Search Results (903)

Background: High-temperature stress is one of the major abiotic stresses limiting cotton production. Identifying genetic loci and genes for heat tolerance is crucial for breeding heat-tolerant varieties. Methods: Given the complexity of heat tolerance phenotypes in cotton, this study, which focused on resource materials, identified an A/C SNP mutation at position 5486185 on chromosome D06 within the heat tolerance interval through genome-wide association studies (GWAS) of natural Gossypium hirsutum populations. Results: A total of 308 resource materials were identified and evaluated for their heat tolerance phenotypes over two years of field research. Kompetitive allele-specific PCR (KASP) molecular markers were developed on the basis of the D06-5486185 SNP to characterize the heat tolerance phenotypes of these 308 resource materials. Genotyping for heat tolerance-related traits and agronomic traits was also performed. Materials with the C/C haplotype at position D06-5486185 presented increased heat tolerance (higher pollen viability (PV), leaf area (LA), chlorophyll (Chl) and number of bolls on the third fruit branch (FB3) and a lower number of dry buds (DBs) and drop rate (DR)) without negatively impacting key yield traits. This locus is located in the intergenic region of two adjacent bZIP transcription factor genes (GH_D06G0408 and GH_D06G0409). Expression analysis revealed that the expression levels of these two genes were significantly greater in heat-tolerant accessions (C/C type) than in sensitive accessions and that their expression levels were significantly correlated with multiple heat-tolerant phenotypes. Conclusions: In summary, this study developed a Kompetitive Allele Specific PCR (KASP) marker associated with heat tolerance in G. hirsutum and identified two key heat tolerance candidate genes. These results provide an efficient marker selection tool and important genetic resources for the molecular breeding of heat-tolerant G. hirsutum, laying an important foundation for further establishing a molecular marker-assisted breeding system for heat tolerance in G. hirsutum. Full article

Background: The TGACG-BINDING FACTORS (TGA) gene family, a key subgroup of bZIP transcription factors, mediates plant stress responses and developmental processes by binding to the as-1 cis-element in target gene promoters to regulate transcriptional activation or repression. Despite its functional significance, systematic characterization of TGA genes in cotton (Gossypium spp.) remains insufficient. Methods: In this study, we performed a comprehensive genome-wide identification and phylogenetic analysis of TGA members across 10 Gossypium species and verified the functions of candidate genes using VIGS technology. Results: A total of 74 TGA homologous genes with conserved DOG1 and bZIP domains were identified. Evolutionary analysis revealed that the cotton TGA gene family can be classified into five distinct branches, suggesting functional diversification. Functional prediction analyses indicated these genes in cotton growth regulation and stress adaptation, potentially through hormone-mediated signaling pathways. Expression profiling demonstrated both tissue-specific expression patterns and salt-stress responsiveness in Gossypium hirsutum TGA genes, and GhTGA2 exhibited the most significant up-regulated expression under salt stress. Virus-induced gene silencing (VIGS)-mediated GhTGA2 silencing significantly reduced the salt tolerance in cotton. Conclusions: The TGA gene family is involved in regulating cotton growth, development, and stress responses, and plays a critical role in mediating salt stress tolerance in cotton. Our results provide mechanistic insights into cotton stress adaptation and establish a valuable genetic resource for developing elite salt-tolerant cotton cultivars, with direct implications for sustainable cotton production. Full article

Efficient allocation of mineral nutrients and photoassimilates is essential for grain development in rice. However, the transcriptional programs governing nutrient transport at key reproductive stages remain largely unresolved. Here, we performed a comprehensive transcriptome analysis of rice (Oryza sativa L.) across spatial (nodes, roots, and five other tissues) and temporal (seven reproductive stages) dimensions to elucidate the molecular basis of nutrient transport and allocation. RNA-seq profiling of node I identified stage-specific gene expression patterns, with the grain filling stage marked by strong induction of transporters involved in mineral allocation (e.g., OsYSL2, OsZIP3, OsSULTR3;3, SPDT) and carbohydrate distribution (e.g., OsSWEET13, OsSWEET14, OsMST6). Comparative analysis with the neck-panicle node (NPN) and root revealed tissue-specific regulatory networks, including nitrate (OsNRT1.1A, OsNRT2.3) and phosphate (OsPHT1;4, OsPHO1;3) transporters enriched at the grain filling stage. Root expression of Cd/As-related transporters (OsNRAMP5, OsCd1, OsLsi1, OsLsi2, OsLsi3) during grain filling highlights the contribution of belowground uptake to grain metal accumulation. Together, our study establishes a spatiotemporal atlas of nutrient transporter gene activity during rice reproductive development and identifies candidate genes regulating upward and lateral nutrient allocation. These findings provide insights into improving nutrient use efficiency and reducing toxic metal accumulation in rice grains through targeted manipulation of nodal and root transport systems. Full article

As the only harvest organ of pepper, fruit size is an important yield determinant. To elucidate the molecular mechanisms underlying pepper fruit size, we performed histological, physiological, and transcriptomic analyses on the pepper varieties QB6 (large fruit) and CXJ82 (small fruit). High contents of auxin and cytokinin in the early stage of fruit development promoted the rapid division of fruit cells in both varieties, which provided sufficient cells for subsequent fruit enlargement. High gibberellin accumulation induced the elongation and expansion of QB6 pericarp cells. Transcriptome analysis showed that genes related to cell division, cell wall polysaccharide degradation, and photosynthesis were highly expressed in QB6 fruit, likely contributing to its larger size. In the hormone–signal transduction factor–gene interaction network, GID6, GID1, IAA12, MYC30, and SAUR36 exhibited high correlations with numerous genes related to cell division, the cell wall, and photosynthesis, emerging as key signal transduction factors for the hormone-mediated regulation of pepper fruit size. Weighted gene co-expression network analysis identified the transcription factors OFP20, HD-ZIP6, and HD-ZIP13 as fundamental for pepper fruit size regulation. Our results expand the understanding of hormone regulation of pepper fruit size, providing a foundation for the breeding and improvement of excellent pepper varieties. Full article

Nitrogen is an essential macronutrient for crop growth. Although sorghum can tolerate poor soils, its low-nitrogen (LN) tolerance mechanisms remain underexplored. We conducted a genome-wide association study (GWAS) and RNA sequencing (RNA-seq) to dissect LN tolerance mechanisms in a diverse panel of 232 sorghum accessions. Phenotypic analyses revealed extensive variation in nitrogen-use efficiency traits, with shoot dry weight and shoot nitrogen accumulation in (SNAcc) showing the highest diversity. GWAS identified 10 quantitative trait loci harboring pleiotropic single-nucleotide polymorphisms (SNPs), including q1 (Chr3: 8.59–8.68 Mb), which is associated with biomass and nitrogen accumulation. Transcriptome profiling under LN stress revealed 6208 differentially expressed genes, with nitrate transporters showing genotype-specific regulation. Integration prioritized SORBI_3004G286700, where Hap2 accessions (14.66%) showed superior agronomic performance under LN conditions. We also identified pivotal transcription factors (TFs) that govern LN tolerance in sorghum, notably bHLH35 (SORBI_3007G051800) and three WRKY TFs, demonstrating constitutive upregulation in tolerant genotypes, whereas three previously uncharacterized TFs (MYB, bZIP, and B3) exhibited > 5-fold genotype-specific induction under LN. The integration of GWAS and transcriptome analyses offers an effective strategy for exploring candidate genes and elucidating nitrogen adaptation mechanisms in sorghum, while providing actionable molecular targets for precise breeding of nitrogen-efficient cultivars. Full article

In fish cells, light exposure elevates levels of reactive oxygen species (ROS) and stress-activated MAP kinase activity and thereby induces gene transcription. However, we lack a complete understanding of the function and evolution of this regulatory mechanism. Here, we reveal that a set of mitochondrial and heme metabolism genes is transcriptionally induced in zebrafish cells upon exposure to light or elevated ROS. The integrity of D-box and E-box enhancers in these gene promoters is essential for their transcriptional activation. Furthermore, light-induced transcription of mitochondrial and heme metabolism genes is absent in a cell line derived from the blind Somalian cavefish (Phreatichthys andruzzii). This fish species has evolved in perpetual darkness and lacks light-dependent circadian and DNA repair responses as well as D-box-mediated and light- and ROS-induced transcription. PAR-bZip transcription factors bind to and activate transcription via the D-box. Cavefish homologs of these factors share extensive homology with their zebrafish counterparts and lack the deletion mutations that characterize other light-dependent genes in this species. These results extend the role of the D-box as a key regulator of light- and ROS-driven transcription in fish, beyond the circadian clock and DNA repair systems, to also encompass metabolic and mitochondrial function. Full article

Background/Objectives: Metal transporter gene SLC39A8 and single nucleotide polymorphism (SNP) rs13107325 are associated with risk factors for atherosclerosis and cardiovascular disease (CVD). However, it is unclear how dietary manganese intake impacts CVD risk factors. The aim of this study was to use the UK Biobank population cohort (276,436 participants, Caucasian genetic ancestry, no genetic kinship) to investigate whether rs13107325 and dietary manganese are associated with CVD risk. Methods: A cross-sectional design and quantile (median) regression was used to determine associations of rs13107325 and dietary manganese intake with indicators of CVD risk. Results: SNP rs13107325 was associated with CVD risk factors, including greater body mass index (BMI) (beta ± SE per rs13107325 allele = 0.283 ± 0.0392, false discovery rate (FDR) < 10⁻¹⁰) and triglycerides (beta ± SE = 0.0308 ± 0.00761, FDR < 0.001) and reduced high density lipoprotein (HDL) (beta ± SE = −0.0298 ± 0.00343, FDR < 10⁻¹⁵). SNP rs13107325 was also associated with lower systolic (beta ± SE = −0.601 ± 0.172, FDR < 10⁻³) and diastolic blood pressure (beta ± SE = −0.531 ± 0.100, FDR < 10⁻⁵). Dietary manganese intake was positively correlated with measures of favorable cardiovascular health, such as lower BMI (beta ± SE per mg dietary manganese = −0.531 ± 0.0118, FDR < 10⁻³⁰⁰), reduced triglycerides (beta ± SE = −0.0451 ± 0.00229, FDR < 10⁻⁵⁰), increased HDL (beta ± SE = 0.00958 ± 0.00103, FDR < 10⁻¹⁵), and lower blood pressure (systolic beta ± SE = −0.529 ± 0.0520, FDR < 10⁻²⁰; diastolic beta ± SE = −0.562 ± 0.0302, FDR < 10⁻⁵⁰). Conclusions: The favorable associations of dietary manganese opposed many deleterious trends associated with rs13107325. Increased dietary manganese may promote cardiovascular health and offset many risks to cardiovascular health linked to SNP rs13107325. Full article

Mitochondria are increasingly recognized as important contributors to immune function, in addition to energy production. They exert this influence through modulation of various signaling pathways that regulate cellular metabolism and immune function in response to pathogens. Peroxisome proliferator-activated receptor (PPAR) coactivator 1 alpha (PGC-1α) is the primary transcription factor and regulator involved in mitochondrial biogenesis. Long known to be involved in immune function, zinc (Zn) is also required for proper mitochondrial function. It is increasingly recognized that many cellular immunometabolic activities are also Zn-dependent. Taken together, we investigated the role of Zn deficiency, both dietary and genetically induced, and Zn supplementation in PGC-1α-mediated macrophage mitochondrial biogenesis and immune function following infection with Mycobacterium avium complex (MAC). Our novel findings show that Zn is an important regulator of PGC-1α, TFAM and mitochondrial biogenesis, leading to enhanced bacterial phagocytosis and bacterial killing in macrophages. Mechanistically, we show that the Zn importer ZIP8 (Zrt/Irt-like protein) orchestrates Zn-mediated effects on PGC-1α and mitochondrial function. Taken together, defective Zn biodistribution may increase susceptibility to infection, whereas Zn supplementation may provide a tractable host-directed therapy to enhance the innate immune response in patients vulnerable to MAC infection. Full article

Access to home- and community-based services (HCBS) is critical for aging in place; yet many older adults continue to experience unmet needs. While individual-level factors are better-studied, less is known about how neighborhood-level place-based factors (PBFs, e.g., poverty, housing conditions, transportation, and internet access) shape access to and adequacy of HCBS. This study addresses that gap by examining the added explanatory value of PBFs in predicting HCBS use and unmet needs. We analyzed data from 6558 community-dwelling adults aged ≥ 65 years using the 2022–2023 National Core Indicators–Aging & Disability Adult Consumer Survey. Outcomes included use of six HCBS types, consumer-reported unmet needs for each type, and overall unmet HCBS needs. PBFs were measured at the ZIP code level using the 2016–2020 American Community Survey. Nested logistic regression models estimated incremental variance (McFadden’s R²) explained by PBFs, adjusting for individual demographics, health status, state, and proxy response. Adding PBFs increased explained variance by 7.98–22.70% for HCBS use, 35.92–48.00% for unmet needs by service type, and 51.85% for overall unmet HCBS needs. PBFs meaningfully influence both access to and adequacy of HCBS. Using PBFs to guide resource allocation and targeting modifiable PBFs could improve HCBS access and efficiency. Full article

This study elucidates the key molecular features underlying the embryogenic initiation divergence between japonica rice Chongxiangjing (CXJ) and indica rice 9311 during isolated microspore culture. Comparative transcriptome analysis across critical timepoints (0, 5, and 10 days post-culture initiation) revealed that while both varieties initially exhibit comparable microspore viability, CXJ maintains transcriptional stability and activates developmental programs (e.g., hormone signaling, DNA replication, cell morphogenesis), enabling sustained callus formation. In contrast, 9311 undergoes drastic transcriptome reorganization by 5 days, characterized by maladaptive activation of stress-response pathways (glutathione metabolism, MAPK signaling, ER stress) and futile metabolic reactivation (photosynthesis, starch degradation), culminating in near-total cell death and failed callus induction. Transcription factor dynamics further explain this divergence: CXJ specifically upregulates regulators coordinating development and stress resilience (NAC, ERF, HSF, GRAS, bZIP), while 9311 exhibits detrimental upregulation of FAR1 and B3, leading to catastrophic energy misallocation. These findings identify master transcriptional networks and stress-response pathways as pivotal indicators of embryogenic initiation efficiency, providing strategic targets for enhancing indica rice microspore culture technology. Full article

ATHB1, an Arabidopsis thaliana homeodomain-leucine zipper (HD-Zip) transcription factor, is involved in the control of leaf development and hypocotyl elongation under short-day conditions. As growth adaptation to environmental conditions is essential for plant resilience, we investigated the role of ATHB1 in the interaction between transcriptional regulatory networks and hormone signaling pathways. We found that wounding, flooding and ethylene induce ATHB1 expression. In addition, we found that the ethylene signal transduction pathway is also involved in an age-dependent ATHB1 expression increase in leaves. Conversely, methyl jasmonate (MeJA) application decreases the ATHB1 transcript level. By exploiting mutant and over-expressing (OE) lines, we also found that the ATHB1 level influences plant sensitivity to the inhibitory effect of MeJA treatment on growth. To gain deeper insights into the regulatory pathways affected by ATHB1, we performed a microarray analysis comparing the transcriptome of wild-type and athb1 mutant plants following exposure to MeJA. Remarkably, although the response to the MeJA treatment was not impaired in athb1, several genes involved in jasmonate and salycilic acid signaling were already downregulated in athb1 seedlings under normal conditions compared to the wild type. Thus, our study suggests that ATHB1 may integrate different hormone signaling pathways to influence plant growth under various stress conditions. Full article

Background and Clinical Significance: Retained intrarenal foreign bodies are rare adverse events after endourological stone surgery. Guidewire fracture or detachment is uncommon and can trigger infection, obstruction, or encrustation if unrecognized. We report antegrade percutaneous snare retrieval of a retained hydrophilic guidewire tip and provide a concise literature review (seven PubMed-indexed intrarenal cases identified by a structured search) to inform diagnosis, management, and prevention. We also clarify the clinical rationale for an antegrade versus retrograde approach and the sequencing of decompression, definitive stone management, and stenting in the context of sepsis. Case Presentation: A 75-year-old woman with diabetes presented with obstructive left pyelonephritis from ureteral and renal calculi. After urgent percutaneous nephrostomy, she underwent semirigid and flexible ureteroscopic lithotripsy with double-J stenting; the nephrostomy remained. During routine tube removal, the stent was inadvertently extracted. Seven days later she re-presented with fever and flank pain. KUB and non-contrast CT showed a linear 4 cm radiopaque foreign body in the left renal pelvis with dilatation. Under local anesthesia and fluoroscopy, a percutaneous tract was used to deploy a 35 mm gooseneck snare and retrieve the distal tip of a hydrophilic guidewire (Sensor/ZIP-type). Inflammatory markers were normalized; the nephrostomy was removed on day 5; six-week imaging confirmed complete clearance without complications. Conclusions: Retained guidewire fragments should be suspected in postoperative patients with unexplained urinary symptoms or infection. Cross-sectional imaging confirms the diagnosis, while minimally invasive extraction—preferably an antegrade percutaneous approach for rigid or coiled fragments—achieves prompt resolution. This case adds to the seven prior PubMed-indexed intrarenal reports identified in our review, bringing the total to eight, underscoring prevention through pre-/post-use instrument checks, immediate fluoroscopy when withdrawal resistance occurs, and structured device accounting to avoid “never events.” Full article

Seed storage proteins (SSPs) play a pivotal role in determining the development, quality, and nutritional value of rice seeds. In this study, we conducted a transcriptome-based correlation analysis to identify novel transcription factors (TFs) potentially involved in the biosynthesis and accumulation of SSPs. Our analysis revealed nine TFs—OsGATA8, OsMIF1, OsMIF2, OsGZF1, OsbZIP58, OsS1Fa1, OsS1Fa2, OsICE2, and OsMYB24—that exhibit strong co-expression with key SSP genes, including those encoding glutelin and prolamin. Gene expression profiling using quantitative RT-PCR and GUS reporter assays revealed that these TFs are predominantly expressed during seed development, with peak expression observed at 10 days after flowering (DAF). Promoter analysis further demonstrated an enrichment of seed-specific and hormone-responsive cis-regulatory elements, reinforcing the seed-preferential expression patterns of these TFs. Collectively, our findings identify a set of candidate TFs likely involved in SSP regulation and seed maturation, providing a foundation for the genetic enhancement of rice seed quality and nutritional content through targeted breeding and biotechnological approaches. Full article

Background/Objectives: Geographical variations in outcomes and oral anticoagulant (OAC) initiation among patients with nonvalvular atrial fibrillation (NVAF) in the United States (US) have been characterized; however, regional effects on OAC persistence are unknown. The study described variation in persistence with OACs among patients with NVAF across different US regions. Methods: The Komodo Healthcare Map was used to evaluate adult patients with NVAF, elevated stroke risk, and ≥1 pharmacy claim for an OAC between 1 January 2015 and 31 August 2022. Patients initiating treatment with an OAC (treatment-naïve) and having ≥12 months continuous enrollment were included. Persistence rates were assessed at 6, 9, 12 and 18 months among OAC- and direct OAC (DOAC)-naïve patients by 3-digit zip codes. Results: Of the 260,001 (Northeast = 72,507, Midwest = 59,979, South = 83,880, West = 42,778, Other/Unknown = 857) OAC-naïve patients identified, 82.2% were DOAC-naïve while 17.8% initiated warfarin. Mean follow-up time was 1101 (median = 964) and 1073 days (median = 938) in OAC and DOAC cohorts, respectively, while mean time to discontinuation was 342 (median = 190) and 329 days (median = 181), respectively. At 12 months, persistence rates ranged from 40.3% to 78.8% for OAC-naïve patients and 40.6% to 81.4% for DOAC-naïve patients. Average OAC and DOAC 12-month persistence rates were highest in the Northeast (63.5% and 63.7%, respectively) and lowest in the South (57.1% and 56.9%, respectively). Conclusions: Variations in 12-month persistence were consistent with existing evidence on geographic variation in NVAF-related disease burden and treatment initiation. Understanding geographic trends in prescribing patterns may provide insights into differences in treatment persistence that are relevant for clinicians seeking to address real-world barriers to care. Full article

Phosphorus deficiency significantly limits soybean production across 74% of China’s arable land. This study investigated the molecular mechanisms enabling soybean to access insoluble phosphorus through transcriptome sequencing of the Heinong 48 variety across four developmental stages (Trefoil, Flower, Podding, and Post-podding). RNA-Seq analysis identified 2755 differentially expressed genes (DEGs), with 2506 up-regulated and 249 down-regulated genes. Notably, early developmental stages showed the most substantial transcriptional reprogramming, with 3825 DEGs in the Trefoil stage and 10,660 DEGs in the Flower stage, compared to only 523 and 393 DEGs in the Podding and Post-podding stages, respectively. Functional enrichment analysis revealed 44 significantly enriched GO terms in the Trefoil stage and 137 in the Flower stage, with 13 GO terms shared between both stages. KEGG pathway analysis identified 8 significantly enriched pathways in the Trefoil stage and 21 in the Flower stage, including key pathways related to isoflavonoid biosynthesis, alpha-linolenic acid metabolism, and photosynthesis. Among 87 differentially expressed transcription factors from 31 families, bHLH (8.08%), bZIP (7.18%), and WRKY (5.94%) were most prevalent. These findings provide genetic targets for developing soybean varieties with improved phosphorus acquisition capacity, potentially reducing fertilizer requirements and supporting more sustainable agricultural practices. Full article