CD22 is predominantly localized to the plasma membrane. Luciferase reporter assays performed in heterologous cell systems showed that overexpression of On-CD22 was associated with changes in the basal transcriptional activities of NF-κB, IFN1, IFN3, and STAT1 responsive promoters under unstimulated conditions. Furthermore, single-cell transcriptomic analysis revealed that On-CD22 expression was mainly confined to the B-cell population within head-kidney leukocytes. Collectively, these findings suggest that On-CD22 may be involved in immune regulatory processes in Nile tilapia. Full article