Current Issue : October-December Volume : 2025 Issue Number : 4 Articles : 5 Articles
Outbreaks of infectious diseases contribute significantly to morbidity and mortality in resource-limited settings, yet the capacity to identify their etiology remains limited. We aimed to characterize microbes and antimicrobial resistance (AMR) genes in Tanzanian children affected by an acute febrile illness (AFI) outbreak using metagenomic next-generation sequencing (mNGS). A cross-sectional study was conducted on archived blood samples from children who presented with AFI between 2018 and 2019. Total nucleic acids were extracted from 200 μL of blood, and complementary DNA (cDNA), along with enriched pathogenic DNA, was sequenced using the Illumina MiSeq platform. mNGS data were analyzed using CZ-ID Illumina mNGS bioinformatics pipeline v7.0. Results were obtained from 25 participants (mean age: 11.6 years; SD ± 5), of whom 36% had a moderate to high-grade fever. The following five potential microbial causes of AFI were identified: Escherichia coli (n = 19), Paraclostridium bifermentans (n = 2), Pegivirus C (n = 2), Shigella flexneri (n = 1) and Pseudomonas fluorescens (n = 1), with E. coli being the most prevalent. Twelve AMR genes were detected, including mdtC, acrF, mdtF, and emrB. E. coli harbored most of the AMR genes previously associated with resistance to commonly used antibiotics. mNGS offers a promising complementary approach to conventional diagnostics for identifying pathogens and AMR profiles in vulnerable populations....
Background: The PDX2 gene serves as a critical catalytic component in vitamin B6 (VB6) biosynthesis pathways and plays pivotal regulatory roles in plant growth. Methods: To investigate the metabolic regulation of PDX2 (GbPDX2) fromGinkgo biloba in VB6 biosynthesis during kernel development, we successfully cloned this gene and conducted systematic expression profiling through qRT-PCR across multiple tissues and developmental stages. Results: Bioinformatic characterization revealed that GbPDX2 contains a 765-bp coding sequence encoding a 254-amino acid polypeptide. The encoded protein displays typical hydrophilic properties (average hydrophobicity index: −0.32) and was predicted to be an unstable cytosolic protein (instability index: 45.7) lacking signal peptides or transmembrane domains with cytoplasmic localization. Phylogenetic analysis demonstrated that GbPDX2’s closest evolutionary relationship was with its ortholog in Picea sitchensis, which had an amino acid sequence similarity of 83.7% with spruce PsPDX2. Tissue-specific expression analysis revealed a gradient expression profile of Kernel > Exocarp > Leaves > Stems > Roots. The expression level in kernels was significantly higher than that in other tissues (19.7 times that in roots, 8.3 times that in stems, and 5.9 times that in leaves; p < 0.01), with peak transcript levels observed in mature kernels. HPLC quantification established a strong positive correlation between GbPDX2 expression dynamics and VB6 accumulation patterns during kernel maturation (r = 0.92, p < 0.01), and the peak period of VB6 reached 288.9 ± 7.1 μg/g. Conclusions: Our findings provide the first experimental evidence that GbPDX2 spatiotemporally regulates VB6 biosynthesis in ginkgo kernels, offering novel insights into the evolutionary adaptation of vitamin metabolism in gymnosperms....
Although necroptosis is an emerging mechanism of multiple organ dysfunction in sepsis, data on the mechanistic link between necroptosis and sepsis are scarce. Bioinformatic analysis was performed to compare the gene profiles between the sepsis (n = 133) and healthy control (n = 12) groups and identify necroptosis- related differentially expressed genes (DEGs). The identified necroptosis- related DEGs were verified by three- step molecular experiments: (1) quantitative real- time PCR and enzymelinked immunosorbent assay; (2) cell culture, transfection and Western blotting; and (3) cytokine array with apoptosis inhibition. Additionally, receiver- operating characteristic curve analyses were performed to evaluate the performance of the corresponding proteins to the necroptosis- related DEGs in diagnosing sepsis and in predicting in- hospital mortality of patients with sepsis. Eight necroptosis- related DEGs, including five upregulated (PYGL, TNF, CYLD, FADD and TLR3) and three downregulated (TP53, FASLG and NLRP6) DEGs, were identified. Moreover, the levels of the corresponding proteins to necroptosis- related DEGs showed excellent or considerable accuracy in diagnosing sepsis and in predicting the mortality of sepsis patients. In cell culture media transfected with plasma from the sepsis and control groups, Western blotting revealed that the levels of the corresponding proteins were increased in the upregulated DEGs and decreased in the downregulated DEGs. The cytokine array revealed cytokines in cell culture media transfected with plasma from patients with sepsis while preventing apoptosis by inhibiting the caspase- 8 activity, wherein the transfected cells potentially underwent necroptosis. Eight necroptosis- related DEGs were identified in patients with sepsis by bioinformatic analysis and verified by molecular experiments, implying that necroptosis may be a key mechanism of sepsis....
Background: Genome sequence databases are growing exponentially, but with high redundancy and uneven data quality. For these reasons, selecting representative subsets of genomes is an essential step for almost all studies. However, most current sampling approaches are biased and unable to process large datasets in a reasonable time. Methods: Here we present MPS-Sampling (Multiple-Protein Similarity-based Sampling), a fast, scalable, and efficient method for selecting reliable and representative samples of genomes from very large datasets. Using families of homologous proteins as input, MPS-Sampling delineates homogeneous groups of genomes through two successive clustering steps. Representative genomes are then selected within these groups according to predefined or user-defined priority criteria. Results: MPS-Sampling was applied to a dataset of 48 ribosomal protein families from 178,203 bacterial genomes to generate representative genome sets of various size, corresponding to a sampling of 32.17% down to 0.3% of the complete dataset. An in-depth analysis shows that the selected genomes are both taxonomically and phylogenetically representative of the complete dataset, demonstrating the relevance of the approach. Conclusion: MPS-Sampling provides an efficient, fast and scalable way to sample large collections of genomes in an acceptable computational time. MPS-Sampling does not rely on taxonomic information and does not require the inference of phylogenetic trees, thus avoiding the biases inherent in these approaches. As such, MPSSampling meets the needs of a growing number of users....
This study reports the construction, expression, and purification of synthetic SARS-CoV-2 spike (S) and nucleoprotein (N) containing immunodominant epitopes. The pET28aS_epit construct included epitopes 287–317, 402, 507, 524–598, and 601–640, while the pET28aN_epit construct included residues 42–62, 153–172, and 355–401. Commercial sequences of both proteins were used as controls. The four constructs were expressed using the Escherichia coli BL21(DE3) star strain at 37 ◦C. The results show that the S protein constructs were insoluble, unlike the N protein constructs. Both recombinant proteins induced immune responses in mice and were recognized by antibodies present in sera from COVID-19-positive and/or SARS-CoV-2-vaccinated humans. No significant differences in immune recognition were observed between our constructs and the commercially available proteins. In conclusion, S_epit and N_epit could be promising starting points for the development of new strategies based on immunological reactions for the control of SARS-CoV-2 infections....
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