Search Results (10)

Coastal shellfish farming areas in northern China seas face frequent starfish outbreaks, particularly from Asterias amurensis and Patiria pectinifera, leading to significant economic losses. Genomic data are key to understanding the population dynamics and adaptive traits and developing effective control measures for these species. Here, we characterized and compared the genomic information of these two starfish using a whole-genome survey approach. The genome size of A. amurensis is ~477 Mb with 1.52% heterozygosity, 53.60% repetitive sequences, and 39.94% GC content, while P. pectinifera has a ~529 Mb genome, 2.90% heterozygosity, 56.02% repetitive sequences, and 40.63% GC content. Scaffold N50 values were 1823 bp for A. amurensis and 1328 bp for P. pectinifera. We identified 161,786 microsatellite motifs in A. amurensis and 316,245 in P. pectinifera, with mononucleotide repeats being the most common. A total of 171 single-copy homologous genes were found in A. amurensis, with 94 in P. pectinifera. For both species, KEGG annotation showed functional similarities in glycan biosynthesis, translation, metabolism, catabolism, and transport. The Pairwise Sequentially Markovian Coalescent (PSMC) analysis unveiled a bottleneck effect during the Pleistocene glaciation. Additionally, phylogenetic analysis of mitochondrial genomes indicates that P. pectinifera and Patiria miniata of the same genus belong to the same branch in the evolutionary tree as sister groups with the closest genetic relationship, while A. amurensis is most closely related to Astropecten polyacanthus within the class Asteroidea. These findings provide valuable genomic insights for both species. Full article

This review summarizes recent findings on the diverse roles of bacterial sialidases in microbial biology. Bacterial sialidases, also known as neuraminidases, are exog α-lycosidases that cleave terminal sialic acid residues from a number of complex compounds designated as sialoglycoconjugates (glycoproteins, glycolipids and oligosaccharides). Metabolically, they are involved in sialic acid catabolism, providing energy, carbon and nitrogen sources. Catabolic degradation of sialic acids is a physiological feature that can be considered an important virulence factor in pathogenic microorganisms. Sialidases play a pivotal role in host–pathogen interactions and promotion of bacterial colonization. The activity of these enzymes enables bacterial adhesion, biofilm formation, tissue invasion, and also provides immune evasion by exposing cryptic receptors and modifying immune components. Many different perspectives are being developed for the potential application of sialidases. In the field of medicine, they are being explored as appropriate targets for antimicrobials, vaccines, diagnostic preparations and in tumor immunotherapy. In the field of enzymatic synthesis, they are used for the regioselective production of oligosaccharide analogs, enzymatic separation of isoenzymes and as a tool for structural analysis of sialylated glycans, among other applications. Full article

Background: Glioblastoma (GBM) uses Glut3 and/or Glut14 and the Leloir pathway to catabolize D-Galactose (Gal). UDP-4-deoxy-4-fluorogalactose (UDP-4DFG) is a potent inhibitor of the two key enzymes, UDP-galactose-4-epimerase (GALE) and UDP-Glucose 6-dehydrogenase (UGDH), involved in Gal metabolism and in glycan synthesis. The Gal antimetabolite 4-deoxy-4-fluorogalactose (4DFG) is a good substrate for Glut3/Glut14 and acts as a potent glioma chemotherapeutic. Methods: Primary GBM cell cultures were used to examine toxicity and alterations in glycan composition via lectin binding in fixed cells and by Western blots. Toxicity/efficacy in vivo data was performed in mouse flank and intracranial models. The effect of 4DFG on D-glucose (Glc) metabolism in GBM cells was assessed by using ¹³C NMR-based tracer studies. Results: 4DFG is moderately potent against GBM cells (IC₅₀: 125–300 µM). GBM glycosylation is disrupted by 4DFG. Survival analysis in an intracranial mouse model showed that treatment with 4DFG (6 × 25 mg/kg of 4DFG, intravenously) improved outcomes by three-fold (p < 0.01). Metabolic flux analysis revealed that both glycolytic and mitochondrial metabolic fluxes of [U-¹³C]Glc were significantly decreased in the presence of 4DFG in GBM cells. Conclusion: A functional Gal-scavenging pathway in GBM allows Gal-based antimetabolites to act as chemotherapeutics. 4DFG is metabolized by GBM in vitro and in vivo, is lethal to GBM tumors, and is well tolerated in mice. Full article

The accurate diagnosis and treatment of oral squamous cell carcinoma (OSCC) requires an understanding of its genomic alterations. Liquid biopsies, especially cell-free DNA (cfDNA) analysis, are a minimally invasive technique used for genomic profiling. We conducted comprehensive whole-exome sequencing (WES) of 50 paired OSCC cell-free plasma with whole blood samples using multiple mutation calling pipelines and filtering criteria. Integrative Genomics Viewer (IGV) was used to validate somatic mutations. Mutation burden and mutant genes were correlated to clinico-pathological parameters. The plasma mutation burden of cfDNA was significantly associated with clinical staging and distant metastasis status. The genes TTN, PLEC, SYNE1, and USH2A were most frequently mutated in OSCC, and known driver genes, including KMT2D, LRP1B, TRRAP, and FLNA, were also significantly and frequently mutated. Additionally, the novel mutated genes CCDC168, HMCN2, STARD9, and CRAMP1 were significantly and frequently present in patients with OSCC. The mutated genes most frequently found in patients with metastatic OSCC were RORC, SLC49A3, and NUMBL. Further analysis revealed that branched-chain amino acid (BCAA) catabolism, extracellular matrix–receptor interaction, and the hypoxia-related pathway were associated with OSCC prognosis. Choline metabolism in cancer, O-glycan biosynthesis, and protein processing in the endoplasmic reticulum pathway were associated with distant metastatic status. About 20% of tumors carried at least one aberrant event in BCAA catabolism signaling that could possibly be targeted by an approved therapeutic agent. We identified molecular-level OSCC that were correlated with etiology and prognosis while defining the landscape of major altered events of the OSCC plasma genome. These findings will be useful in the design of clinical trials for targeted therapies and the stratification of patients with OSCC according to therapeutic efficacy. Full article

We explored the characteristics of soil bacterial communities and their ecological functions under different types of vegetation reclamation in open-pit mines on the Loess Plateau, which is the guiding significance for the selection of vegetation and the improvement of restoration effect in mining areas. The research object was to reclaim the soil of the aluminum mine waste dump in Xiaoyi County, Shanxi. The soil characteristics were measured under different types of vegetation reclamation. The soil bacterial community under different vegetation reclamation was measured using the 16S rRNA gene high-throughput sequencing technology. The ecological function was predicted using the PICRUSt method. The correlation between soil physical and chemical properties and bacterial community structure and function was analyzed. From the results, (1) the bacterial compositions of the reclaimed soil samples were 33 phyla, 90 classes, 121 orders, 207 families, 298 genera, and 140 species. The abundance and diversity of the soil microbial community showed the rule of yellow rose > lespedeza and sweet wormwood herb > alfalfa. (2) Proteobacteria were the dominant bacteria in alfalfa and sweet wormwood herb samples, accounting for 36.09–43.36%. Proteobacteria and actinobacteria were the dominant bacteria in the yellow rose and lespedeza samples accounted for 53.34–53.39%. α-Proteobacteria, actinobacteria, and β-proteobacteria were the dominant bacteria of the four vegetation types. The relative abundance of the α-proteobacteria and β-proteobacteria was positively correlated with soil organic carbon (SOC) and negatively correlated with soil total kalium (TK). Actinobacteria were positively correlated with available kalium (AK) and negatively correlated with SOC and total nitrogen (TN). (3) There was no difference in the primary functions of the soil bacterial community after the reclamation of different plants, and the main functions were metabolism, genetic information processing, and environmental information processing, with the function abundance accounting for 81.52%. (4) The abundance of functional genes in the metabolism of other amino acids, folding, sorting, and degradation and glycan biosynthesis and metabolism were relatively rich in the rhizosphere soil of yellow rose. The abundance of functional genes in signal molecules and interaction, transport, and catabolism in the rhizosphere soil of lespedeza was the highest. The abundance of functional genes in carbohydrate metabolism, translation, and energy metabolism in the rhizosphere soil of alfalfa was the highest. Therefore, there were significant differences in the structure and function of rhizosphere soil microbial communities among yellow rose, lespedeza, sweet wormwood herb, and alfalfa, and they were also affected by the soil properties. Hence, we concluded that the differences and diversity of soil microbial structure and function can help select plants for the sustainable development of soil remediation in mining areas. Full article

A total of 16 crossbred (Duroc × Landrace × Yorkshire) barrows, with an average initial body weight of 8.61 ± 0.24 kg (28 days of age), were randomly allotted into the control group (CON group) and high ambient temperature group (HT group) with 8 replicates per group, 1 pig per replicate. The ambient temperature of the CON group was controlled at 26 ± 1 °C, and the HT group was controlled at 35 ± 1 °C. The study lasted for 21 days. Our results showed that high ambient temperature significantly decreased the average daily feed intake (ADFI) and average daily gain (ADG) of piglets (p < 0.05), and the feed-to-gain ratio was significantly increased (p < 0.05). The liver index, spleen index, and thymus index of piglets in the HT group were significantly decreased (p < 0.05). The villous height (VH) of the duodenum, jejunum, and ileum of piglets in the HT group was significantly decreased (p < 0.05), whereas the crypt depth (CD) of the duodenum was significantly increased (p < 0.05), and the VH-to-CD ratio of the duodenum and ileum was significantly decreased (p < 0.05). The piglets in the HT group showed a higher (p < 0.05) observed-species index, PD whole tree index, and Shannon index, indicating that there was a significant difference in species richness and diversity between the two groups. At the genus level, the piglets in the HT group showed a greater (p < 0.05) percent of Desulfovibrio, Occillibater, and Catenisphaera. HT reduced glycan biosynthesis and metabolism, transport and catabolism, lipid metabolism, amino acids metabolism, secondary metabolites biosynthesis, aging, endocrine system, signaling molecules, and interaction of colon microbiota (p < 0.05), and increased signal transduction, cell motility, transcription, and genetic information processing (p < 0.05). Full article

This experiment investigated the effect of vitamin A supplementation on growth, serum biochemical parameters, jejunum morphology and the microbial community in male growing-furring mink. Thirty healthy male mink were randomly assigned to three treatment groups, with 10 mink per group. Each mink was housed in an individual cage. The mink in the three groups were fed diets supplemented with vitamin A acetate at dosages of 0 (CON), 20,000 (LVitA) and 1,280,000 IU/kg (HVitA) of basal diet. A 7-day pretest period preceded a formal test period of 45 days. The results show that 20,000 IU/kg vitamin A increased the ADG, serum T-AOC and GSH-Px activities, villus height and villus height/crypt depth ratio (p < 0.05). The mRNA expression levels of IL-22, Occludin and ZO-1 in the jejunum of mink were significantly higher in the LVitA group than those in the CON and HVitA groups (p < 0.05). Vitamin A supplementation increased the diversity of jejunum bacteria, decreased the ratio of Firmicutes to Bacteroidetes and increased the relative abundance of Akkermansia, uncultured bacterium f Muribaculaceae, Allobaculum, Lachnospiraceae NK4A136 group, Rummeliibacillus and Parasutterella. The comparison of potential functions also showed enrichment of glycan biosynthesis and metabolism, transport and catabolism pathways in the vitamin A supplementation groups compared with the CON group. In conclusion, these results indicate that dietary vitamin A supplementation could mediate host growth by improving intestinal development, immunity and the relative abundance of the intestinal microbiota. Full article

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism. Full article

The development of infant gut microbiota is strongly influenced by nutrition. Human milk oligosaccharides (HMOSs) in breast milk selectively promote the growth of glycan-degrading microbes, which lays the basis of the microbial network. In this study, we investigated the trophic interaction between Bacteroides thetaiotaomicron and the butyrate-producing Anaerostipes caccae in the presence of early-life carbohydrates. Anaerobic bioreactors were set up to study the monocultures of B. thetaiotaomicron and the co-cultures of B. thetaiotaomicron with A. caccae in minimal media supplemented with lactose or a total human milk carbohydrate fraction. Bacterial growth (qPCR), metabolites (HPLC), and HMOS utilization (LC-ESI-MS²) were monitored. B. thetaiotaomicron displayed potent glycan catabolic capability with differential preference in degrading specific low molecular weight HMOSs, including the neutral trioses (2′-FL and 3-FL), neutral tetraoses (DFL, LNT, LNnT), neutral pentaoses (LNFP I, II, III, V), and acidic trioses (3′-SL and 6′-SL). In contrast, A. caccae was not able to utilize lactose and HMOSs. However, the signature metabolite of A. caccae, butyrate, was detected in co-culture with B. thetaiotaomicron. As such, A. caccae cross-fed on B. thetaiotaomicron-derived monosaccharides, acetate, and d-lactate for growth and concomitant butyrate production. This study provides a proof of concept that B. thetaiotaomicron could drive the butyrogenic metabolic network in the infant gut. Full article

It is well known that the “free” form of glycans that are structurally related to asparagine (N)-linked glycans (“free N-glycans”) are found in a wide variety of organisms. The mechanisms responsible for the formation/degradation of high mannose-type free N-glycans have been extensively studied in mammalian cells. Recent evidence, however, also suggests that sialylated, complex-type free N-glycans are also present in the cytosol of various mammalian-derived cultured cells/tissues. We report herein on an investigation of the mechanism responsible for the degradation of such sialyl free N-glycans. The findings show that the amount of glycans is dramatically reduced upon the co-expression of cytosolic sialidase NEU2 with cytosolic β-glycosidase GBA3 in human stomach cancer-derived MKN45 cells. The physical interaction between NEU2 and GBA3 was confirmed by co-precipitation analyses as well as gel filtration assays. The NEU2 protein was found to be stabilized in the presence of GBA3 both in cellulo and in vitro. Our results thus indicate that cytosolic GBA3 is likely involved in the catabolism of cytosolic sialyl free N-glycans, possibly by stabilizing the activity of the NEU2 protein. Full article