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Polish Journal of Microbiology Jun 2024Shiga toxin-producing (STEC) are zoonotic pathogens causing hemorrhagic colitis and hemolytic uremic syndrome (HUS) in children and the elderly. Stool samples were...
Shiga toxin-producing (STEC) are zoonotic pathogens causing hemorrhagic colitis and hemolytic uremic syndrome (HUS) in children and the elderly. Stool samples were collected from 180 children hospitalized in five pediatric centers in Poland in 2018-2022. Direct / gene detection by PCR in feces and isolates was performed. Antibiotic susceptibility was tested according to EUCAST v.12. Randomly selected isolates were serotyped with O157 antiserum and genotyped by pulsed-field gel electrophoresis (PFGE). A total of 44 isolates were confirmed as STEC by PCR. Among them, 84.4% were positive for , and equally 6,8% for only and both and genes. The gene was also found in one isolate. serotype O157 was present in 97.6% of the isolates. STEC infections most often occurred between June-October with a peak in July and August (51%). The highest, 77.8% of STEC isolates were found in the 1-5 years old group. No extended-spectrum β-lactamases (ESBL) were found. Resistance only to amoxicillin/clavulanic acid (24.4%), piperacillin/tazobactam (3%), cefotaxime (6%), gentamicin (6%), ciprofloxacin (3%), azithromycin (3%), trimethoprim/sulfamethoxazole (24,2%) was detected. PFGE analysis showed 18 PFGE types with no clonal distribution. Eight isolates with A, B, and C PFGE types showed genetic relatedness in the type with no detection of transmission way of distribution. STEC strains pose a serious threat to human health, therefore demographic and epidemiological characteristics are crucial for their surveillance.
Topics: Humans; Poland; Child, Preschool; Shiga-Toxigenic Escherichia coli; Escherichia coli Infections; Child; Infant; Anti-Bacterial Agents; Feces; Female; Male; Microbial Sensitivity Tests; Adolescent; Electrophoresis, Gel, Pulsed-Field; Genotype; Infant, Newborn
PubMed: 38727736
DOI: 10.33073/pjm-2024-016 -
Virus Research Jul 2024To elucidate the epidemiological features of HIV-2 in Hunan Province, China, utilizing sequence analysis.
OBJECTIVE
To elucidate the epidemiological features of HIV-2 in Hunan Province, China, utilizing sequence analysis.
METHODS
Thirteen individuals diagnosed with HIV-2 infection in Hunan Province, China, from 2017 to 2023 were included in this study. Amplification of HIV-2 env and pol regions was conducted, followed by Sanger sequencing. Phylogenetic and molecular transmission network analyses were performed to delineate molecular features and transmission dynamics.
RESULTS
All 14 individuals contracted HIV-2 through heterosexual intercourse, comprising 7 males and 7 females, with a median age of 58 years. Among them, three couples (HN001 and HN013, HN010 and HN011, HN008 and HN009) were identified, along with commercial sexual activity engagement reported for subject HN004. Notably, subjects HN001, HN003, HN008, and HN010 engaged in commercial sexual activities at the same location as subject HN004. Phylogenetic analysis of the pol gene revealed close proximity of sequences from all subjects to reference sequences from Gambia (Sub-type A). Employing a genetic distance threshold of 1.5 %, eight out of the 14 subjects formed a molecular transmission network, with HN002 and HN004 identified as central nodes.
CONCLUSION
From 2017 to 2023, all HIV-2-infected individuals in Hunan Province, China, acquired the virus through identifiable routes, indicating transmission of similar HIV-2 strains among them.
Topics: Humans; China; Male; Female; HIV Infections; HIV-2; Phylogeny; Middle Aged; Adult; Aged; Epidemics; pol Gene Products, Human Immunodeficiency Virus; Sexual Behavior; Genotype; env Gene Products, Human Immunodeficiency Virus
PubMed: 38723949
DOI: 10.1016/j.virusres.2024.199385 -
Acta Biochimica Polonica 2024To explore the difference in intestinal microecology between patients with preeclampsia and pregnant women at different stages of pregnancy. From January 2020 to...
To explore the difference in intestinal microecology between patients with preeclampsia and pregnant women at different stages of pregnancy. From January 2020 to January 2022, clinical data, including blood routine, lipid profile, and renal function indicators, were gathered from a cohort consisting of 5 cases of preeclampsia and 34 cases of non-preeclampsia. The non-preeclampsia group was further categorized into 6 cases in the First trimester, 13 cases in the Second trimester, and 15 cases in the Third trimester. The data collection took place at the Obstetrics Department of the Maternal and Child Health Hospital of Hubei Province. Additionally, fecal samples were obtained from each subject for 16S rDNA gene sequencing and subsequent analysis. The clinical data and composition characteristics of the gut microbiota in each group were analyzed, and the correlation between gut microbiota and clinical data was analyzed by the Spearman correlation analysis method. In comparison to pregnant women without preeclampsia, preeclampsia patients exhibited a statistically significant elevation in blood routine parameters (WBC, N, L, and PLT count), a rise in lipid-related indicators (TC, TG, and LDL-C levels), a reduction in HDL-C levels, and an increase in renal function-related indicators (Cr, BUN, UA and Pro levels). Compared with non-preeclampsia pregnant women, preeclampsia women exhibited an augmented diversity of gut microbiota. Differences in gut microbiota composition between the two groups were observed at the gate and genus levels. Moreover, there are significant differences in the composition of gut microbiota between the preeclampsia group and the third-trimester group in terms of genus and species, and this difference is mainly caused by and _ and . In addition, actinobacteria, bifidobacterium at the genus level, and at the species level are positively correlated with clinically relevant indicators (excluding HDL-C). There are significant differences in gut microbiota between preeclampsia pregnant women and late pregnancy pregnant without preeclampsia, including and and . In addition, these differential bacteria are correlated with most clinical indicators. However, additional comprehensive analysis is required to ascertain the functional correlation between these bacteria and clinical indicators.
Topics: Humans; Pregnancy; Pre-Eclampsia; Female; Gastrointestinal Microbiome; Adult; Feces; RNA, Ribosomal, 16S
PubMed: 38721310
DOI: 10.3389/abp.2024.12020 -
Cell Death & Disease May 2024Metastatic dissemination from the primary tumor is a complex process that requires crosstalk between tumor cells and the surrounding milieu and involves the interplay...
Metastatic dissemination from the primary tumor is a complex process that requires crosstalk between tumor cells and the surrounding milieu and involves the interplay between numerous cellular-signaling programs. Epithelial-mesenchymal transition (EMT) remains at the forefront of orchestrating a shift in numerous cellular programs, such as stemness, drug resistance, and apoptosis that allow for successful metastasis. Till date, there is limited success in therapeutically targeting EMT. Utilizing a high throughput screen of FDA-approved compounds, we uncovered a novel role of the topoisomerase inhibitor, Teniposide, in reversing EMT. Here, we demonstrate Teniposide as a potent modulator of the EMT program, specifically through an IRF7-NMI mediated response. Furthermore, Teniposide significantly reduces the expression of the key EMT transcriptional regulator, Zinc Finger E-Box Binding Homeobox 2 (ZEB2). ZEB2 downregulation by Teniposide inhibited RNA polymerase I (Pol I) activity and rRNA biogenesis. Importantly, Teniposide treatment markedly reduced pulmonary colonization of breast cancer cells. We have uncovered a novel role of Teniposide, which when used at a very low concentration, mitigates mesenchymal-like invasive phenotype. Overall, its ability to target EMT and rRNA biogenesis makes Teniposide a viable candidate to be repurposed as a therapeutic option to restrict breast cancer metastases.
Topics: Epithelial-Mesenchymal Transition; Humans; Breast Neoplasms; Female; Zinc Finger E-box Binding Homeobox 2; Cell Line, Tumor; Down-Regulation; RNA Polymerase I; Teniposide; Animals; Mice; Gene Expression Regulation, Neoplastic
PubMed: 38719798
DOI: 10.1038/s41419-024-06694-7 -
Journal of Bioscience and Bioengineering Jul 2024Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein...
Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. Considering the onsite use of RPA reagents, lyophilized RPA reagents with long storage stability are highly desired. In this study, as one of the approaches to solve this problem, we attempted to use a thermostable pyruvate kinase (PK). PK gene was isolated from a thermophilic bacterium Thermotoga maritima (Tma-PK). Tma-PK was expressed in Escherichia coli and purified from the cells. Tma-PK exhibited higher thermostability than human PK. The purified Tma-PK preparation was applied to RPA as an ATP-regenerating enzyme. Liquid RPA reagent with Tma-PK exhibited the same performance as that with human PK. Lyophilized RPA reagent with Tma-PK exhibited higher performance than that with human PK. Combined with our previous results of RPA reagents of thermostable Pol from a thermophilic bacterium, Aeribacillus pallidus, the results in this study suggest that thermostable enzymes are preferable to mesophilic ones as a component in lyophilized RPA reagents.
Topics: Thermotoga maritima; Freeze Drying; Pyruvate Kinase; Enzyme Stability; Nucleic Acid Amplification Techniques; Humans; Recombinases; Escherichia coli; DNA-Directed DNA Polymerase; Bacterial Proteins
PubMed: 38719683
DOI: 10.1016/j.jbiosc.2024.04.003 -
Frontiers in Genetics 2024-regulatory elements (CREs) play crucial roles in regulating gene expression during erythroid cell differentiation. Genome-wide erythroid-specific CREs have not been...
BACKGROUND
-regulatory elements (CREs) play crucial roles in regulating gene expression during erythroid cell differentiation. Genome-wide erythroid-specific CREs have not been characterized in chicken erythroid cells, which is an organism model used to study epigenetic regulation during erythropoiesis.
METHODS
Analysis of public genome-wide accessibility (ATAC-seq) maps, along with transcription factor (TF) motif analysis, CTCF, and RNA Pol II occupancy, as well as transcriptome analysis in fibroblasts and erythroid HD3 cells, were used to characterize erythroid-specific CREs. An α-globin CRE was identified, and its regulatory activity was validated and by luciferase activity and genome-editing assays in HD3 cells, respectively. Additionally, circular chromosome conformation capture (UMI-4C) assays were used to distinguish its role in structuring the α-globin domain in erythroid chicken cells.
RESULTS
Erythroid-specific CREs displayed occupancy by erythroid TF binding motifs, CTCF, and RNA Pol II, as well as an association with genes involved in hematopoiesis and cell differentiation. An α-globin CRE, referred to as CRE-2, was identified as exhibiting enhancer activity over αD and αA genes and . Induction of terminal erythroid differentiation showed that α-globin CRE-2 is required for the induction of αD and αA. Analysis of TF binding motifs at α-globin CRE-2 shows apparent regulation mediated by GATA-1, YY1, and CTCF binding.
CONCLUSION
Our findings demonstrate that cell-specific CREs constitute a key mechanism that contributes to the fine-tuning gene regulation of erythroid cell differentiation and provide insights into the annotation and characterization of CREs in chicken cells.
PubMed: 38706797
DOI: 10.3389/fgene.2024.1384167 -
Horticulture Research Apr 2024With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. lncRNAs are primarily... (Review)
Review
With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. lncRNAs are primarily transcribed and spliced by RNA polymerase II (Pol II) or plant-specific Pol IV/V, and exhibit limited evolutionary conservation. lncRNAs intricately regulate various aspects of fruit and vegetables, including pigment accumulation, reproductive tissue development, fruit ripening, and responses to biotic and abiotic stresses, through diverse mechanisms such as gene expression modulation, interaction with hormones and transcription factors, microRNA regulation, and involvement in alternative splicing. This review presents a comprehensive overview of lncRNA classification, basic characteristics, and, most importantly, recent advances in understanding their functions and regulatory mechanisms.
PubMed: 38706580
DOI: 10.1093/hr/uhae046 -
Polish Journal of Microbiology Jun 2024This study aimed to investigate azole resistance mechanisms in which involve 51A and 51B genes. Real-time Reverse Transcriptase qPCR method was applied to determine the...
This study aimed to investigate azole resistance mechanisms in which involve 51A and 51B genes. Real-time Reverse Transcriptase qPCR method was applied to determine the overexpression of 51A and 51B genes for 34 isolates. PCR sequencing of these two genes was used to detect the presence of gene mutations. Susceptibility test found sensitivity to voriconazole (VOR) in all strains. 14.7% and 8.8% of isolates were resistant to itraconazole (IT) and posaconazole (POS), respectively, with a cross-resistance in 5.8%. For the double resistant isolates (IT/POS), the expression of 51A was up to 17-fold higher. PCR sequencing showed the presence of 2 mutations in 51A: a synonymous point mutation (P61P) in eight isolates, which did not affect the structure of CYP51A protein, and another non synonymous mutation (G206L) for only the TN-33 strain (cross IT/POS resistance) causing an amino acid change in the protein sequence. However, we noted in 51B the presence of the only non-synonymous mutation (L177G) causing a change in amino acids in the protein sequence for the TN-31 strain, which exhibits IT/POS cross-resistance. A short single intron of 67 bp was identified in the 51A gene, whereas three short introns of 54, 53, and 160 bp were identified in the 51B gene. According to the models provided by PatchDock software, the presence of non-synonymous mutations did not affect the interaction of CYP51A and CYP51B proteins with antifungals. In our study, the overexpression of the 51A and 51B genes is the primary mechanism responsible for resistance in collection. Nevertheless, other resistance mechanisms can be involved.
Topics: Aspergillus flavus; Fungal Proteins; Cytochrome P-450 Enzyme System; Drug Resistance, Fungal; Antifungal Agents; Azoles; Microbial Sensitivity Tests; Humans; Aspergillosis; Mutation; Voriconazole; Triazoles
PubMed: 38700908
DOI: 10.33073/pjm-2024-001 -
Neuron Jun 2024Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in...
Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type (WT) and mutant MECP2 molecules. MECP2 occupies CpG-rich promoter-proximal regions in over four thousand genes in human neurons, including a plethora of autism risk genes, together with RNA polymerase II (RNA Pol II). MECP2 directly interacts with RNA Pol II, and genes occupied by both proteins showed reduced expression in neurons with MECP2 patient mutations. We conclude that MECP2 acts as a positive cofactor for RNA Pol II gene expression at many neuronal genes that harbor CpG islands in promoter-proximal regions and that RTT is due, in part, to the loss of gene activity of these genes in neurons.
Topics: RNA Polymerase II; Methyl-CpG-Binding Protein 2; Humans; Neurons; Transcription, Genetic; Promoter Regions, Genetic; Rett Syndrome; CpG Islands; Mutation; Gene Expression Regulation
PubMed: 38697112
DOI: 10.1016/j.neuron.2024.04.007 -
Expert Opinion on Therapeutic Targets May 2024
Topics: Humans; HIV Infections; Anti-HIV Agents; Molecular Targeted Therapy; HIV-1; Animals
PubMed: 38696265
DOI: 10.1080/14728222.2024.2351510