Search Results (87)

Splicing regulatory sequences are cornerstones for exon recognition. Mutations that modify them can severely compromise mRNA maturation and protein production. A wide range of mutations, including SNPs and InDels, can influence splicing regulatory signals either directly (e.g., altering canonical donor and acceptor dinucleotides) or indirectly (e.g., creating cryptic splice sites). CSN1S1 and CSN1S2 genes encode for the two main milk proteins, αs1 and αs2 caseins, respectively. They represent a remarkable and unique example of the possibilities for alternative splicing of individual genes, both due to the high number of alternative splices identified to date and for recognized allele-specific splicing events. To date, at least 13 alleles of CSN1S1 originating from mutations that affect canonical splice sites have been described in Bos taurus (CSN1S1 A, A1, and H), Ovis aries (E, H, and I), Capra hircus (D and G), Bubalus bubalis (E, F) and Camelidae (A, C, and D). Similarly, allele-specific splicing events have been described at the CSN1S2 locus in B. taurus. (CSN1S2 D), C. hircus (CSN1S2 D), B. bubalis (CSN1S2 B, B1, and B2), Equus asinus (CSN1S2 I B), and Camelidae. This review highlights that mutations affecting canonical splice sites, particularly donor sites, are significant sources of genetic variation impacting the casein production of the main dairy livestock species. Currently, a key limitation on this topic is the lack of detailed functional and proteomic studies. Future research should leverage advanced omics technologies like long-read transcriptomics and allele-resolved RNA sequencing to characterize these splicing mechanisms, guiding precision breeding strategies. Full article

The state path optimization model, alongside strategies like slowing down and waiting, aims to identify optimal aircraft routes that minimize the total taxi time and prevent conflicts. Optimization reduces taxiing times for aircraft YZR7537, CES2558, and CSZ9806, while slightly increasing the times for CSN6310 and CSN3210 due to conflict hotspot avoidance measures. This approach also decreases the number of aircraft passing through key conflict hotspots, effectively reducing both conflicts and risk levels in these areas. Consequently, the total taxiing time for the optimized aircraft is cut by 53 s, enhancing airport operational efficiency. The proposed model serves as a theoretical foundation for developing an intelligent airport operation management system. Full article

Background/Objectives: Breast milk provides essential nutrition and immune protection to support infant growth and development. However, insufficient breast milk remains a serious issue, and bioactive peptides represent a potential strategy to promote lactation. In this study, we investigated the impact of a methionine-containing dipeptide, EM, on MCF-10A mammary epithelial cells. Methods: MCF-10A cells were treated with EM, and cell proliferation and the expression of key milk protein genes were assessed. Integrated transcriptomic and untargeted metabolomic analyses were performed to identify EM-induced changes in metabolic and gene expression pathways. Results: EM treatment significantly enhanced cell proliferation and upregulated the expression of key milk protein genes (CSN1S1 (casein alpha-S1, encoding alpha-S1 casein), CSN2 (casein beta, encoding beta-casein), and CSN3 (casein kappa, encoding kappa-casein)) at both transcriptional and protein levels compared to controls. Integrated transcriptomic and metabolomic analyses revealed that EM reprogrammed amino acid metabolism, lipid biosynthesis, and nutrient transport pathways. Core genes such as SLC7A11, APOE, and ABCA1 were identified as critical nodes linking metabolic and transcriptional networks. Conclusions: These findings indicate that EM may promote lactogenic activity by modulating metabolic and transcriptional networks in vitro, highlighting the potential of dipeptide-based nutritional interventions, which warrants further in vivo validation. Full article

Linear conjugated polymer photocatalysts are still hampered by challenges involving low charge separation efficiency and poor water dispersibility, which are crucial factors during the photocatalytic water splitting process. Herein, we synthesized Poly thieno[3,2-b]thiophene (PTT) nanoparticles with excellent visible light response characteristic. Subsequently, we constructed the gun–bullet model PTT/graphitic carbon nitride (PTT/g-C₃N₄) heterojunctions for photocatalytic hydrogen production, where PTT with good visible light response characteristic serves as the bullets and g-C₃N₄ with good water dispersibility serves as the guns. The as-prepared PTT/g-C₃N₄ heterojunctions show greatly accelerated charge separation and excellent photocatalytic hydrogen production performance. Specifically, 10PTT/g-C₃N₄ demonstrates extraordinary hydrogen production performance, reaching 6.56 mmol g⁻¹ h⁻¹ (2 wt% Pt loading, 0.1 M AA as sacrificial agent, λ > 420 nm), calculated to be 15.3 and 22.6 times those of PTT and g-C₃N₄, respectively. Mechanistic studies reveal that the significantly improved performance of PTT/g-C₃N₄ heterojunctions is ascribed to the accelerated charge transfer, which originates from the C…S/N…S noncovalent interactions among PTT and g-C₃N₄. The C…S/N…S noncovalent interactions act as an efficient interface charge transmission channel (ICTC), accelerating the steady stream of excited electron transfer from the lowest unoccupied molecular orbital (LUMO) of PTT to that of g-C₃N₄. The gun–bullet model heterojunctions proposed here provide a practical strategy for achieving exceptional visible light photocatalytic hydrogen production by combining charge separation with water dispersibility in polymer/polymer heterojunctions via noncovalent interactions. Full article

Background/Objectives: Buffalo populations exhibit distinct genetic variations influenced by domestication history, geographic distribution, and selection pressures. This study investigates the genetic structure and differentiation of 11 buffalo populations, focusing on five loci related to milk protein (CSN1S1 and CSN3) and fat metabolism (LPL, DGAT1 and SCD). The aim is to assess genetic variation between river, swamp, and wild-type buffaloes and identify key loci contributing to population differentiation. Methods: Genetic diversity was analyzed through allele frequency distribution, the Hardy−Weinberg equilibrium testing, and observed (Ho) and expected heterozygosity (He) calculations. Population structure was assessed using principal component analysis (PCA), F_ST statistics, and phylogenetic clustering (k-means and UPGMA tree). The silhouette score (SS) and the Davies−Bouldin index (DBI) were applied to determine optimal population clustering. Results: Significant genetic differentiation was observed between river and swamp buffaloes (p < 0.001). DGAT1 and CSN3 emerged as key markers distinguishing buffalo types. The Italian Mediterranean buffalo exhibited the highest genetic diversity (Ho = 0.464; He = 0.454), while the Indonesian, Chinese, and Vietnamese populations showed low heterozygosity, likely due to selection pressures and geographic isolation. The global F_ST (0.2143; p = 0.001) confirmed moderate differentiation, with closely related populations (e.g., Nepal and Pakistan) exhibiting minimal genetic divergence, while distant populations (e.g., Egypt and Indonesia) showed marked differences, and the Romanian population showed a unique genetic position. Conclusions: These findings contribute to a deeper understanding of buffalo genetic diversity and provide a valuable basis for exploiting the potential of this species in the light of future breeding and conservation strategies specific for each buffalo type. Full article

This study utilized MAC-T cells cultured in vitro as a model to investigate the effects of varying concentrations of valine on α-casein synthesis and its underlying regulatory mechanisms. In this experiment, MAC-T cells were subjected to a 12 h starvation period, followed by the addition of valine in a range of concentrations (a total of seven concentrations: 0.000, 1.596, 3.192, 6.384, 12.768, 25.536, and 51.072 mM, as well as in 10% Fetal Bovine Serum). The suitable range of valine concentrations was determined using enzyme-linked immunosorbent assays (ELISAs). Real-time fluorescent quantitative PCR (RT-qPCR) and Western blot analyses were employed to evaluate the expression levels and phosphorylation states of the casein alpha s1 gene (CSN1S1), casein alpha s2 gene (CSN1S2) and mTOR signaling pathway-related genes. The functionality of the mTOR signaling pathway was further validated through rapamycin (100.000 nM) inhibition experiments. Results indicated that 1× Val (6.384 mM), 2× Val (12.768 mM), 4× Val (25.536 mM), and 8× Val (51.072 mM) significantly enhanced α-casein synthesis (p < 0.01). Within this concentration range, valine significantly upregulated the expression of CSN1S1, CSN1S2, and mTOR signaling pathway-related genes including the RagA gene (RRAGA), RagB gene (RRAGB), RagC gene (RRAGC), RagD gene (RRAGD), mTOR, raptor gene (RPTOR), and 4EBP1 gene (EIF4EBP1), eukaryotic initiation factor 4E (EIF4E), and S6 Kinase 1 (S6K1) (p < 0.01). Notably, the expression of the eukaryotic elongation factor 2 (EEF2) gene peaked at 1× Val (6.384 mM), while the expression of other genes reached their maximum at 4× Val (25.536 mM). Additionally, valine significantly increased the phosphorylation levels of mTOR, S6K1, 4E-binding protein-1 (4EBP1), ribosomal protein S6 (RPS6), and eEF2 (p < 0.01), with the highest phosphorylation levels of mTOR, S6K1, and RPS6 observed at 4× Val (25.536 mM). Rapamycin treatment significantly inhibited mTOR phosphorylation and α-casein synthesis (p < 0.01); however, the addition of 4× Val (25.536 mM) partially mitigated this inhibitory effect. In conclusion, valine promotes α-casein synthesis by activating the mTOR signaling pathway, with an optimal concentration of 4× Val (25.536 mM). Full article

Recent discoveries revealed mechanistic insights into the control of adipogenesis by the Constitutive Photomorphogenesis 9 Signalosome (CSN) and its variants, CSN^CSN7A and CSN^CSN7B, which differ in the paralog subunits, CSN7A and CSN7B. CSN^CSN7A and CSN^CSN7B variants form permanent complexes with cullin-RING-ubiquitin ligases 3 and 4A (CRL3 and CRL4A), respectively. These complexes can be found in most eukaryotic cells and represent a critical reservoir for cellular functions. In an early stage of adipogenesis, mitotic clonal expansion (MCE), CSN-CRL1, and CSN^CSN7B-CRL4A are blocked to ubiquitinate the cell cycle inhibitor p27^KIP, leading to cell cycle arrest. In addition, in MCE CSN-CRL complexes rearrange the cytoskeleton for adipogenic differentiation and CRL3^KEAP1 ubiquitylates the inhibitor of adipogenesis C/EBP homologous protein (CHOP) for degradation by the 26S proteasome, an adipogenesis-specific proteolysis. During terminal adipocyte differentiation, the CSN^CSN7A-CRL3 complex is recruited to a lipid droplet (LD) membrane by RAB18. Currently, the configuration of the substrate receptors of CSN^CSN7A-CRL3 on LDs is unclear. CSN^CSN7A-CRL3 is activated by neddylation on the LD membrane, an essential adipogenic step. Damage to CSN/CUL3/CUL4A genes is associated with diverse diseases, including obesity. Due to the tremendous impact of CSN-CRLs on adipogenesis, we need strategies for adequate treatment in the event of malfunctions. Full article

Chitooligosaccharides (COSs) are a class of functional carbohydrates with significant application prospects in food and medicine. Chitosanase CsnMY002 from the GH46 family has been used to prepare COS with controlled degrees of polymerization. To enhance the industrial applicability of CsnMY002, molecular dynamics (MD) simulations were applied to investigate the structure–property relationship. Guided by the simulation results, the beneficial mutants were screened through a synergistic strategy using a residue-folding free energy calculation and consensus sequence analysis. Iterative combinations constructed the mutant Mut6 (A49G/K70A/S84A/N89G/D199R/N221G) with significantly improved thermal stability, which had a half-life (t_1/2 value) at 55 °C and 75 °C that was 1.80 and 1.62 times higher than that of the wild type, respectively. A highly active mutant, Mut2, was created, exhibiting a 1.52 times catalytic efficiency of the wild type. An MD simulation analysis of the mutants suggested that the improved enzymatic properties were highly correlated with changes in the dynamic behaviours of the enzyme structure. This study generated more suitable CsnMY002 variants for COS production and provided a comprehensive strategy for the optimization of other industrial enzymes with application potential. Full article

Potato common scab (CS) caused by Streptomyces scabiei is a severe disease that threatens tuber quality and its market value. To date, little is known about the mechanism regulating the resistance of potato to CS. In this study, we identified a presequence translocase-associated motor 16 gene from potato (designated StPAM16-1) that is involved in the response to the phytotoxin thaxtomin A (TA) secreted by S. scabiei. The StPAM16-1 protein was localized in the mitochondria, and the expression of the gene was upregulated in potato leaves treated with TA. The suppression of StPAM16-1 in potato led to enhanced resistance to TA and S. scabiei. Protein interaction analyses revealed that StPAM16-1 interacted with the subunit 5b of the COP9 signalosome complex (StCSN5). Similar to that of StPAM16-1, the expression levels of StCSN5 significantly increased in potato leaves treated with TA. These results indicated that StPAM16-1 acted as a negative regulator and was functionally associated with StCSN5 in the immune response of potato plants against CS. Our study sheds light on the molecular mechanism by which PAM16 participates in the plant immune response. Furthermore, both StPAM16-1 and StCSN5 could be potential target genes in the molecular breeding of potato cultivars with increased resistance to CS. Full article

Non-clinical enterococci are relatively poorly studied by means of acquired antibiotic resistance to tetracycline and by the distribution, functionality and role of their CRISPR systems. Background: In our study, 72 enterococcal strains, isolated from various non-clinical origins, were investigated for their phenotypic and genotypic (tet(M), tet(O), tet(S), tet(L), tet(K), tet(T) and tet(W)) tetracycline resistance. Methods: The genetic determinants for HGT (MGEs (Int-Tn and prgW), inducible pheromones (cpd, cop and cff), aggregation substances (agg, asa1, prgB and asa373) and CRISPR–Cas systems were characterized by PCR and whole-genome sequencing. Results: Four tet genes (tetM, tetO, tetS and tetT) were detected in 39% (n = 28) of our enterococcal population, with tetM (31%) being dominant. The gene location was linked to the Tn6009 transposon. All strains that contained tet genes also had genes for HGT. No tet genes were found in E. casseliflavus and E. gilvus. In our study, 79% of all tet-positive strains correlated with non-functional CRISPR systems. The strain E. faecalis BM15 was the only one containing a combination of a functional CRISPR system (cas1, cas2, csn2 and csn1/cas9) and tet genes. The CRISPR subtype repeats II-A, III-B, IV-A2 and VI-B1 were identified among E. faecalis strains (CM4-II-A, III-B and VI-B1; BM5-IV-A2, II-A and III-B; BM12 and BM15-II-A). The subtype II-A was the most present. These repeats enclosed a great number of spacers (1–10 spacers) with lengths of 31 to 36 bp. One CRISPR locus was identified in plasmid (p.Firmicutes1 in strain E. faecalis BM5). We described the presence of CRISPR loci in the species E. pseudoavium, E. pallens and E. devriesei and their lack in E. gilvus, E. malodoratus and E. mundtii. Conclusions: Our findings generally describe the acquisition of foreign DNA as a consequence of CRISPR inactivation, and self-targeting spacers as the main cause. Full article

Goat milk has gained recognition for its medicinal, cosmetic, and health benefits, particularly its potential to improve human skin conditions. Its therapeutic properties are attributed to bioactive compounds influenced by genes such as lactoferrin (LTF), lysozyme (LYZ), and β-casein (CSN2), known for their antimicrobial, immunomodulatory, and anti-inflammatory effects. Genetic factors are hypothesized to shape goat milk’s composition and its effectiveness in managing dermatological conditions like eczema and psoriasis. Understanding these genetic determinants is critical to optimizing the use of goat milk in skin health applications. This review aims to explore the application of genomic tools to elucidate the medicinal properties of goat milk and its implications for skin care. By identifying the specific genes and molecular mechanisms underpinning its therapeutic effects, genomic studies have provided insights into the bioactive constituents of goat milk, such as peptides, proteins, and lipids, which contribute to its dermatological efficacy. Candidate genes, including growth hormone receptor (GHR), butyrophilin (BTN1A1), and lactoglobulin (LGB), have been identified as critical for enhancing milk quality and functionality. Future research should integrate genomic data with functional studies to further investigate goat milk’s immunomodulatory, antimicrobial, and antioxidant activities. Such insights could advance targeted breeding strategies and innovative formulations for managing inflammatory skin conditions and promoting skin health. Full article

Reportedly, the number of κ-casein (κ-CN) B alleles increases the proportion of κ-CN to total protein and the κ-CN content. This phenomenon is caused by single-nucleotide polymorphisms (SNPs) in the promoter region of CSN3, which encodes the B variant. Therefore, a series of 5′-deleted promoter plasmids were constructed to define the core promoter of CSN3. The promoter activity was analyzed by comparing the luciferase activity among the recombinant vectors with truncated promoters. No mutation occurred in the core promoter region (5′-ctatcgtcagatctttcctttctgtcatcttcctattggtg-3′) of CSN3 in 40 cows. A 2092 bp promoter region of CSN3 was re-sequenced for detection, and nine variants were found, of which only three variants had mutation frequencies > 40%, which were −1002T>−, −1654T>A, and −2039T>G. The CSN3 promoter polymorphisms did not correlate with the CSN3 A and B alleles according to the Pearson’s chi-square test (p > 0.05). Moreover, the luciferase activity analysis of the CSN3 promoter showed no difference among pGL3 recombinants with different polymorphic CSN3 promoters (p > 0.05). In the genetic selection of dairy cows, mutations in the CSN3 core promoter should be focused upon. These findings provide a reference for the regulatory mechanism of bovine milk proteins and offer guidance for the genetic selection and breeding of cows. Full article

Paranasal sinus surgery, a common treatment for chronic rhinosinusitis, requires exceptional precision due to the proximity of critical anatomical structures. To ensure accurate instrument control and clear visualization of the surgical site, surgeons utilize computer-aided surgical navigation (CSN). A key component of CSN is the registration process, which is traditionally reliant on manual or marker-based techniques. However, there is a growing shift toward marker-less registration methods. In previous work, we investigated a mesh-based registration approach using a Mixed Reality Head-Mounted Display (MR-HMD), specifically the Microsoft HoloLens 2. However, this method faced limitations, including depth holes and invalid values. These issues stemmed from the device’s low-resolution camera specifications and the 3D projection steps required to upscale RGB camera spaces. In this study, we propose a novel automated marker-less registration method leveraging Neural Radiance Field (NeRF) technology with an MR-HMD. To address insufficient depth information in the previous approach, we utilize rendered-depth images generated by the trained NeRF model. We evaluated our method against two other techniques, including prior mesh-based registration, using a facial phantom and three participants. The results demonstrate our proposed method achieves at least a 0.873 mm (12%) improvement in registration accuracy compared to others. Full article

Rehmannia glutinosa is an important medicinal herb; but its long-term cultivation often leads to continuous cropping problems. The underlying cause can be attributed to the accumulation of and alterations in root exudates; which interact with soil-borne pathogens; particularly Fusarium oxysporum; triggering disease outbreaks that severely affect its yield and quality. It is therefore crucial to elucidate the mechanisms by which root exudates induce F. oxysporum CCS043 outbreaks. In this study; the genome of F. oxysporum CCS043 from R. glutinosa’s rhizosphere microbiota was sequenced and assembled de novo; resulting in a 47.67 Mb genome comprising 16,423 protein-coding genes. Evolutionary analysis suggests that different F. oxysporum strains may adapt to the host rhizosphere microecosystem by acquiring varying numbers of specific genes while maintaining a constant number of core genes.The allelopathic effects of ferulic acid; verbascoside; and catalpol on F. oxysporum CCS043 were examined at the physiological and transcriptomic levels. The application of ferulic acid was observed to primarily facilitate the proliferation and growth of F. oxysporum CCS043; whereas verbascoside notably enhanced the biosynthesis of infection-related enzymes such as pectinase and cellulase. Catalpol demonstrated a moderate level of allelopathic effects in comparison to the other two. Furthermore; 10 effectors were identified by combining the genomic data. Meanwhile; it was found that among the effector-protein-coding genes; ChiC; VRDA; csn; and chitinase exhibited upregulated expression across all treatments. The expression patterns of these key genes were validated using qRT-PCR. Transient overexpression of the two effector-encoding genes in detached R. glutinosa leaves provided further confirmation that ChiC (GME8876_g) and csn (GME9251_g) are key effector proteins responsible for the induction of hypersensitive reactions in R. glutinosa leaf cells. This study provides a preliminary indication that the use of allelochemicals by F. oxysporum CCS043 can promote its own growth and proliferation and enhance infection activity. This finding offers a solid theoretical basis and data support for elucidating the fundamental causes of fungal disease outbreaks in continuous cropping of R. glutinosa and for formulating effective mitigation strategies. Full article

Methylisothiazolinone (MIT) is widely used as a biocide in numerous personal care products, glass-cleaning liquids, paints, and industrial applications. MIT and related isothiazolinones have attracted much attention for their allergenic properties such as contact dermatitis. Although the compound was first prepared in 1964 and has been widely used as a biocide since the 1970s, its crystal structure has so far not been reported. Here we report the solid state structure of MIT as determined by single crystal X-ray diffraction (SC-XRD) analysis of a crystal grown from the melt. MIT crystallizes as a layered structure with short C-H···O hydrogen bonding interactions within the sheets. The average distance between the sheets parallel to (1 0 2) is ca. 3.2 Å. The molecule exhibits a small C-S-N angle of 90.81(2)° and a methyl group that is slightly bent out of the plane of the planar five-membered ring. The sulfur atom does not undergo any significant intermolecular interactions. Full article