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PubMed2003

[Antigenic and genetic characterizations of Victoria like strain of influenza B viruses isolated in China in 2001].

BACKGROUND: To understand the antigenic and genetic characteristics of Victoria like strain of influenza B virus isolated recently and to provide a scientific evidence for influenza surveillance and monitoring of influenza epidemic in future. METHODS: Viruses were passed in embryonated hen eggs and virion RNA was extracted from allantoic fluid and reverse transcribed to synthesize cDNA. cDNA was amplified by PCR and the PCR product was purified with a purification kit. Afterwards RNA sequence analysis was performed by dideoxynucleotide chain termination and a cloning method. Finally, phylogenetic analysis of the sequencing data was performed with MegAlign. RESULTS: B/Sichuan/63/2001 and B/Zhejiang/2/2001 viruses were antigenically different from B/Shandong/7/97 strain. The substitution of nucleotide sequences of HA1genes of them compared with those of B/Shandong/7/97strain resulted in the change of amino acid sequences in antigenic determinants on HA1 protein domain. The phylogenetic analysis also indicated that strains isolated recently were genetically different from B/Shandong/7/97/strain. However, there was neither differences on the antigenicity nor genetic partern between these two isotates. CONCLUSIONS: The antigenic drift of Victoria-like strain of influenza B virus isolated recently in China has further occurred.

Amino Acid Sequence↗
PubMed1993

The maize stripe virus major noncapsid protein messenger RNA transcripts contain heterogeneous leader sequences at their 5' termini.

Primer extension analyses and a PCR-based cloning strategy were used to identify and characterize 5' nucleotide sequences on the maize stripe virus (MStV) RNA4 mRNA transcripts encoding the major noncapsid protein (NCP). Direct RNA sequence analysis by primer extension showed that the NCP mRNA transcripts had 10-15 nucleotides beyond the 5' terminus of the MStV RNA4 nucleotide sequence. MStV genomic RNAs isolated from ribonucleoprotein particles (RNPs) lacked the additional 5' nucleotides. cDNA clones representing the 5' region of the mRNA transcripts were constructed, and the nucleotide sequences of the 5' regions were determined for 16 clones. Each was found to have a distinct 10-15 nucleotide sequence immediately 5' of the MStV RNA4 sequence. Eleven of 16 clones had the correct MStV RNA4 5' nucleotide sequence, while five showed minor variations at or near the 5' most MStV RNA4 nucleotide. These characteristics show strong similarities to other viral mRNA transcripts which are synthesized by cap snatching.

Base Sequence↗
PubMed2006

A method for rapid similarity analysis of RNA secondary structures.

BACKGROUND: Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. RESULTS: Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. CONCLUSION: The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

Algorithms↗
PubMed1987

Phylogenetic diversity and position of the genus Campylobacter.

RNA sequence analysis has been used to examine the phylogenetic position and structure of the genus Campylobacter. A complete 5S rRNA sequence was determined for two strains of Campylobacter jejuni and extensive partial sequences of the 16S rRNA were obtained for several strains of C. jejuni and Wolinella succinogenes. In addition limited partial sequence data were obtained from the 16S rRNAs of isolates of C. coli, C. laridis, C. fetus, C. fecalis, and C. pyloridis. It was found that W. succinogenes is specifically related to, but not included, in the genus Campylobacter as presently constituted. Within the genus significant diversity was noted. C. jejuni, C. coli and C. laridis are very closely related but the other species are distinctly different from one another. C. pyloridis is without question the most divergent of the Campylobacter isolates examined here and is sufficiently distinct to warrant inclusion in a separate genus. In terms of overall position in bacterial phylogeny, the Campylobacter/Wolinella cluster represents a deep branching most probably located within an expanded version of the Division containing the purple photosynthetic bacteria and their relatives. The Campylobacter/Wolinella cluster is not specifically includable in either the alpha, beta or gamma subdivisions of the purple bacteria.

Base Sequence↗
PubMed2006

Transcriptional genomics associates FOX transcription factors with human heart failure.

BACKGROUND: Specific transcription factors (TFs) modulate cardiac gene expression in murine models of heart failure, but their relevance in human subjects remains untested. We developed and applied a computational approach called transcriptional genomics to test the hypothesis that a discrete set of cardiac TFs is associated with human heart failure. METHODS AND RESULTS: RNA isolates from failing (n=196) and nonfailing (n=16) human hearts were hybridized with Affymetrix HU133A arrays, and differentially expressed heart failure genes were determined. TF binding sites overrepresented in the -5-kb promoter sequences of these heart failure genes were then determined with the use of public genome sequence databases. Binding sites for TFs identified in murine heart failure models (MEF2, NKX, NF-AT, and GATA) were significantly overrepresented in promoters of human heart failure genes (P<0.002; false discovery rate 2% to 4%). In addition, binding sites for FOX TFs showed substantial overrepresentation in both advanced human and early murine heart failure (P<0.002 and false discovery rate <4% for each). A role for FOX TFs was supported further by expression of FOXC1, C2, P1, P4, and O1A in failing human cardiac myocytes at levels similar to established hypertrophic TFs and by abundant FOXP1 protein in failing human cardiac myocyte nuclei. CONCLUSIONS: Our results provide the first evidence that specific TFs identified in murine models (MEF2, NKX, NFAT, and GATA) are associated with human heart failure. Moreover, these data implicate specific members of the FOX family of TFs (FOXC1, C2, P1, P4, and O1A) not previously suggested in heart failure pathogenesis. These findings provide a crucial link between animal models and human disease and suggest a specific role for FOX signaling in modulating the hypertrophic response of the heart to stress in humans.

Adult↗
PubMed2005

Roles of Mg2+ in TPP-dependent riboswitch.

We quantified the effect of Mg(2+) on thiamine pyrophosphate (TPP) binding to TPP-dependent thiA riboswitch RNA. The association constant of TPP binding to the riboswitch at 20 degrees C increased from 1.2 x 10(6) to 50 x 10(6) M(-1) as the Mg(2+) concentration increased from 0 to 1 mM. Furthermore, circular dichroic spectra under various conditions showed that 1 mM Mg(2+) induced a local structural change of the riboswitch, which might be pivotal for TPP binding. These results indicate that a physiological concentration of Mg(2+) can regulate TPP binding to the thiA riboswitch.

5' Untranslated Regions↗
PubMed2006

RNA structural motifs: building blocks of a modular biomolecule.

RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common 'structural elements'. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.

Base Sequence↗
PubMed2003

Positive selection on an acrosomal sperm protein, M7 lysin, in three species of the mussel genus Mytilus.

Marine invertebrate sperm proteins are particularly interesting because they are characterized by positive selection and are likely to be involved in prezyogotic isolation and, thus, speciation. Here, we present the first survey of interspecific and intraspecific variation of a bivalve sperm protein among a group of species that regularly hybridize in nature. M7 lysin is found in sperm acrosomes of mussels and dissolves the egg vitelline coat, permitting fertilization. We sequenced multiple alleles of the mature protein-coding region of M7 lysin from allopatric populations of mussels in the Mytilus edulis species group (M. edulis, M. galloprovincialis, and M. trossulus). A significant McDonald-Kreitman test showed an excess of fixed amino acid replacing substitutions between species, consistent with positive selection. In addition, Kolmogorov-Smirnov tests showed significant heterogeneity in polymorphism to divergence ratios for both synonymous variation and combined synonymous and nonsynonymous variation within M. galloprovincialis. These results indicate that there has been adaptive evolution at M7 lysin and, furthermore, show that positive selection on sperm proteins can occur even when postzygotic reproductive isolation is incomplete.

Acrosome Reaction↗
PubMed2006

Marburgvirus genomics and association with a large hemorrhagic fever outbreak in Angola.

In March 2005, the Centers for Disease Control and Prevention (CDC) investigated a large hemorrhagic fever (HF) outbreak in Uige Province in northern Angola, West Africa. In total, 15 initial specimens were sent to CDC, Atlanta, Ga., for testing for viruses associated with viral HFs known to be present in West Africa, including ebolavirus. Marburgvirus was also included despite the fact that the origins of all earlier outbreaks were linked directly to East Africa. Surprisingly, marburgvirus was confirmed (12 of 15 specimens) as the cause of the outbreak. The outbreak likely began in October 2004 and ended in July 2005, and it included 252 cases and 227 (90%) fatalities (report from the Ministry of Health, Republic of Angola, 2005), making it the largest Marburg HF outbreak on record. A real-time quantitative reverse transcription-PCR assay utilized and adapted during the outbreak proved to be highly sensitive and sufficiently robust for field use. Partial marburgvirus RNA sequence analysis revealed up to 21% nucleotide divergence among the previously characterized East African strains, with the most distinct being Ravn from Kenya (1987). The Angolan strain was less different ( approximately 7%) from the main group of East African marburgviruses than one might expect given the large geographic separation. To more precisely analyze the virus genetic differences between outbreaks and among viruses within the Angola outbreak itself, a total of 16 complete virus genomes were determined, including those of the virus isolates Ravn (Kenya, 1987) and 05DRC, 07DRC, and 09DRC (Democratic Republic of Congo, 1998) and the reference Angolan virus isolate (Ang1379v). In addition, complete genome sequences were obtained from RNAs extracted from 10 clinical specimens reflecting various stages of the disease and locations within the Angolan outbreak. While the marburgviruses exhibit high overall genetic diversity (up to 22%), only 6.8% nucleotide difference was found between the West African Angolan viruses and the majority of East African viruses, suggesting that the virus reservoir species in these regions are not substantially distinct. Remarkably few nucleotide differences were found among the Angolan clinical specimens (0 to 0.07%), consistent with an outbreak scenario in which a single (or rare) introduction of virus from the reservoir species into the human population was followed by person-to-person transmission with little accumulation of mutations. This is in contrast to the 1998 to 2000 marburgvirus outbreak, where evidence of several virus genetic lineages (with up to 21% divergence) and multiple virus introductions into the human population was found.

Angola↗
PubMed2025

Identification of GREM-1 and GAS6 as Specific Biomarkers for Cancer-Associated Fibroblasts Derived from Patients with Non-Small-Cell Lung Cancer.

Background/Objectives: Cancer-associated fibroblasts (CAFs) play a pivotal role in the tumor microenvironment. We conducted an analysis using RNA sequencing to identify specific markers for CAFs compared to normal fibroblasts (NFs) in non-small-cell carcinoma (NSCLC). Methods: CAFs and NFs were isolated and cultured from tumor tissues (primary tumor or metastatic lymph nodes) and matched non-tumor tissues, respectively. Bulk RNA sequencing was conducted on isolated CAFs and normal fibroblast NFs. Differential expressions, gene set enrichment, and CAF subpopulation prediction analyses were performed. Results: During the study period, 27 CAFs and 12 NFs were isolated and cultured from tumor and non-tumor tissues in patients with treatment-na&#xef;ve NSCLC. Among them, 22 CAFs and 11 NFs were included in the RNA sequencing analysis. The 22 CAF samples consisted of 12 adenocarcinomas and 10 squamous cell carcinomas (SqCC), with 16 samples from the lungs and 6 samples from the lymph nodes. Notably, COL11A1, GREM1, CD36, and GAS6 showed a higher expression in CAFs than in NFs, whereas TNC and CXCL2 were more abundantly expressed in NFs. CD36 levels were elevated in CAFs from lymph nodes (LN-CAFs) compared with those from lung specimens (Lung-CAFs) and NFs. COL11A1 levels in Lung-CAFs surpassed those in LN-CAFs and NFs. Both GREM1 and GAS6 showed a strong expression in Lung-CAFs and LN-CAFs relative to NFs. CAFs exhibited features of the myofibroblast CAF subpopulation, whereas NFs displayed traits of the antigen-presenting CAF subtype. In the co-culture model of CAFs and THP-1 cells, the knockdown of GREM1 or GAS6 in CAFs significantly decreased the M2 marker expression in macrophages. Conclusions: In NSCLC, GREM1 and GAS6 can be valuable diagnostic targets for CAFs from primary tumors and metastatic sites; they warrant further study.

cancer-associated fibroblast↗
PubMed2003

[Influenza activity in China from 2000 to 2001].

OBJECTIVE: To understand the epidemics and antigenic drift of influenza viruses in China from 2000 to 2001. METHODS: The viruses were grown in embryonated hen eggs with 9 - 10 days old. The egg allantoic fluids with influenza viruses were used. Virion RNA was transcribed into cDNA by reverse transcriptase while cDNA amplified by PCR. Products of PCR were purified. RNA sequence analysis was then performed. Finally, phylogenetic analysis of the sequencing data was performed with MegAlign (Version 1.03) and Editseq (Version 3.69) software. RESULTS: Data from comparison of amino acid sequence on HA1 domain of HA protein molecule between H1N1 viruses isolated in 2001 and A/Shanghai/7/99 (H1N1) strain indicated that there was only one difference of amino acid located at 190 position (antigenic determinant D). However, phylogenetic analysis showed that there were two distinguishable genetically lineages of H1N1 viruses co-circulating in men in China in 2001. Two antigenically distinct genetic lineages of influenza B viruses were still existing in men in China. Most of influenza B viruses were Yamagata-like strain and there were two different amino acid sequences located at 197 and 199 position on HA1 domain of HA protein molecule, between Victoria-like virus isolated and B/Shandong/7/97 strain. When comparing amino acid sequences on HA1 protein domain of H3N2 viruses isolated in 2000 with those of A/Sydeney/5/97 (H3N2) virus, it was revealed that there were 7 - 8 differences of amino acid sequences between them. However, there were four differences related to amino acid sequences on HA1 protein domain between H3N2 viruses isolated in 2000 and in 2001. These results were further demonstrated by analysis of phylogenic tree. CONCLUSIONS: Influenza was not prevalent in China from 2000 to 2001. The antigenic drifts of H3N2 and B/Victoria-like viruses occurred. Two antigenically distinct genetic lineages of influenza B viruses were still co-circulating in men in China. Two genetically distinct lineages of influenza A (H1N1) virus were also co-circulating in men in China.

Antigens, Viral↗
PubMed2026

From transcriptomic profiling to precision oncology: a bibliometric analysis of RNA sequencing in acute myeloid leukemia.

BACKGROUND: RNA sequencing (RNA-seq) has become an important tool for investigating the molecular heterogeneity of acute myeloid leukemia (AML); however, the global development and thematic evolution of this field remain inadequately characterized. OBJECTIVE: To map the global landscape of AML RNA-seq research and identify major knowledge domains, emerging themes, and temporal changes in research priorities. METHODS: Publications indexed in the Web of Science Core Collection and Scopus between January 1, 2007, and August 18, 2025, were retrieved. After database filtering, merging, and deduplication, 3,460 articles and reviews were included. CiteSpace, VOSviewer, the bibliometrix R package, and Microsoft Excel were used to analyze publication trends, collaboration networks, co-citation structures, keyword evolution, and citation bursts. RESULTS: Publication output increased steadily, accelerating after 2014. China contributed the largest number of publications (n&#x202f;=&#x202f;547, 15.8%), whereas the United States had the highest total citation count. Major publication outlets spanned hematology, oncology, genomics, and molecular biology. Co-citation analysis identified prominent themes involving next-generation sequencing, gene mutations, KMT2A rearrangements, epigenetic dysregulation, leukemia-initiating cells, drug resistance, biomarkers, T-cell biology, and single-cell sequencing. Earlier literature emphasized sequencing technologies, gene expression profiling, and molecular alterations, whereas recent publications show increasing representation of cellular heterogeneity, single-cell transcriptomics, drug resistance, biomarker applications, immune-related research, and computational interpretation. CONCLUSION: While molecular characterization remains foundational, AML RNA-seq research has broadened to encompass increasingly prominent cellular, functional, computational, and translational dimensions. This study provides a structured overview of the field; nevertheless, bibliometric prominence should not be interpreted as direct evidence of clinical utility.

RNA sequencing↗
PubMed2000

[Further study on the genetic characteristics of a strain of A/PR/8/34/].

OBJECTIVE: Through the test and analysis of nucleotide sequences of seven different RNA segments of the virion to exclude the possibility that A/Guangdong/6/91 (H1N1) strain might be derived from laboratory contamination and to determine how many RNA segments are there with nucleotide sequence difference between A/Guangdong/6/91 (H1N1) and A/PR/8/34 (H1N1) viruses, as well as to determine is A/Guangdong/6/91 virus a reassortant? METHODS: Virion RNA was transcribed into cDNA by reverse transcriptase, cDNA was amplified by PCR, the products of PCR were purified. Afterward, RNA sequence test was performed by the dideoxynucleotide chain termination method using synthetic oligodeoxynucleotide primers. RESULTS: There are no nucleotide sequence differences in RNA segments 6 and 7 between A/Guangdong/6/91 (H1N1) and PR8 strains, while there are 20,5, 11, 7 and 6 differences in nucleotide sequences of RNA segments 1, 2, 3, 5 and 8 between these two strains, respectively. These differences induce 10, 2, 1, 0 and 4 differences in amino acid sequences on PB2, PB1, PA,NP and NS protein molecules between A/Guangdong/6/91 (H1N1) and PR8 strains, respectively. CONCLUSIONS: The possibility of laboratory contamination of A/Guangdong/6/91 (H1N1) virus can be ruled out completely. A/Guangdong/6/91 (H1N1) virus is a PR8 like strain, but not a reassortant.

China↗
PubMed1992

Peanut stunt virus satellite RNA: analysis of sequences that affect symptom attenuation in tobacco.

The V-satellite RNA (V-satRNA) of peanut stunt virus (PSV) has no effect on symptoms produced in tobacco by PSV. In contast, the G-satRNA induced complete or nearly complete suppression of systemic symptom development. Because G-satRNA differs from V-satRNA in only five nucleotide positions, these two satRNAs provide excellent material for investigating the molecular basis of satRNA-mediated symptom attenuation. For this purpose, we constructed transcription vectors containing full-length cDNA clones from which infectious RNA transcripts can be synthesized in vitro, and produced chimeric and mutant satRNA molecules. Although an A----C substitution at position 362 of the V-satRNA molecule delayed systemic symptom development and reduced symptom severity, changes at both nucleotide positions 226 (C----U) and 362 (A----C) of V-satRNA were required for suppression of systemic symptom development. Our results are consistent with the idea that PSV satRNAs are noncoding molecules that exert their biological activities by directly interacting with host/viral components.

Base Sequence↗
PubMed1999

Cloning and sequencing of peach rosette mosaic virus RNA1.

The complete nucleotide sequence of peach rosette mosaic nepovirus (PRMV) RNA1 has been determined. A grapevine isolate of PRMV from Michigan was propagated and purified and cDNA clones representing 99. 5% of the RNA1 were constructed. The cDNA and direct RNA sequence analysis revealed a RNA species of 8004 nucleotides, excluding a 3' polyadenylated tail. The 5'- and 3'-untranslated regions were 52 and 1474 nucleotides, respectively. Computer analysis of the PRMV RNA1 nucleotide sequence unveiled a single long open reading frame of 6477 nucleotides, which is capable of encoding a 240 kDa polyprotein. Analysis of the predicted amino acid sequence of RNA1 revealed amino acid motifs characteristic of a replicase, proteinase, NTP-binding protein and a proteinase cofactor. The order and identity of these putative proteins are consistent with other nepoviruses. Analysis of PRMV RNA1 further distinguishes the taxonomic subdivisions within the nepovirus group, confirms the subgroup three status of PRMV and lays the groundwork for a replicase-mediated resistance strategy.

Amino Acid Sequence↗
PubMed2005

Accelerated probabilistic inference of RNA structure evolution.

BACKGROUND: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. RESULTS: We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs) is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. CONCLUSION: A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License.

Algorithms↗