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Search Results (1,063)

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Keywords = 18S Ribosomal RNA

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16 pages, 3202 KiB  
Article
Gut Microbiota Composition in Rats Consuming Sucralose or Rebaudioside A at Recommended Doses Under Two Dietary Interventions
by Meztli Ramos-García, Alma Delia Genis-Mendoza, Carlos García-Vázquez, José Jaime Martínez-Magaña, Viridiana Olvera-Hernández, Mirian Carolina Martínez-López, Juan Cuauhtémoc Díaz-Zagoya, Carina Shianya Alvarez-Villagomez, Isela Esther Juárez-Rojop, Humberto Nicolini and Jorge Luis Ble-Castillo
Metabolites 2025, 15(8), 529; https://doi.org/10.3390/metabo15080529 - 4 Aug 2025
Abstract
Background: Artificial non-nutritive sweeteners (NNSs), such as sucralose, have been associated with gut microbiota (GM) alterations. However, the impact of rebaudioside A (reb A), a natural NNS, on GM has received limited scrutiny. Objective: The objective of this study was to examine [...] Read more.
Background: Artificial non-nutritive sweeteners (NNSs), such as sucralose, have been associated with gut microbiota (GM) alterations. However, the impact of rebaudioside A (reb A), a natural NNS, on GM has received limited scrutiny. Objective: The objective of this study was to examine the response of GM composition to sucralose and reb A in rats under two dietary conditions. Methods: Male Wistar rats (150–200 g) fed with a normal diet (ND) or a high-fat diet (HFD) were randomly assigned to receive sucralose (SCL), reb A (REB), glucose (GLU, control), or sucrose (SUC). The NNS interventions were administered in water at doses equivalent to the acceptable daily intake (ADI). After eight weeks, the GM composition in fecal samples was analyzed through 16S ribosomal RNA gene sequencing. Results: The NNSs did not modify the diversity, structure, phylum-level composition, or Firmicutes/Bacteroidetes (F/B) ratio of the GM in rats under ND or HFD. However, REB with HFD decreased Bacilli and increased Faecalibacterium abundance at the class level. SCL and REB in rats receiving ND reduced the genera Romboutsia and Lactobacillus. Conclusions: Our study suggests that when sucralose or reb A is consumed at recommended doses, there is no alteration in the diversity or the composition of the GM at the phylum level. The clinical relevance of these findings lies in the potential modifications of the GM at specific taxonomic levels by the consumption of these NNSs. Further research involving humans and including a broader range of microbial analyses is warranted. Full article
(This article belongs to the Section Nutrition and Metabolism)
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15 pages, 1691 KiB  
Article
tRNA Modifications: A Tale of Two Viruses—SARS-CoV-2 and ZIKV
by Patrick Eldin and Laurence Briant
Int. J. Mol. Sci. 2025, 26(15), 7479; https://doi.org/10.3390/ijms26157479 (registering DOI) - 2 Aug 2025
Viewed by 160
Abstract
tRNA modifications are crucial for efficient protein synthesis, impacting codon recognition, tRNA stability, and translation rates. RNA viruses hijack the host’s translational machinery, including the pool of modified tRNA, to translate their own genomes. However, the mismatch between viral and host codon usage [...] Read more.
tRNA modifications are crucial for efficient protein synthesis, impacting codon recognition, tRNA stability, and translation rates. RNA viruses hijack the host’s translational machinery, including the pool of modified tRNA, to translate their own genomes. However, the mismatch between viral and host codon usage can lead to a limited availability of specific tRNA leading to ribosome stalling, posing a significant challenge for efficient protein translation. While some viruses address this challenge through codon optimization, we show here that SARS-CoV-2 (Coronavirus) and the Zika virus (ZIKV; Flavivirus) adopt a different approach, manipulating the host tRNA epitranscriptome. Analysis of codon bias indices confirmed a substantial divergence between viral and host codon usage, revealing a strong preference in viral genes for codons decoded by tRNAs requiring U34 wobble modification. Monitoring tRNA modification dynamics in infected cells showed that both SARS-CoV2 and ZIKV enhance U34 tRNA modifications during infection. Strikingly, impairing U34 tRNAs profoundly impacted viral replication, underscoring the strict reliance of SARS-CoV-2 and ZIKV on manipulating the host tRNA epitranscriptome to support the efficient translation of their genome. Full article
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12 pages, 1678 KiB  
Article
Molecular Surveillance of Plasmodium spp. Infection in Neotropical Primates from Bahia and Minas Gerais, Brazil
by Luana Karla N. S. S. Santos, Sandy M. Aquino-Teixeira, Sofía Bernal-Valle, Beatriz S. Daltro, Marina Noetzold, Aloma Roberta C. Silva, Denise Anete M. Alvarenga, Luisa B. Silva, Ramon S. Oliveira, Cirilo H. Oliveira, Iago A. Celestino, Maria E. Gonçalves-dos-Santos, Thaynara J. Teixeira, Anaiá P. Sevá, Fabrício S. Campos, Bergmann M. Ribeiro, Paulo M. Roehe, Danilo Simonini-Teixeira, Filipe V. S. Abreu, Cristiana F. A. Brito and George R. Albuquerqueadd Show full author list remove Hide full author list
Pathogens 2025, 14(8), 757; https://doi.org/10.3390/pathogens14080757 (registering DOI) - 31 Jul 2025
Viewed by 267
Abstract
In Brazil, Plasmodium infections in non-human primates (NHPs) have been associated with P. simium and P. brasilianum, which are morphologically and genetically similar to the human-infecting species P. vivax and P. malariae, respectively. Surveillance and monitoring of wild NHPs are crucial [...] Read more.
In Brazil, Plasmodium infections in non-human primates (NHPs) have been associated with P. simium and P. brasilianum, which are morphologically and genetically similar to the human-infecting species P. vivax and P. malariae, respectively. Surveillance and monitoring of wild NHPs are crucial for understanding the distribution of these parasites and assessing the risk of zoonotic transmission. This study aimed to detect the presence of Plasmodium spp. genetic material in Platyrrhini primates from 47 municipalities in the states of Bahia and Minas Gerais. The animals were captured using Tomahawk-type live traps baited with fruit or immobilized with tranquilizer darts. Free-ranging individuals were chemically restrained via inhalation anesthesia using VetBag® or intramuscular anesthesia injection. Blood samples were collected from the femoral vein. A total of 298 blood and tissue samples were collected from 10 primate species across five genera: Alouatta caraya (25), Alouatta guariba clamitans (1), Callicebus melanochir (1), Callithrix geoffroyi (28), Callithrix jacchus (4), Callithrix kuhlii (31), Callithrix penicillata (175), Callithrix spp. hybrids (15), Leontopithecus chrysomelas (16), Sapajus robustus (1), and Sapajus xanthosthernos (1). Molecular diagnosis was performed using a nested PCR targeting the 18S small subunit ribosomal RNA (18S SSU rRNA) gene, followed by sequencing. Of the 298 samples analyzed, only one (0.3%) from Bahia tested positive for Plasmodium brasilianum/P. malariae. This represents the first detection of this parasite in a free-living C. geoffroyi in Brazil. These findings highlight the importance of continued surveillance of Plasmodium infections in NHPs to identify regions at risk for zoonotic transmission. Full article
(This article belongs to the Section Parasitic Pathogens)
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37 pages, 2865 KiB  
Review
Ribosome Biogenesis and Function in Cancer: From Mechanisms to Therapy
by Kezia Gitareja, Shalini S. Chelliah, Elaine Sanij, Shahneen Sandhu, Jian Kang and Amit Khot
Cancers 2025, 17(15), 2534; https://doi.org/10.3390/cancers17152534 - 31 Jul 2025
Viewed by 360
Abstract
Ribosome biogenesis is a highly coordinated, multi-step process that assembles the ribosomal machinery responsible for translating mRNAs into proteins. It begins with the rate-limiting step of RNA polymerase I (Pol I) transcription of the 47S ribosomal RNA (rRNA) genes within a specialised nucleolar [...] Read more.
Ribosome biogenesis is a highly coordinated, multi-step process that assembles the ribosomal machinery responsible for translating mRNAs into proteins. It begins with the rate-limiting step of RNA polymerase I (Pol I) transcription of the 47S ribosomal RNA (rRNA) genes within a specialised nucleolar region in the nucleus, followed by rRNA processing, modification, and assembly with ribosomal proteins and the 5S rRNA produced by Pol III. The ribosomal subunits are then exported to the cytoplasm to form functional ribosomes. This process is tightly regulated by the PI3K/RAS/MYC oncogenic network, which is frequently deregulated in many cancers. As a result, ribosome synthesis, mRNA translation, and protein synthesis rates are increased. Growing evidence supports the notion that dysregulation of ribosome biogenesis and mRNA translation plays a pivotal role in the pathogenesis of cancer, positioning the ribosome as a promising therapeutic target. In this review, we summarise current understanding of dysregulated ribosome biogenesis and function in cancer, evaluate the clinical development of ribosome targeting therapies, and explore emerging targets for therapeutic intervention in this rapidly evolving field. Full article
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20 pages, 2905 KiB  
Article
Redefining Latrogastropoda Again and Searching for Its Sister Group in Hypsogastropoda (Gastropoda: Caenogastropoda)
by Donald J. Colgan and Winston F. Ponder
Diversity 2025, 17(8), 524; https://doi.org/10.3390/d17080524 - 28 Jul 2025
Viewed by 123
Abstract
Caenogastropoda is a highly speciose and ecologically diverse subclass of Gastropoda but its higher order classification remains unclear, especially within its largest constituent group, Hypsogastropoda. Two nominal taxa encompassing most of the great diversity of Hypsogastropoda are in current widespread use: one is [...] Read more.
Caenogastropoda is a highly speciose and ecologically diverse subclass of Gastropoda but its higher order classification remains unclear, especially within its largest constituent group, Hypsogastropoda. Two nominal taxa encompassing most of the great diversity of Hypsogastropoda are in current widespread use: one is Latrogastropoda, which has been repeatedly redefined resulting in changes to the second, Littorinimorpha, which is generally not supposed to be monophyletic. We examined the utility of these divisions by assembling single-gene data sets of nuclear 28S ribosomal RNA (28S rRNA) and mitochondrial 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase subunit I from many genera. Capuloidea was consistently found with strong support within Latrogastropoda, so this taxon is redefined here to include that superfamily. The analyses also suggested the redefinition of some superfamilies within Littorinimorpha, particularly for the clade comprising Truncatelloidea, Vanikoroidea and Rissooidea, and the Littorinoidea. Littorinimorpha was monophyletic (albeit lacking strong support) in the combined analysis of 28S rRNA and 16S rRNA and was resolved as the sister group of Latrogastropoda which was also monophyletic, with bootstrap support of 66%. Littorinimorpha was not monophyletic in other analyses. In these, the sister group of Latrogastropoda comprised clades of multiple littorinimorph superfamilies but these relationships were also not strongly supported. Full article
(This article belongs to the Section Marine Diversity)
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15 pages, 2118 KiB  
Article
Ribosomal Hibernation Factor Links Quorum-Sensing to Acid Resistance in EHEC
by Yang Yang, Xinyi Zhang, Zixin Han, Junpeng Li, Qiaoqiao Fang and Guoqiang Zhu
Microorganisms 2025, 13(8), 1730; https://doi.org/10.3390/microorganisms13081730 - 24 Jul 2025
Viewed by 248
Abstract
The mechanism by which quorum sensing (QS) enhances stress resistance in enterohemorrhagic Escherichia coli (E. coli) O157:H7 remains unclear. We employed optimized exogenous QS signal N-acyl-homoserinelactones (AHL) (100 μM 3-oxo-C6-AHL, 2 h) in EHEC O157:H7 strain EDL933, which was validated with [...] Read more.
The mechanism by which quorum sensing (QS) enhances stress resistance in enterohemorrhagic Escherichia coli (E. coli) O157:H7 remains unclear. We employed optimized exogenous QS signal N-acyl-homoserinelactones (AHL) (100 μM 3-oxo-C6-AHL, 2 h) in EHEC O157:H7 strain EDL933, which was validated with endogenous yenI-derived AHL, to investigate QS-mediated protection against acid stress. RNA-seq transcriptomics identified key upregulated genes (e.g., rmf). Functional validation using isogenic rmf knockout mutants generated via λ-Red demonstrated abolished stress resistance and pan-stress vulnerability. Mechanistic studies employing qRT-PCR and stress survival assays established Ribosomal Hibernation Factor (RMF) as a non-redundant executor in a SdiA–RMF–RpoS axis, which activates ribosomal dormancy and SOS response to enhance EHEC survival under diverse stresses. For the first time, we define ribosomal hibernation as the core adaptive strategy linking QS to pathogen resilience, providing crucial mechanistic insights for developing EHEC control measures against foodborne threats. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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19 pages, 6698 KiB  
Article
Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences
by Moldir Yermagambetova, Akzhunis Imanbayeva, Margarita Ishmuratova, Aidar Sumbembayev and Shyryn Almerekova
Genes 2025, 16(8), 852; https://doi.org/10.3390/genes16080852 - 22 Jul 2025
Viewed by 312
Abstract
Background: Rosa L. is an economically significant genus with species that are notable for their rich content of phenolic compounds. Despite its importance, the taxonomy of Rosa remains complex and unresolved. Methods: We sequenced, assembled, and performed comparative analyses of the complete plastomes [...] Read more.
Background: Rosa L. is an economically significant genus with species that are notable for their rich content of phenolic compounds. Despite its importance, the taxonomy of Rosa remains complex and unresolved. Methods: We sequenced, assembled, and performed comparative analyses of the complete plastomes of four Rosa species: R. acicularis, R. iliensis, R. laxa, and R. spinosissima. In addition to the plastome, we sequenced the nuclear ribosomal internal transcribed spacer (ITS). Results: Plastomes ranged in size from 157,148 bp (R. iliensis) to 157,346 bp (R. laxa). In each plastome, 136 genes were annotated, comprising 90 protein-coding, 38 tRNA, and eight rRNA genes. A total of 905 SSRs were identified, ranging from 224 (R. acicularis) to 229 in R. spinosissima. Nine highly variable regions were detected, including two coding genes (rps16 and ycf1) and seven intergenic spacers (ycf3-trnS(GGA), trnT(UGU)-trnL(UAA), rpl14-rpl16, trnR(UCU)-atpA, trnD(GUC), trnG(UCC)-trnfM(CAU), and psbE-petL). Maximum Likelihood (ML) phylogenetic analyses based on the complete plastome and ycf1 gene datasets consistently resolved the Rosa species into three major clades, with strong bootstrap support. In contrast, the ML tree based on ITS resolved species into four clades but showed lower bootstrap values, indicating reduced resolution compared to plastid datasets. Conclusions: Our findings underscore the value of plastome data in resolving phylogenetic relationships within the genus Rosa. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 1047 KiB  
Article
Protein Functional Effector (pfe) Noncoding RNAS Are Identical to Fragments from Various Noncoding RNAs
by Roberto Patarca and William A. Haseltine
Int. J. Mol. Sci. 2025, 26(14), 6870; https://doi.org/10.3390/ijms26146870 - 17 Jul 2025
Viewed by 269
Abstract
Protein functional effector (pfe)RNAs were introduced in 2015 as PIWI-interacting-like small noncoding (nc)RNAs and were later categorized as a novel group based on being 2′-O-methylated at their 3′-end, directly binding and affecting protein function, but not levels, and not matching known RNAs. Here, [...] Read more.
Protein functional effector (pfe)RNAs were introduced in 2015 as PIWI-interacting-like small noncoding (nc)RNAs and were later categorized as a novel group based on being 2′-O-methylated at their 3′-end, directly binding and affecting protein function, but not levels, and not matching known RNAs. Here, we document that human pfeRNAs match fragments of GenBank database-annotated human ncRNAs. PDLpfeRNAa matches the 3′-half fragment of a mitochondrial transfer (t)RNA, and PDLpfeRNAb matches a 28S ribosomal (r)RNA fragment. These PDLpfeRNAs are known to bind to tumor programmed death ligand (PD-L)1, enhancing or inhibiting its interaction with lymphocyte PD-1 and consequently tumor immune escape, respectively. In a validated 8-pfeRNA-set classifier for pulmonary nodule presence and benign vs. malignant nature, seven here match one or more of the following: transfer, micro, Y, PIWI, long (lnc)RNAs, and a PDLpfeRNAa fragment. The previously identified chromosomal locations of these pfeRNAs and their matches partially overlap. Another 2-pfeRNA set was previously determined to distinguish between controls, patients with pulmonary tuberculosis, and those with lung cancer. One pfeRNA, previously shown to bind p60-DMAD and affect apoptosis, complements small nucleolar RNA SNORD45C, matching smaller 18S rRNA and lncRNA segments. Thus, pfeRNAs appear to have a common origin with known multifunctional ncRNA fragments. Differential modification may contribute to the multifunctionality of ncRNAs. For instance, for tRNA fragments, stabilizing 3′-end 2′-O-methylation, 3′-aminoacylation, and glycosylation modifications may regulate protein function, translation, and extracellular effects, respectively. One ncRNA gene can encode multiple fragments, multiple genes can encode the same fragment, and differentially modified ncRNA fragments might synergize or antagonize each other. Full article
(This article belongs to the Special Issue Targeting RNA Molecules)
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13 pages, 2110 KiB  
Article
Comparison of Rhizosphere Microbial Diversity in Soybean and Red Kidney Bean Under Continuous Monoculture and Intercropping Systems
by Huibin Qin, Aohui Li, Shuyu Zhong, Yingying Zhang, Chuhui Li, Zhixin Mu, Haiping Zhang and Jing Wu
Agronomy 2025, 15(7), 1705; https://doi.org/10.3390/agronomy15071705 - 15 Jul 2025
Viewed by 344
Abstract
The long-term monocropping of red kidney beans in agricultural fields can lead to the occurrence of soil-borne diseases. Alterations in the composition of the soil microbial community are a primary cause of soil-borne diseases and a key factor in continuous cropping obstacles. Research [...] Read more.
The long-term monocropping of red kidney beans in agricultural fields can lead to the occurrence of soil-borne diseases. Alterations in the composition of the soil microbial community are a primary cause of soil-borne diseases and a key factor in continuous cropping obstacles. Research exploring how different cultivation modes can modify the diversity and composition of the rhizosphere microbial community in red kidney beans, and thus mitigate the effects of continuous cropping obstacles, is ongoing. This study employed three cultivation modes: the continuous monocropping of red kidney beans, continuous monocropping of soybeans, and red kidney bean–soybean intercropping. To elucidate the composition and diversity of rhizosphere microbial communities, we conducted amplicon sequencing targeting the V3-V4 hypervariable regions of the bacterial 16S rRNA gene and the ITS1 region of fungal ribosomal DNA across distinct growth stages. The obtained sequencing data provide a robust basis for estimating soil microbial diversity. We observed that, under the intercropping mode, the composition of both bacteria and fungi more closely resembled that of soybean monocropping. The monocropping of red kidney beans increased the richness of rhizosphere bacteria and fungi and promoted the accumulation of pathogenic microorganisms. In contrast, intercropping cultivation and soybean monocropping favored the accumulation of beneficial bacteria such as Bacillus and Streptomyce, reduced pathogenic fungi including Alternaria and Mortierell, and exhibited less microbial variation across different growth stages. Compared to the monocropping of red kidney beans, these systems demonstrated more stable microbial structure and composition. The findings of this study will inform sustainable agricultural practices and soil management strategies. Full article
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21 pages, 1469 KiB  
Article
Comparative Mitogenomic Analysis of Three Chionea Species (Tipulomorpha: Limoniidae): Insights into Phylogenetic Relationships and Selection Pressure
by Yufeng Feng, Wei Cen, Kenneth B. Storey, Lingjuan Liu, Danna Yu and Jiayong Zhang
Insects 2025, 16(7), 720; https://doi.org/10.3390/insects16070720 - 14 Jul 2025
Viewed by 377
Abstract
Chionea is classified within the Tipuloidea superfamily and predominantly inhabits cold regions. However, its phylogenetic relationships remain contentious. In this study, the first three mitogenomes of Chionea (Diptera: Limoniidae) sampled in northeastern China (Jilin region) were sequenced, and their phylogenetic relationships were reconstructed [...] Read more.
Chionea is classified within the Tipuloidea superfamily and predominantly inhabits cold regions. However, its phylogenetic relationships remain contentious. In this study, the first three mitogenomes of Chionea (Diptera: Limoniidae) sampled in northeastern China (Jilin region) were sequenced, and their phylogenetic relationships were reconstructed by integrating these sequences with 30 additional Tipuloidea mitogenomes retrieved from NCBI. Unlike other Tipuloidea species, which are predominantly distributed in relatively warmer regions, this research investigates whether positive selection has acted on the mitogenomes of these three Chionea species due to environmental pressures, thereby elucidating key evolutionary drivers for Chionea. The three mitogenomes of Chionea exhibit characteristic features typical of insect mitogenomes, comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA genes (tRNA), and a single non-coding control region (D-loop). Notably, the secondary structure of trnS1 lacks the DHU arm in all three samples, and UUA (Leu) emerges as the most frequently utilized codon. Furthermore, the COX2 and ND5 genes utilize incomplete stop codons “T”. Utilizing these 13 PCGs, we reconstructed the internal phylogenetic relationships within Tipuloidea, revealing that Chionea tianhuashana and C. sphaerae form sister branches, while (C. tianhuashana + C. sphaerae) constitutes a sister branch to C. crassipes. Moreover, our analysis confirms the monophyly of Tipulidae, Tipula, and Nephrotoma as well as the polyphyly of Tipulinae, Chioneinae, and Limoniidae. In the branch site model analysis, three positively selected sites were detected when Chionea was designated as the foreground branches: COX3 (at position 242), ND5 (at position 535), and ND6 (at position 138). Full article
(This article belongs to the Section Insect Systematics, Phylogeny and Evolution)
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17 pages, 6355 KiB  
Article
Regulation of Hindbrain Vascular Development by rps20 in Zebrafish
by Xinyu Shen, Zhaozhi Wen, Shunze Deng, Yuxuan Qiu, Weijie Ma, Xinyue Dong, Jie Gong, Yu Zhang, Dong Liu and Bing Xu
Cells 2025, 14(14), 1070; https://doi.org/10.3390/cells14141070 - 13 Jul 2025
Viewed by 497
Abstract
During aging, the brain vasculature undergoes significant deterioration characterized by increased arterial tortuosity, compromised blood–brain barrier integrity, and reduced cerebral blood flow, all of which contribute to various neurological disorders. Thus, understanding the mechanisms underlying aging-related cerebrovascular defects is critical for developing strategies [...] Read more.
During aging, the brain vasculature undergoes significant deterioration characterized by increased arterial tortuosity, compromised blood–brain barrier integrity, and reduced cerebral blood flow, all of which contribute to various neurological disorders. Thus, understanding the mechanisms underlying aging-related cerebrovascular defects is critical for developing strategies to alleviate aging-associated neurological diseases. In this study, we investigated the role of aging-related genes in brain vascular development using zebrafish as an in vivo model. By thoroughly analyzing scRNA-seq datasets of mid- and old-aged brain vascular endothelial cells (human/mouse), we found ribosomal protein S20 (rps20) significantly down-regulated during aging. qPCR analysis and whole-mount in situ hybridization validated a high expression of rps20 during early zebrafish development, which progressively decreased in adult and aged zebrafish brains. Functional studies using the CRISPR/Cas9-mediated knockout of rps20 revealed an impaired growth of central arteries in the hindbrain and a marked increased intracranial hemorrhage incidence. Mechanistically, qPCR analysis demonstrated a significant downregulation of vegfa, cxcl12b, and cxcr4a, key signaling molecules required for hindbrain vascular development, in rps20-deficient embryos. In conclusion, our findings demonstrate that rps20 is essential for proper brain vascular development and the maintenance of vascular homeostasis in zebrafish, revealing a novel mechanism by which aging-related genes regulate brain vascular development. This study provides new insights that may aid in understanding and treating aging-associated vascular malformations and neurological pathologies. Full article
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16 pages, 2950 KiB  
Article
Characterization of the Mitochondrial Genome of the Vietnamese Central Highland Wild Boar (Sus scrofa)
by Minh Thi Tran, Anh Le Hong Vo, Chi Nguyen Quynh Ho, Manh Quang Vu, Quan Minh To, Mai Thi Phuong Nguyen, Loan Thi Tung Dang, Nhan Lu Chinh Phan, Chung Chinh Doan, Huy Nghia Quang Hoang, Cuong Phan Minh Le, Son Nghia Hoang, Han Thai Minh Nguyen and Long Thanh Le
Animals 2025, 15(14), 2029; https://doi.org/10.3390/ani15142029 - 10 Jul 2025
Viewed by 347
Abstract
Hybridization between domestic pigs and wild boars of unknown origins has disrupted the precious gene pool of Vietnamese wild boar (Sus scrofa) populations in the Central Highlands. However, the genetic background of Vietnamese wild boars remains largely unknown. This study describes [...] Read more.
Hybridization between domestic pigs and wild boars of unknown origins has disrupted the precious gene pool of Vietnamese wild boar (Sus scrofa) populations in the Central Highlands. However, the genetic background of Vietnamese wild boars remains largely unknown. This study describes the complete mitochondrial genome of the Vietnamese Central Highland wild boar, a circular molecule comprising 16,581 base pairs (bp). The mitogenome contains 37 genes, which encode for 2 ribosomal RNAs, 22 transfer RNAs, and 13 mitochondrial proteins. It has a conserved gene order, gene orientation, and similar nucleotide composition indexes to other boars and pig breeds across the world. Notably, 232 nucleotide substitutions were detected when comparing this genome with 19 previously described Sus scrofa genomes. Partial cytochrome b gene analysis revealed the distribution of Asian haplotypes in the Vietnamese Central Highland Sus scrofa. A phylogenetic tree constructed from 32 Sus scrofa’s whole mitogenome sequences demonstrated the close relationship between Vietnamese wild boars and domestic pig breeds. The study provides additional insights into the genetics of Vietnamese wild boars, paving the way for future research in conservation, evolution, and breeding of Vietnamese wild boar populations. Full article
(This article belongs to the Special Issue Wildlife Genetic Diversity)
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13 pages, 590 KiB  
Review
Potential Shifts in the Oral Microbiome Induced by Bariatric Surgery—A Scoping Review
by Zuzanna Ślebioda, Hélène Rangé, Marta Strózik-Wieczorek and Marzena Liliana Wyganowska
Antibiotics 2025, 14(7), 695; https://doi.org/10.3390/antibiotics14070695 - 10 Jul 2025
Viewed by 403
Abstract
Background: The oral microbiome differs in obese patients compared to normal-weight subjects. Microbiologic shifts very often appear after surgical interventions such as bariatric surgery (BS) and in immunocompromised patients. However, the oral microbiome composition and load in subjects after bariatric surgery are [...] Read more.
Background: The oral microbiome differs in obese patients compared to normal-weight subjects. Microbiologic shifts very often appear after surgical interventions such as bariatric surgery (BS) and in immunocompromised patients. However, the oral microbiome composition and load in subjects after bariatric surgery are unclear. Aim: The aim of this review is to summarize the current state of the art related to the oral microbiome shift induced by bariatric surgery and to discuss its implications on oral cavity health. Methods: Electronic databases: PubMed/Medline, Web of Science, and Cochrane Library were searched for articles published up to March 30, 2025, describing prospective studies focused on changes in the oral microbiota of patients who underwent bariatric surgery. Results: Eight studies measuring the oral microbiome with different approaches—16S ribosomal RNA (16S rRNA) sequencing, polymerase chain reaction (PCR), culture, and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI TOF MS)—were included in this review. The following bariatric techniques were used: sleeve gastrectomy, Roux-en-Y gastric bypass, Omega loop gastric bypass, and laparoscopic gastric plication. The follow-up period ranged from 3 to 12 months. The results of microbiologic studies were unequivocal. There was an increment in Streptococcus mutans reported, high levels of Candida species, and increased rates of some periodontitis-associated bacteria (Porphyromonas gingivalis) in the post-bariatric surgery period, though some studies suggested a shift towards non-pathogenic composition of the oral microbiome in prospective observations. Conclusions: The local oral microbial homeostasis becomes strongly impacted by the bariatric surgical treatment itself as well as its consequences in the further post-operative period. Therefore, obese patients undergoing BS require very careful dental observation. Full article
(This article belongs to the Special Issue Periodontal Bacteria and Periodontitis: Infections and Therapy)
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12 pages, 4263 KiB  
Article
Characterization of a Novel Lentzea Species Isolated from the Kumtagh Desert and Genomic Insights into the Secondary Metabolite Potential of the Genus
by Ying Wen, Jiahui Li, Fujun Qiao, Wanyin Luo, Tuo Chen, Guangxiu Liu and Wei Zhang
Microorganisms 2025, 13(7), 1628; https://doi.org/10.3390/microorganisms13071628 - 10 Jul 2025
Viewed by 293
Abstract
A novel actinobacterial strain, designated E54T, was isolated from a hyper-arid desert soil sample collected from the Kumtagh Desert in Dunhuang, Gansu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain E54T within the genus Lentzea, [...] Read more.
A novel actinobacterial strain, designated E54T, was isolated from a hyper-arid desert soil sample collected from the Kumtagh Desert in Dunhuang, Gansu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain E54T within the genus Lentzea, showing highest similarity to Lentzea waywayandensis DSM 44232T (98.9%) and Lentzea flava NBRC 15743T (98.5%). However, whole-genome comparisons revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between E54T and these related strains were below the thresholds for species delineation. Strain E54T exhibited typical morphological characteristics of the genus Lentzea, forming a branched substrate. It grew optimally at 28–30 °C, pH 7.0–9.0, and tolerated up to 10% NaCl. The cell wall contained meso-diaminopimelic acid, the predominant menaquinone was MK-9(H4), and major fatty acids included iso-C16:0. The polar lipid profile comprised diphosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl inositol, hydroxyphosphatidyl ethanolamine, and an unidentified lipid. The characteristic amino acid type of the cell wall was meso-DAP. Whole-cell hydrolysis experiments revealed the characteristic cell wall sugar fractions: ribose and galactose. The genome of strain E54T is approximately 8.0 Mb with a DNA G+C content of 69.38 mol%. Genome mining revealed 39 biosynthetic gene clusters (BGCs), including non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), terpenes, and siderophores. Comparative antiSMASH-based genome analysis across 38 Lentzea strains further demonstrated the genus’ remarkable biosynthetic diversity. NRPS and type I PKS (T1PKS) were the most prevalent BGC types, indicating a capacity to synthesize structurally complex and pharmacologically relevant metabolites. Together, these findings underscore the untapped biosynthetic potential of the genus Lentzea and support the proposal of strain E54T as a novel species. The strain E54T (=JCM 34936T = GDMCC 4.216T) should represent a novel species, for which the name Lentzea xerophila sp. nov. is proposed. Full article
(This article belongs to the Section Environmental Microbiology)
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Article
Transcriptomic Analysis of Biofilm Formation Inhibition by PDIA Iminosugar in Staphylococcus aureus
by Anna Tomusiak-Plebanek, Łucja Kozień, Estelle Gallienne, Maciej Florczyk, Sławomir Ciesielski, Piotr Heczko and Magdalena Strus
Antibiotics 2025, 14(7), 668; https://doi.org/10.3390/antibiotics14070668 - 1 Jul 2025
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Abstract
Background: Iminosugars are natural or synthetic sugar analogues with a very broad spectrum of activities, including those against the most prominent bacterial pathogens, like P. aeruginosa or S. aureus. In a series of studies, we have demonstrated that one of the synthetic iminosugars, [...] Read more.
Background: Iminosugars are natural or synthetic sugar analogues with a very broad spectrum of activities, including those against the most prominent bacterial pathogens, like P. aeruginosa or S. aureus. In a series of studies, we have demonstrated that one of the synthetic iminosugars, PDIA (beta-1-C-propyl-1,4-dideoxy-1,4-imino-L-arabinitol), possesses the ability to suppress biofilm production by different pathogenic bacteria without inhibiting their growth. Thereby, PDIA is able to influence experimental skin infection caused by S. aureus. Methods: To elucidate molecular mechanisms by which PDIA impedes biofilm formation by S. aureus, a transcriptomic study was performed in which a biofilm-producing S. aureus strain was grown in the presence of PDIA for 24 and 48 h in comparison to a control without the iminosugar. The RNA was then isolated, converted into cDNA, sequenced, and data analysis was performed. Results: It appeared that PDIA caused the down-regulation of many bacteriophage genes responsible for the processes of bacterial cell lysis, and some genes responsible for cell wall degradation were also down-regulated. Among the 25 most upregulated genes were those representing the phosphotransferase system (PTS), which is required for carbohydrate uptake and control of carbon metabolism. The ranking of the most significant down-regulated genes after 24 h exposure to PDIA shows that they predominantly coded for both the synthesis and lysis of the peptidoglycan. Conclusions: We have shown here that the influence of PDIA on the expression of S. aureus genes is broad and affects many genes encoding metabolism and ribosomes. Full article
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