Search Results (24)

Coastal boulder deposits (CBDs) are among the most striking geomorphic signatures of extreme wave activity, recording the action of both tsunamis and severe storms. Their significance extends beyond geomorphology, providing geological archives that capture rare but high-impact events beyond the scope of instrumental or historical records. This review critically examines the origins, emplacement mechanisms, diagnostic morphology, monitoring tools, and global case studies of CBDs with the aim of clarifying the storm–tsunami debate and advancing their application in coastal hazard assessment. A systematic literature survey of 77 peer-reviewed studies published between 1991 and 2025 was conducted using Scopus and Web of Science, with inclusion criteria ensuring relevance to extreme-wave processes, geomorphic analysis, and chronological methods. Multiproxy approaches were emphasized, integrating geomatics (RTK-GPS, UAV-SfM, TLS, LiDAR), geochronology (¹⁴C, U–Th, OSL, cosmogenic nuclides, VRM), and hydrodynamic modeling. Findings show that tsunamis explain the largest and most inland megaclasts, while modern storms have proven capable of mobilizing boulders exceeding 200 t at elevations up to 30 m. Many deposits are polygenetic, shaped by successive high-energy events, complicating binary classification. CBDs emerge as multifaceted archives of extreme marine forcing, essential for refining hazard assessments in a changing climate. Full article

As the residual products of severe chemical weathering, bauxite deposits serve both as essential economic Al-Fe resources and geochemical archives that reveal information about the parent rocks’ composition, paleoenvironments and paleoclimates, and the tectonic settings responsible for their genesis. The well-developed Early Paleocene bauxite deposits of the Salt Range, Pakistan, provide an opportunity for deciphering their ore genesis and parental affinities. The deposits occur as lenticular bodies and are typically composed of three consecutive stratigraphic facies from base to top: (1) massive dark-red facies (L-1), (2) composite conglomeratic–pisolitic facies (L-2), and (3) Kaolinite-rich clayey facies (L-3). Results from optical microscopy, X-ray powder diffraction (XRPD), and scanning electron microscopy with Energy-Dispersive X-Ray Spectroscopy (SEM-EDS) reveal that facies L-1 contains kaolinite, hematite, and goethite as major minerals, with minor amounts of muscovite, quartz, anatase, and rutile. In contrast, facies L-2 primarily consists of kaolinite, boehmite, hematite, gibbsite, goethite, alunite/natroalunite, and zaherite, with anatase, rutile, and quartz as minor constituents. L-3 is dominated by kaolinite, quartz, and anatase, while hematite and goethite exist in minor concentrations. Geochemical analysis reveals elevated concentrations of ${\mathrm{Al}}_2$${\mathrm{O}}_3$, ${\mathrm{Fe}}_2$${\mathrm{O}}_3$, ${\mathrm{SiO}}_2$, and ${\mathrm{TiO}}_2$. Trace elements, including Th, U, Ga, Y, Zr, Nb, Hf, V, and Cr, exhibit a positive trend across all sections when normalized to Upper Continental Crust (UCC) values. Field observations and analytical data suggest a polygenetic origin of these deposits. L-1 suggests in situ lateritization of some sort of precursor materials, with enrichment in stable and ultra-stable heavy minerals such as zircon, tourmaline, rutile, and monazite. This facies is mineralogically mature with bauxitic components, but lacks the typical bauxitic textures. In contrast, L-2 is texturally and mineralogically mature, characterized by various-sized pisoids and ooids within a microgranular-to-microclastic matrix. The L-3 mineralogy and texture suggest that the conditions were still favorable for bauxite formation. However, the ongoing tectonic activities and wet–dry climate cycles post-depositionally disrupted the bauxitization process. The accumulation of highly stable detrital minerals, such as zircon, rutile, tourmaline, and monazite, indicates prolonged weathering and multiple cycles of sedimentary reworking. These deposits have parental affinity with acidic-to-intermediate/-argillaceous rocks, resulting from the weathering of sediments derived from UCC sources, including cratonic sandstone and shale. Full article

The Bighead carp (Hypophthalmichthys nobilis), a primary freshwater aquaculture species in China, faces challenges due to over-exploitation and environmental changes. We leveraged RAD-seq to perform a comprehensive population genetic analysis on 14 H. nobilis populations sampled from the Yangtze River (13 populations) and the Marseilles Reach of the Illinois River (one population). Analysis of genetic diversity showed that different parameters demonstrated varied inferences, and notably, Zhongxian (ZX2), Wanhzou (WZ2), Yangzhou hatchery (YZYZ), Yangzhou (YZ), and Taihu (TH) populations showed apparent heterozygote deficiency. Linkage disequilibrium (LD) analysis exhibited a trend of higher linkage disequilibrium in populations from the upper reaches of the Yangtze River, followed by those from the middle reaches and then those from the lower reaches. Additionally, the reconstructed polygenetic tree and PCA plot clustered all populations into 2 major subgroups, while the results of structure analysis indicated 4 ancestors. The pairwise F_ST values ranged from 0 to 0.5530. Among these, high F_ST values (0.1931–0.5530) were only observed between populations WZ2, YZ, YZYZ, and the remaining 11 populations. Furthermore, genetic bottlenecks were observed in all populations 20–30 thousand years ago. Overall, the research offers insights essential for genetic management practices for sustainable aquaculture and biodiversity conservation of bighead carp. Full article

Schizophrenia (SCZ) is a complex psychiatric disorder with high heritability; identifying risk genes is essential for deciphering the disorder’s pathogenesis and developing novel treatments. Using whole-exome sequencing, we screened for mutations within protein-coding sequences in a single family of patients with SCZ. In a pathway enrichment analysis, we found multiple transmitted variant genes associated with two KEGG pathways: herpes simplex virus 1 (HSV1) infection and the extracellular matrix (ECM)–receptor interaction. When searching for rare variants, six variants, SLC6A19^p.L541R, CYP2E1^p.T376S, NAT10^p.E811D, N4BP1^p.L7V, CBX2^p.S520C, and ZNF460^p.K190E, segregated with SCZ. A bioinformatic analysis showed that three of these mutated genes were associated with chromatin modulation. We found that HSV1 infection, ECM–receptor interaction pathways, and epigenetic mechanisms may contribute to the pathogenesis of SCZ in certain families. The identified polygenetic risk factors from the sample family provide distinctive underlying biological mechanisms of the pathophysiology of SCZ and may be useful in clinical practice and patient care. Full article

Terra rossa is a reddish clay soil which is often present on the surface of limestone in regions with a Mediterranean-type climate. Its genesis is a controversial subject in terms of the origin of the parent material, from the residuum of underlying (carbonate/dolomite) bedrock in the absence/presence of an external silicate contribution (e.g., aeolian dust). Within this context the main goal of the present work was the understanding of the geochemical processes leading to the formation of the terra rossa starting from the carbonate bedrock. We report the results of a multi-method analysis on a terra rossa deposit occupying the bottom of a Quaternary karst depression on Mesozoic limestones exposed in the Murge area (Apulia Foreland, southern Italy). Geological, petrographic, textural, and chemical data were collected on karst products (reddish calcite incrustations and nodules, and fine-grained portion of terra rossa) by a detailed field mapping, optical microscopy, XRF and fusion ICP/MS analyses and by scanning electron microscope. New collected data show that the mineralogical composition of reddish incrustations and nodules is comparable, consisting of fibrous and impure calcite, detrital fragments of quartz, K-feldspar, zircon and authigenic minerals as (Mn, Ba, Ca) phases, (Al, Si, Mn, Fe, Mg, Ba, Ca) minerals, Fe-kaolinite and anatase. The prevailing minerals, instead, in the fine-grained portion of terra rossa are hematite, kaolinite, and goethite. Based on the chemical composition, and especially on REE patterns, a progressive interaction of silicate aqueous solutions (with Al, Si, Fe), containing pelite material, with the calcareous bedrock, as a source of carbonic acid, was the process driving the formation of terra rossa. Obtained results add new elements to the definition of the long-lasting question about the genetic processes responsible for the formation of terra rossa, corroborating their polygenetic origin, as result of limestone alteration in conjunction with the chemical interaction with allochthonous siliciclastic material. Full article

Obesity has become a severe public health challenge globally. The present study aimed to identify separate and interactive dietary, genetic, and other factors that increase the risk of obesity as measured by body fat (BF) mass. We utilized a genome-wide association study to identify genetic variants associated with high fat mass (obesity; n = 10,502) and combined them to generate polygenic risk scores (PRS) of genetic variants interacting with each other in adults aged over 40 while excluding body-fat-related diseases in a city-hospital-based cohort (n = 53,828). It was validated in Ansan/Ansung plus rural cohorts (n = 13,007). We then evaluated dietary and lifestyle factors in subjects to assess what factors might help overcome a genetic propensity for higher BF. The three-SNP model included brain-derived neurotrophic factor (BDNF)_rs6265, fat-mass- and obesity-associated protein (FTO)_rs1421085, and SEC16B_rs509325. The genes with the minor alleles of ADCY3_rs6545790 and BAIAP2_rs35867081 increased their gene expression in the visceral and subcutaneous adipocytes, but their gene expression decreased in the hypothalamus in eQTL analysis. In the three-SNP model, the PRS was associated with BF mass by 1.408 and 1.396 times after adjusting covariates 1 (age, gender, survey year, residence area, education, and income) and 2 (covariates in model 1 plus energy intake, alcohol intake, regular exercise, and smoking status), respectively. However, when separating subjects by PRS of the three-SNP model, a plant-based diet was the most significant factor associated with low BF, followed by high-protein diets and lower energy intakes. They could offset the effects of high genetic risk for high BF. In conclusion, modulating nutrient intakes might overcome a high genetic risk for obesity. Dietary choices favoring more plant-based and higher-protein foods might help prevent increased BF in Asians and potentially people of other ethnicities with high polygenetic risk scores. Full article

Lymphocystic disease affects over 150 species of marine and freshwater fish worldwide. In this study, the lymphocystis pathogen was found in 2 (Amphiprion ocellaris and Amphiprion clarkii) of the 9 species of clownfish. Detection of lymphocystis disease virus (LCDV) was based on histopathological study, electron microscope observation of virus particles and gene sequence analysis from the MCP region. Infected A. ocellaris hosts showed sparse, multifocal, white, stiff, papilloma-like nodules on the body, skin, gills and fins; while, on A. clarkia, nodules were found on the operculum skin. Histopathologic study showed lymphocystic cells with an irregular nucleus, enlarged cytoplasm and intracytoplasmic inclusion bodies surrounded by the cell membrane. The viral particle presents virions 180–230 nm in diameter, hexagonal in shape with an inner dense nucleoid under transmission electron micrographs (TEM). From the ML polygenetic tree, the clownfish LCVD genotype was closely related to the LCDV strain from paradise fish, Macropodus opercularis (KJ408271) (pairwise distance: 92.5%) from China, then followed by the strain from Spain (GU320726 and GU320736) (pairwise distance: 90.8–90.5%), Korea (AB299163, AB212999, AB213004, and AB299164) (pairwise distance: 91.5–80.5%) and lastly Canada (GU939626) (pairwise distance: 83%). This is the first report of lymphocystis disease in A. clarkii in Taiwan. Full article

The phenotypic expression of antibiotic resistance genes (ARGs) can hamper the use of antibiotics as adjuncts to subgingival instrumentation in the treatment of periodontitis patients. The aim of the study was to analyze the relationship between the phenotypic and genotypic resistance against ampicillin-sulbactam, clindamycin, doxycycline and metronidazole of subgingival biofilm samples from 19 periodontitis patients. Samples were analyzed with shotgun sequencing and cultivated anaerobically for 7 days on microbiological culture media incorporating antibiotics. All growing isolates were identified to the species level using MALDI-TOF-MS and sequence analysis of the 16S ribosomal RNA (rRNA) gene. Phenotypic resistance was determined using EUCAST-breakpoints. The genetic profile of eight patients matched completely with phenotypical resistance to the tested antibiotics. The positive predictive values varied from 1.00 for clindamycin to 0.57 for doxycycline and 0.25 for ampicillin-sulbactam. No sample contained the nimI gene. It can be concluded that antibiotic resistance may be polygenetic and genes may be silent. Every biofilm sample harboring erm genes was phenotypic resistant. The absence of cfx and tet genes correlated to 100%, respectively, to 75%, with the absence of phenotypic resistance. The absence of nimI genes leads to the assumption that constitutive resistance among several species could explain the resistance to metronidazole. Full article

Sucrose non-fermenting-1-related protein kinase-1 (SnRK1) and its scaffolding proteins, FCS-like zinc finger proteins (FLZs), are well conserved in land plants and involved in various processes of plant growth and stress responses. Glycyrrhiza inflata Bat. is a widely used licorice species with strong abiotic stress resistance, in which terpenoids and flavonoids are the major bioactive components. Here, we identified 2 SnRK1 catalytic α subunit encoding genes (GiSnRK1α1 and GiSnRK1α2) and 21 FLZ genes in G. inflata. Polygenetic analysis showed that the 21 GiFLZs could be divided into three groups. A total of 10 representative GiFLZ proteins interact with GiSnRK1α1, and they display overlapped subcellular localization (mainly in the nucleus and the cytoplasm) when transiently expressed in Nicotiana benthamiana leaf cells. Coinciding with the existence of various phytohormone-responsive and stress-responsive cis-regulatory elements in the GiSnRK1α and GiFLZ gene promoters, GiFLZs are actively responsive to methyl jasmonic acid (MeJA) and abscisic acid (ABA) treatments, and several GiFLZs and GiSnRK1α1 are regulated by drought and saline-alkaline stresses. Interestingly, GiSnRK1α and 20 of 21 GiFLZs (except for GiFLZ2) show higher expression in the roots than in the leaves. These data provide comprehensive information on the SnRK1 catalytic α subunit and the FLZ proteins in licorice for future functional characterization. Full article

Aphanomyces root rot, caused by Aphanomyces euteiches, causes severe yield loss in field pea (Pisum sativum). The identification of a pea germplasm resistant to this disease is an important breeding objective. Polygenetic resistance has been reported in the field pea cultivar ‘00-2067’. To facilitate marker-assisted selection (MAS), bulked segregant RNA-seq (BSR-seq) analysis was conducted using an F₈ RIL population derived from the cross of ‘Carman’ × ‘00-2067’. Root rot development was assessed under controlled conditions in replicated experiments. Resistant (R) and susceptible (S) bulks were constructed based on the root rot severity in a greenhouse study. The BSR-seq analysis of the R bulks generated 44,595,510~51,658,688 reads, of which the aligned sequences were linked to 44,757 genes in a reference genome. In total, 2356 differentially expressed genes were identified, of which 44 were used for gene annotation, including defense-related pathways (jasmonate, ethylene and salicylate) and the GO biological process. A total of 344.1 K SNPs were identified between the R and S bulks, of which 395 variants were located in 31 candidate genes. The identification of novel genes associated with partial resistance to Aphanomyces root rot in field pea by BSR-seq may facilitate efforts to improve management of this important disease. Full article

Iron-refractory iron deficiency anemia (IRIDA) is an autosomal recessive inherited form of iron deficiency anemia characterized by discrepantly high hepcidin levels relative to body iron status. However, patients with monoallelic exonic TMPRSS6 variants have also been reported to express the IRIDA phenotype. The pathogenesis of an IRIDA phenotype in these patients is unknown and causes diagnostic uncertainty. Therefore, we retrospectively summarized the data of 16 patients (4 men, 12 women) who expressed the IRIDA phenotype in the presence of only a monoallelic TMPRSS6 variant. Eight unaffected relatives with identical exonic TMPRSS6 variants were used as controls. Haplotype analysis was performed to assess the (intra)genetic differences between patients and relatives. The expression and severity of the IRIDA phenotype were highly variable. Compared with their relatives, patients showed lower Hb, MCV, and TSAT/hepcidin ratios and inherited a different wild-type allele. We conclude that IRIDA in monoallelic TMPRSS6-affected patients is a phenotypically and genotypically heterogeneous disease that is more common in female patients. We hypothesize that allelic imbalance, polygenetic inheritance, or modulating environmental factors and their complex interplay are possible causes. This explorative study is the first step toward improved insights into the pathophysiology and improved diagnostic accuracy for patients presenting with IRIDA and a monoallelic exonic TMPRSS6 variant. Full article

The northern slopes of the Vipava Valley are defined by a thrust front of Mesozoic carbonates over Tertiary flysch deposits. These slopes are characterized by a variety of different surface forms, among which recent and fossil polygenetic landslides are the most prominent mass movements. We used the height variability method as a morphometric indicator, which proved to be the most useful among the various methods for quantifying and visualizing fossil landslides. Height variability is based on the difference in elevations derived from a high-resolution lidar-derived DEM. Based on geologic field mapping and geomorphometric analysis, we distinguished two main types of movements: structurally induced movement along the fault zone and movements caused by complex Quaternary gravitational slope processes. The most pronounced element is the sliding of the huge rotational carbonate massif, which was displaced partly along older fault structures in the hinterland of fossil rock avalanches and carbonate blocks. In addition to the material properties of the lithology, the level of surface roughness also depends on the depositional processes of the individual sedimentary bodies. These were formed by complex sedimentary events and are intertwined in the geological past. The sedimentary bodies indicate two large fossil rock avalanches, while the smaller gravity blocks indicate translational–rotational slides of carbonate and carbonate breccia. Full article

Previous studies showed that diet and gut microbiota had a correlation with sleep. However, the potential interaction effects of diet and gut microbiota on sleep are still unclear. The phenotypic data of insomnia (including 374,505 subjects) and sleep duration (including 372,805 subjects) were obtained from the UK Biobank cohort. The Single Nucleotide Polymorphisms (SNPs) associated with 114 gut microbiota, 84 dietary habits, and 4 dietary compositions were derived from the published Genome-wide Association Study (GWAS). We used Linkage Disequilibrium Score Regression (LDSC) to estimate the genetic correlation and colocalization analysis to assess whether dietary habits and insomnia/sleep duration shared a causal variant in a region of the genome. Using UK Biobank genotype data, the polygenetic risk score of gut microbiota, dietary habits, and dietary compositions were calculated for each subject. Logistic regression and linear regression models were used to assess the potential effects of diet-gut microbiota interactions on sleep phenotypes, including insomnia and sleep duration. Insomnia and sleep duration were used as dependent variables, and sex, age, the Townsend Deprivation Index scores, and smoking and drinking habits were selected as covariates in the regression analysis. All statistical analyses were conducted using R-3.5.1 software. Significant genetic correlations were discovered between insomnia/sleep duration and dietary habits. Further, we found several significant dietary compositions-gut microbiota interactions associated with sleep, such as fat × G_Collinsella_RNT (p = 1.843 × 10⁻²) and protein × G_Collinsella_HB (p = 7.11 × 10⁻³). Besides, multiple dietary habits-gut microbiota interactions were identified for sleep, such as overall beef intake × G_Desulfovibrio_RNT (p = 3.26 × 10⁻⁴), cups of coffee per day × G_Escherichia_Shigella_RNT (p = 1.14 × 10⁻³), and pieces of dried fruit per day × G_Bifidobacterium_RNT (p = 5.80 × 10⁻³). This study reported multiple diet-gut microbiota interactions associated with sleep, which may provide insights into the biological mechanisms of diet and gut microbiota affecting sleep. Full article

Porcine Circovirus 2 (PCV2) is a crucial swine pathogen and considered a primary causative agent of porcine circovirus-associated diseases (PCVADs), posing a serious economic threat to the swine industry across globe. The world’s biggest agricultural conglomerates have teamed up to create giant commercial pig farms across Shanghai due to the proximity of this region to more affluent lean-pork markets. Since its discovery, PCV2 has displayed extraordinary genetic diversity, and its genome is swiftly evolving through a series of mutations and recombinations. However, limited information on epidemiology, molecular characteristics, vaccine cross-protection, and the co-infection rate of PCV2 with other lethal swine diseases can adversely impact the pig production in the region. To investigate the molecular epidemic characteristics and genetic evolution of PCV2, pigs with doubtful symptoms of PCVADs were sampled from various commercial pig farms with a history of PWMS and/or PDNS across Shanghai from 2014 to 2018. Our results revealed the coexistence of multiple PCV2 genotypes (PCV2b, PCV2e, and PCV2d) among Shanghai pig herds and dominance of PCV2d among them. We also found critical amino acid substitutions in epitope regions of important capsid proteins in PCV2 isolates involved in viral replication and host immune escape. Spotted mutations may favor the prevalence and survival of various PCV2 genotypes despite availability of commercial vaccines. This study also provides insight into the co-infection status of PCV2 with major lethal swine viral diseases such as PPV and PPRSV. Collectively, these investigations will contribute to understanding the molecular epidemiology and evolution of PCV2 across the region. Full article

Background: Insulin resistance is a common etiology of metabolic syndrome, but receiver operating characteristic (ROC) curve analysis shows a weak association in Koreans. Using a machine learning (ML) approach, we aimed to generate the best model for predicting insulin resistance in Korean adults aged > 40 of the Ansan/Ansung cohort using a machine learning (ML) approach. Methods: The demographic, anthropometric, biochemical, genetic, nutrient, and lifestyle variables of 8842 participants were included. The polygenetic risk scores (PRS) generated by a genome-wide association study were added to represent the genetic impact of insulin resistance. They were divided randomly into the training (n = 7037) and test (n = 1769) sets. Potentially important features were selected in the highest area under the curve (AUC) of the ROC curve from 99 features using seven different ML algorithms. The AUC target was ≥0.85 for the best prediction of insulin resistance with the lowest number of features. Results: The cutoff of insulin resistance defined with HOMA-IR was 2.31 using logistic regression before conducting ML. XGBoost and logistic regression algorithms generated the highest AUC (0.86) of the prediction models using 99 features, while the random forest algorithm generated a model with 0.82 AUC. These models showed high accuracy and k-fold values (>0.85). The prediction model containing 15 features had the highest AUC of the ROC curve in XGBoost and random forest algorithms. PRS was one of 15 features. The final prediction models for insulin resistance were generated with the same nine features in the XGBoost (AUC = 0.86), random forest (AUC = 0.84), and artificial neural network (AUC = 0.86) algorithms. The model included the fasting serum glucose, ALT, total bilirubin, HDL concentrations, waist circumference, body fat, pulse, season to enroll in the study, and gender. Conclusion: The liver function, regular pulse checking, and seasonal variation in addition to metabolic syndrome components should be considered to predict insulin resistance in Koreans aged over 40 years. Full article