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At least 505 records · Page 28Linked to original sources
PubMed1992

Expression pattern of a tobacco lipid transfer protein gene within the shoot apex.

A genomic clone coding for a putative lipid transfer protein was isolated from Nicotiana tabacum. The gene is expressed in all aerial organs of the tobacco plant, with expression being highest in the upper part of the plant and declining towards the base (i.e. with increasing age). In the shoot apex transcript levels are highest in the LI layer, lower in the underlying cell layers, and are again higher in the submeristem region. This pattern is markedly different from those previously described for genes expressed within the shoot apex.

Amino Acid Sequence↗
PubMed2004

[Antigenic and genetic characterizations of group A influenza viruses H3N2 circulated in men in China during 2000-2002].

OBJECTIVE: To understand the antigenic and genetic characteristics of influenza A H3N2 viruses circulated in man in China from 2000 to 2002. METHODS: Embryonated chicken eggs inoculated with virus for amplification of viral yield. The harvesting egg allantoic fluids with influenza viruses were provided for testing antigen and RNA extraction. Virion RNA was transcribed into cDNA by reverse transcriptase, cDNA amplified by PCR, and the product of PCR was purified. Afterward RNA sequence analysis was performed by the dideoxynucleotide chain termination method using synthetic oligodeoxynucleotide primers. Finally the phylogenetic tree was analyzed with MegAlign software. RESULTS: The H3N2 viruses isolated during 2000-2002 were different in amino acid sequences on HA1 domain protein molecule from those of A/Wuhan359/1995 H3N2 as well as those of A/Sydney/7/1997 H3N2 strains. There were four different positions of amino acid sequence on HA1 domain protein molecule among the H3N2 viruses isolated in 2000 and during 2001-2002. They located at 83, 186, 202, 222 and 225 position, respectively. Of them 83 and 186 were in antigenic determinant E and B, respectively. The others located at left wall of the receptor binding site (RBS). CONCLUSION: From the end of 2001 to the beginning of 2002, the influenza epidemic in Northern China caused by H3N2 virus was due to occurrence of antigenic and genetic changes of influenza A(H3N2) virus.

Amino Acid Sequence↗
PubMed2005

[Cloning of mMR-1 gene and expression in Pichia pastoris systems].

hMR-1 (Homo Myofibrillogenesis Regulator 1, AF417001) is a novel homo gene, which was firstly cloned in our laboratory. The former studies revealed that hMR-1 is a transmembrane protein which shows protein interaction with sarcomeric proteins like myomesin I, myosin regulatory light chain, alpha-enolase and some cell regulator proteins such as eukaryotic translation initiation factor3 subunit 5 (eIF3S5) and etc. In this work, we focused on cloning the homologous gene of hMR-1 from mouse C57BL/6J and exploring its expression using Pichia pastoris yeast system. Two pairs of primers were synthesized according to the hMR-1 gene homologous sequence on mouse genome chromosome 1. The mouse MR-1 gene (mMR-1) was cloned by PCR following the first round RT-PCR from mouse C57BL/6J spleen total RNA. Sequence analysis verified that mMR-1 gene and amino acids sequence showed 90.4% and 90.1% identity with hMR-1, respectively. The prediction of hydrophobic transmembrane structure of mMR-1 suggested it is also a transmembrane protein. The mMR-1 Pichia pastoris expression vector pPIC9-mMR-1 was constructed by fusion of the flanking mMR-1 ORF in the pPIC9 plasmid. After linearization of pPIC9-mMR-1 with Sal I, the 8.5kb DNA fragment was transformed into Pichia pastoris GS115 strain by electroporation. GS115/Mut+ pPIC9-mMR-1 transformants were selected on minimal methanol medium. Integration of mMR-1 gene into the yeast genome in the recombinants was verified by PCR from the transformants total DNA. The mMR-1 protein was expressed by induction under the concentration of 0.5 % methanol. The specific induced protein of 25 kD molecular mass in SDS-PAGE was confirmed to be the mMR-1 protein by Western blot rsing hMR-1 polyclonal antibody. The expression level of this recombinant mMR-1 protein was about 50 mg/L. The successful expression of mMR-1 in the Pichia pastoris GS115 will facilitate the further functional analysis of the novel gene MR-1 in animal model.

Amino Acid Sequence↗
PubMed2005

Analysis of progressively overexpressed genes in tumorigenesis of colorectal cancers using cDNA microarray.

The identification of differentially expressed genes has important implications in understanding the biology of colorectal tumorigenesis and progression, as well as developing new diagnostic and therapeutic strategies. In this study, cDNA microarray technology was used to identify colorectal tumor-related functional genes, which are overexpressed continuously from colorectal adenoma to adenocarcinoma. A set of 23 genes with progressive overexpression in the development of colorectal cancer (CRC) was identified by cDNA microarray, then analyzed by sequencing and Northern blot analysis. Validation of our array results was simultaneously performed by exploring the SAGEmap database. Furthermore, the gradually over-expressed genes from adenoma to adenocarcinoma were validated by Northern blot analysis with additional samples from three patients with synchronous colorectal adenocarcinoma and adenoma and four patients with CRC. Of these 23 genes, one was a function-unknown gene, designated as Homo sapiens chromosome 21q22.1 anonymous mRNA sequence (Genbank accession no. AF003738), and 22 were function-known genes. Searching through the Gene Ontology Browser at the Cancer Genome Analysis Project website revealed that the biological roles of these 22 function-known genes are involved in cell motility, cell adhesion, chemokine activity, signal transduction, cytoskeleton organization, proteolysis, apoptosis, and cell proliferation. The genes identified in the present study offer valuable information on colorectal carcinogenesis and metastasis, and represent a potential source of novel targets for new strategies for CRC diagnosis and therapy.

Blotting, Northern↗
PubMed2006

[Analysis and state of HCV genotype 6a infection].

OBJECTIVE: To investigate the infection state of hepatitis C virus genotype 6a in China. METHODS: Three (95, 126, 150)HCV genotype 6a serum samples were identified by digesting 5'NCR with compound enzyme method. Then, HCV 5'NCR and NS5B fragments were amplified from these samples by RT-PCR assay and sequenced. The phylogenetic trees of the samples were analyzed and compared with 24 HCV complete gene sequences from GenBank. RESULTS: The sequencing reports on 5'NCR showed "CA" bases in 3 serum samples (95,126,150) were inserted into -145 site, and the sequences of 3 serum samples had the highest homology with sequence Y12083( 0.934, 0.930, and 0.926, respectively). The results of the phylogenetic trees suggested these 3 serum samples belonged to HCV genotype 6a. The sequencing reports on NS5B showed the 3 serum samples also had the highest homology with HC-J4(0.934, 0.930, and 0.926, respectively), and the results of the phylogenetic trees suggested these 3 serum samples belonged to HCV genotype 1b. To exclude the influence of amplification efficiency of primers, NS5B fragments were amplified by HCV genotype 6a specific primers and no amplification products appeared. CONCLUSION: There are different results of HCV genotype by analyzing 5'NCR and NS5B in 3 samples infected with HCV genotype 6a. It may be related with gene recombination. It suggests HCV genotype should be analyzed on more than two regions.

Base Sequence↗
PubMed1990

Structure, tissue-specific expression, and transforming activity of the mouse met protooncogene.

A 6.7-kilobase met complementary DNA (cDNA) was isolated from a pcD cDNA library prepared from C3H mouse fibroblast cell line polyadenylated RNA. Sequence analysis of 6.7-kilobase met cDNA insert revealed that it contained the entire open reading frame and shared an overall homology of 88.1% with the human met gene. Using the mouse met cDNA as probe, high levels of met expression were observed in the kidney, brain, lung, skin, and embryonic tissue as well as in several factor responsive mouse myeloid cell lines. Under SV40 promoter control, the mouse met protooncogene cDNA in the pCD vector was able to transform NIH 3T3 cells. These transformed cells possess multiple copies of mouse met cDNA and exhibit properties of malignant cells, including growth in soft agar and induction of tumors in nude mice. Tumor explant cell lines analyzed by Western blot also reveal the presence of high levels of Mr 170,000 and 140,000 met protein product(s).

Amino Acid Sequence↗
PubMed1998

Isoleucine:RNA sites with associated coding sequences.

An RNA family that binds isoleucine with Kd = 200-500 microM was repetitively isolated from a ribonucleotide transcript pool containing 50 randomized positions. The RNA site is specific, discriminating against branched side chains of different size (valine--one methylene smaller than isoleucine) by at least 1.3 kcal/mol and against the shape (linear) of norleucine by 0.6 kcal/mol. The binding site was localized by sequence comparison, by synthesis of mutant and truncated active derivatives, and by chemical modification-interference. The binding site is small, no more than 10-12 nt, containing an asymmetric internal loop (6 over 2 nt) that includes the isoleucine codon AUU and a sequence of four G's, two of which are involved in G-U and G-C base pairs. Areas of U/G concentration like these may signal a hydrophobic RNA site.

Amides↗
PubMed2001

Sequence analysis of the RNA polymerase gene of foot-and-mouth disease virus serotype Asia1.

The complete nucleotide (nt.) sequence of the RNA polymerase (3D) gene and 81 nt. in the 3'-untranslated region of foot-and-mouth disease virus (FMDV) serotype Asial (IND63/72) was determined and compared with the sequence of other FMDV serotypes. The 3D genomic region was 1410 nt. long encoding 470 amino acids with an inframe stop codon (TAA) at nt. position 1411-1413. The deduced amino acid sequence of the protein showed 8 conserved motifs as reported in other picornaviruses, 2 of which are 100% identical across the serotypes. Antigenic regions in the polymerase protein were predicted and found to be located at the N-terminus of the protein. The phylogenetic analysis showed that the FMD viruses were segregated into different clusters based on geographical origin; the Asia1 virus did not cluster tightly with any of the geographical groups.

Amino Acid Sequence↗
PubMed1998

Sequence analysis of the RNA polymerase gene of African horse sickness virus.

The gene encoding the inner core protein VP1 of African horse sickness virus (AHSV) serotype 9 has been cloned, expressed in vitro and entirely sequenced, completing molecular characterization of the AHSV genome. An analysis of the sequence supporting the identity of AHSV VP1 as the putative viral RNA polymerase is presented.

African Horse Sickness Virus↗
PubMed2026

A token-pruning framework enables efficient representation of the human genome for RNA modification analysis.

MOTIVATION: Modelling long genomic sequences remains challenging due to extreme sequence length, high redundancy, and the need for biological interpretability. Although Transformer-based architectures have achieved strong performance across genomic tasks, their high computational cost and reliance on fixed tokenization strategies limit their scalability and ability to focus on biologically informative regions. RESULTS: We propose ATSFormer, a token-pruning Transformer framework for efficient and biologically informed genomic sequence modelling. ATSFormer incorporates an attention-guided and parameter-free Adaptive Token Sampling (ATS) module into Transformer layers. Guided by attention-derived importance scores, ATS dynamically retains informative tokens while probabilistically discarding redundant ones, thereby reducing sequence length, FLOPs, and memory usage without introducing additional learnable parameters or extra training procedures. Importantly, the retained tokens correspond to key contributors to model predictions, enabling ATSFormer to highlight biologically meaningful sites and sequence motifs. We evaluated ATSFormer on four benchmark RNA modification datasets derived from RMVar 2.0, covering A-to-I, m1A, m5C, and m7G. Experimental results show that ATSFormer consistently outperforms existing state-of-the-art methods while achieving substantial computational savings. Furthermore, structural analysis using AlphaFold3 supports the biological relevance of the motifs identified by ATSFormer. AVAILABILITY AND IMPLEMENTATION: The source data and code are freely available at GitHub (https://github.com/1gao2/ATSFormer) and Zenodo (https://doi.org/10.5281/zenodo.21813541).

Humans↗
PubMed2003

Sequence analysis of the medium RNA segment of three Simbu serogroup viruses, Akabane, Aino, and Peaton viruses.

The sequence analysis was carried out for the medium (M) RNA segment of the Akabane virus (AKAV), Aino virus (AINV), and Peaton virus (PEAV) of the Simbu serogroup of the genus Orthobunyavirus of the family Bunyaviridae. The complementary sequences of the M RNA segments of AKAV, AINV, and PEAV contain a single large open reading frame (ORF), like other orthobunyaviruses. The ORFs potentially encode 1401 amino acids (aa), 1404 aa, and 1400 aa polypeptides, respectively. The identity of the M segment among these viruses is remarkably low, although previous researchers reported that the small RNA segments are highly conserved. Because the M segment codes for the viral surface glycoproteins G1 and G2, the variability of the M segment may affect the antigenicity of these viruses. Phylogenetic studies based on the M and S segment sequences suggested that genetic reassortment has been occurring among ancestral viruses of the three Simbu serogroup viruses throughout their evolution.

Animals↗
PubMed2005

RNA secondary structural alignment with conditional random fields.

MOTIVATION: The computational identification of non-coding RNA regions on the genome is currently receiving much attention. However, it is essentially harder than gene-finding problems for protein-coding regions because non-coding RNA sequences do not have strong statistical signals. Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational methods are expected for structural alignment of RNA sequences. Several methods have been proposed to accomplish the structural alignment tasks for RNA sequences, and we found that one of the most important points is to estimate an accurate score matrix for calculating structural alignments. RESULTS: We propose a novel approach for RNA structural alignment based on conditional random fields (CRFs). Our approach has some specific features compared with previous methods in the sense that the parameters for structural alignment are estimated such that the model can most probably discriminate between correct alignments and incorrect alignments, and has the generalization ability so that a satisfiable score matrix can be obtained even with a small number of sample data without overfitting. Experimental results clearly show that the parameter estimation with CRFs can outperform all the other existing methods for structural alignments of RNA sequences. Furthermore, structural alignment search based on CRFs is more accurate for predicting non-coding RNA regions than the other scoring methods. These experimental results strongly support our discriminative method employing CRFs to estimate the score matrix parameters. AVAILABILITY: The program which is implemented in C++ is available at http://phmmts.dna.bio.keio.ac.jp/ under the GNU public license.

Base Sequence↗
PubMedDate not supplied

Use of avian myeloblastosis virus reverse transcriptase at high temperature for sequence analysis of highly structured RNA.

Avian myeloblastosis virus reverse transcriptase (AMV RT) is routinely used in the sequence analysis of RNA and DNA templates. We review the various methods for dealing with secondary structures that would otherwise result in premature termination or sequence compression. Based on our experience in sequencing the 11-kb single-stranded RNA genome of lymphocytic choriomeningitis virus, we have found that raising the reaction temperature above 47 degrees C is the simplest way to overcome template secondary structure, and the use of 98% formamide gels is the simplest way to overcome product secondary structure.

Avian Leukosis Virus↗
PubMed1974

Sequence analysis of nonradioactive RNA fragments by periodate-phosphatase digestion and chemical tritium labeling: characterization of large oligonucleotides and oligonucleotides containing modified nucleosides.

A tritium derivative method for sequence analysis of polyribonucleotides is detailed, which is based on borotritide reduction of oligonucleotide dialdehydes generated by treatment of polyribonucleotides with alkaline phosphatase and excess periodate at pH 8 (borate buffer; no primary amine present in the reaction mixture). While neither phosphatase nor periodate possess any intrinsic exonuclease activity their combination mimics an RNA-specific exonuclease ("pseudo-exonuclease"). Procedures are described for separation and characterization of tritiumlabeled oligonucleotide derivatives. The sequence is deduced by identification of labeled 3'-termini following separation of the reduced nucleotide intermediates according to chain length. The sensitivity of the method is indicated by the fact that as little as 0.01 O.D.260 unit of a nonradioactive decanucleotide is sufficient for sequence determination.

Alkaline Phosphatase↗
PubMed2000

Ribosomal small-subunit RNA gene-sequence analysis of Theileria lestoquardi and a Theileria species highly pathogenic for small ruminants in China.

A fatal disease of sheep and goats in the northwestern part of China has been reported to be due to Theileria lestoquardi (syn. T. hirci). However, some characteristics of the causative agent are not in accordance with attributes ascribed to this parasite. We therefore determined the nucleotide sequence of the small-subunit ribosomal RNA (srRNA) gene of T. lestoquardi and the parasite identified in China and compared it with that of other Theileria and Babesia species. In the inferred phylogenetic tree the srRNA sequence of the Chinese parasite was found to be most closely related to T. buffeli and clearly divergent from T. lestoquardi, suggesting that it is an as yet unrecognized Theileria species. Extensive structural similarities were observed between the srRNA sequences of T. lestoquardi and T. annulata, revealing a close phylogenetic relationship between these two Theileria species. On the basis of the srRNA nucleotide sequence, polymerase chain reaction (PCR) primers were designed that specifically amplified genomic DNA of the Chinese Theileria species. These primers may be valuable tools in future epidemiology studies.

Animals↗
PubMed1982

The reaction of human SLE antibodies with native, single stranded RNA: analysis of nucleotide sequence specificities and correlation with Sm and nRNP activities.

The antigenic specificities of RNA reactive IgG autoantibodies from three individual human SLE sera and pooled NZB/NZW mouse serum were studied by competition reactions with synthetic co-polymers and heteropolymers of varying nucleotide compositions. Although minor differences in the individual binding patterns were noted, the RNA reactive immunoglobulins showed a clear preference for G, C and G,C,U containing RNA sequences. All three SLE sera had Sm or RNP activities with rabbit thymus extractable nuclear antigen (ENA). Conversely, all SLE sera that were selected on the basis of their positive ENA reaction could also bind free, single stranded RNA. These results suggest that the autoimmune response to RNA in human and murine SLE is restricted to one or a very few antigenic determinants. They also raise the possibility that autoantibodies to native RNA in SLE sera are partly responsible for ENA reactivity.

Antigen-Antibody Complex↗
PubMed1995

Identification of base-triples in RNA using comparative sequence analysis.

Comparative sequence analysis has proven to be a very efficient tool for the determination of RNA secondary structure and certain tertiary interactions. However, base-triples, an important RNA structural element, cannot be predicted accurately from sequence data. We show here that the poor base correlations observed at base-triple positions are the result of two factors. (1) Base covariation is not as strictly required in triples as it is in Watson-Crick pairs. (2) Base-triple structures are less conserved among homologous molecules. A particularity of known triple-helical regions is the presence of multiple base correlations that do not reflect direct pairing. We suggest that natural mutations in base-triples create structural changes that require compensatory mutations in adjacent base-pairs and triples to maintain the triple-helix conformation. On the basis of these observations, we devised two new measures of association that significantly enhance the base-triple signal in correlation studies. We evaluated correlations between base-pairs and single stranded bases, and correlations between adjacent base-pairs. Positions that score well in both analyses are the best triple candidates. This procedure correctly identifies triples, or interactions very close to the proposed triples, in type I and type II tRNAs and in the group I intron.

Base Composition↗