Search Results (2,256)

The barbel chub (Squaliobarbus curriculus) exhibits remarkable resistance to grass carp reovirus (GCRV), a devastating pathogen in aquaculture. To reveal the molecular basis of this resistance, we investigated complement factor D (DF)—a rate-limiting serine protease governing alternative complement pathway activation. Molecular cloning revealed that the barbel chub DF (ScDF) gene encodes a 1251-bp cDNA sequence translating into a 250-amino acid protein. Crucially, bioinformatic characterization identified a unique N-glycosylation site at Asn¹³⁹ in ScDF, representing a structural divergence absent in grass carp (Ctenopharyngodon idella) DF (CiDF). While retaining a conserved Tryp_SPc domain harboring the catalytic triad (His⁶¹, Asp¹⁰⁹, and Ser²⁰⁴) and substrate-binding residues (Asp¹⁹⁸, Ser²¹⁹, and Gly²²¹), sequence and phylogenetic analyses confirmed ScDF’s evolutionary conservation, displaying 94.4% amino acid identity with CiDF and clustering within the Cyprinidae. Expression profiling revealed constitutive ScDF dominance in the liver, and secondary prominence was observed in the heart. Upon GCRV challenge in S. curriculus kidney (SCK) cells, ScDF transcription surged to a 438-fold increase versus uninfected controls at 6 h post-infection (hpi; p < 0.001)—significantly preceding the 168-hpi response peak documented for CiDF in grass carp. Functional validation showed that ScDF overexpression suppressed key viral capsid genes (VP2, VP5, and VP7) and upregulated the interferon regulator IRF9. Moreover, recombinant ScDF protein incubation induced interferon pathway genes and complement C3 expression. Collectively, ScDF’s rapid early induction (peaking at 6 hpi) and multi-pathway coordination may contribute to barbel chub’s GCRV resistance. These findings may provide molecular insights into the barbel chub’s high GCRV resistance compared to grass carp and novel perspectives for anti-GCRV breeding strategies in fish. Full article

Molecular chaperones, especially heat shock proteins (HSPs) have vital functions in cells’ responses to stress. Here, we cloned and sequenced the complete complementary DNA encoding HSP90 (MjHSP90) from the shrimp Marsupenaeus japonicus. The MjHSP90 cDNA comprised 3162 bp, including a 2172 bp coding region encoding a 724 amino acid-protein (predicted molecular mass = 83.12 kDa). Homology and phylogenetic analyses showed that MjHSP90 was highly conserved and most homologous to Litopenaeus vannamei HSP90. MjHSP90 is expressed in all tested tissues, with high expression in gill tissue and the hepatopancreas. Cold stress significantly upregulated MjHSP90 expression in the gill and hepatopancreas (p < 0.05). Following RNA interference knockdown of MjHSP90, the cold stress-related death rate of the shrimp increased significantly, accompanied by significantly upregulated expression of apoptosis-related genes Mjcaspase-3 and Mjbcl-2 (p < 0.05) and an increase in the number of apoptotic cells. The results indicated that MjHSP90 might play a pivotal role in the shrimp’s immune response to cold stress. Full article

In this study, 14 palynological samples and nine AMS ¹⁴C dating samples were collected from two representative black soil profiles in the Xingkai Lake Plain to examine climate changes and their impacts on environmental evolution since the Holocene. The systematic identification, analysis, and research of palynological data reveal that the black soil profiles in the Xingkai Lake Plain can be categorized into the following three distinct palynological assemblage zones: the lower zone (11.7–7.5 ka BP) is characterized by Pinus-Laevgatomonoleti-Amaranthaceae-Artemisia, having a cold, dry climate; the middle zone (7.5–2.5 ka BP) features Quercus-Juglans-Polygonum-Cyperaceae, with a warm and humid climate; and the upper zone (2.5 ka BP to present) consists of Pinus-Quercus-Betula, indicating a cold and dry climate. Furthermore, field lithostratigraphic observations of the two black soil profiles suggest that late Pleistocene loessial clay serves as the parent material in this region. Quaternary geology, section lithology, palynology, and AMS ¹⁴C dating results indicate that a significant portion of black soil in the Xingkai Lake Plain was primarily formed during the Great Warm Period following the middle Holocene. These insights not only enhance our understanding of Holocene climate dynamics in Northeast China but also provide a substantial scientific foundation for further studies on related topics. Full article

Background: Chronic stress in childhood and adolescence leads to excessive cortisol secretion, adipokines production and obesity with all the negative mental and physical effects on the health of individuals and adulthood. Objectives: The aim of the present non-randomized controlled trial was to investigate the effect of a stress management protocol with diaphragmatic breathing (DB) and physiotherapy exercise on stress, body composition, cardiorespiratory and metabolic markers of children and adolescents with morbid obesity. Methods: The study included 31 children and adolescents (5–18 years old) with morbid obesity (22 in the intervention arm and 9 controls). All participants completed anxiety questionnaires and a self-perception scale. Forced expiratory volume in the first second (FEV1), forced vital capacity (FVC), blood pressure (BP) and SpO₂ were measured. Fasting glucose, uric acid, triglycerides, HbA1c, (AST/SGOT), (ALT/SGPT), HDL, LDL, insulin, ACTH, cortisol, HOMA-IR, 17-OH, S-DHEA, SHBG were assessed, and anthropometric measurements were also performed. Results: In the intervention group, 4 months after the treatment, an improvement was noted in the BMI, BMI z-score, waist-to-height ratio, FEV1, SpO₂, pulse and systolic BP. HDL increased, ALT/SGPT and insulin resistance improved. Positive changes were observed in temporary and permanent stress and self-esteem of children in the intervention group, including anxiety, self-perception, physical appearance, etc. Conclusions: A combined exercise and DB protocol has a positive effect on stress, by improving body composition, reducing insulin resistance, and ameliorating physical and mental health and quality of life of pediatric patients with morbid obesity. Full article

This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The bla_NDM-19 was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes bla_NDM-19 and qnrS11 are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (sul1), trimethoprim (dfrA14), β-lactams (bla_TEM-1B), aminoglycosides (aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, aac(3)-IV, and aph(4)-Ia), tetracycline (tet(A)), and chloramphenicol (floR). It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding bla_NDM-19 includes ISAba125-IS5-bla_NDM-19-ble_MBL-trpF-hp1-hp2-IS26. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 E. coli lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (ISAba125) are critical vehicles for the dissemination of bla_NDM and its related variants. To our knowledge, this is the first genomic report of a bla_NDM-19/IncX3-carrying E. coli isolate of animal origin globally. Full article

Background/Objectives: Scutiger ningshanensis (Fang, 1985) is an endemic Chinese amphibian species within the genus Scutiger (Megophryidae). Despite its ecological significance, its mitochondrial genome architecture and evolutionary relationships remain poorly understood. Given the high structural variability in Megophryidae mitogenomes and unresolved phylogenetic patterns in Scutiger, this study aims to (1) characterize the complete mitogenome of S. ningshanensis, (2) analyze its molecular evolution, and (3) clarify its phylogenetic position and divergence history within Megophryidae. Methods: The complete mitochondrial genome was sequenced and annotated, followed by analyses of nucleotide composition, codon usage bias, and selection pressures (Ka/Ks ratios). Secondary structures of rRNAs and tRNAs were predicted, and phylogenetic relationships were reconstructed using maximum likelihood and Bayesian methods. Divergence times were estimated using molecular clock analysis. Results: The mitogenome of S. ningshanensis is 17,282 bp long, encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region, with a notable AT bias (61.05%) with nucleotide compositions of T (32.51%), C (24.64%), G (14.3%), and A (28.54%). All tRNAs exhibited cloverleaf structures except trnS1, which lacked a DHU stem. Phylogenetic analysis confirmed the monophyly of Scutiger, forming a sister clade to Oreolalax and Leptobrachium, and that S. ningshanensis and S. liubanensis are sister species with a close evolutionary relationship. Positive selection was detected in Atp8 (Ka/Ks > 1), suggesting adaptation to plateau environments, while other PCGs underwent purifying selection (Ka/Ks < 1). Divergence time estimation placed the origin of Megophryidae at~47.97 MYA (Eocene), with S. ningshanensis diverging~32.67 MYA (Oligocene). Conclusions: This study provides the first comprehensive mitogenomic characterization of S. ningshanensis, revealing its evolutionary adaptations and phylogenetic placement. The findings enhance our understanding of Megophryidae’s diversification and offer a genomic foundation for future taxonomic and conservation studies. Full article

Hypertension (HTN) is a major contributor to global morbidity and manifests in several variants, including salt-sensitive hypertension (SSHTN). SSHTN is defined by an increase in blood pressure (BP) in response to high dietary salt, and is associated with heightened cardiovascular risk, renal damage, and immune system activation. However, the role of granulocyte-macrophage colony-stimulating factor (GM-CSF) has not yet been explored in the context of SSHTN. Previously, we reported that GM-CSF is critical in priming bone marrow-derived (BMD)-macrophages (BMD-Macs) and BMD-dendritic cells (BMD-DCs) to become activated (CD38+) in response to salt. Further exploration revealed these cells differentiated into BMD-M1 Macs, CD38+ BMD-M1 Macs, BMD-type-2 conventional DCs (cDC2s), and CD38+ BMD-cDC2s. Additionally, BMD-monocytes (BMDMs) grown with GM-CSF and injected into SSHTN mice traffic to the kidneys and differentiate into Macs, CD38+ Macs, DCs, and CD38+ DCs. In the current study, we treated SSHTN mice with an anti-GM-CSF antibody (aGM) and found that preventive aGM treatment mitigated BP, prevented renal inflammation, and altered renal immune cells. In mice with established SSHTN, aGM treatment attenuated BP, reduced renal inflammation, and differentially affected renal immune cells. Adoptive transfer of aGM-treated BMDMs into SSHTN mice resulted in decreased renal trafficking. Additionally, aGM treatment of BMD-Macs, CD38+ BMD-M1 Macs, BMD-DCs, and CD38+ BMD-cDC2s led to decreased pro-inflammatory gene expression. These findings suggest that GM-CSF plays a role in SSHTN and may serve as a potential therapeutic target. Full article

Reducing the application of chemical fertilizers and remediating heavy metal pollution in soil are important directions in current agricultural research. Utilizing the plant-growth-promoting and remediation capabilities of bacteria can provide more environmentally friendly assistance to agricultural production. In this study, the Burkholderia alba YIM B08401 strain was isolated and identified from rhizospheric soil, subjected to whole-genome sequencing and analysis, and its Cd²⁺ adsorption efficiency and characteristics were confirmed using multiple experimental methods, including atomic absorption spectrometry (AAS), Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS). The results showed that the genome of strain YIM B08401 has a total length of 7,322,157 bp, a GC content of 66.39%, and predicts 6504 protein-coding sequences. It contains abundant functional genes related to nutrient conversion (phosphate solubilization, sulfur metabolism, zinc solubilization, siderophore production), plant hormone regulation (indole-3-acetic acid secretion, ACC deaminase production), phenolic acid degradation, root colonization, heavy metal tolerance, pathogen antagonism, and the production of antagonistic secondary metabolites. Additionally, strain YIM B08401 can specifically bind to Cd²⁺ through various functional groups on the cell surface, such as C-O-C, P=O, and O-H, enabling biosorption. In conclusion, strain YIM B08401 is an excellent strain with plant-growth-promoting, disease-resistant, and bioremediation capabilities, warranting further development as a biofertilizer for agricultural applications to promote green and sustainable agricultural development. Full article

Three novel Aeromonas phages vB_AerVS_332-Yuliya, vB_AerVM_332-Vera, and vB_AerVM_332-Igor and their host Aeromonas veronii CEMTC7594 were found in the same water + sediments sample collected in a freshwater pond. Complete genome sequencing indicated that vB_AerVS_332-Yuliya (43,584 bp) is a siphophage, whereas vB_AerVM_332-Vera (294,685 bp) and vB_AerVM_332-Igor (237,907 bp) are giant phages. The host strain can grow at temperatures from 5 °C to 37 °C with an optimum of 25–37 °C; siphophage vB_AerVS_332-Yuliya effectively reproduced at temperature ≤ 25 °C, the optimal temperature for giant phage vB_AerVM_332-Igor was 25 °C, and giant phage vB_AerVM_332-Vera infected host cells at 5–10 °C. The genomes of these phages differed significantly from known phages; their level of nucleotide identity and values of intergenomic similarity with the corresponding neighboring phages indicated that each of these phages is a member of a new genus/subfamily. Giant phage vB_AerVM_332-Vera is a member of the proposed Chimallinviridae family, which forms Cluster D of giant phages that possibly evolved from phages with shorter genomes. Giant phage vB_AerVM_332-Igor is part of Cluster E, the known members of which preserve the size of genomes. Phages from Cluster F, containing Aeromonas phages among others, show a gradual decrease and/or increase in genomes during evolution, which indicates different strategies for giant phages. Full article

Carassius auratus var. suogu, an endemic fish in southern China, is a natural triploid crucian carp mutant. In this study, the characteristics of mitochondrial DNA sequences were analyzed to understand their taxonomic status and genetic background at the gene level. The complete mitochondrial genome of C. auratus var. suogu (length, 16,580 bp) comprises 37 genes (13 protein-coding genes, 22 transfer RNA (tRNAs) genes, and 2 ribosomal RNA (rRNAs) genes) and a non-coding control region. The RSCU of the mtDNA of Carassius was similar. Ka/Ks analyses showed the ND4 gene had the highest evolutionary rate. Moreover, the whole mitogenome sequences and D-loop region were employed to examine phylogenetic relationships among C. auratus var. suogu and other closely related species. The result indicated that Carassius auratus suogu var clustered with Carassius auratus auratus and divided Carassius into four clades, providing new insights and data support for the taxonomic status of Carassius. Full article

Accurate and reliable detection of coal mine gases is the key to ensuring the safe service of coal mine production. Fourier Transform Infrared (FTIR) spectroscopy, due to its high sensitivity, non-destructive nature, and potential for online monitoring, has emerged as a key technique in gas detection. However, the complex underground environment often causes baseline drift in IR spectra. Furthermore, the variety of gas species and uneven distribution of concentrations make it difficult to achieve precise and reliable online analysis using existing quantitative methods. This paper aims to perform a quantitative analysis of coal mine gases by FTIR. It utilized the adaptive smoothness parameter penalized least squares method to correct the drifted spectra. Subsequently, based on the infrared spectral distribution characteristics of coal mine gases, they could be classified into gases with mutually distinct absorption peaks and gases with overlapping absorption peaks. For gases with distinct absorption peaks, three spectral lines, including the absorption peak and its adjacent troughs, were selected for quantitative analysis. Spline fitting, polynomial fitting, and other curve fitting methods are used to establish a functional relationship between characteristic parameters and gas concentration. For gases with overlapping absorption peaks, a wavelength selection method bassed on the impact values of variables and population analysis was applied to select variables from the spectral data. The selected variables were then used as input features for building a model with a backpropagation (BP) neural network. Finally, the proposed method was validated using standard gases. Experimental results show detection limits of 0.5 ppm for CH₄, 1 ppm for C₂H₆, 0.5 ppm for C₃H₈, 0.5 ppm for n-C₄H₁₀, 0.5 ppm for i-C₄H₁₀, 0.5 ppm for C₂H₄, 0.2 ppm for C₂H₂, 0.5 ppm for C₃H₆, 1 ppm for CO, 0.5 ppm for CO₂, and 0.1 ppm for SF₆, with quantification limits below 10 ppm for all gases. Experimental results show that the absolute error is less than 0.3% of the full scale (F.S.) and the relative error is within 10%. These results demonstrate that the proposed infrared spectral quantitative analysis method can effectively analyze mine gases and achieve good predictive performance. Full article

Protein association and aggregation are fundamental processes that play critical roles in a variety of biological phenomena from cell signaling to the development of incurable diseases, including amyloidoses. Understanding the basic biophysical principles governing protein aggregation processes is of crucial importance for developing treatment strategies for diseases associated with protein aggregation, including sarcopenia, as well as for the treatment of pathological processes associated with the disruption of functional protein complexes. This work, using a set of methods such as atomic force microscopy (AFM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction, as well as bioinformatics analysis, investigated the structures of complexes formed by titin and myosin-binding protein C (MyBP-C). TEM revealed the formation of morphologically ordered aggregates in the form of beads during co-incubation of titin and MyBP-C under close-to-physiological conditions (175 mM KCl, pH 7.0). AFM showed the formation of a relatively homogeneous film with local areas of relief change. Fluorimetry with thioflavin T, as well as FTIR spectroscopy, revealed signs of an amyloid-like structure, including a signal in the cross-β region. X-ray diffraction showed the presence of a cross-β structure characteristic of amyloid aggregates. Such structural features were not observed in the control samples of the investigated proteins separately. In sarcomeres, these proteins are associated with each other, and this interaction plays a partial role in the formation of a strong sarcomeric cytoskeleton. We found that under physiological ionic-strength conditions titin and MyBP-C form complexes in which an amyloid-like structure is present. The possible functional significance of amyloid-like aggregation of these proteins in muscle cells in vivo is discussed. Full article

Westernization of traditional diets has been implicated in the rising burden of overweight/obesity and type 2 diabetes, especially in developing countries. In recent times, diet therapy is increasingly being recognized as an essential component of diabetes care. This study assessed the effect of diet therapy on body composition, antioxidant nutrient intake, and glycemic status in individuals living with type 2 diabetes (ILWT2D). In this prospective observational cohort study, 45 ILWT2D who were receiving diet therapy (personalized dietary counseling) in addition to standard medical treatment (intervention group) were compared with 45 ILWT2D receiving only standard medical treatment (comparator group). Antioxidant micronutrient intake was assessed using a 24-h dietary recall. Body composition indices, including body mass index (BMI), percentage body fat (%BF), and visceral fat (VF), were assessed. Participants’ fasting blood glucose (FBG), glycated hemoglobin (HbA1C) levels, and blood pressure (BP) were measured. All measurements were performed before and after a three-month period. There were significant improvements in BMI (27.8 ± 6.0 kg/m² vs. 26.9 ± 5.5 kg/m², p = 0.003), %BF (37.8 ± 11.9% vs. 35.5 ± 10.5%, p < 0.001), visceral fat (9.8 ± 3.4 vs. 9.1 ± 3.2, p < 0.001), systolic BP (136.9 ± 19.9 mmHg vs. 124.6 ± 13.0 mmHg, p < 0.001), FBG (8.8 ± 2.8 mmol/L vs. 6.7 ± 1.5 mmol/L, p < 0.001), and HbA1c (7.3 ± 1.0% vs. 6.4 ± 0.8%, p < 0.001) in the intervention group from baseline to endline, but not in the comparator group. In contrast, %BF increased within the comparator group (39.9 ± 7.8 vs. 40.7 ± 7.4; p = 0.029). Vitamin A intake increased significantly (227.5 ± 184.3 µg vs. 318.8 ± 274.7 µg, p = 0.038) within the intervention group but not in the comparator group (174.9 ± 154.3 µg, 193.7 ± 101.4 µg, p = 0.54). There were no significant changes in zinc, copper, selenium, and vitamin C intakes (p > 0.05) in the intervention group from the baseline to endline, unlike those in the comparator group who showed a significant increase in the intake of these nutrients. There was a significant increase in vitamin A intake among the ILWT2D who received dietary counseling as an intervention compared to those who did not. Additionally, the ILWT2D who received dietary counseling had significant improvements in their body composition (BMI, body fat, and visceral fat) and systolic blood pressure, compared to those who did not. The ILWT2D who received the intervention had significantly better glycemic control (FBG and HbA1c) than their counterparts who did not. Thus, this study suggests the potential of diet therapy as a viable non-pharmacological treatment approach for individuals living with type 2 diabetes. Full article

Phytoene synthase (PSY) is a multimeric enzyme that serves as the first enzyme in carotenoid synthesis within plant tissues and plays a crucial role in the production of carotenoids in plants. To understand the function of the PSY gene in Panax japonicus C. A. Meyer. fruit, the gene’s transcript was obtained by analyzing the transcriptome sequencing data of Panax japonicus fruit. The CDS sequence of the gene was cloned from Panax japonicus fruit using the RT-PCR cloning technique and named PjPSY1, which was then subjected to biosynthetic analysis and functional verification. The results showed that the open reading frame of the gene was 1269 bp, encoding 423 amino acids, with a protein molecular mass of 47,654.67 KDa and an isoelectric point (pI) of 8.63; the protein encoded by these amino acids was hydrophilic and localized in chloroplasts, and its three-dimensional structure was predicted by combining the pymol software to annotate the N site of action and active centre of the protein. Phylogenetic analysis demonstrated that PjPSY1 had the closest affinity to DcPSY from Daucus carota. Overexpression of PjPSY1 led to a significant increase in the content of carotenoid-related monomers in Arabidopsis thaliana, with Violaxanthin being synthesized in transgenic Arabidopsis thaliana but not in wild-type Arabidopsis thaliana. The PjPSY1 clone obtained in this study was able to promote carotenoid synthesis in the fruits of Panax japonicus, revealing that the mode of action of PjPSY1 in the carotenoid biosynthesis pathway of Panax japonicus fruits has a positive regulatory effect. Full article

Artificial insemination (AI) is a key breeding technique in the swine industry; however, the lack of reliable biomarkers for semen quality limits its effectiveness. Seminal plasma (SP) contains extracellular vesicles (EVs) that present a promising, non-invasive biomarker for semen quality. This study explores the biochemical profiles of boar SP to assess semen quality through near-infrared spectroscopy (NIRS) and proteomics of SP-EVs. Fresh semen from mature Duroc boars was evaluated based on sperm motility, classifying samples as Passed (≥70%) or Failed (<70%). NIRS analysis identified distinct variations in water structures at specific wavelengths (C1, C5, C12 nm), achieving high accuracy (92.2%), sensitivity (94.2%), and specificity (90.3%) through PCA-LDA. Proteomic analysis of SP-EVs revealed 218 proteins in Passed and 238 in Failed samples. Nexin-1 and seminal plasma protein pB1 were upregulated in Passed samples, while LGALS3BP was downregulated. The functional analysis highlighted pathways associated with single fertilization, filament organization, and glutathione metabolism in Passed samples. Integrating NIRS with SP-EV proteomics provides a robust approach to non-invasive assessment of semen quality. These findings suggest that SP-EVs could serve as effective biosensors for rapid semen quality assessment, enabling better boar semen selection and enhancing AI practices in swine breeding. Full article