Search Results (4,729)

Türkiye has a unique position globally as it connects the Asian and European continents. In this study, the genetic diversity of a total of 27 mulberry (Morus alba) genotypes collected from northeastern Türkiye was evaluated in terms of morphological, biochemical, and molecular characteristics. In the fruits of the mulberry genotypes, the fruit weight (FW) ranged from 2.00 to 5.13 g, fruit width (Fw) ranged from 12.64 to 16.93 mm, and fruit length (FL) ranged from 20.89 to 32.34 mm. Total soluble solids (TSS) ranged from 16.56% to 26.00%, fruit pH ranged from 3.87 to 5.10, total phenolic content (TPC) ranged from 72.69 to 171.34 mg GAE/100 g, total flavonoid content (TFC) ranged from 75.55 to 86.85 mg QE 100/g, and antioxidant activity (AA) ranged from 42.35% to 74.93%. According to principal component analysis (PCA), the first three principal components (eigenvalue ≥ 1.00) explain 54.05% of the total variation. In general, the fruit and leaf characteristics were more effective in the first two principal components, while the biochemical traits were more effective in the third principal component. As a result of molecular analysis using 13 inter-simple sequence repeat (ISSR) primers, 94.23% of the total of 76 bands was polymorphic. Molecular variance analysis (AMOVA) showed that within the population, genetic variation was 79%, and among the populations, the variation was 21%. The similarities of the genotypes in the UPGMA dendrogram created according to the results of the molecular analysis varied between 0.74 and 0.98, and the genotypes were divided into two main groups. This study guides breeders in future studies by evaluating mulberry genotypes from morphological, biochemical, and molecular perspectives and explaining the wide variation among genotypes. Full article

Agropyron michnoi is a perennial grass with rhizomes in the genus Agropyron. It has a strong tolerance to drought and low temperature, and it is an established species in sandy flat and hilly slope lands, which constitute sandy grassland. So, it is an important forage species in dry grassland and desert steppes. Rhizomes not only enable asexual reproducibility but also confer strong resilience to stresses in A. michnoi. However, during production and utilization, it has been found that there are significant differences in the development of rhizomes among individuals of A. michnoi, yet the regulatory mechanism remains unclear. Therefore, in this study, the A. michnoi ‘Baiyinxile’ was used as the material, and the anatomical structures of the rhizomes, roots, and stems were analyzed using the paraffin sectioning technique. The results showed that the anatomical structure composition of the cross-section of the rhizome was similar to that of the root, while the arrangement of the vascular bundles in the stele was different from that of the root but similar to that of the stem. Subsequently, the Agropyron michnoi plants were classified into two types: plants with rhizomes and plants without rhizomes. Root, stem, and rhizome samples were collected from each type, and RNA sequencing was conducted. De novo transcriptomic analysis was performed to identify the candidate genes involved in rhizome development. From the RNA sequencing, a total of 103.73 Gb clean bases were obtained, from which 215,282 unigenes with an average length of 905.67 bp were assembled. Among these unigenes, 161,175 (74.87%) were functionally annotated based on seven common public databases. From pairwise comparisons of differentially expressed genes between the five samples, 129 candidate genes that are potentially specifically expressed in rhizomes were selected. Pathway enrichment analysis revealed that the rhizome-expressed genes are highly enriched in pathways of phenylpropanoid biosynthesis and starch and sucrose metabolism. The rhizome-specific expression pattern of 10 of the 129 candidate genes was further validated using qRT-PCR. Through the analysis of metabolites, 11 metabolites closely related to rhizome development, such as choline and betaine, were successfully identified. CYP family genes were selected for functional verification, and phylogenetic analysis revealed that CYP86B1 was grouped with CYP 86B1 of species such as Triticum aestivum and Lolium rigidum and was named AmrCYP86B1. The cloning results showed that its size was 1599 bp, and its subcellular localization was in the endoplasmic reticulum. Through stable genetic transformation, the study found that AmrCYP86B1 can promote the development of plant roots and stems and increase the dry matter content of the roots. Hormone detection showed that overexpression of AmrCYP 86B1 decreased the content of ABA hormone and increased the content of GA3 hormone in the plants. Combined with previous studies, it was determined that AmrCYP 86B1 promoted rhizome elongation by regulating ABA and GA3 hormones. The selected candidate genes involved in rhizome development, along with the preliminary functional verification, provide a preliminary mechanistic interpretation of rhizome development. This will contribute to in-depth research on the molecular mechanism of rhizome development in A. Michnoi. Full article

Statistically significant multiple sequence alignment construction is an important task that has many biological applications. We applied the method for multiple alignments of highly divergent sequences (MAHDS) to construct multiple sequence alignments (MSAs) for 490 protein families with less than 20% identity between family members. The method uses random symmetric position–weight matrices (PWMs) and a genetic algorithm to construct a multiple alignment. PWM symmetry is essential because it makes PWMs comparable and recoverable at all steps of the MAHDS algorithm, which reduces the optimal MSA search task to a PWM optimization task. A Monte Carlo method is applied to assess the statistical significance of the resulting alignments. The statistical significance of the constructed MSAs was compared with that of MSAs obtained using T-Coffee and MUSCLE algorithms. The results showed that for 476 of the 490 families, the MAHDS method created much more statistically significant MSAs than T-Coffee and MUSCLE, whereas for 138 families, only MAHDS could construct statistically significant MSAs. These findings indicate that MAHDS calculate statistically significant alignments in cases when the other methods create purely random MSAs and are, therefore, the most appropriate method to construct MSAs for families of proteins with weak sequence similarities for amino acid annotation. Full article

In this study, we present the first-ever comparison of the effectiveness of SRAP and ISSR markers on three Allium species. In addition, to visualize the results of each dataset in a simpler way, the Fruchterman–Reingold algorithm was used to generate a link graph and neighbor-joining methods were used to obtain a phylogenetic tree. The genetic similarity matrices were compared using the Mantel test. Primers generated 59 ISSR and 72 SRAP fragments. There was no statistically significant difference between the polymorphism information content of the marker sets. In terms of the effective multiplex ratio, SRAP markers were higher than ISSR markers, with values of 6.700 for garlic, 6.400 for onion, and 5.800 for leek (3.490, 4.316, and 2.573, respectively). Similarly, the marker index was calculated as 2.820, 3.056, and 2.505 for SRAP and 1.903, 1.523, and 1.050 for ISSR in onion, garlic, and leek species, respectively. The highest value regarding cophenetic correlation coefficients was obtained from the Jaccard method. According to the neighbor-joining method, the tree drawn using SRAP and ISSR data together shows a more distinct hierarchical structure of genotypes. The results obtained proved that SRAPs have higher values in terms of sign efficiency criteria, but they are not sufficient for the homogeneous grouping of different Allium species. Full article

Background: Interstitial deletions of chromosome 1q are rare, with about 30 cases reported in the literature. The phenotypical features of the affected subjects described so far include microcephaly, pre- and post-natal growth retardation, psychomotor delays, ear anomalies, brachydactyly, in addition to small hands and feet, and rarely a congenital diaphragmatic hernia (CDH). Case presentation: Here, we report on a neonate with CDH, dysmorphic features, and multiple midline anomalies including a cleft palate, in whom an array-comparative genomic hybridization (a-CGH) analysis allowed the identification of an interstitial deletion of the long arm of chromosome 1. Our patient underwent a surgical correction of CDH on the fourth day of life, while that of cleft palate has been planned to be performed at 12 months. Conclusions: The few subjects suffering such rearrangement reported to date, along with the clinical and genetic profile of the present newborn, show that 1q deletions should be considered within the context of the “interstitial 1q deletion syndrome”. Comparing our case with those described in previous studies, the involved genomic regions and the phenotypic traits are partially overlapping, although the clinical picture of the present patient is among the few ones including a congenital diaphragmatic hernia within the phenotypical spectrum. A more extensive comparative analysis of a larger number of patients with similar genetic profiles may allow for a more precise clinical and genomic characterization of this rare syndrome, and for genotype–phenotype correlations. Full article

Parkinson’s Disease (PD) is the most frequent movement disorder and is second only to Alzheimer’s Disease as the most frequent neurodegenerative pathology. Early onset Parkinson’s disease (EOPD) is less common and may be characterized by genetic predisposition. NGS testing might be useful in the diagnostic assessment of these patients. A panel of eight genes (SNCA, PRKN, PINK1, DJ1, LRRK2, FBXO7, GBA1 and HFE) was validated and used as a diagnostic tool. A total of 38 in sequence EOPD patients of the Parkinson’s Disease Unit of our Hospital Institution were tested. In addition, the number of the hexanucleotide repeats of the C9ORF72 gene and the frequency of main HFE mutations were evaluated. Six patients were carriers of likely pathogenic mutations in heterozygosity in the analyzed genes, one of them presented mutations in association and another had a complex genetic background. Their clinical symptoms were correlated with their genotypes. In the cohort of patients, only the p.Cys282Tyr of HFE was significantly decreased in the dominant model and allele contrast comparison. Only one patient with one allele of C9ORF72 containing 10 repeats was identified and clinically described. The clinical signs of sporadic and monogenic PD are often very similar; for this reason, it is fundamental to correlate genotypes and phenotypes, as we tried to describe here, to better classify PD patients with the aim to deepen our knowledge in the molecular mechanisms involved and collaborate in reaching a personalized management and treatment. Full article

Growing food insecurity can in part be attributed to a lack of diversity in arable crops, with most African countries now focused on the production of a few “green revolution crops”. Indigenous knowledge of traditional food types could hold the key to the genetic diversification of crop production systems. Wild yams are indigenous crops that have been relegated to the background. This study aimed to assess the state of knowledge in, and cultivation of, wild yams collectively called “Kumbu” by the Bakweris of the Mount Cameroon Region. Following reconnaissance surveys, semi-structured questionnaires were administered to 583 interviewees across 41 villages in this region. Data were analysed in the SPSS version 21 statistical package with significance at α = 0.05 where necessary. Results showed that the study population was fairly balanced in terms of gender (SD = 0.534), with males representing 56.8% of the sample. A majority of the interviewees (53.3%) were married, and most had received at least primary education (85.2%). Most (61.6%) of the interviewees do not cultivate Kumbu due to a lack of available seeds (69.3%) and a preference for other yams (30.7%). Of those who cultivate Kumbu (38.4% of the interviewees), a majority (89.6%) have less than five stands of Kumbu. The different names (10) and types (13) of Kumbu could represent linguistic polymorphism, requiring further studies for proper identification. A majority (68.1%) of the interviewees had no idea of the differences between Kumbu types. Agronomic practices, pests, and disease management reported for Kumbu are similar to those of other mainstream yam types. We conclude that the state of knowledge on Kumbu in the Mt Cameroon Region is limited and on the decline. Bringing Kumbu production to the mainstream requires research on molecular taxonomy, propagation techniques, and agronomic practices for better yields. Full article

We describe a method tailored to the in-cell selection of protease inhibitors. In this method, a target protease is co-expressed with a selective substrate, the product of which kills host cells. Therefore, the method can be applied to identify potential inhibitors based on cell host survival when inhibition of the target protease occurs. The TEV protease was chosen for this proof-of-concept experiment. The genetically encoded selective substrate is a single polypeptide chain composed of three parts: (1) a ccdB protein, which can cause host cell death when it accumulates inside the cell; (2) a protease cleavage sequence that can be changed according to the target protease, in this case the TEV substrate ENLYFQ↓G (↓-predicted cleavage site); and (3) the ssrA sequence (AANDENYALAA), which drives the polypeptide to degradation by the ClpX/ClpP complex inside host E. coli cells. In our experiment, co-expression of the active TEV protease and this selective substrate (ccdB-ENLYFQG-ssrA) caused the death of a significant host cell population, while control assays with an inactive mutant TEV Asp81Asn did not. Details of the methodology used are given, providing the basis for the application of similar systems for other proteases of interest. Full article

Muskellunge (Esox masquinongy) are a recreationally and ecologically important apex predator found throughout North America. In West Virginia, the genetic structuring and diversity of native muskellunge is poorly understood. The supplementary stocking of non-native muskellunge has further complicated the issue, as the introgression of non-native alleles and prevalence of non-native muskellunge post stocking remains unclear as well. Using ddRAD sequencing, several datasets were generated to investigate the population structure and genomic diversity of muskellunge in West Virginia. Populations stocked with New York-strain muskellunge exhibited significant introgression, with genetic composition diverging from unstocked native West Virginia populations. However, one population showed greater genetic similarity to native and unstocked populations despite New York-strain prevalence, suggesting resilience against genetic alteration. Fixed SNPs between the New York and West Virginia strains were identified that can be used for broodstock screening and the enhancement of native populations. A genetically distinct population was identified in the Little Kanawha River system, with this population having the highest levels of genomic diversity among native populations as well as a high number of private alleles. However, elevated inbreeding coefficients highlight potential conservation concerns for this unique population. This study establishes a genomic baseline for muskellunge in West Virginia and underscores the importance of preserving native genomic diversity while balancing the demands of recreational fishing programs. Full article

Background and Objectives: Mucinous adenocarcinoma (MAC) and mucinous components (MCP) in colorectal cancers (CRC) have shown conflicting results regarding their prognostic impact. This study aims to evaluate survival differences between MAC, MCP, and non-mucinous adenocarcinoma (nMAC) in stage II and III CRC patients. Materials and Methods: 224 CRC patients who underwent surgery between 2013 and 2021 were analyzed retrospectively. Patients were classified as nMAC, MCP, or MAC based on the percentage of extracellular mucin. Those who received neoadjuvant therapy, had stage I or IV TNM disease, and emergency cases were excluded. Survival analysis was performed using Kaplan–Meier curves and Cox regression models. Results: MAC patients showed worse survival outcomes compared to nMAC (p = 0.025). No difference in survival was found between MCP and nMAC (p = 0.055). Multivariate analysis identified MAC (OR: 2.814; p = 0.014) and perineural invasion (PNI) (OR: 2.283; p = 0.008) as independent factors associated with worse survival. Kaplan–Meier analysis revealed MAC’s worse prognosis than nMAC (p = 0.027). Conclusions: MAC was shown to have a worse prognosis than nMAC in stage II and III CRC patients, while MCP survival rates were similar with nMAC. These findings suggest that MAC requires more careful treatment approaches, while MCP and nMAC have better survival rates. Further studies focusing on molecular and genetic profiles are needed to better understand these outcomes. Full article

Background/Objectives: Autosomal dominant polycystic kidney disease (ADPKD) is a progressive genetic disorder marked by bilateral renal cysts and extrarenal manifestations, ultimately resulting in renal failure. Emerging research indicates that metformin might influence the intracellular mechanisms of ADPKD, though its clinical significance remains uncertain. Methods: We applied the Taiwan National Health Insurance Database (NHIRD) to investigate the clinical impact of metformin utilization in ADPKD patients in real-world practice. The metformin user group was defined by more than 90 days of usage. To mitigate selection bias, we established a non-user group with a 1:2 ratio, matching for age, sex, and comorbidities by a propensity score matching method. Results: A total of 10,222 ADPKD cases were identified in the NHIRD between 2009 and 2018. After matching, the metformin user group was composed of 778 cases with a mean age of 59.5 ± 13.9 years, and the non-user group of 1546 cases with a mean age of 59.3 ± 14.4 years. The time from the index date to the outcome of ESKD in ADPKD was 5.3 ± 2.2 years in the metformin user group and 5.3 ± 2.3 years in the metformin non-user group, respectively. The metformin user group exhibited a significant reduction in the risk of end-stage kidney disease (ESKD), as indicated in the fully adjusted model (0.75, 95% CI 0.58–0.97, p = 0.03). A decreased risk of major adverse cardiovascular events (MACEs) was noted in metformin users, with an adjusted hazard ratio (HR) of 0.78 (95% CI 0.65–0.95, p = 0.01). Sensitivity analysis showed similar results by excluding late-stage CKD (CKD stage 5 or erythropoietin-stimulating agents use). Conclusions: Metformin usage in real-world practice showed lower hazards of ESKD and MACEs in patients with ADPKD, except for those with advanced CKD. Full article

The growing reliance on chemical pesticides in agriculture has raised significant concerns about their environmental and health impacts. This study investigates the potential of Indigenous entomopathogenic nematodes (EPNs), specifically Steinernema pakistanense and Heterorhabditis indica, as biological control agents for Leucinodes orbonalis, the brinjal fruit and shoot borer, a major pest in Karachi, Sindh, Pakistan. A comprehensive soil sampling was carried out across 30 locations. Molecular identification via PCR and sequencing confirmed the taxonomic classification of the isolated strains, showing high genetic similarity to known EPN species. The reproductive potential of the isolated strains varied, with Pak.S.SA.22 exhibiting the highest fecundity, averaging 91,944 offspring per larva, indicating strong biocontrol potential. Laboratory bioassays at different concentrations showed that Pak.S.SA.22 achieved 100% mortality of L. orbonalis at a concentration of 200 IJs/mL, confirming its effectiveness. Field trials further validated these findings, demonstrating up to 90% pest control efficacy over multiple application intervals, highlighting the practical applicability of this strain in field conditions. These results advocate for the inclusion of indigenous EPNs in integrated pest management (IPM) programs as a sustainable, environmentally friendly alternative to chemical pesticides, contributing to the promotion of sustainable agricultural practices. Full article

Obesity arises from a complex interplay of genetic and environmental factors. Even among individuals with the same genetic predisposition, diet-induced obesity (DIO) exhibits varying degrees of susceptibility, which are categorized as DIO and diet-induced obesity resistance (DR). The hypothalamus plays a pivotal role in regulating energy homeostasis. This study performed a comparative hypothalamic proteomic analysis in DIO and DR rats to identify differentially expressed proteins (DEPs) associated with alterations in body weight. Male Sprague Dawley rats were fed either a standard chow diet or a high-fat diet for 12 weeks. DIO rats exhibited the most rapid weight gain compared to both the control and DR rats. Despite consuming similar caloric intake, DR rats exhibited less weight gain relative to DIO rats. Proteomic analysis revealed 31 DEPs in the hypothalamus of DR rats compared to DIO rats (with a false discovery rate (FDR) < 1%). Notably, 14 proteins were upregulated and 17 proteins were downregulated in DR rats. Gene ontology analysis revealed an enrichment of ion-binding proteins, such as those binding to Fe²⁺, Zn²⁺, Ca²⁺, and Se, as well as proteins involved in neuronal activity and function, potentially enhancing neuronal development and cognition in DR rats. The DEPs pathway analysis via the Kyoto Encyclopedia of Genes and Genomes (KEGG) implicated starch and sucrose metabolism, antigen processing and presentation, and the regulation of inflammatory mediator affecting TRP channels. Western blotting confirmed the proteomic findings for TRPV4, CaMKV, RSBN1, and BASP1, which were consistent with those obtained from Tandem Mass tag (TMT) proteomic analysis. In conclusion, our study highlights the hypothalamic proteome as a critical determinant in the susceptibility to DIO and provides novel targets for obesity prevention and treatment. Full article

Chile holds ~50% of temperate forests in the Southern Hemisphere, thus constituting a genetic–ecological heritage. However, intense anthropogenic pressures have been inducing distinct forest structural-regeneration patterns. Accordingly, we evaluated 22 soil properties at 0–5 and 5–20 cm depths in two protected sites, with similar perturbation records but contrasting post-disturbance regeneration stages: long-term secondary forest (~50 y) (SEC_FORST) (dominated by Chusquea sp.-understory) and a short-term forest after disturbance (~5 y) (FAD_IST) within a Nothofagus spp. forest to determine the potential of these soils to promote nutrient availability, water cycling, soil organic carbon (SOC) sequestration (CO₂→SOC), and microbiome. Results detected 93 correlations (r ≥ 0.80); however, no significant differences (p < 0.05) in physical or chemical properties, except for infiltration velocity (+27.97%), penetration resistance (−23%), SOC (+5.64%), and % Al saturation (+5.64%) relative to SEC_FORST, and a consistent trend of suitable values 0–5 > 5–20 cm were estimated. The SOC→CO₂ capacity reached 4.2 ± 0.5 (FAD_IST) and 2.7 ± 0.2 Mg C y⁻¹ (SEC_FORST) and only microbial abundance shifts were observed. These findings provide relevant insights on belowground resilience, evidenced by similar ecosystem services provision capacities over time, which may be influenced progressively by opportunistic Chusquea sp. Full article

Rubber dandelion (Taraxacum kok-saghyz Rodin, TKS), also referred to as Russian dandelion, is one of the most promising natural rubber (NR)-producing plants that produce high-quality NR comparable to that from the Pará rubber tree (Hevea brasiliensis, Hb), currently the only commercial source. It needs further breeding to improve the agricultural traits. However, little has been known about the genetic mechanisms underlying the regulation of floral induction and flower development in TKS, an important trait that remains to be improved for commercial production. The MADS-box gene AGAMOUS-LIKE 24 (AGL24) plays important roles in floral induction and flower development. As the first step in understanding its roles in TKS, this study isolated and characterized the AGL24-homologous gene TkAGL24 in TKS. The TkAGL24 gene had a 705 bp coding sequence (CDS) that encoded a protein of 234 amino acids containing the conserved classic MADS-box type II domain and K-box domain, sharing 55.32% protein sequence identity with the AtAGL24 protein from Arabidopsis. TkAGL24 was highly expressed in leaf, latex, root, and peduncle but rarely or not in mature flower. The TkAGL24 protein was located in the nucleus and cytoplasm and did not have transcription activation activity in yeast cells. The overexpression of TkAGL24 in Arabidopsis could promote flowering and cause the abnormal development of flowers, similar to other AGL24-homologous genes from other species. Furthermore, the overexpression of TkAGL24 in TKS also affected the development of ligulate flowers. These results suggested that the cloned TkAGL24 gene is functional and may play important roles in floral induction and flower development in TKS, providing an insight into the possibility for the further studies of its roles and application to breeding. Full article