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1.
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
2.
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
3.
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
4.
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
5.
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
6.
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
7.
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
8.
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 , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces pombe Proteins/genetics , DNA Helicases/metabolism , DNA Helicases/genetics , Hydroxyurea/pharmacology , Stress, Physiological , DNA, Ribosomal/genetics , DNA, Ribosomal/metabolism , Chromosomal Instability
9.
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
10.
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
11.
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
12.
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
13.
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
14.
Mycologia ; 116(4): 509-535, 2024.
Article in English | MEDLINE | ID: mdl-38742888

ABSTRACT

South Africa has an indigenous rust (Pucciniales) funga of approximately 460 species. This funga was sampled with species from as many genera as possible. The nuclear ribosomal large subunit (28S) region was amplified from samples representing 110 indigenous species, as well as the small subunit (18S) region and the cytochrome c oxidase subunit 3 (CO3) in some cases, and these were used in phylogenetic analyses. One new species is described, 12 new combinations made, six names reinstated, and two life history connections made. The life histories of this funga were summarized; it is dominated by species with contracted life histories. The majority of species are autoecious, with a small proportion being heteroecious. Of the autoecious species, many will likely be homothallic with no spermagonia. A shortened life history with homothallism allows for a single basidiospore infection to initiate a local population buildup under the prevailing unpredictable climatic conditions. Suggestions are made as to the possible origin of this funga based on the development of the modern South African flora. It is postulated that the rusts of South Africa are of relatively recent origin, consisting of three groups. Firstly, there is an African tropical element with members of the Mikronegerineae (Hemileia), the Sphaerophragmiaceae (Puccorchidium, Sphaerophragmium), and certain Uredinineae (Stomatisora). Their immediate ancestors likely occurred in the tropical forests of Africa during the Paleogene. Secondly, there is a pantropical element including the Raveneliaceae (e.g., Diorchidium, Maravalia, Ravenelia sensu lato, Uropyxis). This likely diversified during the Neogene, when the mimosoids became the dominant trees of the developing savannas. Thirdly, the Pucciniaceae invaded Africa as this continent pushed northward closing the Tethys Sea. They diversified with the development of the savannas as these become the dominant habitat in most of Africa, and are by far the largest component of the South African rust funga.


Subject(s)
Basidiomycota , DNA, Fungal , Phylogeny , South Africa , Basidiomycota/genetics , Basidiomycota/classification , DNA, Fungal/genetics , Sequence Analysis, DNA , RNA, Ribosomal, 28S/genetics , DNA, Ribosomal/genetics , Electron Transport Complex IV/genetics , RNA, Ribosomal, 18S/genetics
15.
Genes (Basel) ; 15(5)2024 05 20.
Article in English | MEDLINE | ID: mdl-38790276

ABSTRACT

This study was conducted to evaluate the 5S rDNA site number, position, and origin of signal pattern diversity in 42 plant species using fluorescence in situ hybridization. The species were selected based on the discovery of karyotype rearrangement, or because 5S rDNA had not yet been explored the species. The chromosome number varied from 14 to 160, and the chromosome length ranged from 0.63 to 6.88 µm, with 21 species having small chromosomes (<3 µm). The chromosome numbers of three species and the 5S rDNA loci of nineteen species are reported for the first time. Six 5S rDNA signal pattern types were identified. The 5S rDNA varied and was abundant in signal site numbers (2-18), positions (distal, proximal, outside of chromosome arms), and even in signal intensity. Variation in the numbers and locations of 5S rDNA was observed in 20 species, whereas an extensive stable number and location of 5S rDNA was found in 22 species. The potential origin of the signal pattern diversity was proposed and discussed. These data characterized the variability of 5S rDNA within the karyotypes of the 42 species that exhibited chromosomal rearrangements and provided anchor points for genetic physical maps.


Subject(s)
Chromosomes, Plant , In Situ Hybridization, Fluorescence , Karyotype , RNA, Ribosomal, 5S , Chromosomes, Plant/genetics , RNA, Ribosomal, 5S/genetics , In Situ Hybridization, Fluorescence/methods , Chromosome Mapping/methods , DNA, Ribosomal/genetics , Plants/genetics , Karyotyping/methods
16.
Parasitol Res ; 123(6): 230, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38822199

ABSTRACT

Cryptosporidium is an important water-borne and food-borne parasite with a high burden of disease. This organism has been shown to contaminate various leafy vegetables; however, studies assessing the presence of Cryptosporidium spp in pre-washed and ready-to-eat vegetables are limited. Routine surveillance in the UK revealed a nationwide exceedance of human cases of Cryptosporidium. Therefore, this study aims to assess the presence of this parasite in pre-washed vegetables from supermarkets in the UK. A total of 36 samples were purchased from four different supermarkets. A nested PCR targeting the SSU rRNA was carried out on 24 samples, 58% were PCR-positive for Cryptosporidium. Sanger sequencing confirmed that, of these sequences, 4/24 (17%) produced significant similarities to Cryptosporidium parvum. This study provides evidence for the presence of C. parvum in pre-washed and ready-to-eat vegetables. Future work to identify the point of contamination is required.


Subject(s)
Cryptosporidium parvum , Vegetables , Cryptosporidium parvum/isolation & purification , Cryptosporidium parvum/genetics , Cryptosporidium parvum/classification , Vegetables/parasitology , England , Pilot Projects , Supermarkets , Polymerase Chain Reaction , DNA, Protozoan/genetics , Sequence Analysis, DNA , RNA, Ribosomal, 18S/genetics , Humans , DNA, Ribosomal/genetics
17.
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
18.
Cell Genom ; 4(6): 100562, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38749448

ABSTRACT

The phenotypic impact of genetic variation of repetitive features in the human genome is currently understudied. One such feature is the multi-copy 47S ribosomal DNA (rDNA) that codes for rRNA components of the ribosome. Here, we present an analysis of rDNA copy number (CN) variation in the UK Biobank (UKB). From the first release of UKB whole-genome sequencing (WGS) data, a discovery analysis in White British individuals reveals that rDNA CN associates with altered counts of specific blood cell subtypes, such as neutrophils, and with the estimated glomerular filtration rate, a marker of kidney function. Similar trends are observed in other ancestries. A range of analyses argue against reverse causality or common confounder effects, and all core results replicate in the second UKB WGS release. Our work demonstrates that rDNA CN is a genetic influence on trait variance in humans.


Subject(s)
Biological Specimen Banks , DNA Copy Number Variations , Humans , DNA Copy Number Variations/genetics , United Kingdom , Glomerular Filtration Rate/genetics , DNA, Ribosomal/genetics , Kidney/metabolism , Male , Female , Whole Genome Sequencing , Genome, Human , UK Biobank
19.
Eur J Protistol ; 94: 126091, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38772052

ABSTRACT

Acanthamoeba castellanii (Douglas, 1930) Page, 1967 is the type species of a widespread genus of free-living amoebae, potentially pathogenic for humans and animals. The Neff strain is one of the most widely used in biological research, serving as a model for both A. castellanii and the whole genus in general. The Neff strain, isolated in California, closely resembles another strain found in France and originally described as a separate species, Acanthamoeba terricola Pussard, 1964, but both were successively synonymized with A. castellanii. Molecular sequence analysis has largely replaced morphological diagnosis for species identification in Acanthamoeba, and rDNA phylogenies show that the Neff strain forms a distinct lineage from that of the type strain of A. castellanii. In this study, we compared the type strain of A. terricola with the Neff strain and A. castellanii, and analysed the available molecular data including new sequences obtained from A. terricola. Here we provide molecular evidence to validate the species A. terricola. The Neff strain is therefore transferred to A. terricola and should no longer be considered as belonging to A. castellanii.


Subject(s)
Acanthamoeba , DNA, Protozoan , Phylogeny , Acanthamoeba/classification , Acanthamoeba/genetics , DNA, Protozoan/genetics , DNA, Ribosomal/genetics , Species Specificity , Sequence Analysis, DNA , Molecular Sequence Data , Animals
20.
Parasitol Res ; 123(5): 219, 2024 May 23.
Article in English | MEDLINE | ID: mdl-38780821

ABSTRACT

The genus Hepatozoon Miller (1908) contains a wide range of obligate parasitic organisms with complex life cycles involving vertebrates and hematophagous invertebrates. Despite over 300 species being described, only a small percentage has been characterized in snakes using morphological and molecular techniques. The prevalence of these parasites in snakes is significant, highlighting the need for molecular descriptions in such elusive hosts. Thus, the objective of this study was to determine molecularly the presence of Hepatozoon species in snakes from the Northeastern region of Argentina. Thirty-two specimens of eight snake species (Bothrops alternatus, Dryophylax hypoconia, Erythrolamprus jaegeri coralliventris, Erythrolamprus poecilogyrus, Erythrolamprus semiaureus, Philodryas olfersii latirostris, Pseudablabes (ex Philodryas) patagoniensis and Palusophis (ex Mastigodryas) bifossatus were collected and examined. PCR analysis of the 18S rRNA locus detected four samples (12% prevalence) positive for the presence of Hepatozoon DNA. Phylogenetic analysis positioned the 18S rRNA Hepatozoon sequences obtained in three different clades, one with Hepatozoon musa, another with sequences of Hepatozoon cuestensis, while the third was placed as a sister taxon to a clade including Hepatozoon cevapii and Hepatozoon massardi. This study presents the first documentation of Hepatozoon infecting snakes in Argentina, thereby expanding their distribution within southern South America. Additionally, B. alternatus and Pa. bifossatus are reported as new hosts of Hepatozoon.


Subject(s)
DNA, Protozoan , Eucoccidiida , Phylogeny , RNA, Ribosomal, 18S , Snakes , Animals , Argentina , Snakes/parasitology , RNA, Ribosomal, 18S/genetics , Eucoccidiida/genetics , Eucoccidiida/isolation & purification , Eucoccidiida/classification , DNA, Protozoan/genetics , Coccidiosis/parasitology , Coccidiosis/veterinary , Coccidiosis/epidemiology , Sequence Analysis, DNA , DNA, Ribosomal/genetics , Prevalence , Polymerase Chain Reaction
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