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1.
J Infect Dev Ctries ; 18(6): 978-981, 2024 Jun 30.
Article in English | MEDLINE | ID: mdl-38990993

ABSTRACT

INTRODUCTION: Mycetoma is a chronic granulomatous inflammatory disease of the subcutaneous tissue, which affects deep structures and bone. Most cases of actinomycetoma are caused by members of the genus Nocardia. CASE PRESENTATION: Here we report the case of a 43-year-old male who presented a disseminated mycetoma on the forearm, chest and neck, characterized by enlarged and erythematous lesions through which seropurulent material drains, and numerous atrophic scars. Molecular identification was performed by 16S gene amplification and sequencing. Nocardia mexicana was identified with 100% identity. Trimethoprim-sulfamethoxazole, diaminodiphenyl sulfone and amikacin was a successful treatment after 6 months. CONCLUSIONS: Nocardia mexicana is a rare organism that causes mycetoma. We report a case of extensive mycetoma on the forearm with spread to the neck and thorax associated with manipulation of the mouth of a calf.


Subject(s)
Anti-Bacterial Agents , Forearm , Mycetoma , Neck , Nocardia Infections , Nocardia , RNA, Ribosomal, 16S , Thorax , Humans , Male , Adult , Nocardia/isolation & purification , Nocardia/genetics , Mycetoma/microbiology , Mycetoma/drug therapy , Mycetoma/diagnosis , Nocardia Infections/microbiology , Nocardia Infections/drug therapy , Nocardia Infections/diagnosis , Forearm/microbiology , Forearm/pathology , Thorax/diagnostic imaging , Thorax/microbiology , Neck/pathology , Anti-Bacterial Agents/therapeutic use , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , Treatment Outcome , Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use , Amikacin/therapeutic use , DNA, Ribosomal/genetics , DNA, Ribosomal/chemistry
2.
Parasitol Res ; 123(7): 268, 2024 Jul 12.
Article in English | MEDLINE | ID: mdl-38992328

ABSTRACT

This study describes the first detection of Ixodes ventalloi in Slovakia. Two engorged females of I. ventalloi were collected from Dunnocks (Prunella modularis) captured in eastern Slovakia. The identification of females was based on morphological and molecular 16S rRNA gene features. Phylogenetic analysis revealed a classification of the females into distinct genogroups. Moreover, comparative morphological analysis highlighted variations between the two females, particularly in the curvature of the auriculae, the shape of coxa I, and the internal spur. These findings suggest the potential for varied phenotypes of I. ventalloi correlated with their genogroups. Nonetheless, I. ventalloi population establishment within Slovakia necessitates further investigation through flagging or drag sampling.


Subject(s)
Ixodes , Phylogeny , RNA, Ribosomal, 16S , Animals , Slovakia , Ixodes/classification , Ixodes/anatomy & histology , Ixodes/genetics , Ixodes/physiology , Female , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tick Infestations/parasitology , Tick Infestations/veterinary , Bird Diseases/parasitology , Galliformes/parasitology , DNA, Ribosomal/genetics , Cluster Analysis
3.
Front Cell Infect Microbiol ; 14: 1402329, 2024.
Article in English | MEDLINE | ID: mdl-38947125

ABSTRACT

Introduction: In infants with cholestasis, variations in the enterohepatic circulation of bile acids and the gut microbiota (GM) characteristics differ between those with biliary atresia (BA) and non-BA, prompting a differential analysis of their respective GM profiles. Methods: Using 16S rDNA gene sequencing to analyse the variance in GM composition among three groups: infants with BA (BA group, n=26), non-BA cholestasis (IC group, n=37), and healthy infants (control group, n=50). Additionally, correlation analysis was conducted between GM and liver function-related indicators. Results: Principal component analysis using Bray-Curtis distance measurement revealed a significant distinction between microbial samples in the IC group compared to the two other groups. IC-accumulated co-abundance groups exhibited positive correlations with aspartate aminotransferase, alanine aminotransferase, total bilirubin, direct bilirubin, and total bile acid serum levels. These correlations were notably reinforced upon the exclusion of microbial samples from children with BA. Conclusion: The varying "enterohepatic circulation" status of bile acids in children with BA and non-BA cholestasis contributes to distinct GM structures and functions. This divergence underscores the potential for targeted GM interventions tailored to the specific aetiologies of cholestasis.


Subject(s)
Bile Acids and Salts , Biliary Atresia , Cholestasis , Gastrointestinal Microbiome , RNA, Ribosomal, 16S , Humans , Biliary Atresia/microbiology , Cholestasis/microbiology , Infant , Bile Acids and Salts/metabolism , Bile Acids and Salts/blood , Male , Female , RNA, Ribosomal, 16S/genetics , Bilirubin/blood , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , DNA, Ribosomal/genetics , Feces/microbiology
4.
J Vis Exp ; (208)2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38975778

ABSTRACT

All ribosomal genes of Naegleria trophozoites are maintained in a closed circular extrachromosomal ribosomal DNA (rDNA) containing element (CERE). While little is known about the CERE, a complete genome sequence analysis of three Naegleria species clearly demonstrates that there are no rDNA cistrons in the nuclear genome. Furthermore, a single DNA origin of replication has been mapped in the N. gruberi CERE, supporting the hypothesis that CERE replicates independently of the nuclear genome. This CERE characteristic suggests that it may be possible to use engineered CERE to introduce foreign proteins into Naegleria trophozoites. As the first step in exploring the use of a CERE as a vector in Naegleria, we developed a protocol to transfect N. gruberi with a molecular clone of the N. gruberi CERE cloned into pGEM7zf+ (pGRUB). Following transfection, pGRUB was readily detected in N. gruberi trophozoites for at least seven passages, as well as through encystment and excystment. As a control, trophozoites were transfected with the backbone vector, pGEM7zf+, without the N. gruberi sequences (pGEM). pGEM was not detected after the first passage following transfection into N. gruberi, indicating its inability to replicate in a eukaryotic organism. These studies describe a transfection protocol for Naegleria trophozoites and demonstrate that the bacterial plasmid sequence in pGRUB does not inhibit successful transfection and replication of the transfected CERE clone. Furthermore, this transfection protocol will be critical in understanding the minimal sequence of the CERE that drives its replication in trophozoites, as well as identifying regulatory regions in the non-ribosomal sequence (NRS).


Subject(s)
DNA, Ribosomal , Naegleria , Transfection , Naegleria/genetics , Transfection/methods , DNA, Ribosomal/genetics , Trophozoites , DNA, Protozoan/genetics , Cloning, Molecular/methods
5.
RNA Biol ; 21(1): 42-51, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38958280

ABSTRACT

The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II and III). Although TBP is central to transcription by the three RNA Pols in various species, the emergence of TBP paralogs throughout evolution has expanded the complexity in transcription initiation. Furthermore, recent studies have emerged that questioned the centrality of TBP in mammalian cells, particularly in Pol II transcription, but the role of TBP and its paralogs in Pol I transcription remains to be re-evaluated. In this report, we show that in murine embryonic stem cells TBP localizes onto Pol I promoters, whereas the TBP paralog TRF2 only weakly associates to the Spacer Promoter of rDNA, suggesting that it may not be able to replace TBP for Pol I transcription. Importantly, acute TBP depletion does not fully disrupt Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells.


Subject(s)
Mitosis , Promoter Regions, Genetic , RNA Polymerase I , TATA-Box Binding Protein , Transcription, Genetic , Animals , RNA Polymerase I/metabolism , RNA Polymerase I/genetics , TATA-Box Binding Protein/metabolism , TATA-Box Binding Protein/genetics , Mice , Mouse Embryonic Stem Cells/metabolism , Mouse Embryonic Stem Cells/cytology , Protein Binding , DNA, Ribosomal/genetics , DNA, Ribosomal/metabolism
6.
Front Cell Infect Microbiol ; 14: 1420389, 2024.
Article in English | MEDLINE | ID: mdl-38983117

ABSTRACT

The intestinal microbiota assumes a pivotal role in modulating host metabolism, immune responses, overall health, and additional physiological dimensions. The structural and functional characteristics of the intestinal microbiota may cause alterations within the host's body to a certain extent. The composition of the gut microbiota is associated with environmental factors, dietary habits, and other pertinent conditions. The investigation into the gut microbiota of yaks remained relatively underexplored. An examination of yak gut microbiota holds promise in elucidating the complex relationship between microbial communities and the adaptive responses of the host to its environment. In this study, yak were selected from two distinct environmental conditions: those raised in sheds (NS, n=6) and grazed in Nimu County (NF, n=6). Fecal samples were collected from the yaks and subsequently processed for analysis through 16S rDNA and ITS sequencing methodologies. The results revealed that different feeding styles result in significant differences in the Alpha diversity of fungi in the gut of yaks, while the gut microbiota of captive yaks was relatively conserved. In addition, significant differences appeared in the abundance of microorganisms in different taxa, phylum Verrucomicrobiota was significantly enriched in group NF while Firmicutes was higher in group NS. At the genus level, Akkermansia, Paenibacillus, Roseburia, Dorea, UCG_012, Anaerovorax and Marvinbryantia were enriched in group NF while Desemzia, Olsenella, Kocuria, Ornithinimicrobium and Parvibacter were higher in group NS (P<0.05 or P<0.01). There was a significant difference in the function of gut microbiota between the two groups. The observed variations are likely influenced by differences in feeding methods and environmental conditions both inside and outside the pen. The findings of this investigation offer prospective insights into enhancing the yak breeding and expansion of the yak industry.


Subject(s)
Bacteria , Feces , Gastrointestinal Microbiome , RNA, Ribosomal, 16S , Animals , Cattle , Gastrointestinal Microbiome/genetics , Feces/microbiology , RNA, Ribosomal, 16S/genetics , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , China , Phylogeny , DNA, Bacterial/genetics , Fungi/classification , Fungi/isolation & purification , Fungi/genetics , DNA, Ribosomal/genetics , DNA, Ribosomal/chemistry , Sequence Analysis, DNA , Biodiversity
7.
Int J Mol Sci ; 25(12)2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38928039

ABSTRACT

Different developmental genes shape frequent dynamic inter-chromosomal contacts with rDNA units in human and Drosophila cells. In the course of differentiation, changes in these contacts occur, coupled with changes in the expression of hundreds of rDNA-contacting genes. The data suggest a possible role of nucleoli in the global regulation of gene expression. However, the mechanism behind the specificity of these inter-chromosomal contacts, which are rebuilt in every cell cycle, is not yet known. Here, we describe the strong association of rDNA-contacting genes with numerous long intergenic non-coding RNAs (lincRNAs) in HEK293T cells and in initial and differentiated K562 cells. We observed that up to 600 different lincRNAs were preferentially co-expressed with multiple overlapping sets of rDNA-contacting developmental genes, and there was a strong correlation between the genomic positions of rDNA-contacting genes and lincRNA mappings. These two findings suggest that lincRNAs might guide the corresponding developmental genes toward rDNA clusters. We conclude that the inter-chromosomal interactions of rDNA-contacting genes with nucleoli might be guided by lincRNAs, which might physically link particular genomic regions with rDNA clusters.


Subject(s)
Cell Nucleolus , DNA, Ribosomal , RNA, Long Noncoding , Humans , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , DNA, Ribosomal/genetics , DNA, Ribosomal/metabolism , Cell Nucleolus/metabolism , Cell Nucleolus/genetics , HEK293 Cells , K562 Cells
8.
An Acad Bras Cienc ; 96(3): e20230629, 2024.
Article in English | MEDLINE | ID: mdl-38922254

ABSTRACT

The current study proposes to investigate the diversity and phylogeny of trypanosomes parasitizing wild birds from the Brazilian Atlantic Forest. Cytological examination was carried out by light microscopy of blood smears and positive birds were selected for amplification of the 18S rDNA sequence through PCR. The resulting amplicons were subjected to purification, cloning, and sequencing analysis. Phylogenetic reconstruction was conducted, including all avian trypanosomes representative's lineages. A total of ten bird samples from species of Turdus flavipes (N=1/12), T. albicollis (N=1/8), Tachyphonus coronatus (N=6/121), Thamnophilus caerulescens (N=1/22) and Synallaxis spixi (N=1/8) were positive for Trypanosoma spp. In the six specimens of T. coronatus, five distinct lineages of Trypanosoma spp. 18S-rRNA were observed in ninety sequences obtained, and using the strategy of cloning independent PCR, it was possible to observe that two of them were related to T. avium (JB01/JB02), and three were closed related to T. bennetti (JB03/ JB04/JB05). Addionaly, all fifteen sequences obtained from T. caerulescens/ S. spixi/T. flavipes/T. albicollis were identical. The present research is the first study to access molecular diversity and polyparasitism by avian trypanosomes in Brazil. The current research exhibits the wide genetic variability in avian trypanosomes and its non-specific relationship with its avian hosts.


Subject(s)
Birds , Phylogeny , Polymerase Chain Reaction , Trypanosoma , Animals , Brazil , Trypanosoma/classification , Trypanosoma/genetics , Trypanosoma/isolation & purification , Birds/parasitology , Rainforest , RNA, Ribosomal, 18S/genetics , DNA, Protozoan/genetics , Trypanosomiasis/veterinary , Trypanosomiasis/parasitology , Bird Diseases/parasitology , Genetic Variation , DNA, Ribosomal/genetics , Sequence Analysis, DNA
9.
Sci Rep ; 14(1): 13161, 2024 06 07.
Article in English | MEDLINE | ID: mdl-38849440

ABSTRACT

Physella acuta is a freshwater snail native to North America. Understanding the phylogeography and genetic structure of P. acuta will help elucidate its evolution. In this study, we used mitochondrial (COI and 16S rDNA) and nuclear (ITS1) markers to identify the species and examine its genetic diversity, population structure, and demographic history of P. acuta in Thailand. Phylogenetic and network analyses of P. acuta in Thailand pertained to clade A, which exhibits a global distribution. Analysis of the genetic structure of the population revealed that the majority of pairwise comparisons showed no genetic dissimilarity. An isolation-by-distance test indicates no significant correlation between genetic and geographical distances among P. acuta populations, suggesting that gene flow is not restricted by distance. Demographic history and haplotype network analyses suggest a population expansion of P. acuta, as evidenced by the star-like structure detected in the median-joining network. Based on these results, we concluded that P. acuta in Thailand showed gene flow and recent population expansion. Our findings provide fundamental insights into the genetic variation of P. acuta in Thailand.


Subject(s)
Genetic Variation , Phylogeny , Phylogeography , RNA, Ribosomal, 16S , Animals , Thailand , RNA, Ribosomal, 16S/genetics , Gastropoda/genetics , Gastropoda/classification , Gene Flow , Electron Transport Complex IV/genetics , Haplotypes , Genetic Markers , Genetics, Population , DNA, Mitochondrial/genetics , DNA, Ribosomal/genetics , Snails/genetics , Snails/classification , Genes, Mitochondrial
10.
Cell Death Dis ; 15(6): 457, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38937439

ABSTRACT

In eukaryotes, the nucleolus is the critical non-membranous organelle within nuclei that is responsible for ribosomal DNA (rDNA) transcription and ribosome biogenesis. The transcription of rDNA, a rate-limiting step for ribosome biogenesis, is tightly regulated to meet the demand for global protein synthesis in response to cell physiology, especially in neurons, which undergo rapid changes in morphology and protein composition during development and synaptic plasticity. However, it is unknown how the pre-initiation complex for rDNA transcription is efficiently assembled within the nucleolus in neurons. Here, we report that the nucleolar protein, coronin 2B, regulates rDNA transcription and maintains nucleolar function through direct interaction with upstream binding factor (UBF), an activator of RNA polymerase I transcriptional machinery. We show that coronin 2B knockdown impairs the formation of the transcription initiation complex, inhibits rDNA transcription, destroys nucleolar integrity, and ultimately induces nucleolar stress. In turn, coronin 2B-mediated nucleolar stress leads to p53 stabilization and activation, eventually resulting in neuronal apoptosis. Thus, we identified that coronin 2B coordinates with UBF to regulate rDNA transcription and maintain proper nucleolar function in neurons.


Subject(s)
Apoptosis , Cell Nucleolus , Neurons , Pol1 Transcription Initiation Complex Proteins , Apoptosis/genetics , Cell Nucleolus/metabolism , Neurons/metabolism , Animals , Pol1 Transcription Initiation Complex Proteins/metabolism , Pol1 Transcription Initiation Complex Proteins/genetics , Humans , DNA, Ribosomal/metabolism , DNA, Ribosomal/genetics , Microfilament Proteins/metabolism , Microfilament Proteins/genetics , Transcription, Genetic , Tumor Suppressor Protein p53/metabolism , Tumor Suppressor Protein p53/genetics , Mice , Stress, Physiological
11.
Nat Commun ; 15(1): 5006, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38866738

ABSTRACT

Body mass results from a complex interplay between genetics and environment. Previous studies of the genetic contribution to body mass have excluded repetitive regions due to the technical limitations of platforms used for population scale studies. Here we apply genome-wide approaches, identifying an association between adult body mass and the copy number (CN) of 47S-ribosomal DNA (rDNA). rDNA codes for the 18 S, 5.8 S and 28 S ribosomal RNA (rRNA) components of the ribosome. In mammals, there are hundreds of copies of these genes. Inter-individual variation in the rDNA CN has not previously been associated with a mammalian phenotype. Here, we show that rDNA CN variation associates with post-pubertal growth rate in rats and body mass index in adult humans. rDNA CN is not associated with rRNA transcription rates in adult tissues, suggesting the mechanistic link occurs earlier in development. This aligns with the observation that the association emerges by early adulthood.


Subject(s)
Body Mass Index , DNA Copy Number Variations , DNA, Ribosomal , Animals , Humans , DNA, Ribosomal/genetics , Male , Rats , Female , Adult , Mammals/genetics , RNA, Ribosomal/genetics , RNA, Ribosomal/metabolism
12.
Parasitol Res ; 123(6): 237, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38856825

ABSTRACT

Mastophorus muris (Gmelin, 1790) is a globally distributed parasitic nematode of broad range mammals. The taxonomy within the genus Mastophorus and the cryptic diversity among the genus are controversial among taxonomists. This study provides a detailed morphological description of M. muris from Mus musculus combined with a molecular phylogenetic approach. Moreover, descriptions and molecular data of M. muris from non-Mus rodents and wildcats complement our findings and together provide new insights into their taxonomy. The analysis of M. muris was based on light microscopy and scanning electron microscopy. The morphological description focused on the dentition pattern of the two trilobed pseudolabia. Additionally, we described the position of the vulva, arrangement of caudal pairs of papillae, spicules and measured specimens from both sexes and the eggs. For the molecular phylogenetic approach, we amplified the small subunit ribosomal RNA gene and the internal transcribed spacer, and the cytochrome c oxidase subunit 1. Mastophorus morphotypes based on dentition patterns and phylogenetic clustering indicate a subdivision of the genus in agreement with their host. We recognize two groups without a change to formal taxonomy: One group including those specimens infecting Mus musculus, and the second group including organisms infecting non-Mus rodents. Our genetic and morphological data shed light into the cryptic diversity within the genus Mastopohorus. We identified two host-associated groups of M. muris. The described morphotypes and genotypes of M. muris allow a consistent distinction between host-associated parasites.


Subject(s)
Microscopy, Electron, Scanning , Phylogeny , Animals , Female , Male , Mice , Spiruroidea/classification , Spiruroidea/genetics , Spiruroidea/anatomy & histology , Spiruroidea/isolation & purification , Spiruroidea/ultrastructure , Electron Transport Complex IV/genetics , Genetic Variation , Sequence Analysis, DNA , Microscopy , DNA, Helminth/genetics , DNA, Ribosomal/genetics , DNA, Ribosomal Spacer/genetics , Cluster Analysis , Molecular Sequence Data
13.
Parasitol Res ; 123(6): 231, 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38829429

ABSTRACT

Cryptosporidium spp. are protozoa commonly found in domestic and wild animals. Limited information is available on Cryptosporidium in deer worldwide. In this study, 201 fecal samples were collected from Alpine musk deer on three farms in Gansu Province, China. Detection and subtyping of Cryptosporidium were performed by PCR and sequence analysis of the SSU rRNA and gp60 genes. The prevalence of Cryptosporidium infection in Alpine musk deer was 3.9% (8/201), with infection rates of 1.0% (1/100), 2.8% (1/36), and 9.2% (6/65) in three different farms. All positive samples for Cryptosporidium were from adult deer. Two Cryptosporidium species were identified, including C. parvum (n = 2) and C. xiaoi (n = 6). The C. parvum isolates were subtyped as IIdA15G1, while the C. xiaoi isolates were subtyped as XXIIIa (n = 2) and XXIIIg (n = 4). The IIdA15G1 subtype of C. parvum was found for the first time in deer. These results provide important insights into the identity and human infectious potential of Cryptosporidium in farmed Alpine musk deer.


Subject(s)
Cryptosporidiosis , Cryptosporidium , Deer , Feces , Animals , Deer/parasitology , Cryptosporidiosis/parasitology , Cryptosporidiosis/epidemiology , Cryptosporidium/genetics , Cryptosporidium/isolation & purification , Cryptosporidium/classification , China/epidemiology , Feces/parasitology , Prevalence , DNA, Protozoan/genetics , Phylogeny , Polymerase Chain Reaction , Sequence Analysis, DNA , Genotype , DNA, Ribosomal/genetics , DNA, Ribosomal/chemistry
14.
Parasitol Res ; 123(6): 250, 2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38910209

ABSTRACT

Hepatozoon spp. are tick-borne apicomplexan parasites of terrestrial vertebrates that occur worldwide. Tissue samples from small rodents and their parasitizing fleas were sampled for molecular detection and phylogenetic analysis of Hepatozoon-specific 18S rRNA gene region. After alignment and tree inference the Hepatozoon-sequences retrieved from a yellow-necked mouse (Apodemus flavicollis) placed into a strongly supported single clade demonstrating the presence of a novel species, designated Hepatozoon sp. SK3. The mode of transmission of Hepatozoon sp. SK3 is yet unknown. It is important to note that this isolate may be identical with the previously morphologically described Hepatozoon sylvatici infecting Apodemus spp.; however, no sequences are available for comparison. Furthermore, the previously reported variants Hepatozoon sp. BV1/SK1 and BV2/SK2 were detected in bank voles (Clethrionomys glareolus). It has been suggested that these variants should be identified as Hepatozoon erhardovae leading to the assumption that BV1 and BV2 are paralogous 18S rRNA gene loci of this species. Evidence has also been presented that fleas are vectors of H. erhardovae. In this study, we show with high significance that only the Hepatozoon sp. BV1 variant, but not BV2, infects the studied flea species Ctenophthalmus agyrtes, Ctenophthalmus assimilis, and Megabothris turbidus (p < 0.001). This finding suggests that Hepatozoon sp. BV2 represents an additional species besides H. erhardovae (= Hepatozoon sp. BV1), for which alternative arthropod vectors or non-vectorial modes of transmission remain to be identified. Future studies using alternative molecular markers or genome sequencing are required to demonstrate that BV1/SK1 and BV2/SK2 are different Hepatozoon species.


Subject(s)
Coccidiosis , Eucoccidiida , Phylogeny , RNA, Ribosomal, 18S , Animals , RNA, Ribosomal, 18S/genetics , Coccidiosis/parasitology , Coccidiosis/veterinary , Coccidiosis/epidemiology , Eucoccidiida/genetics , Eucoccidiida/classification , Eucoccidiida/isolation & purification , Europe , DNA, Protozoan/genetics , Rodentia/parasitology , Siphonaptera/classification , Sequence Analysis, DNA , DNA, Ribosomal/genetics , Rodent Diseases/parasitology , Rodent Diseases/epidemiology , Murinae/parasitology
15.
PLoS One ; 19(6): e0300434, 2024.
Article in English | MEDLINE | ID: mdl-38905307

ABSTRACT

Homologous recombination is a key process that governs the stability of eukaryotic genomes during DNA replication and repair. Multiple auxiliary factors regulate the choice of homologous recombination pathway in response to different types of replication stress. Using Schizosaccharomyces pombe we have previously suggested the role of DNA translocases Rrp1 and Rrp2, together with Srs2 helicase, in the common synthesis-dependent strand annealing sub-pathway of homologous recombination. Here we show that all three proteins are important for completion of replication after hydroxyurea exposure and provide data comparing the effect of overproduction of Srs2 with Rrp1 and Rrp2. We demonstrate that Srs2 localises to rDNA region and is required for proper replication of rDNA arrays. Upregulation of Srs2 protein levels leads to enhanced replication stress, chromosome instability and viability loss, as previously reported for Rrp1 and Rrp2. Interestingly, our data suggests that dysregulation of Srs2, Rrp1 and Rrp2 protein levels differentially affects checkpoint response: overproduction of Srs2 activates simultaneously DNA damage and replication stress response checkpoints, while cells overproducing Rrp1 mainly launch DNA damage checkpoint. On the other hand, upregulation of Rrp2 primarily leads to replication stress response checkpoint activation. Overall, we propose that Srs2, Rrp1 and Rrp2 have important and at least partially independent functions in the maintenance of distinct difficult to replicate regions of the genome.


Subject(s)
DNA Damage , DNA Helicases , DNA Replication , Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Chromosomal Instability , DNA Helicases/metabolism , DNA Helicases/genetics , DNA, Ribosomal/genetics , DNA, Ribosomal/metabolism , Hydroxyurea/pharmacology , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces pombe Proteins/genetics , Stress, Physiological
16.
Parasites Hosts Dis ; 62(2): 180-192, 2024 May.
Article in English | MEDLINE | ID: mdl-38835259

ABSTRACT

Free-living amoebae (FLA) are found in diverse environments, such as soils, rivers, and seas. Hence, they can be used as bioindicators to assess the water quality based solely on their presence. In this study, we determined the presence of FLA in river water by filtering water samples collected from various sites and culturing the resulting filtrates. FLA were detected in all the water samples with varying quality grades (Grades Ι-V). The significant increase in the size of the amoebae population with the deterioration in the water quality. Monoxenic cultures of the amoebae were performed, and genomic DNAs were isolated, among which 18S rDNAs were sequenced to identify the amoeba species. Of the 12 species identified, 10 belonged to the Acanthamoeba genus; of the remaining 2 species, one was identified as Vannella croatica and the other as a species of Vermamoeba. Acanthamoeba was detected in samples with Grades Ι to VI quality, whereas the Vermamoeba species was present only in Grade Ι water. V. croatica was found exclusively in water with Grade ΙΙ quality. Following morphological observations, genomic DNA was sequenced using 16S rDNA to determine whether the species of Acanthamoeba harbored endosymbionts. Most of the isolated Acanthamoeba contained endosymbionts, among which 4 species of endogenous bacteria were identified and examined using transmission electron microscopy. This study provides evidence that the distribution of amoebae other than Acanthamoeba may be associated with water quality. However, further confirmation will be required based on accurate water quality ratings and assessments using a more diverse range of FLA.


Subject(s)
Amoeba , Water Quality , Amoeba/genetics , Amoeba/isolation & purification , Amoeba/classification , Phylogeny , Rivers/parasitology , DNA, Protozoan/genetics , Acanthamoeba/genetics , Acanthamoeba/isolation & purification , Acanthamoeba/classification , RNA, Ribosomal, 18S/genetics , DNA, Ribosomal/genetics , Biodiversity , Sequence Analysis, DNA/methods , RNA, Ribosomal, 16S/genetics
17.
Front Endocrinol (Lausanne) ; 15: 1397402, 2024.
Article in English | MEDLINE | ID: mdl-38872962

ABSTRACT

Graphene-based warm uterus acupoint paste (GWUAP) is an emerging non-drug alternative therapy for the treatment of primary dysmenorrhea (PD), but the underlying mechanism is still unclear. SD female rats were randomly divided into control group, model group and treatment group to explore the mechanism of GWUAP in the treatment of PD. Combined with 16S rDNA and fecal metabolomics, the diversity of microbiota and metabolites in each group was comprehensively evaluated. In this study, GWUAP reduced the torsion score of PD model rats, improved the pathological morphology of uterine tissue, reduced the pathological damage score of uterine tissue, and reversed the expression levels of inflammatory factors, pain factors and sex hormones. The 16 S rDNA sequencing of fecal samples showed that the abundance of Lactobacillus in the intestinal flora of the model group decreased and the abundance of Romboutsia increased, while the abundance of Lactobacillus in the intestinal flora of the treatment group increased and the abundance of Romboutsia decreased, which improved the imbalance of flora diversity in PD rats. In addition, 32 metabolites related to therapeutic effects were identified by metabolomics of fecal samples. Moreover, there is a close correlation between fecal microbiota and metabolites. Therefore, the mechanism of GWUAP in the treatment of PD remains to be further studied.


Subject(s)
Acupuncture Points , Dysmenorrhea , Metabolomics , Rats, Sprague-Dawley , Animals , Female , Dysmenorrhea/therapy , Dysmenorrhea/drug therapy , Rats , Gastrointestinal Microbiome/drug effects , RNA, Ribosomal, 16S/genetics , Feces/microbiology , DNA, Ribosomal/genetics
18.
Front Cell Infect Microbiol ; 14: 1394663, 2024.
Article in English | MEDLINE | ID: mdl-38873099

ABSTRACT

In this study, we report the first isolation of Hanseniaspora opuntiae obtained from four pregnant women in Brazil. Clinical isolates were obtained from four samples taken between 35 and 37 gestational weeks, as part of the routine antenatal care for maternal colonization screening for Streptococcus agalactiae group B. The patients were immunocompetent, with two of them diagnosed with gestational diabetes mellitus. Species identification was performed by MALDI-TOF MS and rDNA sequencing. While Hanseniaspora species have not traditionally been considered a typical opportunist pathogen, our findings emphasize the importance of investigating and screening for Hanseniaspora in pregnant populations, highlighting H. opuntiae as a potential agent of human infections.


Subject(s)
Pregnancy Complications, Infectious , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Humans , Female , Pregnancy , Brazil , Adult , Pregnancy Complications, Infectious/microbiology , Pregnancy Complications, Infectious/diagnosis , Vagina/microbiology , DNA, Ribosomal/genetics , Sequence Analysis, DNA , Streptococcus agalactiae/isolation & purification , Streptococcus agalactiae/genetics , Streptococcus agalactiae/classification , Diabetes, Gestational/microbiology , Diabetes, Gestational/diagnosis , Young Adult
19.
J Vector Borne Dis ; 61(2): 259-266, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38922661

ABSTRACT

BACKGROUND OBJECTIVES: Vector-borne haemoprotozoan diseases comprise diverse group of single celled organism transmitted by haematophagus invertebrates. The current study was aimed at the identification of major haemoprotozoan (Babesia, Theileria and Trypanosoma) in dromedary camel of North Gujarat region in India using microscopy and Polymerase Chain Reaction (PCR). METHODS: A total of 234 blood samples were screened by the microscopic and molecular detection assays. Molecular prevalence studies of Theileria, Trypanosoma spp and Babesia was undertaken using 18s ribosomal DNA, RoTat 1.2 and SS rRNA gene respectively. The data relating to microscopic and molecular prevalence along with associated risk factors were analysed by statistical methods. RESULTS: The overall prevalence of hamoprotozoan disease based on microscopic and molecular investigation was 23.50%. The sensitivity and specificity (95% Confidence Interval) of PCR assay was 100% in comparison to microscopy (45.45 % sensitive and 100 % specific). The kappa coefficient between PCR and microscopy indicated good level of agreement with a value of 0.704 and SE of 0.159. INTERPRETATION CONCLUSION: Despite holding much significance to the animal sector, little work has been undertaken in regional parts of India regarding camel parasites. The present study offers first preliminary research data investigating haemoprotozoan disease using parasitological and molecular methods in camels in the region.


Subject(s)
Babesia , Camelus , Microscopy , Polymerase Chain Reaction , RNA, Ribosomal, 18S , Theileria , Theileriasis , Trypanosoma , Animals , Camelus/parasitology , India/epidemiology , Trypanosoma/genetics , Trypanosoma/isolation & purification , Trypanosoma/classification , Theileria/genetics , Theileria/isolation & purification , Theileria/classification , Babesia/genetics , Babesia/isolation & purification , Babesia/classification , Theileriasis/epidemiology , Theileriasis/parasitology , RNA, Ribosomal, 18S/genetics , DNA, Protozoan/genetics , Babesiosis/epidemiology , Babesiosis/parasitology , Prevalence , Male , Sensitivity and Specificity , Trypanosomiasis/veterinary , Trypanosomiasis/epidemiology , Trypanosomiasis/parasitology , Female , Vector Borne Diseases/epidemiology , Vector Borne Diseases/parasitology , DNA, Ribosomal/genetics
20.
Braz J Microbiol ; 55(2): 1897-1911, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38727923

ABSTRACT

Plant growth promoting rhizobacteria (PGPR) are also known to colonize in the soil rhizosphere and prevent the development of other soil borne pathogens residing in the root surface. These microorganisms play a vital role in growth and development of the plant and also enhances the soil fertility by enriching the soil with different beneficial nutrients. This study was aimed at isolation of different rhizobacteria and their molecular characterization in search of efficient bacterial strains with multiple growth regulating activities. A total 36 bacteria were isolated from lentil root nodule as well as soil from different lentil growing fields with a view to screen/evaluate their plant growth promoting potential. Morphological characterization of isolated rhizobacterial candidates were done by observing the colonies on YEMA and nutrient agar media. Determination of CFU, Congo red test and gram staining tests were done to further screen them according to their morphology. All the isolates were then undergone molecular phylogenetic analysis using the partial sequences of the 16 S rDNA. Based upon the Gram staining test, all the isolates were negative in gram reaction except six Bacillus isolates, PSB2 and AB3. Results of Ribosomal Database Project (RDP) and Basic Local Alignment Search Tool for Nucleotide Sequences (BLASTn) from 16 S rDNA gene sequences showed that these isolates are genetically diverse. A total of 15 isolates of Rhizobium, 6 isolates of Bacillus, 3 isolates of Pseudomonas, 2 isolates of Phosphate Solubilizing Bacteria, 4 isolates of actinomycetes were identified by molecular sequencing of their 16 S rDNA region and comparing them with the other isolates enlisted in the database of NCBI for the similarity percentage, query coverage. The purpose of the present study was to select native rhizosphere bacteria from the lentil nodule and soil of Lentil field and to evaluate their plant growth promoting potential as an alternative of chemical fertilizer for sustainable, environment friendly agriculture and assessment of their phylogenetic characterization.


Subject(s)
Bacteria , DNA, Bacterial , Lens Plant , Phylogeny , RNA, Ribosomal, 16S , Rhizosphere , Soil Microbiology , Lens Plant/microbiology , Bacteria/classification , Bacteria/isolation & purification , Bacteria/genetics , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Plant Roots/microbiology , India , DNA, Ribosomal/genetics
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