Search Results (1,717)

Photosynthesis (PS) is the cornerstone of crop productivity, directly influencing yield potential. Photosynthesis remains an underexploited target in soybean breeding, partly because field-based photosynthetic traits are difficult to measure at scale. Also, it is unclear which reproductive stage(s) provide the most informative physiological signals for yield. Few studies have evaluated soybean PS in elite germplasm under field conditions, and the integration of chlorophyll fluorescence (CF) with UAV imaging for PS traits remains largely unexplored. This study evaluated genotypic variation in photosynthetic and canopy traits among elite soybean germplasm across environments and developmental stages using CF and UAV imaging. Linear mixed-model analysis revealed significant genotypic and G×E effects for yield, canopy and several photosynthetic parameters. Broad-sense heritability (H²) estimates indicated dynamic genetic control, ranging from 0.12 to 0.77 at the early stage (S1) and 0.20–0.81 at the mid-reproductive stage (S2). Phi2, SPAD and FvP/FmP exhibited the highest heritability, suggesting their potential as stable selection targets. Correlation analyses showed that while FvP/FmP and SPAD were modestly associated with yield at S1, stronger positive relationships with Phi2, PAR and FvP/FmP emerged during S2, underscoring the importance of sustained photosynthetic efficiency during pod formation. Principal component analysis identified photosynthetic efficiency and leaf structural traits as key axes of physiological variation. UAV-derived indices such as NDRE, MTCI, SARE, MExG and CIRE were significantly correlated with CF-based traits and yield, highlighting their utility as high-throughput proxies for canopy performance. These findings demonstrate the potential of integrating CF and UAV phenotyping to enhance physiological selection and yield improvement in soybean breeding. Full article

Research into longevity and aging involves comparing the size of cohorts at certain points on survival curves. However, this analysis is oversimplified because it provides limited information about the sample structure and the distribution of lifespan as a trait. Here, we introduce a method for estimating lifespan across the entire data range using distribution analysis. More specifically, we propose dividing the lifespan series into intervals, obtaining the frequencies of phenotypes by lifespan within the sample, followed by distribution analysis using the normality criterion. Additionally, to visualize the differences, we propose describing the resulting distributions formally using the normal distribution function and the β-distribution function. We demonstrate that the proposed methodology enables to extract additional information from survival data, providing new insights into the processes that occur in populations in response to genetic interventions and shedding light on their impact on ontogenesis. In particular, we observed that the lifespan distribution in Drosophila may not meet the normality criterion and may take different shapes depending on the line’s genotype or in response to genetic interventions. The proposed approach adds a new layer of information to studies of longevity and aging and expands the toolkit of methods used to analyze survival data. Full article

Analysis of coding areas has long been used to study monogenic illnesses, but despite the extensive use of whole-exome sequencing (WES), up to half of suspected cases remain genetically unexplained. Variants outside coding areas can alter splicing, transcript stability, or gene regulation, compromising normal gene activity. These include mutations in noncoding RNAs, promoters, enhancers, deep intronic sequences, and untranslated regions (UTRs). Several well-known disorders have been linked to these mechanisms, including β-thalassemia caused by deep intronic mutations leading to aberrant splicing, familial hypercholesterolemia caused by promoter defects affecting LDLR expression, and inherited retinal diseases driven by noncoding variants influencing retinal gene regulation. These instances show that pathogenic variation is not limited to the exome and can have significant clinical implications. This review summarizes current understanding of noncoding and regulatory variants in monogenic diseases, discusses how they influence diagnosis and therapy, and highlights integrative approaches combining genomic, transcriptomic, and epigenomic data. Multi-layered research has increased diagnostic accuracy and unveiled new therapeutic potentials, although noncoding variations make the connection between genotype and phenotype more complex. Noncoding regions will need to be incorporated into standard diagnostic procedures to convert molecular insights into concrete therapeutic applications in the future. Predictive algorithms, patient-derived model systems, and functional validation testing will all help to simplify this process. Full article

Purpose: Zollinger–Ellison syndrome (ZES) is the most frequent, functional, malignant pancreatic neuroendocrine tumor syndrome (pNET), which is due to ectopic secretion of gastrin by a pNET/NET (i.e., gastrinomas) resulting in severe, refractory acid-peptic disease (ulcer, GERD). ZES has several unique management features, which lead to a number of unresolved controversies. Areas covered: Whereas both medical and surgical controversies exist, they have not been examined in detail for some time. This review contains an analysis of a number of the main current, medical controversies that are unresolved in ZES patients, including insights into the basis of these controversies and possible insights into their resolution from recent studies in patients with gastrinomas or from recent studies in other pNET syndromes or other neuroendocrine tumors (NETs). These include the following: controversies in the long-term control of acid secretion and acid antisecretory drug side-effects; controversies related to the difficulty in making the diagnosis of ZES; nonsurgical MEN1/ZES controversies related to the management of gastric carcinoids (Type II); nonsurgical MEN1/ZES controversies related to whether genotype–phenotype correlations exist in MEN1 patients including MEN1/ZES patients; nonsurgical MEN1/ZES controversies related to the roles of imaging/tumor localization in MEN1 patients for gastrinomas/pNETs in their initial/follow-up management; controversies related to the role of non-surgical tumor ablation for treatment of ZES/gastrinomas; and controversies related to medical treatment selection for advanced, metastatic disease in patients with ZES/gastrinomas/other malignant pNETs. Conclusions: In this paper, the basis for the development of each of these unique ZES-related controversies is discussed and insights into progress that could lead to their resolution are reviewed. Full article

Low temperature exerts severe adverse effects on maize growth, particularly during the seedling stage. Screening for cold-tolerant maize genotypes is highly significant for identifying genes associated with cold tolerance and enhancing maize performance under low, suboptimal temperature conditions. The identification of representative cold tolerance-related genes is of great significance for the breeding of cold-resistant maize varieties. In this study, a diversity panel of 205 materials was evaluated and classified for cold tolerance at the seedling stage. The coefficients of variation of all materials ranged from 14.53% to 35.71%, reflecting considerable genetic diversity within the panel. The correlation coefficients for each phenotypic trait between the cold-treated (CT) and control (CK) maize materials ranged from 0.60 to 0.90, further indicating that all traits displayed varying degrees of sensitivity to cold stress. A comprehensive evaluation of cold tolerance using the D value was conducted. The D values of all materials ranged from 0.355 to 0.863, with a mean value of 0.64. A hierarchical clustering analysis was performed to classify all materials into five categories based on their cold tolerance. Further, 17 SNPs were identified using GWAS analysis, and 12 candidate genes were located within the regions related to the SNPs. Some candidate genes were closely associated with cold tolerance, such as genes encoding MYB and GRAS transcription factors, leucine-rich repeat (LRR) proteins, and protein kinases. Validation by qRT-PCR confirmed that the expression of some genes was induced under cold stress conditions. These findings lay a crucial foundation for breeding cold-tolerant maize varieties and for further exploration of genes associated with cold tolerance. Full article

Background: Pathogenic variants in interphotoreceptor matrix proteoglycan 1 (IMPG1) have been associated with autosomal dominant and recessive retinitis pigmentosa (RP) and autosomal dominant adult vitelliform macular dystrophy (AVMD). Monoallelic pathogenic variants in IMPG2 have been linked to maculopathy and biallelic variants to RP with early onset macular atrophy. Herein we characterise the phenotypic and genotypic features of patients with IMPG1/IMPG2 retinopathy and report novel variants. Methods: Patients with IMPG1 and IMPG2 variants and compatible phenotypes were retrospectively identified. Clinical data were obtained from reviewing the medical records. Phenotypic data included visual acuity, imaging included ultra-widefield pseudo-colour, fundus autofluorescence, and optical coherence tomography (OCT). Genetic testing was performed using next generation sequencing (NGS). Variant pathogenicity was investigated using in silico analysis (SIFT, PolyPhen-2, mutation taster, SpliceAI). The evolutionary conservation of novel missense variants was also investigated. Results: A total of 13 unrelated patients were identified: 2 (1 male; 1 female) with IMPG1 retinopathy and 11 (7 male; 4 female) with IMPG2 retinopathy. Both IMPG1 retinopathy patients were monoallelic: one patient had adult vitelliform macular dystrophy (AVMD) with drusenoid changes while the other had pattern dystrophy (PD), and they presented to clinic at age 81 and 72 years, respectively. There were 5 monoallelic IMPG2 retinopathy patients with a maculopathy phenotype, of whom 1 had PD and 4 had AVMD. The mean age of symptom onset of this group was 54.2 ± 11.8 years, mean age at presentation was 54.8 ± 11.5 years, and mean BCVAs were 0.15 ± 0.12 logMAR OD and −0.01 ± 0.12 logMAR OS. Six biallelic IMPG2 patients had RP with maculopathy, where the mean age of onset symptom onset was 18.4 years, mean age at examination was 68.7 years, and mean BCVAs were 1.90 logMAR OD and 1.82 logMAR OS. Variants in IMPG1 included one missense and one exon deletion. A total of 11 different IMPG2 variants were identified (4 missense, 7 truncating). A splicing defect was predicted for the c.871C>A p.(Arg291Ser) missense IMPG2 variant. One IMPG1 and five IMPG2 variants were novel. Conclusions: This study describes the phenotypic spectrum of IMPG1/IMPG2 retinopathy and six novel variants are reported. The phenotypes of PD and AVMD in monoallelic IMPG2 patients may result from haploinsufficiency, supported by the presence of truncating variants in both monoallelic and biallelic cases. The identification of novel variants expands the known genetic landscape of IMPG1 and IMPG2 retinopathies. These findings contribute to diagnostic accuracy, informed patient counselling regarding inheritance pattern, and may help guide recruitment for future therapeutic interventions. Full article

Background: Colorectal cancer (CRC) remains a major global health problem, with rising incidence among younger individuals. The implementation of next-generation sequencing (NGS) has enabled comprehensive multigene analysis to identify cancer-predisposing variants and molecular alterations in tumors. However, data on age-related genetic differences in CRC from Central and Eastern European populations, including Poland, remain limited. Methods: This study aimed to explore molecular differences in CRC between patients aged ≤50 and >50 years in a Polish cohort. Tumor DNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue samples obtained from 54 treatment-naive patients. Targeted sequencing of hot spot regions of 50 genes with known association to cancer was performed using an AmpliSeq for Illumina Cancer Hotspot Panel v2. Results: Variant frequencies in younger vs. older patients were: TP53 (71.4% vs. 57.6%), APC (57.1% vs. 45.5%), KRAS (28.1% vs. 72.7%), NRAS (28.6% vs. 0%), SMAD4 (9.5% vs. 12.1%), PIK3CA (14.3% vs. 24.2%), and FBXW7 (4.8% vs. 14.7%). Co-occurrence of APC/KRAS/TP53 variants was observed in 20% of cases. KRAS mutations were significantly more frequent in older patients (p-value = 0.001), while NRAS mutations occurred exclusively in younger patients (29% vs. 0%, p = 0.021). Overall, 46% of patients exhibited multiple gene alterations (≥3 mutations). Notably, IDH1 and CTNNB1 variants were found only in patients with better prognosis, whereas TP53 variants were nearly five times more frequent in patients with worse outcomes. Conclusions: Multigene panel sequencing revealed distinct age-related molecular patterns in CRC. Younger patients were more likely to harbor NRAS variants, whereas KRAS alterations predominated in older individuals. These findings underscore the relevance of NGS-based multigene profiling for risk stratification and personalized therapy in colorectal cancer. Full article

Background: Pathogenic variants in the TRIP12 gene are associated with Clark-Baraitser syndrome, a condition characterized by neurodevelopmental disorders, including intellectual disability, autism spectrum disorder (ASD), and speech delay. Phenotypic expression is variable, and facial features are not consistently present. Familial inheritance is rare. Methods: Whole-exome sequencing (WES) was performed on a proband with speech disorder and ASD, as well as on her parents. Clinical assessment included developmental, cognitive, and physical evaluations. Results: A heterozygous missense variant c.3404A>T (p. Asp1135Val) in the TRIP12 gene was identified in both the proband and her father. Both presented with speech disorder and ASD without facial features or severe intellectual disability. Conclusions: In line with recent genotype–phenotype studies, missense TRIP12 variants tend to be associated with milder neurodevelopmental presentations, typically characterized by mild to moderate intellectual impairment, variable autistic traits, limited or absent facial features, and a low incidence of epilepsy. This familial case further presents the phenotypic spectrum of TRIP12 missense variants and highlights that ASD and speech disorder may occur as isolated neurodevelopmental findings without syndromic features. The report reinforces the relevance of TRIP12 analysis in the differential diagnosis of ASD and language disorders, even in individuals lacking physical traits, supporting more accurate genetic counseling and broader awareness of inherited TRIP12-related conditions. Full article

The aim of this study was to assess the energy potential of woody grapevine (Vitis vinifera L.) shoots depending on the cultivation system, cultivar, and fruit colour. Field studies were conducted in 2024 at the Mendel University Vineyard in Lednice (Czech Republic) on Chardonnay, Merlot, Riesling, and Zweigelt cultivars, cultivated using the Guyot and Cordon systems. The cultivar analysis covered both the amount of biomass produced during pruning and its energy and emission properties. Laboratory tests of the energy potential of the biomass obtained were carried out at the University of Life Sciences in Lublin. The results showed that the varietal factor significantly influenced the biomass parameters—Chardonnay was characterised by the highest total plant weight (773.57 g), while Zweigelt (8.60 pcs.) had the highest number of shoots with the lowest unit weight (74.82 g). The Cordon system generated significantly higher biomass yields and more favourable combustion properties compared to Guyot. Differences in fruit colour indicate that, among the studied cultivars, white-berried varieties produce heavier shoots, whereas red varieties produce a greater number of shoots. The analysis of gas emissions showed a significant influence of the cultivar and training system, with the highest CO, CO₂, and NOx emissions recorded for the Zweigelt cultivar. The results emphasise that an integrated approach, taking into account both genotypic factors, training systems and phenotypic characteristics of the vines, is crucial for optimising the use of wine biomass as an energy source in the context of a circular economy. Full article

Chlorophyll content is a key physiological indicator reflecting photosynthetic capacity, and the Soil–Plant Analysis Development (SPAD) meter is a commonly used tool for its rapid and non-destructive estimation. Hyperspectral imaging (HSI) is a non-destructive technique that captures fine spectral characteristics and thus holds great potential for high-throughput phenotyping and early stress detection. This study aimed to explore the potential of HSI combined with ensemble learning (EL) to estimate SPAD of rapeseed seedlings under different durations of waterlogging. Hyperspectral images and corresponding SPAD values were collected from six rapeseed cultivars at 0, 2, 4 and 6 days of waterlogging. The mutual information was employed to select the top 30 most relevant spectral and vegetation index features. The EL model was constructed using partial least squares, support vector machine, random forest, ridge regression and elastic net as the first-layer learners and a multiple linear regression as the second-layer learner. The results showed that the EL model showed superior stability and higher prediction accuracy compared to single models across various genotypes and waterlogging treatment datasets. As waterlogging duration increased, the overall model accuracy improved; notably, under 6 days of waterlogging, the EL model achieved an R² of 0.79 and an RMSE of 3.27, indicating strong predictive capability. This study demonstrated that combining EL with HSI enables stable and accurate estimation of SPAD values, therefore providing an effective approach for early stress monitoring in crops. Full article

Danon Disease (DD) is a rare X-linked autophagic vacuolar myopathy caused by pathogenic variants in the lysosome-associated membrane protein 2 (LAMP-2) gene. Alternative splicing of the terminal exon 9 leads to the creation of three different isoforms, each with essential roles in regulating autophagy. DD is characterized by cardiomyopathy, skeletal myopathy, cognitive impairment, and retinal disorders, with cardiac involvement being the primary cause of morbidity and mortality. Muscle biopsy may reveal signs of vacuolar myopathy, but the diagnosis is typically confirmed through sequencing and deletion/duplication analysis of the LAMP-2 gene using peripheral blood. Although few genotype–phenotype correlations have been described, with most being limited to isoform 2B of exon 9, the most significant prognostic indicator remains sex. The disease manifests earlier and with a more severe systemic presentation in males due to their hemizygous status, whereas in females, the typical presentation is late-onset hypertrophic or dilated cardiomyopathy, generally without extracardiac involvement. Cases of severely affected women have been described, potentially due to non-random or defective X-inactivation. The less typical and delayed clinical presentation in females can result in incorrect or missed diagnoses. The aim of this narrative review is to summarize the natural history, diagnostic criteria, management strategies, and recent advancements in the understanding of DD in women. Full article

Carbapenem-resistant Gram-negative (CR-GN) pathogens pose a critical threat to patient outcomes in high-dependency and intensive care environments. This study aimed to delineate species prevalence, antimicrobial resistance phenotypes, carbapenemase genotypes, and clinical–environmental transmission dynamics across critical-care units. Cross-sectional surveillance was conducted in six ICUs and HDUs of a tertiary-care hospital in Karachi, Pakistan. We identified predominant species, quantified resistance patterns, and detected carbapenemase genes using PCR, exclusively on meropenem-resistant isolates. Network analysis highlighted high-centrality contamination hubs across ICUs and HDUs. Acinetobacter baumannii (36.7%) and Klebsiella pneumoniae (33.9%) were predominant, with 58% originating from environmental reservoirs. Meropenem non-susceptibility was 55% (60/109), and colistin non-susceptibility was 68.6% (35/51), based on standardized CLSI testing. ICU isolates exhibited significantly higher meropenem resistance than HDU isolates. Among carbapenem-resistant isolates, blaOXA-48-like (52.8%) and blaNDM (25%) were most prevalent. Network topology revealed ICU1 and HDU2 as high-centrality transmission nodes. These findings highlight pervasive environmental colonization and heightened antimicrobial pressure in ICUs, necessitating reinforced decontamination protocols, antimicrobial stewardship, and continuous molecular surveillance. This study provides the first integrated clinical–environmental surveillance of MDR Gram-negative bacteria in Pakistan, revealing that over half of isolates originated from surfaces and that network-based mapping can pinpoint contamination hubs driving hospital transmission. Full article

This study aims to investigate the genotype characteristics of newborns with biallelic GJB2 mutations and their correlation with hearing phenotypes, providing a basis for clinical genetic counseling and hearing management. A retrospective study was conducted on 652 newborns with biallelic GJB2 mutations detected at the Newborn Diseases Screening Center of Shenzhen Maternal and Child Health Care Hospital from January 2022 to December 2024. The differences in mutation types, hearing screening, and diagnostic results were analyzed and compared between the homozygous and compound heterozygous mutation groups to assess their correlation with hearing phenotypes. Genotype analysis identified 543 cases of homozygous mutations, mainly the c.109G>A/c.109G>A genotype (98.90%). Compound heterozygous mutations were identified in 109 cases, with the majority being c.109G>A/c.235delC (76.15%). Following two-stage hearing screening, 227 (34.82%) of the 652 cases were referred, with bilateral failure accounting for the majority (81.94%) of these cases. The referral rates showed no significant difference between the homozygous (35.54%) and compound heterozygous (31.19%) groups (p > 0.05). The overall hearing loss detection rate was 6.90% (45/652); among these, eight infants who had initially passed the newborn hearing screening were later found to have hearing loss between 2.5 and 6 months of age. Among the 45 confirmed deaf children, hearing loss was mainly mild to moderate (87.50%), and profound deafness was only seen in the homozygous mutation group (10.29%, 7/68 ears). Most newborns with biallelic GJB2 mutations passed the two-stage hearing screening, and associated hearing loss was typically mild to moderate. Long-term auditory monitoring remains essential for all genetically confirmed infants to monitor late-onset progression. Full article

Japanese apricot (Prunus mume Sieb. et Zucc.) is a dicotyledonous plant from the Rosaceae family that originated in China. Functional genomic studies in Japanese apricot are essential to elucidate the molecular mechanisms underlying key agronomic traits and to accelerate crop improvement. However, the lack of an efficient genetic transformation system has hindered gene function analysis and impeded molecular breeding efforts. Agrobacterium rhizogenes-mediated transformation has emerged as a robust tool for functional gene validation and studying root-specific processes across diverse plant species, due to its simple protocol and rapid turnaround time. Notably, Agrobacterium-mediated transformation remains notoriously recalcitrant in Rosaceae species, particularly in Japanese apricot. Through screening of ten Japanese apricot varieties, we identified ‘Muguamei’ (MGM) as the optimal cultivar for tissue culture. Using its genotype, we established an Agrobacterium rhizogenes-mediated transformation system for Japanese apricot via an in vitro approach. The binary vector incorporated the RUBY reporter for visual selection and eYGFPuv for fluorescent validation of transformation events. Furthermore, CRISPR/Cas9-mediated knockout of PmPDS in ‘Muguamei’ calli generated albino phenotypes, confirming successful genome editing. Through optimization of antibiotics, the study achieved an 80% explant survival rate using Woody Plant Medium (WPM) supplemented with 6-BA (0.5 mg/L) and TDZ (0.05 mg/L). For in vitro micropropagation, we found that ‘Muguamei’ exhibited optimal shoot growth in the presence of 6-BA (0.06 mg/L) and TDZ (0.1 mg/L), and up to 8 bud proliferation lines could be reached under 4.0 mg/L 6-BA. During the rooting of micro shoots, ½MS medium performed better and reached the optimum root length (35.70 ± 4.56 mm) and number (6.00 ± 1.00) under IAA (0.5 mg/L) and IBA (0.4 mg/L). Leaf explants were cultured on WPM supplemented with TDZ (4.0 mg/L) and NAA (0.2 mg/L). 50 mg/L kanamycin concentrations were the suitable screening concentration. Full article

Objectives: To investigate the phenotypic and genotypic changes of Acinetobacter baumannii collected from the tertiary oncology setting in Lithuania. Methods:A. baumannii isolates (n = 61) were collected in the years 2013–2014 (n = 28) and 2017–2019 (n = 33) from a tertiary care cancer center in Lithuania. Antimicrobial susceptibility was determined according to EUCAST and for piperacillin/tazobactam and cefepime, according to CLSI guidelines. PCR, pulsed-field gel-electrophoresis, and multi-locus sequence typing were used for resistance gene detection and genotyping. The biofilm formation ability was determined by a microtiter plate assay. Results: Of 61 A. baumannii isolates obtained, 84% (51/61) and 71% (43/61) were multi-(MDR) and extensively (XDR) drug-resistant, respectively. Carbapenem-resistant isolates comprised 77% (47/61); of these, 92% (43/47) harbored genes encoding the OXA-23-like, and 4% (2/47) OXA-24-like carbapenemases. All isolates were susceptible to colistin. Genotyping analysis revealed six groups with the highest prevalence of international clones 1 (IC1) and 2 (IC2), which dominated during 2013–2014 and 2017–2019, respectively. Notably, the A. baumannii diversity increased in 2017–2019 with the emergence of 3-LST groups G4, G8, G12, and G14, which included isolates of ST276, ST78, ST1463, and ST1336 sequence types, respectively. The IC1 and IC2 isolates displayed characteristic gene profiles aacC1, aacC2, aphA6, sul1, and armA, strA-strB, bla_TEM, respectively, whereas isolates from other groups had lesser resistance gene content. Isolates from IC2, G12, and G14 groups were strong biofilm producers; IC1, G4, and G8 isolates displayed no/weak biofilm formation capacity. Conclusions: A. baumannii from the cancer center showed a high prevalence of MDR and XDR phenotypes. Clonal dominance and diversity changed during the surveillance periods with the replacement of IC1 by IC2 clone isolates and the emergence of higher clonal diversity of isolates with stronger biofilm-forming capacity. The observed changes indicate a concerning trend of the establishment of a more virulent A. baumannii in the cancer setting. Full article