Life time of some RNA products of rDNA intergenic spacer in HeLa cells.

In human cells, the intergenic spacers (IGS), which separate ribosomal genes, are complex approximately 30 kb-long loci. Recent studies indicate that all, or almost all, parts of IGS may be transcribed, and that at least some of them are involved in the regulation of the ribosomal DNA (rDNA) transcription, maintenance of the nucleolar architecture, and response of the cell nucleus to stress. However, since each cell contains hundreds not quite identical copies of IGS, the structure and functions of this locus remain poorly understood, and the dynamics of its products has not been specially studied. In this work, we used quantitative PCR to measure the expression levels of various rDNA regions at different times after inhibition of the transcription by Actinomycin D applied in high doses. This approach allowed us to measure real or extrapolated half-life times of some IGS loci. Our study reveals characteristic dynamic patterns suggestive of various pathways of RNA utilization and decay.

Fluctuations of pol I and fibrillarin contents of the nucleoli.

Nucleoli are formed on the basis of ribosomal DNA (rDNA) clusters called Nucleolus Organizer Regions (NORs). Each NOR contains multiple genes coding for RNAs of the ribosomal particles. The prominent components of the nucleolar ultrastructure, fibrillar centers (FC) and dense fibrillar components (DFC), together compose FC/DFC units. These units are centers of rDNA transcription by RNA polymerase I (pol I), as well as the early processing events, in which an essential role belongs to fibrillarin. Each FC/DFC unit probably corresponds to a single transcriptionally active gene. In this work, we transfected human-derived cells with GFP-RPA43 (subunit of pol I) and RFP-fibrillarin. Following changes of the fluorescent signals in individual FC/DFC units, we found two kinds of kinetics: 1) the rapid fluctuations with periods of 2-3 min, when the pol I and fibrillarin signals oscillated in anti-phase manner, and the intensities of pol I in the neighboring FC/DFC units did not correlate. 2) fluctuations with periods of 10 to 60 min, in which pol I and fibrillarin signals measured in the same unit did not correlate, but pol I signals in the units belonging to different nucleoli were synchronized. Our data indicate that a complex pulsing activity of transcription as well as early processing is common for ribosomal genes.

Nucleolar DNA: the host and the guests.

Nucleoli are formed on the basis of ribosomal genes coding for RNAs of ribosomal particles, but also include a great variety of other DNA regions. In this article, we discuss the characteristics of ribosomal DNA: the structure of the rDNA locus, complex organization and functions of the intergenic spacer, multiplicity of gene copies in one cell, selective silencing of genes and whole gene clusters, relation to components of nucleolar ultrastructure, specific problems associated with replication. We also review current data on the role of non-ribosomal DNA in the organization and function of nucleoli. Finally, we discuss probable causes preventing efficient visualization of DNA in nucleoli.

Separation of replication and transcription domains in nucleoli.

In mammalian cells, active ribosomal genes produce the 18S, 5.8S and 28S RNAs of ribosomal particles. Transcription levels of these genes are very high throughout interphase, and the cell needs a special strategy to avoid collision of the DNA polymerase and RNA polymerase machineries. To investigate this problem, we measured the correlation of various replication and transcription signals in the nucleoli of HeLa, HT-1080 and NIH 3T3 cells using a specially devised software for analysis of confocal images. Additionally, to follow the relationship between nucleolar replication and transcription in living cells, we produced a stable cell line expressing GFP-RPA43 (subunit of RNA polymerase I, pol I) and RFP-PCNA (the sliding clamp protein) based on human fibrosarcoma HT-1080 cells. We found that replication and transcription signals are more efficiently separated in nucleoli than in the nucleoplasm. In the course of S phase, separation of PCNA and pol I signals gradually increased. During the same period, separation of pol I and incorporated Cy5-dUTP signals decreased. Analysis of single molecule localization microscopy (SMLM) images indicated that transcriptionally active FC/DFC units (i.e. fibrillar centers with adjacent dense fibrillar components) did not incorporate DNA nucleotides. Taken together, our data show that replication of the ribosomal genes is spatially separated from their transcription, and FC/DFC units may provide a structural basis for that separation.

Nucleolus: the ribosome factory.

The nucleolus is a nuclear compartment and represents the most obvious and clearly differentiated nuclear structure seen in the microscope. Within nucleoli most events of ribosome biogenesis, such as ribosomal RNA synthesis, processing, and ribosome subunit assembly, take place. Several lines of evidence now show that the nucleolus has also numerous non-ribosomal functions. This review is focused on the recent progress in our knowledge of how to correlate the known biochemical processes taking place in the nucleolus with nucleolar structures observed in the microscope. We still lack detailed enough information to understand fully the organization and regulation of the processes taking place in the nucleolar sub-structures. However, the present power of microscopy techniques should allow for an in situ description of the organization of nucleolar processes at the molecular level in the years to come.

Analysis of specificity of interaction between synthetic key saccharide components of lipopolysaccharides and monoclonal antibodies to Coxiella burnetii.

Two monoclonal antibodies (MAbs) against the lipopolysaccharides (LPSs) of Coxiella burnetii (C.b.) strains Priscilla and Nine Mile were prepared characterized by their interaction with synthetic glycoconjugates representing parts of LPSs of C.b. in virulent phase. Both MAbs were directed against immunodominant epitopes comprising core constituent of LPSs, Kdo (3-deoxy-alpha-D-manno-2-octulo-pyranosylonic acid). ELISA showed that the anti-Nine Mile MAb 4/11 bound preferably to disaccharides (alpha-Kdo (2 --> 4) alpha-Kdo and alpha-Kdo (2 --> 4) alpha-(5d) Kdo), while the anti-Priscilla MAb 1/4/H bound to all conjugates, though with various intensity. On the other hand, immunoelectron microscopy revealed a positive binding of only one glycoconjugate, namely the trisaccharide alpha-Kdo (2 --> 4) alpha-Kdo (2 --> 4) alpha-Kdo-BSA, to both MAbs. In competitive ELISA (cELISA), the anti-Priscilla MAb 1/4/H distinguished the strains Nine Mile and Priscilla, while the anti Nine Mile MAb 4/11 did not.

Resistance to nucleoside analog reverse transcriptase inhibitors mediated by human immunodeficiency virus type 1 p6 protein.

Resistance of human immunodeficiency virus type 1 (HIV-1) to antiretroviral agents results from target gene mutation within the pol gene, which encodes the viral protease, reverse transcriptase (RT), and integrase. We speculated that mutations in genes other that the drug target could lead to drug resistance. For this purpose, the p1-p6(gag)-p6(pol) region of HIV-1, placed immediately upstream of pol, was analyzed. This region has the potential to alter Pol through frameshift regulation (p1), through improved packaging of viral enzymes (p6(Gag)), or by changes in activation of the viral protease (p6(Pol)). Duplication of the proline-rich p6(Gag) PTAP motif, necessary for late viral cycle activities, was identified in plasma virus from 47 of 222 (21.2%) patients treated with nucleoside analog RT inhibitor (NRTI) antiretroviral therapy but was identified very rarely from drug-naïve individuals. Molecular clones carrying a 3-amino-acid duplication, APPAPP (transframe duplication SPTSPT in p6(Pol)), displayed a delay in protein maturation; however, they packaged a 34% excess of RT and exhibited a marked competitive growth advantage in the presence of NRTIs. This phenotype is reminiscent of the inoculum effect described in bacteriology, where a larger input, or a greater infectivity of an organism with a wild-type antimicrobial target, leads to escape from drug pressure and a higher MIC in vitro. Though the mechanism by which the PTAP region participates in viral maturation is not known, duplication of this proline-rich motif could improve assembly and packaging at membrane locations, resulting in the observed phenotype of increased infectivity and drug resistance.

Fine structural in situ analysis of nascent DNA movement following DNA replication.

Nascent DNA (newly replicated DNA) was visualized in situ with regard to the position of the previously replicated DNA and to chromatin structure. Localization of nascent DNA at the replication sites can be achieved through pulse labeling of cells with labeled DNA precursors during very short periods of time. We were able to label V79 Chinese Hamster cells for as shortly as 2 min with BrdU; Br-DNA, detected by immunoelectron microscopy, occurs at the periphery of dense chromatin, at individual dispersed chromatin fibers, and within dispersed chromatin areas. In these regions DNA polymerase alpha was also visualized. After a 5-min BrdU pulse, condensed chromatin also became labeled. When the pulse was followed by a chase, a larger number of gold particles occurred on condensed chromatin. Double-labeling experiments, consisting in first incubating cells with IdU for 20 min, chased for 10 min and then labeled for 5 min with CldU, reveal CldU-labeled nascent DNA on the periphery of condensed chromatin, while previously replicated IdU-labeled DNA has been internalized into condensed chromatin. Altogether, these results show that the sites of DNA replication correspond essentially to perichromatin regions and that the newly replicated DNA moves rapidly from replication sites toward the interior of condensed chromatin areas.

Ultrastructural analysis of nucleolar transcription in cells microinjected with 5-bromo-UTP.

In situ sites of nucleolar transcription in cells microinjected with 5-bromo-UTP (BrUTP) were visualized at an ultrastructural level. After injection the cells were maintained for 4-90 min at 37 degrees C, fixed, and embedded in LR White resin. Postembedding immunoelectron microscopic visualization with colloidal gold has been used for localizing both Br-labeled precursor incorporated into pre-rRNA and different nucleolar transcription or processing factors. This high resolution approach allowed us to identify significant signal as early as after 4-min incubation periods following BrUTP microinjection. It revealed the dense fibrillar component (DFC) as being the first nucleolar compartment labeled with anti-bromodeoxyuridine antibody. Moreover, RNA polymerase I, nucleolar transcription factor UBF, and fibrillarin were also detected almost exclusively in this same nucleolar compartment. From 30 min onward, following microinjection, Br-labeled rRNA occurred also in the granular component. The results indicate that the DFC is the site of pre-rRNA transcription and of initial steps of pre-rRNA processing. Moreover, it demonstrates that BrUTP microinjection followed by postembedding detection of Br-labeled RNA is a useful technique for high resolution studies of structure-function associations in the nucleolus.

Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection.

In this study we demonstrate, at an ultrastructural level, the in situ distribution of heterogeneous nuclear RNA transcription sites after microinjection of 5-bromo-UTP (BrUTP) into the cytoplasm of living cells and subsequent postembedding immunoelectron microscopic visualization after different labeling periods. Moreover, immunocytochemical localization of several pre-mRNA transcription and processing factors has been carried out in the same cells. This high-resolution approach allowed us to reveal perichromatin regions as the most important sites of nucleoplasmic RNA transcription and the perichromatin fibrils (PFs) as in situ forms of nascent transcripts. Furthermore, we show that transcription takes place in a rather diffuse pattern, without notable local accumulation of transcription sites. RNA polymerase II, heterogeneous nuclear ribonucleoprotein (hnRNP) core proteins, general transcription factor TFIIH, poly(A) polymerase, splicing factor SC-35, and Sm complex of small nuclear ribonucleoproteins (snRNPs) are associated with PFs. This strongly supports the idea that PFs are also sites of major pre-mRNA processing events. The absence of nascent transcripts, RNA polymerase II, poly(A) polymerase, and hnRNPs within the clusters of interchromatin granules rules out the possibility that this domain plays a role in pre-mRNA transcription and polyadenylation; however, interchromatin granule-associated zones contain RNA polymerase II, TFIIH, and Sm complex of snRNPs and, after longer periods of BrUTP incubation, also Br-labeled RNA. Their role in nuclear functions still remains enigmatic. In the nucleolus, transcription sites occur in the dense fibrillar component. Our fine structural results show that PFs represent the major nucleoplasmic structural domain involved in active pre-mRNA transcriptional and processing events.

A new immunocytochemical technique for ultrastructural analysis of DNA replication in proliferating cells after application of two halogenated deoxyuridines.

We describe a colloidal gold immunolabeling technique for electron microscopy which allows one to differentially visualize portions of DNA replicated during different periods of S-phase. This was performed by incorporating two halogenated deoxyuridines (IdUrd and CldUrd) into Chinese hamster cells and, after cell processing, by detecting them with selected antibodies. This technique, using in particular appropriate blocking solutions and also Tris buffer with a high salt concentration and 1% Tween-20, prevents nonspecific background and crossreaction of both antibodies. Controls such as digestion with DNase and specific staining of DNA with osmium ammine show that labeling corresponds well to replicated DNA. Different patterns of labeling distribution, reflecting different periods of DNA replication during S-phase, were characterized. Cells in early S-phase display a diffuse pattern of labeling with many spots, whereas cells in late S-phase show labeling confined to larger domains, often at the periphery of the nucleus or associated with the nucleolus. The good correlation between our observations and previous double labeling results in immunofluorescence also proved the technique to be reliable.

Effects of brefeldin A on the expression and transport of influenza A virus haemagglutinin, M1 and M2 proteins within the cell.

Brefeldin A (BFA) decreased the expression of influenza A virus haemagglutinin (HA) and M2 protein on the plasma membrane of virus-infected MDCK cells. It caused a retention of M1 protein in the cell nucleus and a decrease of its expression on the plasma membrane. On the other hand, an increased labelling of the cytoplasmic domain of M2 protein on the plasma membrane in BFA-treated cells was observed in contrast to the labelling in BFA-untreated cells. The effects of BFA on the microtubules and cellular motors are discussed.

[Morphological analysis of synovial exsudate in rheumatoid arthritis. II. Transmission electron microscopy]. / Morfologická analýza synoviálneho výpotku pri reumatoidnej artritíde. II. Transmisná elektrónová mikroskopia.

Synovial exsudate cells from patients with rheumatoid arthritis were investigated by transmission electron microscopy. Most of them represented polymorphous leukocytes. They contained vacuoles full of material reminding of immune complexes (in addition to typical granules) and plentiful alpha and beta glycogen granules. Some lymphoid cells nuclei were alike to those of Sézary disease with frequent ring-shaped nucleoli and enlarged mitochondria. Variegated non-lymphoid mononuclear cells had lateralized nuclei with marginated chromatin, mitochondria with sparse crists, short membranes of reticulum, conspicuous cisterns in trans-Golgi area and lysosomes with myeline bodies as a sign of big capacity of phagocytosis. Importance of using transmission electron microscopy in analysis of synovial exudate was discussed.

[Morphologic analysis of synovial effusion in rheumatoid arthritis. I. Light microscopy--cytology, histochemistry and semi-thin sections]. / Morfologická analýza synoviálneho výpotku pri reumatoidnej artritíde. I. Svetelná mikroskopia--cytológia, histochémia a polotenké rezy.

Inflammatory synovial fluid in patients with rheumatoid arthritis contained IgG, IgM and C3 component of complement, unspecific esterase and acid phosphatase and affinity to Pisum sativum agglutinin (PSA). Various forms of a degeneration of polymorphs, giant non-lymphoid mononuclear cells with cerebriphorm nuclei in different stages of phagocytosis and lymphocytes, sometimes with numerous nuclear invaginations, were found. All the cells of synovial fluid contained IgG, not the IgM. C3 component of complement was limited to non-lymphoid non-lymphoid mononuclear cells. Both the enzymatic activities were especially stressed in polymorphs. PSA was bound to all cells.

Influenza virus M2 protein and haemagglutinin conformation changes during intracellular transport.

The influenza virus M2 protein has an ion channel activity that permits ions to enter the virion during its uncoating and also modulates pH of intracellular compartments. M2 protein is a homotetramer consisting of either a pair of disulfide-linked dimers or a disulfide-linked tetramer. The M2 trans-membrane domain peptide adopts an alfa helical secondary structure. In polarized cells, M2 protein is expressed at the apical cell surface. The amantadine-induced, M2-mediated conversion of influenza A virus haemagglutinin (HA) to the low pH conformation occurs in an acidic trans-Golgi compartment. The M2 protein ion channel activity can affect the conformation of cleaved HA during intracellular transport. The equine influenza virus 1 HA expressed from cDNA does not require coexpression of a functional M2 protein to maintain HA in its native conformation.

Ultrastructural lectinocytochemistry of fowl plague virus-infected and uninfected MDCK cells.

Using horseradish peroxidase (HRP)-conjugated lectins for pre-embedding labelling we have shown differences in ultrastructural localization of saccharides in cell compartments of fowl plague (FP) virus-infected and uninfected MDCK cells. Lectinochemical staining of the cell compartments in the case of FP virus-infected MDCK cells was less intensive as compared with uninfected cells. Also certain differences in the staining of subcompartments of cell organells were seen. Staining of uninfected cells with Pisum sativum agglutinin (PSA)-HRP revealed an extensive visualization of Golgi complex, mainly its cis-part, TGN vesicles and lysosomes. Staining of FP virus-infected cells with the same lectin marked very lightly rough endoplasmic reticulum and not at all the Golgi complex. Staining with Erythrina cristagalli agglutinin (ECA)-HRP revealed a picture very similar to PSA-HRP staining of uninfected and FP virus-infected cells. The differences in the lectinochemical staining of cell organelles of FP virus-infected and uninfected cells may be connected with the inhibition of cell protein synthesis during FP virus morphogenesis.