Search Results (1,061)

Background and Rationale: Tinospora crispa (L.) Hook.f. & Thomson (T. crispa) is a climbing medicinal plant with long-standing ethnopharmacological use, particularly in inflammatory and hepatic disorders and cancer-related conditions. There is a knowledge gap regarding how wild versus cultivated ecotypes differ in chemotype, bioactivity, and safety, and how this might support or refine traditional use. Study Objectives: This study aimed to compare wild and cultivated ecotypes of T. crispa from the Nile Delta (Egypt) in terms of quantitative and qualitative phytochemical profiles; selected in vitro biological activities (especially antioxidant and cytotoxic actions); genetic markers potentially associated with metabolic variation; and short-term oral safety in an animal model. Core Methodology: Standardized extraction of plant material from wild and cultivated ecotypes. Determination of total phenolics, total flavonoids, and major phytochemical classes (alkaloids, tannins, terpenoids). Metabolomic characterization using UHPLC-ESI-QTOF-MS, supported by NMR, to confirm key compounds such as berberine, palmatine, chlorogenic acid, rutin, and borapetoside C. In vitro bioassays including: Antioxidant activity (e.g., radical-scavenging assay with EC₅₀ determination). Cytotoxicity against human cancer cell lines, with emphasis on HepG2 hepatoma cells and calculation of IC₅₀ values. Targeted genetic analysis to detect single-nucleotide polymorphisms (SNPs) in the gen1 locus that differentiate ecotypes. A 14-day oral toxicity study in rats, assessing liver and kidney function markers and performing histopathology of liver and kidney tissues. Principal Results: The wild ecotype showed a 43–65% increase in total flavonoid and polyphenol content compared with the cultivated ecotype, as well as substantially higher levels of key alkaloids, particularly berberine (around 12.5 ± 0.8 mg/g), along with elevated chlorogenic acid and borapetoside C. UHPLC-MS and NMR analyses confirmed the identity of the main bioactive constituents and defined a distinct chemical fingerprint for the wild chemotype. Bioassays demonstrated stronger antioxidant activity of the wild extract than the cultivated one and selective cytotoxicity of the wild extract against HepG2 cells (IC₅₀ ≈ 85 µg/mL), being clearly more potent than extracts from cultivated plants. Genetic profiling detected a C → T SNP within the gen1 region that differentiates the wild ecotype and may be linked to altered biosynthetic regulation. The 14-day oral toxicity study (up to 600 mg/kg) revealed no evidence of hepatic or renal toxicity, with biochemical markers remaining within physiological limits and normal liver and kidney histology. Conclusions and Future Perspectives: The wild Nile-Delta ecotype of T. crispa appears to be a stress-adapted chemotype characterized by enriched levels of multiple bioactive metabolites, superior in vitro bioactivity, and an encouraging preliminary safety margin. These findings support further evaluation of wild T. crispa as a candidate source for standardized botanical preparations targeting oxidative stress-related and hepatic pathologies, while emphasizing the need for: More comprehensive in vivo efficacy studies. Cultivation strategies that deliberately maintain or mimic beneficial stress conditions to preserve phytochemical richness. Broader geographical and genetic sampling to assess how generalizable the present chemotypic and bioactivity patterns are across the species. Full article

Soybean is the world’s foremost oilseed crop, and leaf morphology significantly influences yield potential by affecting light interception, canopy structure, and photosynthetic efficiency. In this study, leaf length, leaf width, maximum leaf width, leaf apex opening angle, and leaf area were measured in 216 soybean accessions, and genome-wide association studies (GWAS) were conducted using genomic resequencing data to identify genetic variants associated with leaf morphological traits. A total of 824 SNP loci were found to be significantly associated with leaf shape, and 130 candidate genes were identified in the genomic regions flanking these significant loci. KEGG enrichment analysis revealed that the above candidate genes were significantly enriched in arginine biosynthesis (ko00220), nitrogen metabolism (ko00910), carbon metabolism (ko01200), pyruvate metabolism (ko00620), glycolysis/glycogenolysis (ko00010), starch and sucrose metabolism (ko00500), plant–pathogen interaction (ko04626), and amino acid biosynthesis (ko01230). By combining KEGG and GO enrichment analysis as well as expression level analysis, four candidate genes related to leaf shape (Glyma.10G141600, Glyma.13G062700, Glyma.16G041200 and Glyma.20G115500) were identified. Further, through candidate gene association analysis, it was found that the Glyma.10G141600 gene was divided into two major haplotypes. The leaf area of haplotype 1 was significantly smaller than that of haplotype 2. Subsequently, the cutting amplification polymorphism sequence (CAPS) molecular marker was developed. The marker Chr.10:37502955 can effectively distinguish the differences in leaf size through enzymatic digestion technology, and has excellent typing ability and application potential. The above results can provide a theoretical basis for molecular-assisted selection (MAS) of soybean leaf morphology. Full article

This study identified genomic regions associated with carcass traits and primal cut yields in Hanwoo cattle using weighted single-step genome-wide association study (WssGWAS). A total of 50,227 carcass records and genomic data from 23,573 animals with 45,057 single-nucleotide polymorphisms were analyzed. Heritability estimates were 0.24 for carcass weight, 0.22 for eye muscle area, 0.31 for backfat thickness, and 0.36 for marbling score, while those for primal cut yields ranged from 0.02 to 0.26. For carcass traits, candidate genes were identified for carcass weight (XKR4 2.35%, COBL 1.26%), eye muscle area (LCORL 1.56%, TGFBR2 1.49%), backfat thickness (ATG7 1.27%, MYPN 1.33%), and marbling score (TWIST2 1.16%, BMP4 1.14%). For primal cut yields, the chromosome 6 region containing WDR1 was commonly identified across six traits and the chromosome 4 region containing CACNA2D1 across five traits; the chromosome 28 region containing SIRT1 explained the highest genetic variance (6.46%) for striploin. These pleiotropic regions are potential targets for genomic selection to improve production efficiency and carcass value in Hanwoo. Full article

Background: Osteoporosis is highly prevalent in postmenopausal women, yet genome-wide association studies often miss disease-relevant variants because of incomplete single nucleotide polymorphism (SNP) coverage and platform-specific limitations. We aimed to identify genetic contributors to osteoporosis risk by integrating two exome-based genotyping platforms with multilayer analytic approaches. Methods: We analyzed extreme osteoporosis phenotypes in Korean postmenopausal women from the Korean Genome and Epidemiology Study (KoGES) Ansan–Anseong cohorts using the Illumina Infinium HumanExome BeadChip and the Affymetrix Axiom Exome Array. After standard quality control, single-SNP logistic regression, cross-platform overlap analysis, and three machine-learning models were applied. Predicted functional impact was evaluated using multiple in silico algorithms and conservation scores. Finally, datasets from both platforms were merged, and cross-platform linkage disequilibrium (LD) blocks were defined to identify loci containing SNPs with p < 1 × 10⁻⁴. Results: No overlapped SNP reached genome-wide significance, but rs2076212 in PNPLA3 achieved suggestive significance (p < 1 × 10⁻⁵) only on the Illumina array. Cross-platform analysis identified 111 overlapping SNPs in 70 genes. Integrated machine-learning, in silico, and conservation evidence prioritized ARMS2, CCDC92, NQO1, ZNF510, PTPRB, and DYNC2H1 as candidate genes. LD-block analysis revealed 10 blocks with at least one SNP at p < 1 × 10⁻⁴, including four chromosome 12 loci (NAV2, BICD1, CCDC92, ZNF664) that became apparent only when LD patterns were evaluated jointly across platforms. Conclusions: Combining dual exome arrays with LD-block analysis, machine learning, and functional prediction improved sensitivity for detecting low bone mineral density-related loci and highlighted CCDC92, DYNC2H1, NQO1, and related genes as biologically plausible candidates for future validation. Full article

Background/Objectives: Common vetch (Vicia sativa L.) is a globally cultivated leguminous crop, valued for its high nutritional content and role in sustainable agriculture. Methods: To identify loci or genes significantly associated with salt tolerance, we conducted a genome-wide association study (GWAS) using 172 common vetch accessions primarily from diverse geographic regions. Single-nucleotide polymorphisms (SNPs) were obtained through re-sequencing, and five salt tolerance-related traits, including the germination rate (GR), germination potential (GP), germination index (GI), shoot length (SL), and root length (RL), were evaluated under salt stress conditions. We have identified 20 loci significantly associated with salt tolerance-related traits, and explaining 9.7–21.8% of the phenotypic variation. Notably, 13 loci exhibited pleiotropic effects on multiple traits; include qST1.1 (associated with SL, GR, GI), qST1.3 (RL, SL, GP), qST2.5 (SL, GR, GI, GP), and qST2.7 (SL, RL, GP, GI), and should be prioritized in future breeding programs. All 20 loci are novel compared to previous reports. Furthermore, we identified 7 candidate genes encoding key regulatory proteins, including a zinc finger MYM-type protein, ubiquitin-like domain-containing protein, transcription factor bHLH, ethylene-responsive transcription factor, auxin-responsive protein, and serine/threonine-protein kinase, as potential regulators of salt tolerance. Conclusions: This study advances our understanding of the genetic basis of salt tolerance in common vetch and provides valuable loci, molecular tools, and elite accessions. HZMC1352, GLF303, GLF301, HZMC1387, GLF306, GLF368, GLF342, HZMC1384, HZMC1355, GLF307, HZMC1366 are used for improving salt tolerance in breeding programs. Full article

Sea cucumber (Apostichopus japonicus) is a commercially important mariculture species in northern China. Papilla number has been recognized as a key economic trait in sea cucumbers. Notably, significant variation in papilla count exists among different populations. The genetic mechanisms controlling papilla development are not fully understood. In this study, 72 individuals from six geographically distinct sea cucumber populations (Group N1) and 35 individuals from their offspring (Group N2) were analyzed using reduced-representation genome sequencing (RRGS) and whole-genome resequencing (WGS), respectively. Genome-wide association studies (GWAS) and selective sweep analysis were conducted to identify the biological pathways and genetic basis underlying variation in papilla number. The GWAS analysis identified two single-nucleotide polymorphism (SNP) loci on chromosomes 4 and 14 in the Group N1 that were significantly associated with papilla number. Within the vicinity of two SNPs, 48 genes were annotated as putative candidate genes, six of which have been reported to be associated with growth in A. japonicus or other aquatic animals. Selective sweep analysis identified 23 candidate genes in the JZ vs. YT within Group N1 and 39 candidate genes in the G1 vs. G3 within Group N2. Notably, functional enrichment analysis revealed that the Calcium signaling pathway was significantly enriched in both Group N1 and Group N2. This pathway has been demonstrated to regulate key cellular processes such as cell proliferation and differentiation through the activation of downstream signaling cascades. The intersection of results from parental Group N1 and progeny Group N2 yielded a total of six key biological pathways, including biological process, cellular process, cellular anatomical entity, cellular component, membrane, and binding. Collectively, our findings contribute to a deeper understanding of the genetic mechanisms underlying papilla number variation in A. japonicus and provide valuable insights for genomic selection in breeding programs. Full article

Background/Objectives: Prostate cancer is the most frequent male malignancy. The incidence of disease varies among different ethnic groups. CYP3A polymorphisms are candidates for prostate cancer susceptibility studies. The aim of the present study is to investigate the ethnicity-related clinical impact of CYP3A4 variants on prostate cancer risk. Methods: A systematic literature search and meta-analysis were conducted according to PRISMA guidelines. A total of 10 eligible studies, including 3116 prostate cancer cases and 3008 healthy controls, were analyzed. We evaluated the association between the CYP3A4*1B (rs2740574, −392 A > G) variant and prostate cancer risk in European Caucasians. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using six genetic models. Data were analyzed using fixed and random-effects models based on the I2 value of heterogeneity magnitude. Funnel plots and Egger’s linear regression tests were used to assess publication bias. Results: CYP3A4*1B was associated with prostate cancer susceptibility in the allele (G vs. A: OR = 1.32, CI = 0.91–1.93), dominant (AG + GG vs. AA OR = 1.41, CI = 0.95–2.09), recessive (GG vs. AA + AG, OR = 1.82, CI = 1.26–2.63), homozygous (GG vs. AA, OR = 1.92, CI = 1.32–2.77), heterozygous model (AG vs. AA, OR = 1.31, CI = 0.89–1.93) and co-dominant model (AG vs. AA + GG; OR = 1.27, CI = 0.88–1.85). Significant heterogeneity characterized the allele, as well as the dominant model (I2 = 84.1%, I2 = 80.0%). Egger’s tests (p < 0.05) and funnel plots did not identify publication bias. Conclusions: The present meta-analysis indicates that the G allele and GG genotype might affect prostate cancer susceptibility in European Caucasians; however, the validity and reliability of the results need to be examined in future research. Full article

The Xinjiang Brown cattle (XJBC) is one of China’s five major dual-purpose dairy and beef breeds. Analyzing the genetic diversity of the Xinjiang Brown cattle population lays the theoretical groundwork for identifying and conserving its genetic resources. This study employed the Illumina Bovine SNP 150K chip to analyze genetic diversity, inbreeding coefficient, kinship, and genetic distance in a population of 750 Xinjiang Brown cattle from three breeding farms in Xinjiang. Genetic diversity was assessed by calculating minimum allele frequency (MAF), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and linkage disequilibrium (LD). Population structure was analyzed using PCA. ROH was calculated to derive ROH-based inbreeding coefficients, pedigree-based inbreeding coefficients (F_PED) were estimated using CFC software for comparison, and candidate genes within high-frequency ROH regions in Xinjiang Brown cattle were identified. A G matrix was constructed to analyze population kinship. Results revealed 94,173 high-quality SNP loci in Xinjiang Brown cattle, with an average MAF of 0.276, PIC of 0.376, Ho of 0.345, and He of 0.376. Breeding farm 3 exhibited the fastest LD decay, indicating relatively high genetic diversity across Xinjiang Brown cattle populations, with farm 3 demonstrating greater diversity. The IBS genetic distance was 0.313. The G matrix results aligned with the IBS distance matrix, both indicating close kinship among some individuals within the Xinjiang Brown cattle population. The ranges for average F_PED and average F_ROH across farms were 0.0017–0.0189 and 0.0609–0.0878, respectively. Short ROH segments (0.5–2 Mb) constituted the largest proportion (51.31%) of all ROHs. Within high-frequency ROH enrichment regions, 61 genes, including LCORL, FAM110B, NR4A1, and PER2, were identified as potentially associated with economic traits in Xinjiang Brown cattle. These findings provide relevant marker sites for genomic selection in Xinjiang Brown cattle and lay a theoretical foundation for subsequent research. Full article

Background/Objectives: Many studies in the literature are increasingly focusing on how genes influence the development of individual behaviors and personality traits through genome sequencing. Most research indicates that complex behaviors and their characteristics are influenced by multiple genes, highlighting the crucial role of genetic studies in this field. Behavioral genetics, as a scientific discipline, investigates how genetic factors shape individuals’ behaviors and personality traits. The concepts of violence and aggression, observable in various contexts, have been extensively studied, with a particular focus on the underlying causes of these behaviors. In sports, where physical strength plays a significant role, regulations designed to prevent violent behaviors and aggressive attitudes contribute to the establishment of appropriate behavior patterns and discipline. Methods: This study aims to identify correlations between polymorphisms found in athletes and their responses to questionnaires, focusing on candidate genes known to influence personality and behavior traits, such as catechol-O-methyltransferase (COMT), serotonin transporter (5-HTT), monoamine oxidase (MAO-A), and serotonin 1A transporter (5-HT1A). A total of twenty licensed athletes participated in the study. Participants completed three standardized instruments: the Sportsmanship Behavior Scale (27 items), the Sports Emotion Scale (22 items), and the Anger-Control Scale (34 items). Following the acquisition of informed consent, buccal swab samples were collected for single nucleotide polymorphism (SNP) analysis targeting the COMT, MAO-A, 5- HT1A, and 5-HTT genes. Subsequent to sample collection and questionnaire administration, statistical analyses were conducted to evaluate the relationships among behavioral measures and genetic variants. Results: Overall, the findings point to gene-specific patterns in 5-HTT, MAO-A, and COMT, while no clear pattern emerged for 5-HT1A. Conclusions: Ultimately, this study provides an early exploration of aggression-related genetic patterns within the context of forensic sciences, highlighting preliminary trends and potential associations that may inform the design of future research. Full article

Background: BTB and CNC homology 1 (Bach1) are transcriptional regulators involved in the oxidative response and inflammation. Although its biological functions are well characterized, the clinical impact of Bach1 gene polymorphisms (rs2300301, rs1153285, and rs2070401) on respiratory outcomes in preterm infants remains unclear. Methods: This multicenter study included 212 Japanese preterm infants born at <32 weeks of gestation with birth weights <1250 g. Three Bach1 single-nucleotide polymorphisms (SNPs; rs2300301, rs1153285, and rs2070401) were genotyped using TaqMan polymerase chain reaction (PCR). The requirements for home oxygen therapy (HOT) were compared across genotypes. Logistic regression analyses were performed after adjusting for the gestational age, sex, birth weight, and histological chorioamnionitis status. Results: Infants requiring HOT had a significantly lower gestational age (26 ± 1.7 weeks vs. 27 ± 2.2 weeks, p = 0.015) and lower birth weight (774 ± 235 g vs. 818 ± 233 g, p = 0.043) than those who did not. Histological chorioamnionitis was more prevalent in the HOT group (p = 0.022). rs2300301 was associated with HOT in univariate analysis (OR = 1.78, 95% CI: 1.20–2.04, p = 0.015). However, this association did not remain statistically significant after adjustment for gestational age, sex, birth weight, and histological chorioamnionitis (OR = 2.48, 95% CI: 0.90–6.80, p = 0.079). The rs1153285 and rs2070401 SNPs were not significantly associated with HOT expression. Conclusions: Our findings suggest a potential association between the Bach1 rs2300301 polymorphism and prolonged oxygen requirement in preterm infants. Although the adjusted analysis did not confirm the statistical significance, this SNP may serve as a candidate genetic marker for respiratory morbidity. Further studies are required to validate these findings. Full article

Background: Sarcopenia and sarcopenic obesity are increasingly recognized in kidney transplant recipients (KTRs), yet their molecular underpinnings remain poorly defined. We sought to synthesize current evidence on biomarker associations with muscle loss and function in the post renal transplant setting. Methods: A comprehensive search of PubMed/MEDLINE and Cochrane databases was conducted according to PRISMA guidelines. Studies evaluating biomarkers related to sarcopenia or sarcopenic obesity in adult and pediatric KTRs were included. Quality assessment was performed with the NHLBI tool. Results: Seven studies were included, encompassing 548 KTRs. Myostatin levels predicted sarcopenia in KTRs (cut-off: 390 pg/mL) and inversely correlated with Metabolic equivalent of Tasks (METs), handgrip strength (HGS), and graft performance. Although adiponectin was negatively correlated with body fat, its high-molecular-weight isoform was linked to lower muscle mass and long-term graft decline. Leptin was associated with sarcopenic obesity and lower estimated Glomerular Filtration Rate (eGFR). Insulin like Growth Factor-1 (IGF-1) independently predicted HGS but not muscle mass. Brain-derived neurotrophic factor (BDNF) levels predicted sarcopenia (cut off: 17.8 ng/mL) and reflected physical activity levels. Visfatin showed no association with sarcopenia but it was positively correlated with eGFR. Lastly, certain polymorphisms of Alpha-actinin-3 (ACTN3) were shown to genetically predispose to post-transplant sarcopenia. Conclusions: These emerging candidate biomarkers provide promising mechanistic insight into post-transplant muscle decline and may ultimately support more personalized risk assessment. Further validation is needed, and functional measures remain the most reliable clinical tools at present. Full article

Cannabis sativa L. has been cultivated for millennia as a source of food and fibre. Increasing demand for functional foods has renewed interest in C. sativa seeds (hempseeds), which are rich in essential fatty acids and amino acids. However, a near-global moratorium on C. sativa cultivation and research throughout most of the 20th century has delayed crop improvement using modern breeding approaches. As a result, genetic loci contributing to key agronomic traits, including with respect to maximizing yield as a seed crop, remain largely unknown. In this study, a feminized segregating F₂ mapping population, derived from a tall parent with spacious inflorescences and large seeds and a short-stature parent with compact inflorescences and small seeds, was phenotyped for key seed and agronomic traits related to yield. A mid-density Single Nucleotide Polymorphism (SNP) genotyping panel was used to generate a genetic linkage map of 291.5 cM with 455 SNPs. Quantitative Trait Locus (QTL) mapping identified major loci for hundred-seed weight—qHSW3, 26.59 percent variance explained (PVE), seed volume—qSV1, 33.24 PVE, and plant height—qPH9, 46.99 PVE. Our results provide novel target regions, associated molecular markers, and candidate genes for future breeding efforts to improve C. sativa. Full article

Pigs play a vital role in global food security as a major source of animal protein. Enhancing growth and reproductive traits is of great economic importance to the swine industry. To systematically identify genetic determinants underlying key economic traits, we performed an integrative multi-omics analysis in a population of 1624 Duroc pigs, focusing on backfat thickness (BF), loin muscle area (LMA), and total teat number (TTN). Our genome-wide association study (GWAS) identified twenty-one significant single nucleotide polymorphisms (SNPs)—fourteen for BF, three for LMA, and seven for TTN. Candidate genes located within 1 Mb of these SNPs, such as ZC3HAV1L and FAM3A for BF, PTGR2 for LMA, and VRTN and ABCD4 for TTN, were further investigated. Functional genomic annotations revealed that genetic variants near the significant SNPs were enriched in tissue-specific enhancer elements, implying regulatory potential. Transcriptome-wide association study (TWAS) further supported the candidate genes such as ABCD4 and YLPM1 for TTN and predicted several putative functional mutations that may affect transcription factor binding sites. This study demonstrates the power of integrative genomics to prioritize candidate genes and causal variants for animal complex traits, offering valuable resources for future precision breeding in pigs. Full article

Soybean [Glycine max (L.) Merr.] is a commercially important oil and protein-producing crop. This study explored genetic variation in seed traits to improve soybean productivity. Phenotypic data, including seed size, length, width, thickness, and weight, were analyzed across 344 Korean soybean accessions, identifying 100-seed weight (100SW) as one of the important yield components in soybean. Using 4,472,823 high-density single-nucleotide polymorphism (SNP) markers, a genome-wide association study detected 10 novel loci associated with 100SW on chromosomes 3, 4, and 19. Haplotype analysis revealed that the accessions with alternative alleles at nine candidate loci displayed significant variation in 100SW, either increasing or decreasing weight. Allele stacking analysis further highlighted that favorable variants, particularly on chromosomes 3 and 19, had additive genetic effects on 100SW. Functional annotations suggest these genes influence seed weight through gibberellin synthesis and developmental pathways. By leveraging high-density genomic data, this study overcomes the limitations of previous studies relying on low-density markers, offering a foundation for more efficient soybean breeding strategies. These findings offer valuable insight into marker-assisted selection, providing a foundation to enhance soybean yield and adaptability under diverse environmental conditions and addressing the growing global demand for sustainable food production. Full article

Recent advancements in nanotechnology have intensified research efforts to address security concerns like hardware trojans and intellectual property (IP) piracy, particularly by exploring novel alternatives to traditional MOSFET devices. Spin-based devices, known for their low power consumption, non-volatility, and seamless integration with silicon substrates, have emerged as promising candidates. This research proposes a novel approach to enhance the security of integrated circuits using spin-based devices known as magnetic tunnel junctions (MTJs). A Non-volatile Polymorphic Logic (NPL) is optimized and designed to perform multiple operations, effectively concealing its true functionality. The analytical studies conducted on the Cadence Virtuoso platform using TSMC 65 nm MOS technology demonstrate the feasibility and efficacy of the proposed approach. The proposed NPL circuit enables polymorphism by allowing the circuit to perform all one- and two-input Boolean logic operations, including NOT, AND/NAND, OR/NOR, and XOR/XNOR, through adjustments of applied keys. This dynamic functionality makes it challenging for attackers to determine the circuit’s true operation. The proposed design exhibits similar timing characteristics for different logic operations, which further complicates the tampering attempts. Additionally, the circuit’s layout is designed to be symmetric, ensuring the execution of all possible operations by the same physical layout. This provides post-manufacturing security from reverse engineering and finds its applications in securing custom IC designs against the evolving landscape of hardware-based threats. Full article