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Results for “Ribosome Profiling”

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PubMed2003

Evaluation of hypothalamic gene expression in mice divergently selected for heat loss.

Mouse lines divergently selected for heat loss were evaluated for correlated responses in the hypothalamic transcriptome. High (MH) heat loss mice have approximately 50% greater heat loss, approximately 35% less body fat, approximately 20% greater feed intake, approximately 100% greater locomotor activity levels, and higher core body temperature compared with low (ML) heat loss mice. We evaluated hypothalamic expression between inbred lines derived from MH and ML lines (IH and IL, respectively) using cDNA microarrays and selected genes previously isolated in a large differential-display PCR experiment. Northern analysis was used to confirm differences, revealing higher hypothalamic mRNA expression of oxytocin (Oxt) and tissue inhibitor of metalloproteinase 2 (Timp-2) in the IH line. Real-time PCR assays were developed for Oxt, Timp-2, and ribosomal protein L3 (Rpl3, previously found to be upregulated in IL) and confirmed differential expression of these genes with potential physiological relevance in energy balance. These results provide information on correlated responses in the transcriptome of mice selected for high and low energy expenditure and reveal new information regarding genetic regulation of energy balance.

Animals↗

PubMed2006

Specific effects of ribosome-tethered molecular chaperones on programmed -1 ribosomal frameshifting.

The ribosome-associated molecular chaperone complexes RAC (Ssz1p/Zuo1p) and Ssb1p/Ssb2p expose a link between protein folding and translation. Disruption of the conserved nascent peptide-associated complex results in cell growth and translation fidelity defects. To better understand the consequences of deletion of either RAC or Ssb1p/2p, experiments relating to cell growth and programmed ribosomal frameshifting (PRF) were assayed. Genetic analyses revealed that deletion of Ssb1p/Ssb2p or of Ssz1p/Zuo1p resulted in specific inhibition of -1 PRF and defects in Killer virus maintenance, while no effects were observed on +1 PRF. These factors may provide a new set of targets to exploit against viruses that use -1 PRF. Quantitative measurements of growth profiles of isogenic wild-type and mutant cells showed that translational inhibitors exacerbate underlying growth defects in these mutants. Previous studies have identified -1 PRF signals in yeast chromosomal genes and have demonstrated an inverse relationship between -1 PRF efficiency and mRNA stability. Analysis of published DNA microarray experiments reveals conditions under which Ssb1, Ssb2, Ssz1, and Zuo1 transcript levels are regulated independently of those of genes encoding ribosomal proteins. Thus, the findings presented here suggest that these trans-acting factors could be used by cells to posttranscriptionally regulate gene expression through -1 PRF.

DNA-Binding Proteins↗

PubMedDate not supplied

Molecular characterization of Bulinus globosus and B. nasutus on Zanzibar, and an investigation of their roles in the epidemiology of Schistosoma haematobium.

The ribosomal internal transcribed spacer (ITS) regions of both Bulinus globosus and B. nasutus from Zanzibar were amplified and restricted with 6 enzymes. Restriction products were separated by polyacrylamide gel electrophoresis and visualized by ethidium bromide staining. Considerable genetic variation was observed at 3 levels: (i) between species, (ii) among populations and (iii) among individuals. In addition, the 18S ribosomal deoxyribonucleic acid gene was amplified from both species and the products were also restricted with several enzymes. No variation was detected. Nucleotide diversity of the ITS was estimated to be approximately 0.019 for both species and nucleotide divergence between species was estimated to be 0.03. Restriction profiles differentiated these snail species and may prove useful for identification purposes. Only B. globosus populations were found to be naturally infected with Schistosoma haematobium. From laboratory infection studies of progeny snails, B. nasutus appeared to be refractory to S. haematobium, whereas certain B. globosus populations were susceptible to laboratory challenge.

Animals↗

PubMed2006

Diversity of bacteria contaminating paper machines.

Formation of microbial biofilms and slimes is a general and serious problem in the operation of paper machines. Studies of microbial populations in paper machine-derived biofilms have been conducted using standard microbiological procedures; however, the bacterial genera present in this type of samples as well as their diversity are quite poorly known. Here, the bacterial diversity of 38 process water and 22 biofilm samples from four different Finnish paper machines were analyzed by length heterogeneity analysis of PCR-amplified 16S ribosomal DNA (LH-PCR). In addition, sequencing of the amplified 16S rRNA gene from 69 clones was conducted for characterization of the bacterial genera present in biofilm and slime samples. The LH-PCR profiles of both the free-living (process waters) and immobilized (biofilms) bacteria were diverse at all stages of the papermaking process. Out of the 69 sequenced clones, 44 belonged to alpha-Proteobacteria, most of which were close to the nitrogen-fixing root nodule genera Sinorhizobium, Rhizobium and Azorhizobium. Other clones were assigned to beta- and gamma-Proteobacteria and the phylum Bacteroidetes. In addition, eight of the clones were assigned to a yet uncultivated phylum, TM7. Finally, epifluorescence microscopy revealed that Gram-negative bacteria were predominant in both the biofilm (65%) and process water (54%) samples and a small coccoid cell morphology was most common in all samples. Together, our results show that the analysis of microbial samples from paper machines using modern molecular biology techniques adds valuable information and should, therefore, be useful as a more specific and sensitive microbiological method for the paper industry. This information could further be applied, e.g., in the development of more specific and environmental friendly antimicrobial agents for paper mills.

Bacteria↗

PubMed2002

Transcript profiling of human platelets using microarray and serial analysis of gene expression.

Human platelets are anucleate blood cells that retain cytoplasmic mRNA and maintain functionally intact protein translational capabilities. We have adapted complementary techniques of microarray and serial analysis of gene expression (SAGE) for genetic profiling of highly purified human blood platelets. Microarray analysis using the Affymetrix HG-U95Av2 approximately 12 600-probe set maximally identified the expression of 2147 (range, 13%-17%) platelet-expressed transcripts, with approximately 22% collectively involved in metabolism and receptor/signaling, and an overrepresentation of genes with unassigned function (32%). In contrast, a modified SAGE protocol using the Type IIS restriction enzyme MmeI (generating 21-base pair [bp] or 22-bp tags) demonstrated that 89% of tags represented mitochondrial (mt) transcripts (enriched in 16S and 12S ribosomal RNAs), presumably related to persistent mt-transcription in the absence of nuclear-derived transcripts. The frequency of non-mt SAGE tags paralleled average difference values (relative expression) for the most "abundant" transcripts as determined by microarray analysis, establishing the concordance of both techniques for platelet profiling. Quantitative reverse transcription-polymerase chain reaction (PCR) confirmed the highest frequency of mt-derived transcripts, along with the mRNAs for neurogranin (NGN, a protein kinase C substrate) and the complement lysis inhibitor clusterin among the top 5 most abundant transcripts. For confirmatory characterization, immunoblots and flow cytometric analyses were performed, establishing abundant cell-surface expression of clusterin and intracellular expression of NGN. These observations demonstrate a strong correlation between high transcript abundance and protein expression, and they establish the validity of transcript analysis as a tool for identifying novel platelet proteins that may regulate normal and pathologic platelet (and/or megakaryocyte) functions.

Base Sequence↗

PubMed2004

Regulation of translation and cancer.

One of the effects of oncogenic signaling appears to be differentiated recruitment of mRNA's to ribosomes. The mRNA's so affected frequently encode proteins involved in growth regulation cell-cell interaction. These functions are critical for both cancer and development, potentially suggesting that the normal role of differential translation may be during development. It is not known whether this effect is sufficient to induce cancer from cells with an initial non-neoplastic gene expression profile.

Adaptor Proteins, Signal Transducing↗

PubMed2001

Ribotyping of Burkholderia pseudomallei from clinical and soil isolates in Thailand.

Burkholderia pseudomallei is a soil saprophyte that causes melioidosis in humans and animals. Restriction fragment length polymorphism of the ribosomal DNA regions (ribotyping) were analyzed in 577 isolates comprising 371 clinical and 206 soil isolates collected throughout Thailand in 1997. A total of 77 distinct ribotype patterns consisting of 2-9 bands with sizes ranging from 2.8 to >23 kb were found. Twelve major ribotypes were identified of which types 3, 8 and 23 were commonly found (278/577, 48.2%) in both clinical (217/371, 58.5%) and environmental isolates (61/206, 29.6%). Three unique environmental types were found whereas a unique clinical type was not observed. Even though ribotypes show high heterogeneity in the rDNA region, the unique environmental patterns were clearly different from the clinical patterns as clearly seen by UPGMA dendrogram. Moreover, the three major types (types 3, 8 and 23) were discovered in nearly half of B. pseudomallei isolates. Subtyping of these major ribotypes in correlation with clinical profiles may help researchers to identify the virulence factor of the organism.

Arabinose↗

PubMed2003

High-content profiling of drug-drug interactions: cellular targets involved in the modulation of microtubule drug action by the antifungal ketoconazole.

Drug-drug interactions play an important role in the discovery and development of therapeutic agents. High-content profiling was developed to unravel the complexity of these interactions by providing multiparameter measurements of target activity at the cellular and subcellular levels. Two microtubule drugs, vinblastine and curacin A, were shown to modulate multiple cellular processes, including nuclear condensation, the activation of the extracellular signal-regulated kinase pathway as measured by RSK90 phosphorylation, and the regulation of the microtubule cytoskeleton as measured in detergent-extracted cells. The heterogeneity of the response, addressed through population analysis and multiparameter comparisons within single cells, was consistent with vinblastine and curacin A having similar effects on nuclear morphology and 90 kDa ribosomal s6 kinase (RSK90) phosphorylation despite having distinct effects on the microtubule cytoskeleton. Ketoconazole, originally developed as an antifungal agent, exhibited concentration-dependent inhibitory and potentiating effects on both drugs in HeLa and PC-3 cells at concentration ranges near the plasma levels of ketoconazole attained in human subjects. Thus, high-content profiling was used to dissect the cellular and molecular responses to interacting drugs and is therefore a potentially important tool in the selection, characterization, and optimization of lead therapeutic compounds.

Animals↗

PubMed2005

Virulence and molecular diversity in Colletotrichum graminicola from Brazil.

Genetic diversity among 37 isolates of the sorghum anthracnose pathogen Colletotrichum graminicola, from four geographically distinct regions of Brazil, was evaluated by RAPD and RFLP-PCR markers and virulence characters on a set of 10 differential sorghum genotypes. Twenty-two races were identified and race 13B was the most frequent, but present in only two regions. RAPD analysis revealed 143 polymorphic bands that grouped the isolates according to their geographic origin, but not by their virulence phenotypes. RFLP with HaeIII, MspI, HinfI, HhaI, HpaII, EcoRI, HindIII, PstI, RsaI, Taq alphaI, and AluI enzymes over ITS domains and 5.8 rDNA genes of C. graminicola did not show differences among the isolates, indicating high conservation of these restriction sites. Molecular polymorphism was observed among isolates belonging to the same race. No association between virulence phenotypes and molecular profiles was observed.

Brazil↗

PubMed1997

Hormonema schizolunatum, a new species of dothideaceous black yeasts from phyllosphere.

Two black yeast isolates from plants from the Canary Islands (Spain) are described and illustrated. Absence of Woronin bodies at simple septal pores, local coralloid terminal hyphal cells, indeterminate thallus maturation, the presence of budding cells and local conversion to meristematic growth all indicate a relationship to the Dothideaceae (Dothideales, Ascomycota). Morphological properties were consistent with the genus Hormonema Lagerberg & Melin, as defined by presence of percurrent conidiogenous loci alongside undifferentiated hyphae, and results of PCR-ribotyping supported this classification. The isolates were judged to belong to a hitherto undescribed species, characterized in particular by curved conidia soon developing transverse septa. The physiological profile of this species is also described.

Cell Differentiation↗

PubMed1998

Analysis of sequence homogenisation in rDNA arrays of Haemonchus contortus by denaturing gradient gel electrophoresis.

Testing different theories of concerted evolution experimentally has been hampered mainly due to the lack of appropriate model systems and technical limitations. In this study, we employed a denaturing gradient gel electrophoresis (DGGE) approach for the display and definition of nucleotide variations in the second internal transcribed spacer (ITS-2) of ribosomal DNA (rDNA) of the parasitic nematode, Haemonchus contortus. The ITS-2 was amplified from individual adult nematodes by PCR and subjected to DGGE. Of the 94 individuals (representing nine different populations) analysed, 13 different DGGE profiles were displayed. Eighteen bands representing those profiles were excised and sequenced. Sequencing defined 13 different types of ITS-2 with 12 nucleotide variations (4 transitions, 5 transversions, 1 insertion and 2 deletions) which could be related to particular positions of the predicted secondary structure for the ITS-2 pre-rRNA. The results showed that individuals of interbreeding populations of H. contortus can have rDNA arrays that are partially or fully homogenised for different sequence variants (despite interindividual variation), suggesting that the homogenisation process is driven mainly by intrachromosomal exchange. The findings also demonstrated the capacity of the DGGE-sequencing strategy to quantify the frequency of ITS-2 sequence types within individual nematodes from different populations without the need for cloning or Southern blot procedures. This has important implications for studying the mechanisms of sequence homogenisation in rDNA and pre-rRNA processing as well as for elucidating speciation events and population differentiation at the molecular level.

Animals↗

PubMed2002

Differential display of vincristine-resistance-related genes in gastric cancer SGC7901 cell.

AIM: To isolate and clone the vincristine-resistance-related genes in gastric cancer SGC7901 cell line and to clarify the multidrug-resistant molecular mechanism of gastric cancer cells. METHODS: The modified differential-display polymerase chain reaction (DD-PCR) was used to examine differences in the mRNA composition of Vincristine-resistant gastric cancer SGC 7901 cells (SGC7901/VCR), induced by vincristine sulfate versus SGC7901cells. The differentially expressed cDNA fragments were confirmed by reverse Northern analysis, sequencing, BLAST analysis and Northern bolt analysis. RESULTS: The DD-PCR identified that 54 cDNA fragments were preferentially expressed in SGC 7901/VCR cells. When these cDNA fragments were analyzed by reverse Northern blot, twenty were reproducibly expressed at high level in SGC7901/VCR. Sequencing and BLAST analysis revealed that seven of the genes were known genes:ADP-ribosylation factor 4, Cytochrome oxidase subunit II, Ss-A/Ro ribonucleoprtein autoantigen 60kd subunit,ribosomal protein S13, galaectin-8 gene, oligophrenin 1 mRNA, ribosomal protein L23 mRNA; thirteen of the genes were unknown genes. The length and abundance of the four unknown genes were further confirmed by Northern blot analysis. CONCLUSION: The twenty differential known and unknown genes may be related to the vincristine-resistant mechanism in human gastric cancer SGC7901 cell line.

ADP-Ribosylation Factors↗

PubMed2005

Molecular characterization of cyanobacterial diversity in a shallow eutrophic lake.

We have studied the diversity of pelagic cyanobacteria in Lake Loosdrecht, The Netherlands, through recovery and analysis of small subunit ribosomal RNA gene sequences from lake samples and cyanobacterial isolates. We used an adapted protocol for specific amplification of cyanobacterial rDNA for denaturing gradient gel electrophoresis (DGGE) analysis. This protocol enabled direct comparison of cyanobacterial community profiles with overall bacterial profiles. The theoretical amplification specificity of the primers was supported by sequence analysis of DNA from excised DGGE bands. Sequences recovered from these bands, in addition to sequences obtained by polymerase chain reaction (PCR) and cloning from lake DNA as well as from cyanobacterial isolates from the lake, revealed a diverse consortium of cyanobacteria, among which are representatives of the genera Aphanizomenon, Planktothrix, Microcystis and Synechococcus. One numerically important and persistent cyanobacterium in the lake, Prochlorothrix hollandica, appeared to co-occur with an unknown but related species. However, the lake is dominated by filamentous species that originally have been termed 'Oscillatoria limnetica-like'. We show that this is a group of several related cyanobacteria, co-occurring in the lake, which belong to the Limnothrix/Pseudanabaena group. The available variation among the coexisting strains of this group can explain the persistent dominance of the group under severe viral pressure.

Bacterial Typing Techniques↗

PubMed2001

N-myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis.

The myc oncogenes are frequently activated in human tumors, but there is no comprehensive insight into the target genes and downstream cellular pathways of these transcription factors. We applied serial analysis of gene expression (SAGE) to identify targets of N-myc in neuroblastomas. Analysis of 42,000 mRNA transcript tags in SAGE libraries of N-myc- transfected and control neuroblastoma cells revealed 114 up-regulated genes. The majority of these genes have a role in ribosome assembly and activity. Northern blot analysis confirmed up-regulation of all tested transcripts. Induction was complete within 4 h after N-myc expression. The large majority of the ribosomal proteins were induced, as well as genes controlling rRNA maturation. Cellular rRNA content was 45% induced. SAGE libraries and northern blot analysis confirmed up-regulation of many of these genes in N-myc-amplified neuroblastomas. As N-myc can functionally replace c-myc, we analyzed whether N-myc targets were induced by c-myc as well. Approximately 40% of these N-myc targets were up-regulated in a c-myc-transfected melanoma cell line. These data suggest that myc genes function as major regulators of the protein synthesis machinery.

Gene Expression Profiling↗

PubMed2002

Epidermal growth factor receptor dependence of radiation-induced transcription factor activation in human breast carcinoma cells.

Ionizing radiation (1-5 Gy) activates the epidermal growth factor receptor (EGFR), a major effector of the p42/44 mitogen-activated protein kinase (MAPK) pathway. MAPK and its downstream effector, p90 ribosomal S6 kinase (p90RSK), phosphorylate transcription factors involved in cell proliferation. To establish the role of the EGFR/MAPK pathway in radiation-induced transcription factor activation, MDA-MB-231 human breast carcinoma cells were examined using specific inhibitors of signaling pathways. Gel-shift analysis revealed three different profile groups: 1) transcription factors that responded to both radiation (2 Gy) and epidermal growth factor (EGF) (CREB, Egr, Ets, and Stat3); 2) factors that responded to radiation, but not EGF (C/EBP and Stat1); and 3) those that did not respond significantly to either radiation or EGF (AP-1 and Myc). Within groups 1 and 2, a two- to fivefold maximum stimulation of binding activity was observed at 30-60 min after irradiation. Interestingly, only transcription factors that responded to EGF had radiation responses significantly inhibited by the EGFR tyrosine kinase inhibitor, AG1478; these responses were also abrogated by farnesyltransferase inhibitor (FTI) or PD98059, inhibitors of Ras and MEK1/2, respectively. Moreover, radiation-induced increases in CREB and p90RSK phosphorylation and activation of Stat3 and Egr-1 reporter constructs by radiation were all abolished by AG1478. These data demonstrate a distinct radiation response profile at the transcriptional level that is dependent on enhanced EGFR/Ras/MAPK signaling.

Binding Sites↗

PubMed2006

Quantitative analysis of messenger RNA abundance for ribosomal protein L-15, cyclophilin-A, phosphoglycerokinase, beta-glucuronidase, glyceraldehyde 3-phosphate dehydrogenase, beta-actin, and histone H2A during bovine oocyte maturation and early embryogenesis in vitro.

Real-time reverse transcription PCR has greatly improved the ease and sensitivity of quantitative gene expression studies. However, measurement of gene expression generally requires selection of a valid reference (housekeeping gene) for data normalization to compensate for inherent variations. Given the dynamic nature of early embryonic development, application of this technology to studies of oocyte and early embryonic development is further complicated due to limited amounts of starting material and a paucity of information on constitutively expressed genes for data normalization. We have validated quantitative procedures for real-time reverse transcription polymerase chain reaction (RT-PCR) analysis of mRNA abundance during bovine meiotic maturation and early embryogenesis and utilized this technology to determine temporal changes in mRNA abundance for ribosomal protein L-15, cyclophilin-A, phosphoglycerokinase, beta-glucuronidase, glyceraldehyde-3-phosphate dehydrogenase, beta-actin, and histone H2A. Quantification of amounts of specific exogenous RNAs added to samples revealed acceptable rates of RNA recovery and efficiency of reverse transcription with minimal variation. Progression of bovine oocytes to metaphase II resulted in reduced abundance of polyadenylated, but not total transcripts for majority of above genes; however phosphoglycerokinase exhibited a significant decline in both RNA populations. Abundance of mRNAs for above genes in early embryos generally remained low until the blastocyst stage, but abundance of ribosomal protein L-15 mRNA was increased at the morula stage and histone H2A mRNA showed dynamic changes prior to embryonic genome activation. Results demonstrate a valid approach for quantitative analysis of mRNA abundance in oocytes and embryos, but do not support constitutive expression of above genes during early embryonic development.

Actins↗

PubMed2003

Hypervariable spacer regions are good sites for developing specific PCR-RFLP markers and PCR primers for screening actinorhizal symbionts.

While the ribosomal RNA like highly conserved genes are good molecular chronometers for establishing phylogenetic relationships, they can also be useful in securing the amplification of adjoining hyper-variable regions. These regions can then be used for developing specific PCR primers or PCR-RFL profiles to be used as molecular markers. We report here the use of ITS region of rrn operon of Frankia for developing PCR-RFL profiles capable of discriminating between closely related frankiae. We have also made use of the ITS1 region of the nuclear rrn operon of Alnus nepalensis (D Don) for designing a PCR primer for specific amplification of nuclear DNA of this tree.

Alnus↗

PubMed2005

Ribosomal RNA probes and microarrays: their potential use in assessing microbial biodiversity.

The awareness that global biological diversity is affected by numerous, mostly human-made threats has made biodiversity assessment an important scientific issue for decades. Biodiversity includes different levels of complexity, such as community diversity, habitat diversity, genetic diversity, and species diversity. The application of molecular methods to answer ecological questions permits issues of biodiversity to be addressed at all levels. Microorganisms dominate global biological diversity in terms of their species numbers. However, their small size and limited morphological features make it challenging to obtain a comprehensive view of their biodiversity. The application of ribosomal RNA (rRNA) probes contributes significantly to the assessment of biodiversity at the molecular level. DNA microarrays offer a great potential to facilitate the application of molecular probes and other DNA analytical methods to answer ecological and biodiversity questions. We provide an introduction into the application of rRNA probes and DNA microarrays for the assessment of microbial biodiversity, as well as protocols for the implementation of DNA microarrays.

Base Sequence↗