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RNA Sequences (rna + sequence)
Selected AbstractsMolecular Phylogeny of Stentor (Ciliophora: Heterotrichea) Based on Small Subunit Ribosomal RNA SequencesTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2007YING-CHUN GONG ABSTRACT. To determine the phylogenetic position of Stentor within the Class Heterotrichea, the complete small subunit rRNA genes of three Stentor species, namely Stentor polymorphus, Stentor coeruleus, and Stentor roeseli, were sequenced and used to construct phylogenetic trees using the maximum parsimony, neighbor joining, and Bayesian analysis. With all phylogenetic methods, the genus Stentor was monophyletic, with S. roeseli branching basally. [source] Morphological, Small Subunit rRNA, and Physiological Characterization of Trimyema minutum (Kahl, 1931), an Anaerobic Ciliate from Submarine Hydrothermal Vents Growing from 28°C to 52°CTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2002MANUELA BAUMGARTNER ABSTRACT. A thermophilic strain of Trimyema minutum was isolated from the hydrothermally heated sea floor at Vulcano Island (Italy) and cultivated monoxenically on Marinobaaer sp. and Methanococcus thermolithotrophicus. It can be propagated strictly an aerobically and is sensitive to oxygen: if exposed to air at 48°C all cells die within 60 min. It grows from 0.45,7.2% (w/v) salt and at pH 6.0,8.0. The isolate is the most extreme thermophilic ciliate which ever has been cultivated, exhibiting an optimal growth temperature of 48°C (doubling time 6 h). Growth occurs between 28°C and 52°C. Trimyema minutum is redescribed using live observation and silver impregnation. Its morphology and the small subunit ribosomal RNA sequence is distinctly different from that of T. compressum, but morphology is highly similar to that of T. shoalsiaNerad et al. 1995, which is thus probably a junior synonym of T. minutum. To stabilize the bewildering species taxonomy in Trimyema. we suggest to recognize our population as a neotype of T. minutum. [source] Human telomeric G-quadruplex: structures of DNA and RNA sequencesFEBS JOURNAL, Issue 5 2010Anh Tuân Phan Telomeres play an important role in cellular aging and cancer. Human telomeric DNA and RNA G-rich sequences are capable of forming a four-stranded structure, known as the G-quadruplex. Such a structure might be important for telomere biology and a good target for drug design. This minireview describes the structural diversity or conservation of DNA and RNA human telomeric G-quadruplexes, discusses structural views on targeting these G-quadruplexes and presents some future challenges for structural studies. [source] pyr RNA binding to the Bacillus caldolyticus PyrR attenuation protein , characterization and regulation by uridine and guanosine nucleotidesFEBS JOURNAL, Issue 4 2008Casper M. Jørgensen The PyrR protein regulates expression of pyrimidine biosynthetic (pyr) genes in many bacteria. PyrR binds to specific sites in the 5, leader RNA of target operons and favors attenuation of transcription. Filter binding and gel mobility assays were used to characterize the binding of PyrR from Bacillus caldolyticus to RNA sequences (binding loops) from the three attenuation regions of the B. caldolyticus pyr operon. Binding of PyrR to the three binding loops and modulation of RNA binding by nucleotides was similar for all three RNAs. The apparent dissociation constants at 0 °C were in the range 0.13,0.87 nm in the absence of effectors; dissociation constants were decreased by three- to 12-fold by uridine nucleotides and increased by 40- to 200-fold by guanosine nucleotides. The binding data suggest that pyr operon expression is regulated by the ratio of intracellular uridine nucleotides to guanosine nucleotides; the effects of nucleoside addition to the growth medium on aspartate transcarbamylase (pyrB) levels in B. subtilis cells in vivo supported this conclusion. Analytical ultracentrifugation established that RNA binds to dimeric PyrR, even though the tetrameric form of unbound PyrR predominates in solution at the concentrations studied. [source] Barley yellow dwarf viruses (BYDVs) preserved in herbarium specimens illuminate historical disease ecology of invasive and native grassesJOURNAL OF ECOLOGY, Issue 6 2007CAROLYN M. MALMSTROM Summary 1In plant invasion ecology, viruses and other pathogens are often considered in terms of the enemy release hypothesis, which predicts that plants become invasive in new ranges if they escape pathogens from their home range. However, pathogens may sometimes facilitate host spread rather than hinder it. 2Previously, we hypothesized that apparent competition mediated by barley and cereal yellow dwarf viruses (Luteoviridae: BYDVs, CYDVs) may have facilitated historical grassland invasion in California, USA, where Eurasian grasses displaced native grasses in the 18th and 19th centuries (the disease facilitation hypotheses). However, this could have happened only if the viruses were present during the invasion, which is unknown. 3To investigate the historical ecology of BYDVs in California grasses, we analysed preserved virus infections in herbarium specimens and used the historical virus sequences to determine rough time estimates of relevant phylogenetic events. 4The historical viral RNA sequences we identified in invasive and native grasses date from 1917 and are among the oldest recovered from plants thus far and the oldest from North America. 5Herbarium evidence and phylogenetic analysis suggest that BYDVs were likely to have been present in wild grasses during the California grassland invasion and to have shared some functional characteristics with present-day isolates, supporting the disease facilitation hypothesis. 6We found evidence of virus spread from California to Australia (or, less likely, from Australia to California) in the late 19th century, when much horticultural exchange occurred, as well as potential correspondence in the timing of virus diversification events and the beginning of extensive human exchange between the Old and New Worlds. 7Synthesis. Increasing evidence indicates that viruses are important in the ecology of grasslands and may, in some cases, mediate apparent competition among species. Historical data provide essential insight into plant virus ecology and suggest the need to examine human influence on plant virus diversification and spread within natural ecosystems. [source] Frequent detection of cell-associated HIV-1 RNA in patients with plasma viral load <50 copies/mlJOURNAL OF MEDICAL VIROLOGY, Issue 10 2007Bernd Kupfer Abstract Despite prolonged undetectable plasma viral load some HIV-1 infected patients have been reported to develop resistance-associated mutations leading to treatment failure. The mechanisms for this phenomenon and the point of origin for residual viral evolution are still not elucidated. In order to quantify cell-associated HIV-1 RNA in patients with different levels of plasma viremia paired cell-associated HIV-1 RNA loads and plasma viral loads were determined. Weak inverse correlation between these parameters and the amounts of CD4+ T cells was observed, whereas there was no correlation between viral loads and CD8+ T cells or CD14+ monocytes, respectively. In a subset of patients, cell-associated and plasma HIV-1 env V3 sequences were analyzed. Plasma viral load and the amount of cell-associated HIV-RNA correlated strongly. However, in 62.3% of patients with undetectable plasma viral load cell-associated HIV-RNA could be detected. Analyses of HIV-RNA in plasma and blood cells showed identical sequences in 4/19 patients, whereas the majority of patients had differing HIV-1 RNA sequences in plasma and cells, respectively. In summary, this study shows that residual viral replication in peripheral blood still occurs in the majority of patients with undetectable plasma viral load. Since these replication events could lead to ongoing viral evolution it should be considered to optimize antiretroviral therapy in order to minimize the development of drug resistance. J. Med. Virol. 79:1440,1445, 2007. © Wiley-Liss, Inc. [source] Engineered 5S ribosomal RNAs displaying aptamers recognizing vascular endothelial growth factor and malachite greenJOURNAL OF MOLECULAR RECOGNITION, Issue 2 2009Xing Zhang Abstract In previous work, Vibrio proteolyticus 5S rRNA was shown to stabilize 13,50 nucleotide "guest" RNA sequences for expression in Escherichia coli. The expressed chimeric RNAs accumulated to high levels in E. coli without being incorporated into ribosomes and without obvious effects on the host cells. In this work, we inserted sequences encoding known aptamers recognizing a protein and an organic dye into the 5S rRNA carrier and showed that aptamer function is preserved in the chimeras. A surface plasmon resonance competitive binding assay demonstrated that a vascular endothelial growth factor (VEGF) aptamer/5S rRNA chimera produced in vitro by transcriptional runoff could compete with a DNA aptamer for VEGF, implying binding of the growth factor by the VEGF "ribosomal RNA aptamer." Separately, a 5S rRNA chimera displaying an aptamer known to increase the fluorescence of malachite green (MG) also enhanced MG fluorescence. Closely related control rRNA molecules showed neither activity. The MG aptamer/5S rRNA chimera, like the original MG aptamer, also increased the fluorescence of other triphenyl methane (TPM) dyes such as crystal violet, methyl violet, and brilliant green, although less effectively than with MG. These results indicate that the molecular recognition properties of aptamers are not lost when they are expressed in the context of a stable 5S rRNA carrier. Inclusion of the aptamer in a carrier may facilitate production of large quantities of RNA aptamers, and may open an approach to screening aptamer libraries in vivo. Copyright © 2009 John Wiley & Sons, Ltd. [source] Divergent modulation of iron regulatory proteins and ferritin biosynthesis by hypoxia/reoxygenation in neurones and glial cellsJOURNAL OF NEUROCHEMISTRY, Issue 5 2005Carlo Irace Abstract Ferritin, the main iron storage protein, exerts a cytoprotective effect against the iron-catalyzed production of reactive oxygen species, but its role in brain injury caused by hypoxia/reoxygenation is unclear. Ferritin expression is regulated mainly at post-transcriptional level by iron regulatory proteins (IRP1 and IRP2) that bind specific RNA sequences (IREs) in the 5,untranslated region of ferritin mRNA. Here, we show that hypoxia decreases IRP1 binding activity in glial cells and enhances it in cortical neurons. These effects were reversed by reoxygenation in both cell types. In glial cells there was an early increase of ferritin synthesis during hypoxia and reoxygenation. Conversely, in cortical neurons, ferritin synthesis increased during the late phase of reoxygenation. Steady-state analysis of ferritin mRNA levels suggested that ferritin synthesis is regulated mainly post-transcriptionally by IRPs in glioma cells, both transcriptionally and post-transcriptionally in type-1 astrocytes, and mainly at transcriptional level in an IRP-independent way in neurons. The different regulation of ferritin expression may account for the different vulnerability of neurons and glial cells to the injury elicited by oxygen and glucose deprivation (OGD)/reoxygenation. The greater vulnerability of cortical neurons to hypoxia-reoxygenation was strongly attenuated by the exogenous administration of ferritin during OGD/reoxygenation, suggesting the possible cytoprotective role exerted by this iron-segregating protein. [source] Noninvasive prenatal diagnosis of aneuploidy using cell-free nucleic acids in maternal blood: promises and unanswered questionsPRENATAL DIAGNOSIS, Issue 1 2008William M. Puszyk Abstract The discovery of cell-free fetal (cff) DNA and RNA in the maternal circulation has driven developments in noninvasive prenatal diagnosis (NIPD) for the past decade. Detection of paternally derived alleles in cff DNA is becoming well established. Now much interest is focussing on NIPD of fetal chromosomal abnormalities, such as trisomy 21, which is a considerable challenge because this demands accurate quantitative measurements of the amounts of specific cff DNA or cff RNA sequences in maternal blood samples. Emerging strategies for distinguishing and quantifying the fetal nucleic acids in the maternal circulation promise continued development of the field, and pose a number of unanswered questions. Copyright © 2007 John Wiley & Sons, Ltd. [source] Molecular Evidence that Phylogenetically Diverged Ciliates Are Active in Microbial Mats of Deep-Sea Cold-Seep SedimentTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2010KIYOTAKA TAKISHITA ABSTRACT. Cold seeps are areas of the seafloor where hydrogen sulfide- and methane-rich fluid seepage occurs, often sustaining chemosynthetic ecosystems. It is well known that both archaea and bacteria oxidize sulfides and methane to produce chemical energy and that several endemic animals use this energy to thrive in cold seeps. On the other hand, there is little knowledge regarding diversity and ecology of microbial eukaryotes in this ecosystem. In this study we isolated environmental RNA and DNA from microbial mats of cold-seep sediment in Sagami Bay, Japan, and retrieved eukaryotic small-subunit ribosomal RNA sequences with polymerase chain reaction methods followed by clone library construction. Most RNA-derived clones obtained were from ciliates, although DNA-derived clones were mainly from the fungus Cryptococcus curvatus, suggesting that ciliates are active in the environment. The ciliate sequences were phylogenetically diverse, and represented eight known class lineages as well as undesignated lineages. Because most ciliates are bacterivorous, it is highly likely that the ciliates for which sequences were recovered play a role in the food web of this ecosystem as grazers of microbial mats. In addition, given that the environment studied is under highly reduced (anoxic) conditions, based on the prokaryotic community structure deduced from T-RFLP profiles, the ciliates detected may be obligatory or facultative anaerobes. [source] Linkage and Association Study of Late-Onset Alzheimer Disease Families Linked to 9p21.3ANNALS OF HUMAN GENETICS, Issue 6 2008S. Züchner Summary A chromosomal locus for late-onset Alzheimer disease (LOAD) has previously been mapped to 9p21.3. The most significant results were reported in a sample of autopsy-confirmed families. Linkage to this locus has been independently confirmed in AD families from a consanguineous Israeli-Arab community. In the present study we analyzed an expanded clinical sample of 674 late-onset AD families, independently ascertained by three different consortia. Sample subsets were stratified by site and autopsy-confirmation. Linkage analysis of a dense array of SNPs across the chromosomal locus revealed the most significant results in the 166 autopsy-confirmed families of the NIMH sample. Peak HLOD scores of 4.95 at D9S741 and 2.81 at the nearby SNP rs2772677 were obtained in a dominant model. The linked region included the cyclin-dependent kinase inhibitor 2A gene (CDKN2A), which has been suggested as an AD candidate gene. By re-sequencing all exons in the vicinity of CDKN2A in 48 AD cases, we identified and genotyped four novel SNPs, including a non-synonymous, a synonymous, and two variations located in untranslated RNA sequences. Family-based allelic and genotypic association analysis yielded significant results in CDKN2A (rs11515: PDT p = 0.003, genotype-PDT p = 0.014). We conclude that CDKN2A is a promising new candidate gene potentially contributing to AD susceptibility on chromosome 9p. [source] A serological and virological survey for evidence of infection with Newcastle disease virus in Australian chicken farmsAUSTRALIAN VETERINARY JOURNAL, Issue 6 2007VG Kite Objective, To determine the prevalence and distribution of antibodies to Newcastle disease virus on Australian chicken farms and to determine the pathotype and relationships of the Newcastle disease viruses present on those farms. Design, A cross-sectional survey of 753 commercial chicken farms. Procedure, The survey comprised a detailed questionnaire and collection of venous blood samples. The titre of antibodies to Newcastle disease virus was determined by haemagglutination inhibition. Virus isolation was conducted from cloacal and tracheal swabs taken from chickens in serologically positive flocks. Virus isolates were pathotyped on the basis of the deduced Fusion protein cleavage site determined by nucleotide sequencing of a 265 bp region of the genome in the region of the cleavage site. Results, Antibody evidence of Newcastle disease virus infection was found on 300 of the 753 surveyed farms throughout all 11 geographic regions of the survey. The highest prevalence occurred in the Sydney basin, New South Wales and Victoria east regions. Antibody titres were also highest in the regions where serologically positive flocks were most prevalent. The 259 virus isolates revealed nine different RNA sequences. Of the nine virus groups isolated, the most common group W was identical in sequence to the V4 vaccine strain. Five of the other groups had novel RNA sequences in the region of the F protein cleavage site. Conclusions, Antibodies to Newcastle disease virus are highly prevalent in the Australian chicken flock but all identified strains were avirulent in nature. [source] Cover Picture: Targeting RNA with Small Molecules (ChemBioChem 10/2003)CHEMBIOCHEM, Issue 10 2003Yitzhak Tor Prof. Dr. Abstract The cover picture shows the processes involved in the search for small molecules as potent and selective RNA binders. Motivation comes from the desire to control cell function at the RNA level and to identify novel approaches to specifically combat pathogens by targeting their unique RNA sequences or RNA,protein complexes. Inspiration comes from nature; in particular, from aminoglycosides, a family of naturally occurring antibiotics that has been shown to target the bacterial ribosome. The discovery process involves identifying RNA targets (schematically shown as a ribosome or a virus), devising unique assays (e.g. a solid-phase assay), and generating the necessary knowledge and lead structures through design, synthesis, and systematic evaluation of biological activity. Further details can be found in the article by Y. Tor on p. 998 ff. [source] | |||||||||||||