Frontiers in bioscience (Scholar edition)最新文献

{"title":"Post-COVID Versus Non-COVID Myocarditis: Comparison of Morphological Activity, Toll-like Receptor Distribution and Responses to Immunosuppressive Therapy.","authors":"Olga V Blagova, Evgenia A Kogan, Vladimir M Novosadov, Valeriy A Bryukhanov, Nikolay V Zharkov","doi":"10.31083/FBS28262","DOIUrl":"https://doi.org/10.31083/FBS28262","url":null,"abstract":"<p><strong>Background: </strong>A prior direct clinical and morphological comparison between non-coronavirus disease (COVID) myocarditis diagnosed before the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) pandemic and post-COVID myocarditis has not been performed.</p><p><strong>Purpose: </strong>To compare morphological activity, Toll-like receptor distribution, and response to immunosuppressive therapy in patients with non-COVID and post-COVID myocarditis.</p><p><strong>Methods: </strong>In total, 77 patients (52 male and 25 female, 48.7 ± 11.7 years old) with biopsy-proven myocarditis, New York Heart Association (NYHA) class 2 or higher heart failure diagnoses, and an ejection fraction (EF) <45% were included. The exclusion criteria comprised a history of myocardial infarction, verified cardiomyopathies, systemic autoimmune diseases, and viral DNA in the myocardium, except parvovirus B19. A right ventricular endomyocardial biopsy was performed using hematoxylin and eosin and Van Gieson staining assays, alongside the polymerase chain reaction (PCR) for viruses (herpes viruses, parvovirus B19, adeno-, enteroviruses, and SARS-CoV-2). Moreover, immunohistochemical assays were conducted for CD3, CD45, CD68, CD20, nucleocapsid/spike proteins of SARS-CoV-2, and the subcellular distribution of Toll-like receptors (TLRs) type 4 and 9 (in 38 patients). The steroids (methylprednisolone 24-40 mg per day), azathioprine, and mycophenolate mofetil were prescribed. This study was observational and non-interventional. The mean follow-up was 15.0 [6.0; 35.5] months.</p><p><strong>Results: </strong>Myocarditis was diagnosed in 45 patients before the SARS-CoV-2 pandemic (giant cell in one case and lymphocytic in the others). Another 32 patients had post-COVID myocarditis that was positive for RNA or/and proteins of SARS-CoV-2 (giant cell in one case, eosinophilic in three cases, and lymphocytic in the others). There were no differences in age, NYHA classification, C-reactive protein (CRP) and anti-heart antibodies levels, echocardiographic parameters (mean EF: 30.2 ± 7.8 vs. 28.7 ± 6.7%), parvovirus B19 positivity (22 vs. 34%), methylprednisolone dosages (24-40 mg/day), and death/transplantation rate (11.1 vs. 9.4%). Differences between non-COVID and post-COVID myocarditis focused on higher CD3, CD 45*, and toll-like receptors (TLR)-4 (4+ vs. 6+) and TLR-9 (0 vs. 2+) levels, alongside subcellular distribution and a better response to therapy ((10% or more increase in EF in 53 vs. 86%* of patients, mean EF (43.9 ± 12.3 vs. 49.8 ± 7.6%*) by the end of follow-up); *<i>p</i> < 0.05).</p><p><strong>Conclusion: </strong>Post-COVID myocarditis is characterized by different morphological types, higher morphological activity, the tendency to increase TLR expression, and an improved response to immunosuppressive therapy compared to non-COVID myocarditis.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"28262"},"PeriodicalIF":0.0,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>CYP3A4</i> and <i>CYP3A5</i> Genes in Cyclophosphamide-treated Chronic Lymphocytic Leukemia Patients: A Pharmacogenetics Study.","authors":"Heba M Elmaraghy, Menna Al-Adl, Eman R Saifeldein, Sahar M Elashmony, Magdy M Youssef, Afaf El-Said, Sherif Refaat, Abdallah E Mohammed","doi":"10.31083/FBS36269","DOIUrl":"https://doi.org/10.31083/FBS36269","url":null,"abstract":"<p><strong>Background: </strong>Approximately 75% of drug metabolism in clinical settings is attributed to cytochrome P450 enzymes. This study aimed to assess the effects of the <i>CYP3A4*1B</i> and <i>CYP3A5*3</i> genetic variations on the clinical results of individuals with chronic lymphocytic leukemia (CLL) following cyclophosphamide treatment. Furthermore, we aimed to ascertain how well the inflammatory condition affects the therapeutic response.</p><p><strong>Methods: </strong><i>CYP3A4*1B</i> and <i>CYP3A5*3</i> polymorphisms were examined in 150 Egyptian CLL patients using allele-specific amplification (ASA)-polymerase chain reaction (PCR); serum interleukin 6 (IL-6) and tumor necrosis factor-alpha (TNF-α) levels were also measured to assess the non-genetic inflammatory effect on <i>CYP3A4</i> and <i>CYP3A5</i> genes. Patients further received chemotherapy and were subsequently followed up.</p><p><strong>Results: </strong>The allelic frequencies of the <i>CYP3A4*1B</i> gene were (74.3% <i>A-allele</i> vs. 25.7% <i>G-allele</i>), and for <i>CYP3A5*3,</i> these frequencies were (73.4% <i>A-allele</i> vs. 26.6% <i>G-allele</i>). Patients with the <i>CYP3A4*1B</i> and <i>CYP3A5*3</i> genes, or both variants, were less likely to respond than the normal patients (<i>p</i> < 0.001). Regarding the non-genetic inflammatory effect, patients in the response group who achieved partial remission were characterized by higher IL-6 and TNF-α values than those who achieved complete remission (<i>p</i> < 0.001), and patients in the non-response group who had a progressive disease were characterized by higher IL-6 and TNF-α values than those who had a stable disease (<i>p</i> < 0.001).</p><p><strong>Conclusion: </strong><i>CYP3A4*1B</i> and <i>CYP3A5*3</i> variants could be helpful indicators in predicting the response to cyclophosphamide chemotherapy. <i>CYP3A4</i> and <i>CYP3A5</i> variability should be factored into personalized medicine, which attempts to optimize drug dosing for individual patients by considering genetic and non-genetic factors affecting the response.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"36269"},"PeriodicalIF":0.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inhibitory Effect of Novel Dihydroxamate Derivatives for Histone Deacetylase 1.","authors":"Jhawn G Saul, Andrew E Huckleby, Maia C Gugello, Jonathan Urbanczyk, Staci Desmarais, Hyunshun Shin, Apparao Bokka, Junha Jeon, Jatindra N Tripathy, Sung-Kun Kim","doi":"10.31083/FBS38998","DOIUrl":"https://doi.org/10.31083/FBS38998","url":null,"abstract":"<p><strong>Background: </strong>Histone deacetylase 1 (HDAC1) is a critical epigenetic regulator involved in chromatin remodeling and transcriptional repression, making it a valuable target for cancer therapy. Selective inhibition of HDAC1 represents a promising approach to cancer treatment, as it modulates gene expression and induces apoptosis in tumor cells.</p><p><strong>Methods: </strong>Two novel hydroxamate-based HDAC1 inhibitors, compounds 4 and 6, were designed and evaluated using molecular docking, molecular dynamics (MD) simulations, and enzymatic inhibition assays. Molecular docking assessed binding interactions, while MD simulations evaluated the stability of the ligand-protein complexes. Enzymatic inhibition assays were used to determine the IC₅₀ values and evaluate the potency of the compounds.</p><p><strong>Results: </strong>Molecular docking revealed that both compounds exhibited significant interactions with HDAC1, including hydrophobic contacts, hydrogen bonding, and zinc coordination. Compound 4 demonstrated a stronger binding affinity (-6.2 kcal/mol) compared to compound 6 (-5.7 kcal/mol). The MD simulations confirmed that compound 4 exhibited greater stability, with divalent zinc coordination (4.3 Å and 4.8 Å), whereas compound 6 showed weaker monovalent coordination (4.4 Å). Enzymatic assays demonstrated that compound 4 had an IC₅₀ of 2.96 ± 0.4 μM, while compound 6 exhibited an IC₅₀ of 4.76 ± 0.5 μM; thus, compound 4 possesses superior inhibitory potency.</p><p><strong>Conclusions: </strong>Compound 4 exhibits enhanced binding affinity, stability, and enzymatic inhibition compared to compound 6, suggesting that this compound may serve as a promising lead for the development of selective HDAC1 inhibitors.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"38998"},"PeriodicalIF":0.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Modifiers of HbF in HbAA and HbAS Women From São Tomé e Príncipe: An Association Study of Common Genetic Variants in <i>BCL11A</i>, <i>MYB</i>, <i>HBG2</i>, and <i>BGLT3</i>.","authors":"Licínio Manco, Afonso Marques Morais, Sara Miguel Almeida, Inês Salgado, Luís Relvas, Celdidy Monteiro, Guilherme Queiroz, Celeste Bento","doi":"10.31083/FBS38388","DOIUrl":"https://doi.org/10.31083/FBS38388","url":null,"abstract":"<p><strong>Background: </strong>While an increase in fetal hemoglobin (HbF) has no consequences in healthy adults, clinical benefits can be promoted in sickle cell disease (SCD) and β-thalassemia patients. Single-nucleotide polymorphisms (SNPs) in three genomic regions: the <i>HBB</i> gene cluster, the <i>BCL11A</i> gene, and the <i>HBS1L-MYB</i> (<i>HMIP</i>) intergenic region, have been associated with HbF regulation. Therefore, the present study aimed to examine the potential association of SNPs in <i>BCL11A</i> (rs11886868 and rs1427407), <i>HMIP</i> (rs66650371 and rs4895441), <i>HBG2</i> (rs7482144), and <i>BGLT3</i> (rs7924684) with HbF levels in an adult population sample from São Tomé e Príncipe (Central Africa).</p><p><strong>Methods: </strong>A total of 145 women aged 18 to 49 years were involved in this study, comprising 98 women with the normal hemoglobin (Hb) genotype (HbAA) and 47 with sickle cell trait (HbAS). From the HbAA individuals, we selected a control group of 60 subjects with normal HbF levels, ranging from 0.2% to 1.4% (mean: 0.75%), and a case group of 38 subjects with elevated HbF levels, ranging from 1.8% to 3.7% (mean: 2.35%). In the group of HbAS individuals, the HbF levels ranged from 0.4% to 3.7% (mean: 1.56%). SNP genotyping was conducted using standard molecular methods.</p><p><strong>Results: </strong>Logistic regression, in the additive model, revealed significant associations with increased levels of HbF for the minor alleles of the two <i>BCL11A</i> SNPs, rs11886868 [C] and rs1427407 [T], in HbAA women (<i>p</i> = 0.00018 and <i>p</i> = 0.00076, respectively). When comparisons of HbF levels were conducted among genotypes in the HbAA women, significant differences were observed for <i>BCL11A</i> SNPs rs11886868 and rs1427407, as well as for the <i>HBG2</i> rs7482144 and <i>BGLT3</i> rs7924684 variants. We found no association between HbF levels and the two <i>HMIP</i> variants rs66650371 and rs4895441 in the HbAA women. Among the HbAS women, no statistically significant associations were observed between the six analyzed polymorphisms and HbF levels (<i>p ></i> 0.05).</p><p><strong>Conclusions: </strong>We successfully replicated the association between the two well-known <i>BCL11A</i> SNPs, rs11886868 and rs1427407, with HbF levels in women with the normal HbAA genotype from São Tomé e Príncipe. Other signals of association with HbF levels were identified for the SNPs <i>HBG2</i> (rs7482144) and <i>BGLT3</i> (rs7924684).</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"38388"},"PeriodicalIF":0.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HER2-low Breast Cancer: Salivary Metabolic Features and Therapeutic Perspectives.","authors":"Lyudmila V Bel'skaya","doi":"10.31083/FBS36652","DOIUrl":"https://doi.org/10.31083/FBS36652","url":null,"abstract":"<p><strong>Background: </strong>The features of metabolic processes associated with low human epidermal growth factor receptor 2 (HER2) expression (HER2-low) in breast cancer have not been described to date, including characteristic features of immune system reactivity, the presence and content of tumor markers, and the amino acid profile.</p><p><strong>Methods: </strong>The case-control study involved 660 volunteers with breast cancer. Saliva was used as a biological fluid; at the time of collection, the patients were not receiving any treatment. Concentrations of 7 cytokines, 4 tumor markers, 12 amino acids, and 11 biochemical parameters were determined in the saliva.</p><p><strong>Results: </strong>It was found that the HER2-low group was characterized by the highest pro-inflammatory activity, but the lowest metabolic activity. Three functional groups of amino acids were identified, which showed reliable differences in the HER2-low subgroup. The cancer antigen 19-9 (CA 19-9) tumor marker in the HER2-low group showed the greatest deviations from normal values compared to patients in the HER2 (-) and HER2 (+) groups.</p><p><strong>Conclusions: </strong>Thus, patients with HER2-low breast cancer status had their own characteristic features in the course of the disease, immune response and metabolic activity. Understanding the features of metabolic processes in the HER2-low subgroup can help identify new therapeutic targets for this group of patients.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"36652"},"PeriodicalIF":0.0,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Soybean <i>E1</i>-<i>E4</i> Gene Orthologs in the Guar Genome Using Comprehensive Transcriptome Assembly and Annotation.","authors":"Luisa Criollo Delgado, Aleksei Zamalutdinov, Elena Potokina","doi":"10.31083/FBS26548","DOIUrl":"https://doi.org/10.31083/FBS26548","url":null,"abstract":"<p><strong>Background: </strong>We publish the first available transcriptome assembly of guar (<i>Cyamopsis tetragonoloba</i> (L.) Taub.), a well-known source of guar gum (food additive E 412). At high latitudes, e.g., in Russia, the main challenge for guar cultivation is the long photoperiod during summer, which delays flowering and maturation of guar plants. Meanwhile, identifying of genes affecting the photoperiod sensitivity of guar would have a major impact on the development of marker-assisted breeding of this valuable food crop.</p><p><strong>Methods: </strong>RNA isolated from leaves of early and late flowering guar plants grown under long-day conditions were used to generate <i>de novo</i> transcriptome assembly. A similarity search was conducted using BLASTN 2.2.31+ with default settings to identify homologous sequences of soybean maturity genes <i>E1</i>-<i>E4</i> in guar transcriptome and genome assembly. Gene prediction tools such as AUGUSTUS and FGENESH+ were used to predict the exon-intron structure of the candidate genes. Functional annotation of the amino acid sequence was performed using InterProScan v. 5.68-100.</p><p><strong>Results: </strong>The transcriptome assembly contained sequences of 96,447 clustered transcript isoforms in the leaves of guar plants grown under long-day conditions. The transcriptome assembly was annotated using BLAST against the <i>Glycine max</i> genome, and 42,615 guar transcripts (44.2%) were found to be similar to soybean genes. We used the developed transcriptome assembly to discover orthologs of the <i>E1</i>-<i>E4</i> soybean loci in the guar genome that have the greatest impact on the flowering and maturation of this closely related, short-day legume crop. A high level of identity was detected between peptide sequences encoding by orthologous genes <i>E1</i> and <i>CtE1</i> (80%), <i>E2</i> and <i>CtE2</i> (93%), <i>E3</i> and <i>CtE3</i> (83%), and <i>E4</i> and <i>CtE4</i> (91%). The sequences and the intron-exon structure of the genes in soybean and guar were similar, suggesting that the genetic pathways underlying basic flowering mechanisms are conserved between these two legume crops.</p><p><strong>Conclusions: </strong>The revealed intron-exon structure of the guar genes <i>CtE1</i>-<i>CtE4</i> creates possibilities for their targeted mutagenesis, e.g., using CRISPR-Cas and developing new guar germplasm with low sensitivity to photoperiod.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"26548"},"PeriodicalIF":0.0,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sanger Sequencing of <i>Borrelia burgdorferi flaB</i> Paralogs Detected Spirochetemia at the Early Localized Stage of Lyme Disease.","authors":"Sin Hang Lee","doi":"10.31083/FBS31280","DOIUrl":"https://doi.org/10.31083/FBS31280","url":null,"abstract":"<p><strong>Background: </strong>The general assumption that spirochetemia does not occur at the early localized stage of Lyme disease is due to a lack of sensitive and specific methods for molecular diagnosis.</p><p><strong>Methods: </strong>During a Lyme disease season in 2023, the platelet-rich plasma specimens of 145 people residing in Lyme disease-endemic areas in the United States were immediately separated from the blood cells following venous blood collection to prevent the spirochetes, if any, from invading the lymphocytes in the test tube. The entire DNA content was extracted from the platelet pellet and used for split sample polymerase chain reaction (PCR) amplification; Sanger sequencing was performed on the nested PCR products to detect the <i>Borrelia burgdorferi flaB</i> and <i>16S rRNA</i> genes.</p><p><strong>Results: </strong>In 98 of the people who were clinically suspected of having early localized Lyme disease irrespective of the presence or absence of a skin lesion, 33 of their blood specimens (33.7%) were positive for <i>Borrelia burgdorferi</i> (<i>B. burgdorferi</i>), including 17 positive for <i>flaB</i> gene only, 15 positive for both the <i>flaB</i> and <i>16S rRNA</i> genes, and one positive for <i>16S rRNA</i> gene only. Eight (17.0%) of the 47 asymptomatic resident controls were positive for <i>flaB</i> PCR only.</p><p><strong>Conclusions: </strong>The <i>flaB</i> gene is a more sensitive chromosomal target than the <i>16S</i> <i>rRNA</i> gene for molecular detection of one to three <i>B. burgdorferi</i> cells due to spirochetes gaining or retaining <i>flaB</i> paralogs at the early localized stage of Lyme disease.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"31280"},"PeriodicalIF":0.0,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circulating Tumor DNA in Primary and Secondary Liver Cancers: A Comprehensive Review.","authors":"Hanna Hong, Chase J Wehrle, Omer Faruk Karakaya, Noah Tocci, Pranav Kumar, Keyue Sun, Chunbao Jiao, Sangeeta Satish, Rebecca Panconesi, Jamak Modaresi Esfeh, Maureen Whitsett Linganna, Koji Hashimoto, Andrea Schlegel, Charles Miller, David C H Kwon, Federico Aucejo","doi":"10.31083/FBS26972","DOIUrl":"https://doi.org/10.31083/FBS26972","url":null,"abstract":"<p><p>Similar to many other cancer types, liver malignancies pose the common challenges of late detection of primary tumors and recurrences. Liquid biopsies, which assess the presence of circulating tumor DNA, have emerged as a novel, non-invasive clinical tool for diagnostic and surveillance purposes. This review represents an introductory and comprehensive overview of the current circulating tumor DNA (ctDNA) literature relevant to primary and secondary liver malignancies. Herein, we highlight key findings, landmark discoveries, challenges, and future directions.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"26972"},"PeriodicalIF":0.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Staphylococcus aureus</i> Strains With a Negative Coagulase Tube Test are Associated With Staphylocoagulase Genotypes.","authors":"Carly L Botheras, Dieter Bulach, Eugene Athan","doi":"10.31083/FBS33398","DOIUrl":"https://doi.org/10.31083/FBS33398","url":null,"abstract":"<p><strong>Background: </strong><i>Staphylococcus aureus</i> is a significant human pathogen. Therefore, differentiating <i>Staphylococcus aureus</i> (<i>S.</i> <i>aureus</i>) from coagulase-negative staphylococcal species is an important step in the diagnostics procedure. The coagulase tube test assay is used as a preliminary identification test; however, there are instances of <i>S. aureus</i> isolates testing negative. We hypothesized that this might affect clinical outcomes and that particular staphylocoagulase genotypes are not detected by the coagulase tube test.</p><p><strong>Methods: </strong>In total, 122 clinical bloodstream <i>S. aureus</i> isolates with clinical metadata were examined for coagulating ability. The <i>coa</i> genotype was determined for each isolate using whole genome sequencing, and regions flanking the <i>coa</i> gene in the genome sequence were examined for synteny to identify differences that may indicate possible differences in <i>coa</i> gene regulation. In addition, a subset of isolates was assessed for <i>coa</i> gene expression using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR).</p><p><strong>Results: </strong>All 122 isolates were found to have the <i>coa</i> gene, and all but one tested positive in the coagulase slide test. Comparatively, 18.9% of the isolates tested negative in the coagulase tube test assay. There was no association between an isolate having a negative tube test and having a complicated bloodstream infection. Among the 122 isolates, 11 <i>coa</i> genotypes were present, with similarities between the <i>coa</i> gene and comparative genome phylogenies and grouping of multilocus sequence types (MLST, abbreviated to ST), indicating that the <i>coa</i> gene may be vertically inherited. Staphylocoagulase type X and XI isolates were more likely to test negative in the coagulase tube test despite evidence of an intact functional <i>coa</i> gene.</p><p><strong>Conclusions: </strong>The <i>S. aureus</i> lineages may be negative in the coagulase tube test, especially ST15 and ST3911 (from staphylocoagulase genotype X). Our analysis suggests that the observed negativity in the coagulase tube test is due to the inability of particular coagulase types to coagulate the substrate provided in the commercial test. This has implications for using the tube test in differentiating <i>Staphylococcus</i> <i>aureus</i> isolates from other species. The Illumina genome sequencing read-set for each isolate was submitted to the National Center for Biotechnology Information (NCBI) under the accession number PRJNA611667.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 2","pages":"33398"},"PeriodicalIF":0.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of Fish Species Detection in the Northwestern Pacific using eDNA Metabarcoding: A Mock Community Approach.","authors":"Sergei V Turanov, Olesia A Rutenko","doi":"10.31083/FBS26247","DOIUrl":"10.31083/FBS26247","url":null,"abstract":"<p><strong>Background: </strong>Metabarcoding of environmental DNA (eDNA), a technique using high-throughput sequencing, has transformed biodiversity monitoring by identifying organisms from DNA fragments present in the environment. This method, particularly useful for aquatic ecosystems, allows for non-invasive species monitoring, helping to provide insight into ecosystem composition and taxonomic diversity. The objective of this study was to assess the efficacy of eDNA metabarcoding for fish species identification in a model community from the northeast Pacific Ocean using <i>12S</i> ribosomal RNA (<i>12S</i> rRNA) marker.</p><p><strong>Methods: </strong>Water samples were collected from the tank of the Primorsky Aquarium, which contains fish species from the Sea of Japan, Sea of Okhotsk, and Bering Sea. DNA was extracted using syringe filters and enriched with polymerase chain reaction (PCR) of mitochondrial <i>12S</i> rRNA fragment, followed by sequencing on Illumina platform. The resulting reads were processed using the bayesian generalized uncertainty modeling (BEGUM) pipeline and their taxonomic diversity was assessed by basic local alignment search tool (BLAST) search. Using <i>in silico</i> PCR, we also assessed the possible association of detection failures of some species with the presence of primer-to-target sequence mismatches.</p><p><strong>Results: </strong>From a fish community of only 20 species in the tank, we identified 56 operational taxonomic units (OTUs) corresponding to 28 genera. Among these OTUs, 20 species were unambiguously classified by BLAST-based analysis, though only 9 of them corresponded to the species actually present in the tank. Significant problems included inconsistent reference data and marker biases that affected the accuracy of species identification. In addition to DNA contamination from feed, contamination from the water source may have introduced extraneous DNA into the samples. Also, using <i>in silico</i> PCR analysis with a small number of available reference sequences, we demonstrated a significantly higher number of primer mismatches for species that were not identified.</p><p><strong>Conclusions: </strong>This study highlights the relative efficacy of eDNA metabarcoding for fish species identification, but also highlights the need to improve reference databases and minimise contamination, searching for references and primers to improve accuracy. Further research should focus on optimising marker selection and controlling methodological bias to ensure robust biodiversity estimates.</p>","PeriodicalId":73070,"journal":{"name":"Frontiers in bioscience (Scholar edition)","volume":"17 1","pages":"26247"},"PeriodicalIF":0.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}