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At least 217 records · Page 12Linked to original sources
PubMed2003

[Serum antibody response and Hantavirus RNA sequencing in patients with hemorrhagic fever renal syndrome in Yantai areas].

OBJECTIVE: To understand antibody responses to and RNA sequences of Hantavirus in patients with hemorrhagic fever renal syndrome (HFRS) in Yantai areas and to demonstrate the type of the prevalent viruses caused HFRS. METHODS: Serum specimens collected at acute and convalescent stages from 90 patients with HFRS and IgM and IgG antibodies against Hantavirus were detected with ELISA, and cross plaque reduction neutralizing tests were performed to detect neutralizing antibody. Viral RNA was extracted from the patients? sera by using Trizol method and nested PCR was utilized to amplify the specific segments of the viral cDNA and the products of the PCR were TA cloned and then the nucleotide sequences were determined. RESULTS: The IgM antibody was positive in 82.2% (88/107) of the patients while the IgG antibody was positive in 85.7% (66/77) of the patients. Both the serologic and sequence analyses demonstrated that the epidemic of HFRS in Yantai areas was caused by mixed types of Hantavirus. The prevalent strains of Hantavirus had higher homology with the strains isolated in Korea than with those isolated previously in China. CONCLUSIONS: The serologic and sequencing analyses indicated that the epidemic of HFRS in Yantai areas was caused by mixed types of Hantavirus dominated by type SEO.

Antibodies, Viral↗
PubMed1995

The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides.

Based on biochemical and ultrastructural data, hyphochytriomycetes are believed to share an ancestor with oomycetes and heterokont algae. In order to study the phylogeny of the hyphochytriomycetes, we determined both the small- and large-subunit ribosomal RNA sequence of Hyphochytrium catenoides. Phylogenetic trees were constructed using the neighbor-joining and maximum-parsimony method and include representatives of Chlorobionta, Fungi, Metazoa, Alveolata, and all known Heterokonta. Our main conclusion is that the hyphochytriomycetes form a monophyletic group with the oomycetes and heterokont algae and that they are probably the closest relatives of the oomycetes. However, the order of divergence between the various heterokont algal phyla and the oomycete-hyphochytriomycete cluster remains uncertain.

Base Sequence↗
PubMed1989

Rapid ribosomal RNA sequencing and the phylogenetic analysis of protists.

A newly described technique for rapidly obtaining the partial nucleotide sequence of ribosomal RNA is being applied to investigate phylogenetic relationships among living organisms. Alan Johnson and Peter Boverstock describe the importance of this method to parasitology in providing new information on the phylogenetic relationships of parasitic organisms previously placed in groups of convenience. The phylum Apicomplexo in particular, has been the object of much study using this technique, but the technology is likely to extend soon to the restructuring of the phylogenetic trees of many groups of parasites.

Journal Article↗
PubMed2025

Analysis of ferroptosis-related genes in cerebral ischemic stroke via immune infiltration and single-cell RNA-sequencing.

Ischemic stroke (IS) represents a harmful neurological disorder with limited treatment options. Ferroptosis accounts for the iron-dependent, nonapoptotic cell death pattern, which shows the feature of fatal lipid ROS accumulation. Nonetheless, ferroptosis-related biomarkers for identifying IS early are currently lacking. The present study focused on investigating the possible ferroptosis-related biomarkers for IS and analyzing their effects on immune infiltration. Altogether five hub differentially expressed ferroptosis-related genes (DEFRGs) were identified from the relevant databases. Additionally, single-cell RNA-sequencing (seq) analysis was conducted for the comprehensive mapping of cell populations based on the IS database. These five hub DEFRGs were analyzed using gene set enrichment analysis, miRNA prediction, and single-cell RNA-seq analysis. A transient middle cerebral artery occlusion mouse model was constructed. We also adopted bioinformatics methods combined with western blot, changes to mitochondria, hematoxylin & eosin staining, Nissl staining, ROS fluorescence staining, immunohistochemistry, and quantitative real-time polymerase chain reaction (qRT-PCR) to show the involvement of ferroptosis in IS progression. The results revealed that nuclear factor erythroid-derived 2-like 2 (Nfe2l2) was the potential candidate biomarker for IS diagnosis, and ferroptosis may be suppressed via the Nfe2l2/HO-1 pathway. Thus, drug targeting Nfe2l2 can shed novel lights on IS treatment.

Ferroptosis↗
PubMed1991

Ribozymes that cleave an RNA sequence from human immunodeficiency virus: the effect of flanking sequence on rate.

Ribozymes designed to cleave sequences specific to viral RNA may be better antiviral agents than simple antisense oligonucleotides. High catalytic activity with the lowest possible chain length is desired for this purpose. We have synthesized several hammerhead ribozymes that cleave sequences from HIV-1 RNA. On reducing from 20 to 12 the base pairs formed with the substrate, the rate of cleavage at 37 degrees C increased 10-fold. Deletions from the stem/loop structure in the ribozyme also increased the initial rate of reaction.

Base Sequence↗
PubMed1994

Oligonucleotide probes for Bordetella bronchiseptica based on 16S ribosomal RNA sequences.

Bordetella bronchiseptica 16S ribosomal RNA (rRNA) gene was cloned and identified. On the basis of information from computer-assisted sequence comparison of the B. bronchiseptica 16S RRNA sequences with that of other bacterial species, we constructed B. bronchiseptica-specific oligonucleotide probes complementary to variable regions in the 16S rRNA molecule. Specificity of these 32P-labeled oligo-nucleotide probes was tested in a RNA/DNA hybridization with B. bronchiseptica strains and other bacterial strains. Probe BB4 was more specific than three other oligonucleotide probes. This probe BB4 was sensitive enough to be able to detect 10(4) bacterial cells.

Base Sequence↗
PubMed1978

Specific RNA sequences and gene products of MC29 avian acute leukemia virus.

The 28S RNA of the defective avian acute leukemia virus MC29 contains two sets of sequences: 60% are hybridized by DNA complementary to other avian tumor virus RNAs (group-specific cDNA) and 40% are hybridized only by MC29-specific cDNA. Specific and group-specific sequences of viral RNA, defined in terms of their large RNase T(1)-resistant oligonucleotides, were located on a map of all large T(1) oligonucleotides of viral RNA. Oligonucleotides representing MC29-specific sequences of viral RNA mapped between 0.4 and 0.7 unit from the 3'-poly(A) end. Oligonucleotides of group-specific sequences mapped between 0 and 0.4 and between 0.7 and 1 map unit. Cell-free translation of viral RNA yielded three proteins with approximate molecular weights of 120,000, 56,000, and 37,000, termed P120(mc), P56(mc), and P37(mc). P120(mc) contained both MC29-specific peptides and serological determinants and peptides of the conserved, internal group-specific antigens of avian tumor viruses. P120(mc) is translated only from full-length 28S RNA. Furthermore, MC29 RNA contains sequences related to the group-specific antigen gene (gag), near the 5' end, which are followed by MC29-specific sequences. We conclude that this protein is translated from the 5' 60% of the RNA, and that it includes a segment translated from the specific sequences. It is suggested that the transforming (onc) gene of MC29 may consists of the specific and some group-specific RNA sequences and that P120(mc), which is also found in transformed cells, may be the onc gene product.

Avian Leukosis Virus↗
PubMed1982

Papovavirus-related RNA sequences in human neurogenic tumours.

Thirty-two human brain tumours were investigated for the presence of papovavirus-related RNA sequences. Radiolabelled viral DNAs isolated from SV40, BKV, HDV, and BPV were hybridized in-situ on to tumour kryostat sections under conditions that detect complementary RNA. SV40-related RNA was detectable in 34% of all tumours tested but was not found in normal human brain tissue. SV40-positive tumours included 1/1 angiofibroma, 1/4 astrocytomas, 2/4 metastatic brain tumours, 1/1 melanoma, 3/7 meningiomas, 2/4 neurinomas, 1/2 oligodendrogliomas. Bovine papilloma virus-, BKV-, and HDV-related RNAs were absent from all tissues tested. The presence of SV40-related nucleic acids in a large number of human neurogenic tumours may reflect a viral involvement in the etiology of these tumours.

Astrocytoma↗
PubMed1982

Detection of bovine leukaemia virus RNA sequences in non-cultivated peripheral lymphocytes by in situ hybridization with 3H-labelled viral cDNA.

Bovine leukaemia virus (BVL) in circulating lymphatic cells of the blood is repressed and has to be activated for its expression. After in situ hybridization of BLV-3HcDNA with a specific activity of 3.9 X 10 dpm/micrograms to noncultivated blood cells from 5 leukotic cattle, in 4 of these animals from 0.96% to 1.5% lymphocytes were found to contain BLV-specific RNA sequences. Non-hybridized lymphocytes as well as calf thymus cells, used as controls, gave only 0.47% and 0.39% labelled cells, respectively. After short-term cultivation of white blood cells from these leukotic animals the percentage of labelled cells increased. During the short-term cultivation the number of hybridizing cells from one and the same animal and from all animal, when compared with each other, varied to a high extent. The highest values of BLV-RNA sequences-containing cells from all 5 animals at different cultivation times were within the range of from 2.4 to 16.2%.

Animals↗
PubMed2025

Transcriptome-Wide Analysis of the 5' Cap Status of RNA Using 5' Monophosphate-Dependent Exonuclease Digestion and RNA Sequencing.

Eukaryotic mRNAs carry an N7-methylguanosine (m7G) cap structure at their 5' extremity, which protects them from the degradation by 5'-3' exoribonucleases and plays a pivotal role in mRNA metabolism, promoting splicing, nuclear export, and translation. Decapping, the enzymatic process that removes this structure, is a key event during cytoplasmic mRNA 5'-3' decay, leading to the degradation of the transcript body by Xrn1. In this chapter, we describe a procedure to assess the cap status of RNA at the transcriptome level. It is based on a treatment of total RNA extracts with a 5' monophosphate-dependent exonuclease, which like Xrn1 specifically degrades decapped RNAs harboring 5' monophosphate extremities, but not RNAs with intact m7G cap. The digested RNAs are then analyzed by RNA sequencing.

Exoribonucleases↗
PubMed1982

Cytoplasmic RNA sequences complementary to cloned chick delta-crystallin cDNA show size heterogeneity.

Double-stranded complementary DNA (cDNA) sequences were prepared from day-old chick lens total polysomal RNA and inserted into the unique PstI restriction site of the plasmid pBR322. Colonies containing sequences complementary to abundant lens poly(A)-containing RNA sequences were identified by using lens 32P-labelled cDNA. Some of these clones have been characterized as containing delta-crystallin mRNA coding sequences by genomic DNA blot hybridization and RNA blot hybridizations. Hybridization of labelled DNA from such clones to RNA blots detected four size classes of delta-crystallin RNA sequences, although Southern blots indicated that there are probably only two delta-crystallin genes.

Animals↗
PubMed2025

Cell-type-specific response to silicon treatment in soybean leaves revealed by single-nucleus RNA sequencing and targeted gene editing.

Mineral nutrient uptake and deposition profoundly influence plant development, stress resilience, and productivity. Silicon (Si), though classified as a non-essential element, significantly influences a plant's physiology, particularly in fortifying defense responses and mitigating stress. While the genetic and molecular mechanisms of Si uptake and transport are well studied in monocots, particularly rice, their role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. In this study, we utilized single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. We identified distinct cellular populations, including a unique Si-induced or Si-associated cell cluster within vascular cells, suggesting a specialized mechanism of Si distribution. Si treatment notably induced the expression of defense-related genes, with a pronounced enrichment in vascular cells, underscoring their pivotal role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in phytoalexin biosynthesis, salicylic acid, and immune receptor signaling, suggesting transcriptional priming of genes involved in defense responses. Further investigation of Si transporters revealed precise expression of an Si efflux gene in epidermal cells in response to Si treatment. We also validated the role of efflux Si transporters using a Xenopus oocyte assay and CRISPR/Cas9 genome editing of composite soybean plant roots. This study provides critical insights into the biotic stress regulatory networks influenced by Si treatment in soybean leaves at the single-cell level, thus laying the foundation for enhancing stress tolerance through optimized mineral nutrient uptake.

Glycine max↗
PubMed1991

The relationship between the flaviviruses Skalica and Langat as revealed by monoclonal antibodies, peptide mapping and RNA sequence analysis.

The flavivirus Skalica was isolated from a bank vole in Czechoslovakia in 1976. It can be serologically distinguished from prototype strains of tick-borne encephalitis (TBE) virus and has a decreased virulence for adult mice. We have further defined the relationship of Skalica virus to other members of the TBE serocomplex (TBE European and Far Eastern subtypes, Langat and louping ill virus) by using a panel of 22 monoclonal antibodies, peptide mapping and RNA sequence analyses. By these criteria Skalica virus proved to be distinct from TBE virus and to be very closely related to Langat virus, differing by only two bases among a total of 416 nucleotides compared. The sequence of 22% of the Langat genome was determined and the encoded amino acid sequences were derived. Comparison of these with the corresponding amino acid sequences of TBE virus revealed a similarity of 85%, as opposed to 93% similarity between the European and Far Eastern subtypes of TBE virus.

Amino Acid Sequence↗
PubMed2005

MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence.

Regulation of post-transcriptional gene expression by microRNAs (miRNA) has so far been validated for only a few mRNA targets. Based on the large number of miRNA genes and the possibility that one miRNA might influence gene expression of several targets simultaneously, the quantity of ribo-regulated genes is expected to be much higher. Here, we describe the web tool MicroInspector that will analyse a user-defined RNA sequence, which is typically an mRNA or a part of an mRNA, for the occurrence of binding sites for known and registered miRNAs. The program allows variation of temperature, the setting of energy values as well as the selection of different miRNA databases to identify miRNA-binding sites of different strength. MicroInspector could spot the correct sites for miRNA-interaction in known target mRNAs. Using other mRNAs, for which such an interaction has not yet been described, we discovered frequently potential miRNA binding sites of similar quality, which can now be analysed experimentally. The MicroInspector program is easy to use and does not require specific computer skills. The service can be accessed via the MicroInspector web server at http://www.imbb.forth.gr/microinspector.

Base Pairing↗
PubMed1993

Discrimination between six species of Theileria using oligonucleotide probes which detect small subunit ribosomal RNA sequences.

The complete small subunit ribosomal RNA (srRNA) gene of Theileria parva was cloned and sequenced. Two primers were designed which permitted the specific amplification of part of the Theileria srRNA gene from Theileria-infected cell line samples which were predominantly (> 95%) bovine DNA. The sequence of the central (variable) region of the srRNA genes of T. annulata, T. taurotragi, T. mutants and two unidentified parasites referred to as Theileria sp. (buffalo) and Theileria sp. (Marula) were obtained. An alignment of the sequences was generated from which 6 oligonucleotide probes, corresponding to species-specific regions, were designed. These probes were demonstrated to provide unequivocal identification of each of the 6 species either by direct detection of parasite srRNA or by hybridization to amplified parasite srRNA genes. The probes were not able to distinguish buffalo-derived T. parva, the causal agent of Corridor disease, from cattle-derived T. parva, the causal agent of East Coast fever.

Animals↗
PubMed1982

Adenovirus-related RNA sequences in human neurogenic tumours.

Thirty two human tumours, mainly neurogenic, have been investigated for the presence of adenovirus-related RNA sequences. 3H-labelled tumour virus DNA probes derived from human adenoviruses types 2 and 12, bovine adenovirus type 3, and avian adenovirus CELO were hybridized in-situ on tumour kryostat sections under conditions that detect complementary RNA. Tumour virus-related RNA was detected in 62% of all tumours tested, but was not detectable in normal human brain tissues. Expression of tumour virus-related RNA was found in 2/4 astrocytomas, 2/4 metastatic brain carcinomas, 2/2 glioblastomas, 1/1 melanoma, 5/7 meningiomas, 4/4 neurinomas, 1/2 oligodendrogliomas, and 1/1 rhabdomyosarcoma. The presence of adenovirus-related RNA in the majority of human neurogenic tumours may reflect a viral involvement in the pathogenesis of these tumours.

Adenoviridae↗
PubMed1983

Differences among the polyadenylated RNA sequences of human leucocyte populations: an approach to the objective classification of human leukaemias.

We have constructed a complementary DNA (cDNA) library representing expressed sequences of the white blood cells from a patient with chronic granulocytic leukaemia. The library was screened by colony hybridization of 32P-labelled cDNAs synthesized from the polyadenylated RNAs of the white blood cells from patients with chronic granulocytic or chronic lymphocytic leukaemia. The autoradiographic patterns were compared and 70 recombinants were selected to comprise a panel which distinguished between these two types of leukaemia. Hybridization of this panel with complementary DNAs transcribed from the polyadenylated RNAs of a variety of normal and neoplastic leucocyte populations showed that the RNA sequences in high abundance in leucocytes from chronic granulocytic leukaemias differ quite radically from those in other leucocytes. The patterns of hybridization seen when this panel was challenged with cDNAs representing the RNAs of normal and leukaemic leucocyte populations were sufficiently different to distinguish clearly the peripheral blood leucocytes of chronic granulocytic leukaemias from other populations of white blood cells, both normal and leukaemic. We suggest that this approach might provide additional markers useful in the classification of the acute leukaemias, especially the undifferentiated leukaemias whose identification by conventional methods is uncertain.

Gene Library↗
PubMed1990

Detection of enterovirus specific RNA sequences in muscle biopsy specimens from patients with adult onset myositis.

A subgenomic cDNA probe with broad specificity for a range of enteroviruses was used to test by an in situ hybridisation technique for the presence of enterovirus specific genomic sequences in muscle biopsy samples obtained from patients with chronic adult myositis. Virus specific RNA sequences were detected in 6/13 (46%) patients with idiopathic polymyositis or dermatomyositis. Control samples obtained from an equal number of patients suffering from other muscle disorders were negative. A monoclonal antibody specific for an enterovirus group was used to probe for viral antigens by indirect immunoperoxidase staining; all biopsy samples from test and control groups were negative.

Adult↗