Ribosomal DNA Research Articles

Antibacterial and Anticancer Properties of Endophenazines from Streptomyces prasinus ZO16, an Endophyte in Zingiber officinale Rosc.

<b>Background and Objective:</b> This study investigated a bacterial strain, ZO16, isolated from ginger (<i>Zingiber officinale</i>) roots. Analysis of its 16S ribosomal DNA (rDNA), along with chemical and physical properties, revealed it to be <i>Streptomyces prasinus</i>. This study aimed to isolate and characterize the main bioactive compounds from ZO16, evaluating their antibacterial and anticancer properties. <b>Materials and Methods:</b> Techniques like column chromatography and thin-layer chromatography (TLC) were used to purify the key compounds from ZO16's culture extract. Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry were utilized to confirm the identities of the purified compounds as endophenazine A (compound 1) and endophenazine B (compound 2). The antibacterial and anticancer properties of these compounds were then evaluated. <b>Results:</b> The isolated compounds displayed antibacterial activity against <i>Staphylococcus aureus</i> ATCC 25923 and Methicillin-Resistant <i>Staphylococcus aureus</i> (MRSA). The minimum inhibitory concentration (MIC) of the isolated compounds against bacteria ranged from 8 to 32 μg/mL, while the minimum bactericidal concentration (MBC) was between 32 and 128 μg/mL. These compounds exhibited effectiveness against tested cancer cells with IC<sub>50</sub> values ranging from 30.40 to 32.51 μg/mL for cervical cancer (HeLa), 78.32 to 86.45 μg/mL for liver cancer (HepG2) and 23.41 to 28.26 μg/mL for breast cancer (MDA-MB-231) cells. However, these compounds also showed moderate toxicity towards non-cancerous Vero cells (IC<sub>50</sub> = 317.44-328.63 μg/mL). <b>Conclusion:</b> The findings of this study suggest that <i>Streptomyces prasinus</i> strain ZO16 produces compounds with antibacterial and anticancer properties. Further investigation of these compounds has the potential to contribute to the development of improved methods for controlling and treating bacterial infections and some cancers.

Assessing management strategies for mitigating Rhizoctonia damping-off in sugar beet cultivation

Rhizoctonia solani is recognized as one of the most economically significant pathogens that can cause both crown root rot (CRR) and damping-off (DO) in the sugar beet (SB) plant. This report details the first investigative study on R. solani as a fungus causing DO of SB in Morocco. The identification of the fungal pathogen was done both based on morphological features as well as on molecular tools utilizing internal transcribed spacer region of ribosomal DNA (ITS rDNA) and specific primers. In vitro evaluation of the antifungal effect of four commonly used fungicides, tebuconazole, azoxystrobin, trifloxystrobin, and difenoconazole, revealed their effectiveness in inhibiting the growth of pathogenic strains on potato dextrose agar (PDA) medium. Bacillus subtilis Y1336, available in the market, was tested as a potential biocontrol agent (BCA) against R. solani-induced DO. The effectiveness of the BCA was confirmed through double culture tests on PDA, in vitro seed inoculation with both B. subtilis and R. solani, and by employing the antagonist agent as a seed coat in greenhouse settings. This marks the first instance of the effectiveness of B. subtilis Y1336 against R. solani-induced DO in SB. B. subtilis Y1336 should be integrated into SB damping-off control strategies, in conjunction with the fungicides that have been shown to be more effective.

Case of tinea corporis caused by a terbinafine-sensitive Trichophyton indotineae strain in a Vietnamese worker in Japan.

A 42-year-old Vietnamese egg factory worker in Ishikawa prefecture, Japan, presented with itchy concentric erythema on the trunk and left calf. The lesions tested positive by direct potassium hydroxide examination, and two fungal strains were isolated. The isolates produced conidia abundantly and were morphologically indistinguishable from Trichophyton mentagrophytes/interdigitale, but were identified as Trichophyton indotineae by internal transcribed spacer sequence of ribosomal DNA. The lesions were refractory to treatment with topical luliconazole (LLCZ) cream for 4 weeks but subsided with oral itraconazole (ITCZ) 100 mg/day for 4 weeks in combination with topical lanoconazole (LCZ) cream. The lesions recurred 6 weeks after discontinuation of oral ITCZ, and an additional isolate was cultured. The minimum inhibitory concentrations of antimycotics for the isolate cultured at the first visit were: terbinafine (TBF) 0.03 μg/mL, ITCZ 0.015 μg/mL, LLCZ 0.0005 μg/mL, and LCZ 0.002 μg/mL. No TBF-resistant mutation in the amino acid sequence of squalene epoxidase, i.e., Leu 393 Ser/Phe or Phe 397 Leu, was detected in the isolate. The reason for recalcitrance in this case, despite the isolate's sensitivity to antimycotics, was unclear. Possible factors include insufficient use of the antimycotics, incomplete removal of abundantly produced conidia from the lesions, the patient's environment, and a language gap between the patient and physician hindering communication.

MARKER REGIONS OF THE GENOME FOR MOLECULAR DIAGNOSTICS OF OPISTHORCHIIDAE FAMILY

Infectious diseases caused by representatives of the Opisthorhidae family rank 8th in terms of health concern in the world among all food parasites. According to FAO data, studies of representatives of the Opisthorhidae family rank first and range from 0.66 to 88.7%. When performing a PCR analysis, a molecular marker plays an important role. In our studies, ribosomal genome clusters and mitochondrial genes were used as molecular markers. In eukaryotic organisms, ribosomal genes are presented in the form of clusters located in groups on different chromosomes. Each cluster includes three ribosomal genes (18S, 5.8S and 28S), separated by spacer regions. The ribosomal gene cluster consists of a transcribed region, internal transcribed spacers (ITS - Internal Transcribed Spacer) and flanking external transcribed spacers (ETS - Eternal Transcribed Spacer) The ITS noncoding sequence differs greatly among closely related organisms and is therefore used to classify parasites at the genus, species, and subspecies level. The ribosomal nuclear gene 5.8S forms the complete transcribed internal spacer region together with the molecular markers ITS1 and ITS2. This region of the genome is used in species studies of 19 families of digenetic flukes. Mitochondrial genes are also one of the most commonly used mtDNA gene fragments in the molecular identification of the family Opisthorchiidae. The advantage of using COX in research is the high degree of mutation, which makes it possible to differentiate closely related species The use of these genome regions makes it possible to quickly and accurately identify pathogens of the family Opishorchiidae, even for such individuals with practically indistinguishable morphological stages of the life cycle, such as parasite eggs and capsules in fish muscles. Therefore, in our studies, primers were used for the nuclear regions of ribosomal DNA ITS1, ITS2 and mitochondrial genes COX1, COX3.

MARKER REGIONS OF THE GENOME FOR MOLECULAR DIAGNOSTICS OF OPISTHORCHIIDAE FAMILY

Infectious diseases caused by representatives of the Opisthorhidae family rank 8th in terms of health concern in the world among all food parasites. According to FAO data, studies of representatives of the Opisthorhidae family rank first and range from 0.66 to 88.7%. When performing a PCR analysis, a molecular marker plays an important role. In our studies, ribosomal genome clusters and mitochondrial genes were used as molecular markers. In eukaryotic organisms, ribosomal genes are presented in the form of clusters located in groups on different chromosomes. Each cluster includes three ribosomal genes (18S, 5.8S and 28S), separated by spacer regions. The ribosomal gene cluster consists of a transcribed region, internal transcribed spacers (ITS - Internal Transcribed Spacer) and flanking external transcribed spacers (ETS - Eternal Transcribed Spacer) The ITS noncoding sequence differs greatly among closely related organisms and is therefore used to classify parasites at the genus, species, and subspecies level. The ribosomal nuclear gene 5.8S forms the complete transcribed internal spacer region together with the molecular markers ITS1 and ITS2. This region of the genome is used in species studies of 19 families of digenetic flukes. Mitochondrial genes are also one of the most commonly used mtDNA gene fragments in the molecular identification of the family Opisthorchiidae. The advantage of using COX in research is the high degree of mutation, which makes it possible to differentiate closely related species The use of these genome regions makes it possible to quickly and accurately identify pathogens of the family Opishorchiidae, even for such individuals with practically indistinguishable morphological stages of the life cycle, such as parasite eggs and capsules in fish muscles. Therefore, in our studies, primers were used for the nuclear regions of ribosomal DNA ITS1, ITS2 and mitochondrial genes COX1, COX3.

Early inhibition of BRD4 facilitates iPSC reprogramming via accelerating rDNA dynamic expression

BackgroundiPSC reprogramming technology exhibits significant promise in the realms of clinical therapeutics, disease modeling, pharmaceutical drug discovery, and various other applications. However, the extensive utilization of this technology has encountered impediments in the form of inefficiency, prolonged procedures, and ambiguous biological processes. Consequently, in order to improve this technology, it is of great significance to delve into the underlying mechanisms involved in iPSC reprogramming. The BET protein BRD4 plays a crucial role in the late stage of reprogramming; however, its precise function in the early stage remains unclear.ResultsOur study aims to investigate BRD4’s role in the early stages of iPSC reprogramming. Our investigation reveals that early inhibition of BRD4 substantially enhances iPSC reprogramming, whereas its implementation during the middle-late stage impedes the process. During the reprogramming, ribosome DNA expression initially increases before decreasing and then gradually recovers. Early inhibition of BRD4 improved the decline and restoration of rDNA expression in the early and middle-late stages, respectively. Additionally, we uncovered the mechanism of BRD4’s regulation of rDNA transcription throughout reprogramming. Specifically, BRD4 interacts with UBF and co-localizes to both the rDNA promoter and enhancer regions. Ultimately, BRD4 facilitates rDNA transcription by promoting the enrichment of histone H3 lysine 27 acetylation in the surrounding chromatin. Moreover, we also discovered that early inhibition of BRD4 facilitates cells’ transition out of the somatic cell state and activate pluripotent genes.ConclusionsIn conclusion, our results demonstrate that early inhibition of BRD4 promotes sequential dynamic expression of rDNA, which improves iPSC reprogramming efficiency.

The effect of the nucleolar protein ZNF385A on the ribosomal DNA copy number variation in response to Cr(VI)-induced DNA damage

Hexavalent chromium [Cr(VI)] is a widely distributed carcinogen in industrial contexts and general environmental contexts. Emerging research highlights the central role of ribosomal DNA (rDNA) in DNA Damage Responses (DDRs). However, there remains a lack of investigation into the potential dose-dependent relationship between exposure to Cr(VI) and alterations in rDNA copy number (CN), as well as the related mechanisms underlying these effects. A molecular epidemiological investigation involving 67 workers exposed to Cr(VI) and 75 unexposed controls was conducted. There was a notable increase in ZNF385A expression, variations in rDNA CN, and elevated γH2AX levels in the peripheral blood of Cr(VI)-exposed workers. Restricted cubic spline (RCS) models showed that blood Cr levels in the exposed population exhibited non-linear dose-dependent relationships with γH2AX, rDNA CN, and ZNF385A. Of considerable interest, there were robust and positive associations between ZNF385A and both γH2AX and rDNA CN. Further in vitro experiments provided concrete evidence that Cr(VI) simultaneously caused an increase in ZNF385A expression and variations in rDNA CN. ZNF385A-depleted cells showed increased sensitivity to Cr(VI)-mediated DDRs and alterations in rDNA CN. This study indicated that ZNF385A played a highly significant role in the rDNA CN variation in response to Cr(VI)-induced DNA damage.

Molecular Identification of Species Belonging to Culex vishnui Subgroup (Diptera: Culicidae), Vectors of Japanese Encephalitis Virus, in Taiwan.

Classification of mosquitoes with overlapping features remains problematic when using traditional morphological identification alone. In this study, we used molecular methods to elucidate the taxonomic status of Culex tritaeniorhynchus, Culex annulus, and Culex pseudovishnui species as vectors of the Japanese encephalitis virus belonging to the Culex vishnui subgroup and gene flow among them. In this study, 76, 59, and 3 samples of Cx. annulus, Cx. tritaeniorhynchus, and Cx. pseudovishnui, respectively, were collected around Taiwan. Phylogenetic analysis and genetic divergence were based on genomic sequence variations in ribosomal DNA and the internal transcribed spacer (rDNA) and cytochrome c oxidase subunit I (COI). Our results revealed that Cx. annulus and Cx. vishnui are genetically similar and share a gene pool among the species from Taiwan and other Asian countries. However, two hidden taxa of Cx. tritaeniorhynchus, which clustered together according to the rDNA sequences, were discovered based on the COI sequences. In addition, Cx. pseudovishnui has different gene pools from those of the strains from other countries, implying that the population from Taiwan is probably either a unique strain or a sibling species. This study provides molecular information on the taxonomic status of the species in the Cx. vishnui subgroup in Taiwan and gene flow between these species, providing valuable information for vector control operations and the delineation of the evolutionary process.

Bifidobacterium longum subsp. infantis NKU FB3-14 attenuates loperamide-induced constipation through regulation of gut microbiota

Abstract Objectives Constipation is a prevalent gastrointestinal issue, and the efficacy of probiotics in alleviating constipation has been well proved. This study aimed to investigate the impact of Bifidobacterium longum subsp. infantis NKU FB3-14 on loperamide- induced constipation by focusing on improving intestinal barrier function and modulating gut microbiota composition Materials and Methods The constipated model mice induced by loperamide were treated with NKU FB3-14, and the laxative effect was assessed based on the fecal water content, first black stool time and gastrointestinal transit rate. Gastrointestinal regulatory peptides in serum, intestinal neurotransmitter and inflammatory cytokines in colon tissues were measured using ELISA kits. Changes of gut microbiota composition were analyzed through 16S ribosomal DNA sequencing identification. Additionally, HPLC detection was performed to quantify short chain fatty acids levels in feces Results Treatment with NKU FB3-14 led to increase the fecal water content, shorten the first black stool time and improve small intestine transit rate. Motilin and substance-P significantly decreased in the model group, and only motilin increased in FB3-14 group; somatostatin and vasoactive intestinal peptide were decreased in model mice and both increased in FB3-14 group; 5-HT levels in the colon tissue were upregulated following NKU FB3-14 treatment. Histological examination revealed thinner colonic mucosa in the model group along with significant in TNF-α, IL-1β and IL-17 levels form the colon tissues which were all relieved by NKU FB 3-14 treatment. Furthermore, NKU FB3-14 intervention resulted in reduced abundance of Desulfobacterota and Desulfovibrio while increasing the abundance of Ruminococcaceae and Eubacterium; higher level of butyric acid was observed in feces Conclusions In summary, our findings demonstrated that NKU FB3-14 treatment significantly enhanced the intestinal motility, regulated the expression levels of gastrointestinal regulatory peptides, prevented damage to colonic barriers as well as ameliorated gut microbiota imbalance associated with loperamide-induced constipation.

Molecular identification of Baylisascaris melis (Gedoelst, 1920) from the Eurasian badger (Meles meles) and ascarids from other wild carnivores in Kazakhstan.

The presence of gastrointestinal nematodes, including zoonotic ascarids, in wild canids, felids and mustelids as definitive hosts in Central Asian countries has been documented in many studies based on traditional morphological methods. In contrast, relevant data for the badger are scarce. The aim of this study was the molecular identification of ascarid nematodes from five wild carnivore species in different regions of Kazakhstan. A total of 211 adult ascarids were collected from gray wolves (Canis lupus, 8 of 83 infected with 2-6 Toxascaris leonina), red foxes (Vulpes vulpes, 26 of 53, with 2-8 Toxascaris leonina), corsac foxes (Vulpes corsac, 6 of 11, 3-6 Toxascaris leonina), lynx (Lynx lynx, 2 of 3, with 2-5 Toxocara cati) and badgers (Meles meles, 2 of 4, with 2-7 Baylisascaris melis). Genomic DNA was extracted from the worms and ribosomal DNA, including the first and second internal transcribed spacer genes, was amplified by polymerase chain reaction using specific oligonucleotide primers and then sequenced. Toxascaris leonina, but not Toxocara canis, was molecularly identified in the wild canids, Toxocara cati in the lynx and Baylisascaris melis in the badger. The maximum likelihood phylogenetic tree showed three distinct clades: the canid Toxascaris leonina was placed in one clade, Toxocara cati in another and Baylisascaris melis in a third. The study provides the world's first molecular data and phylogenetic analysis of Baylisascaris melis, identified for the second time since its description over 100 years ago. This species was shown to be genetically distinct from other Baylisascaris spp. (B. columnaris, B. procyonis, B. transfuga, B. devosi). The possible zoonotic significance of ascarids from wild carnivores is discussed in the light of conditions in Central Asia.

Phylogeography and Population Variation in Prunus discoidea (Prunus subg. Cerasus) in China.

Prunus discoidea is a unique cherry blossom germplasm resource native to China. It is widely distributed across the provinces of Anhui, Zhejiang, Jiangxi, Jiangsu, and Henan, with significant variation. We employed phylogeographic analysis to reveal the evolutionary history of P. discoidea to better understand its genetic diversity and structure. This study provides more accurate molecular insights for the effective conservation and utilization of this germplasm resource. We conducted a phylogeographic analysis of 348 individual plants from 13 natural populations using three fragments (rpoB, rps16, and trnD-E) of chloroplast DNA (cpDNA) and one fragment (ITS) of ribosomal DNA. The results revealed that P. discoidea demonstrates a significant level of genetic diversity (Hd = 0.782; Rd = 0.478). Gene flow among populations was limited, and the variation within populations was the main source of genetic diversity in P. discoidea (among populations: 34.26%, within populations: 65.74%). Regarding genetic differences among populations, Nst (0.401) showed greater differences than Gst (0.308; p < 0.05), demonstrating that there was a significant geographical structure of lineage. One lineage was the central region of Anhui and the western region of Hubei. The other lineage was the Jiangsu region and the Zhejiang region. P. discoidea diverged from Prunus campanulata approximately 1.5 million years ago, during the Pleistocene epoch. This study provides a scientific theoretical basis for the conservation and utilization of germplasm resources of P. discoidea.

Hyper-recombination in ribosomal DNA is driven by long-range resection-independent RAD51 accumulation

Ribosomal DNA (rDNA) encodes the ribosomal RNA genes and represents an intrinsically unstable genomic region. However, the underlying mechanisms and implications for genome integrity remain elusive. Here, we use Bloom syndrome (BS), a rare genetic disease characterized by DNA repair defects and hyper-unstable rDNA, as a model to investigate the mechanisms leading to rDNA instability. We find that in Bloom helicase (BLM) proficient cells, the homologous recombination (HR) pathway in rDNA resembles that in nuclear chromatin; it is initiated by resection, replication protein A (RPA) loading and BRCA2-dependent RAD51 filament formation. However, BLM deficiency compromises RPA-loading and BRCA1/2 recruitment to rDNA, but not RAD51 accumulation. RAD51 accumulates at rDNA despite depletion of long-range resection nucleases and rDNA damage results in micronuclei when BLM is absent. In summary, our findings indicate that rDNA is permissive to RAD51 accumulation in the absence of BLM, leading to micronucleation and potentially global genomic instability.

Comprehensive analysis of microbiome biodiversity in popular date palm (Phoenix dactylifera L.) fruit varieties

Due to its nutritional value and health benefits, the date palm (Phoenix dactylifera L.) is an essential dietary food crop throughout Middle Eastern and African countries. Consumers are concerned about the possible microbial contamination of dates, especially since most dates arriving in local markets are unprocessed. The absence of processing increases the possibility of microbial contamination, which raises the probability of microbial contamination. This study aims to analyze and evaluate the variability of fungal and bacterial microbiota identified in the most popular date palm fruits in Saudi Arabia. The study assessed ten date variety fruits from the most popular date palm varieties for consumption in Saudi Arabia and analyzed the microbial count. Morphological and molecular characterization and comparison of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences identified 78 fungi, including 36 distinct species across 15 fungal genera. Alternaria, Fusarium, Curvilaria, Aspergillus, and Penicillium were the most frequent genera among the ten fruit cultivars studied, according to ITS-rDNA sequence analysis. Furthermore, 36 bacterial isolates were obtained from ten date varieties studied, each with a unique colony morphology. These isolates were identified based on sequence alignment and comparison of their 16S rDNA internal spacer regions to those available in public databases. The results showed that the bacterial isolates included 15 species from five bacterial genera. The results suggested that Bacillus, Stenotrophomonas, and Brucella were the prevailing genera among the ten tested fruit varieties. Some bacterial genera, such as Brucella, Achromobacter, and Stenotrophomonas, are well-known potential human pathogens. Chaetomium globosum was also recognized as air pollution causing adverse health effects such as allergies and as the causal agent of human fungal infections among the tested date varieties; the Rashodiah type exhibited the highest fungal contamination, whereas the Sagai variety displayed the lowest fungal contamination. Conversely, the Sukkari, Barhi, and Mejdool varieties were the most contaminated with bacteria among the ten tested varieties, while the Khalas variety showed the least bacterial contamination. To the best of the authors' knowledge, this study provides the initial comprehensive account of the molecular and morphological identification of all fungal and bacterial genera associated with date palm (P. dactylifera) fruits.

The rhizobacterial Priestia megaterium strain SH-19 mitigates the hazardous effects of heat stress via an endogenous secondary metabolite elucidation network and molecular regulation signalling

Global warming is a leading environmental stress that reduces plant productivity worldwide. Several beneficial microorganisms reduce stress; however, the mechanism by which plant–microbe interactions occur and reduce stress remains to be fully elucidated. The aim of the present study was to elucidate the mutualistic interaction between the plant growth-promoting rhizobacterial strain SH-19 and soybeans of the Pungsannamul variety. The results showed that SH-19 possessed several plant growth-promoting traits, such as the production of indole-3-acetic acid, siderophore, and exopolysaccharide, and had the capacity for phosphate solubilisation. The heat tolerance assay showed that SH-19 could withstand temperatures up to 45 °C. The strain SH-19 was identified as P. megaterium using the 16S ribosomal DNA gene sequence technique. Inoculation of soybeans with SH-19 improved seedling characteristics under high-temperature stress. This may be due to an increase in the endogenous salicylic acid level and a decrease in the abscisic acid level compared with the negative control group. The strain of SH-19 increased the activity of the endogenous antioxidant defense system, resulting in the upregulation of GSH (44.8%), SOD (23.1%), APX (11%), and CAT (52.6%). Furthermore, this study involved the transcription factors GmHSP, GmbZIP1, and GmNCED3. The findings showed upregulation of the two transcription factors GmbZIP1 (17%), GmNCED3 (15%) involved in ABA biosynthesis and induced stomatal regulation, similarly, a downregulation of the expression pattern of GmHSP by 25% was observed. Overall, the results of this study indicate that the strain SH-19 promotes plant growth, reduces high-temperature stress, and improves physiological parameters by regulating endogenous phytohormones, the antioxidant defense system, and genetic expression. The isolated strain (SH-19) could be commercialized as a biofertilizer.

Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae).

In order to understand the bias and main affecting factors of codon usage in the plastid genome of Diplandrorchis sinica, which is a rare and endangered plant species in the Orchidaceae family, the complete plastid genome sequence of D. sinica was downloaded from the GenBank database and 20 protein-coding sequences that met the analysis requirements were finally selected. The GC content, length of the amino acid (Laa), relative synonymous codon usage (RSCU), and effective number of codon (ENC) of each gene and codon were calculated using the CodonW and EMBOSS online programs. Neutral plot analysis, ENC-plot analysis, PR2-plot analysis, and correspondence analysis were performed using Origin Pro 2024 software, and correlation analysis between various indicators was performed using SPSS 23.0 software. The results showed that the third base of the codon in the plastid genome of D. sinica was rich in A and T, with a GC3 content of 27%, which was lower than that of GC1 (45%) and GC2 (39%). The ENC value ranged from 35 to 57, with an average of 47. The codon usage bias was relatively low, and there was a significant positive correlation between ENC and GC3. There were a total of 32 codons with RSCU values greater than 1, of which 30 ended with either A or U. There were a total of nine optimal codons identified, namely, UCU, UCC, UCA, GCA, UUG, AUA, CGU, CGA, and GGU. This study indicated that the dominant factor affecting codon usage bias in the plastid genome of D. sinica was natural selection pressure, while the impact of base mutations was limited. The codon usage patterns were not closely related to gene types, and the distribution of photosynthetic system genes and ribosomal protein-coding gene loci was relatively scattered, indicating significant differences in the usage patterns of these gene codons. In addition, the codon usage patterns may not be related to whether the plant is a photosynthetic autotrophic or heterotrophic nutritional type. The results of this study could provide scientific references for the genomic evolution and phylogenetic research of plant species in the family Orchidaceae.

Identification of ribosome biogenesis genes and subgroups in ischaemic stroke.

Ischaemic stroke is a leading cause of death and severe disability worldwide. Given the importance of protein synthesis in the inflammatory response and neuronal repair and regeneration after stroke, and that proteins are acquired by ribosomal translation of mRNA, it has been theorised that ribosome biogenesis may have an impact on promoting and facilitating recovery after stroke. However, the relationship between stroke and ribosome biogenesis has not been investigated. In the present study, a ribosome biogenesis gene signature (RSG) was developed using Cox and least absolute shrinkage and selection operator (LASSO) analysis. We classified ischaemic stroke patients into high-risk and low-risk groups using the obtained relevant genes, and further elucidated the immune infiltration of the disease using ssGSEA, which clarified the close relationship between ischaemic stroke and immune subgroups. The concentration of related proteins in the serum of stroke patients was determined by ELISA, and the patients were divided into groups to evaluate the effect of the ribosome biogenesis gene on patients. Through bioinformatics analysis, we identified potential IS-RSGs and explored future therapeutic targets, thereby facilitating the development of more effective therapeutic strategies and novel drugs against potential therapeutic targets in ischaemic stroke. We obtained a set of 12 ribosome biogenesis-related genes (EXOSC5, MRPS11, MRPS7, RNASEL, RPF1, RPS28, C1QBP, GAR1, GRWD1, PELP1, UTP, ERI3), which play a key role in assessing the prognostic risk of ischaemic stroke. Importantly, risk grouping using ribosome biogenesis-related genes was also closely associated with important signaling pathways in stroke. ELISA detected the expression of C1QBP, RPS28 and RNASEL proteins in stroke patients, and the proportion of neutrophils was significantly increased in the high-risk group. The present study demonstrates the involvement of ribosomal biogenesis genes in the pathogenesis of ischaemic stroke, providing novel insights into the underlying pathogenic mechanisms and potential therapeutic strategies for ischaemic stroke.

Phlebotomine sand fly (Diptera: Psychodidae) fauna, blood meal source, and detection of Leishmania (Kinetoplastida: Trypanosomatidae) DNA in the Gurupi Biological Reserve, Eastern Amazon, Brazil.

This study was conducted in the Gurupi Biological Reserve (REBIO-Gurupi), the largest area of Amazon rainforest in Maranhão State, Brazil. The objectives were to survey the sand fly (Diptera: Psychodidae) fauna of REBIO-Gurupi, identify blood meal sources, and investigate the presence of Leishmania (Ross, 1903) (Kinetoplastida: Trypanosomatidae) DNA. Individuals were collected using Centers for Disease Control (CDC) light traps and black and white Shannon traps in May and Jun 2022 and Jan 2023. DNA was extracted from female sand flies and subjected to amplification and sequencing of cytochrome b molecular marker (CYTB) for identification of blood meal sources and the first internal transcribed spacer (ITS-1) of ribosomal DNA for Leishmania detection. A total of 514 sand flies individuals were sampled, of which 93 were identified at the genus or series level (9 taxa) and 421 were identified at the species level (24 taxa). Psychodopygus davisi (Root, 1934) (41.1%), Nyssomyia antunesi (Coutinho, 1939) (10.3%), and Psychodopygus (Mangabeira, 1941) Chagasi Series Barretto, 1962 (9.7%) were the most frequently collected. Human (Homo sapiens, Primates, Hominidae) and tapir (Tapirus terrestris, Perissodactyla, Tapiridae) DNA was detected in 10 female sand flies. Leishmania (Leishmania) infantum Cunha and Chagas, 1937 DNA was detected in 2 specimens of Ps. davisi. Given the presence of vectors of Leishmania in REBIO-Gurupi, it is imperative to conduct more comprehensive studies on the interactions among sand flies, Leishmania, and pathogen reservoirs in the area.

Biodiversity study of the genus Bysmatrum from the South China Sea and France reveals a new benthic dinoflagellate, Bysmatrum ingrilense sp. nov. (Peridiniales, Dinophyceae)

ABSTRACT The dinoflagellate genus Bysmatrum is an unusual member of the Peridiniales and cannot be attributed to any known family. Bysmatrum differs from typical peridinialean genera in that the second and third anterior intercalary plates are separated and both antapical plates are asymmetrical. Currently, Bysmatrum encompasses six epibenthic or tide-pool species, but information on their genetic diversity and biogeography remains limited. In the present study, we obtained five strains of Bysmatrum from the South China Sea by isolating single cells and three strains from Ingril, a French Mediterranean lagoon by incubating sediments. Strains from Ingril Lagoon displayed the plate formula Po, cp, X, 4′, 3a, 7′′, 6C, 4S, 5′′′, 2′′′′. They also exhibited an elongated nucleus in the hypocone and a type B eyespot. Smooth and spherical cysts were produced in culture. Small and/or partially large subunit ribosomal DNA sequences were obtained for all eight strains. Molecular phylogeny was inferred using these concatenated sequences through maximum likelihood and Bayesian inference methods. Bysmatrum granulosum and B. subsalsum were identified from Thailand and China for the first time, each of them comprising of two ribotypes. Bysmatrum ingrilense sp. nov. was monophyletic and closest to B. subsalsum ribotype B. Pinnatoxin and related toxins were examined in two strains of Bysmatrum ingrilense by LC-MS/MS, but none were detected. Our results highlight that the diversity of Bysmatrum might be underestimated.

Increased risk of Pneumocystis jirovecii colonization in rheumatoid arthritis patients on biologics and Janus kinase inhibitor

BackgroundThe prevalence of Pneumocystis jirovecii (PJ) pneumonia among rheumatic patients is rising. PJ colonization serves as a reservoir for transmission and precedes the development of PJ pneumonia. We aim to clarify the association of PJ colonization in patients of rheumatoid arthritis (RA) treated with biologics or Janus kinase inhibitors (JAKi). MethodsA prospective cohort study was performed from March 2021 to July 2022 in the rheumatology outpatient department of National Cheng Kung University Hospital. We obtained oral-wash samples from asymptomatic RA patients treated with biologic disease-modifying antirheumatic drugs (bDMARDs) and JAKi. A real-time quantitative polymerase chain reaction assay focusing on the mitochondrial large subunit ribosomal ribonucleic acid gene of PJ was applied to detect colonization. ResultsOne hundred and ten RA patients were enrolled. Adjusted odds ratios (ORs) of PJ colonization were 6.40 (95% CI 1.34-30.57, p-value =0.02) in patients receiving bDMARDs or JAKi. Specifically, in patients treated with bDMARDs the adjusted OR was 8.08 (95% CI 1.57-41.51, p-value=0.012), and a trend toward developing PJ colonization was further identified in patients receiving JAKi (adjusted OR: 4.79, 95% CI 0.89-25.91, p=0.069). Among patients treated with bDMARDs or JAKi, medication duration >3 years and age >60 y/o are risk factors for PJ colonization. ConclusionRA patients on bDMARDs or JAK inhibitors have an approximately 6-fold higher risk of developing P. jirovecii colonization. Patients treated with bDMARDs had an 8-fold higher risk of P. jirovecii colonization. Risk factors of PJ colonization are medication duration >3 years and age > 60 y/o.

Faecal source apportionment using molecular methods: A proof of concept using the FEAST algorithm

Faecal contamination of freshwater and marine environments represents a significant risk for public health, recreational activity and food safety, and tools for evaluating complex multi-source contamination remain largely in the development phase. We evaluated the efficacy of the Fast Expectation Maximization (FEAST) microbial source tracking (MST) algorithm to apportion sources of faecal contamination among four mammalian species of interest in coastal waters in New Zealand. Using 16S ribosomal DNA metabarcoding of faecal samples from cows, fur seals, and sheep, as well as human wastewater, we aimed to differentiate and quantify the contribution of these sources in mixed faecal samples. Multivariate analysis confirmed significant differences in the microbial communities associated with each mammalian source, with specific bacterial classes indicative of different sources. The FEAST algorithm was tested using mixed DNA and mixed faecal samples, and we found that the algorithm correctly assigned the dominant source from all samples, but underestimated the dominant source's proportional contribution. This underestimation suggests the need for further refinement and validation to ensure accurate source apportionment in environmental samples where the faecal signal is likely to be a minor component. Despite these limitations, the findings of our study, in combination with the evidence from others who have tested the FEAST algorithm in environmental settings, indicates that it represents an advance on existing tools for microbial source tracking and may become a useful addition to the toolbox for environmental management.