A multiple-staining procedure for the detection of different DNA fragments on a single blot

We have developed a method that implies the use of a particular type of substrate which can be used in combination with alkaline phosphatase in detecting nucleic acid on filters. The method allows the detection of several different nucleic acid sequences on a single filter. In consecutive steps, the target DNA molecules are hybridized with different digoxigenin-labeled DNA probes. After each hybridization step, digoxigenin is detected with an antibody-alkaline phosphatase conjugate. This enzyme is subsequently visualized by a color reaction using different 2-hydroxy-3-naphthoic acid anilide (naphthol AS) phosphates as substrates in combination with varying diazonium salts. The multiple-staining procedure is based on the fact that the probe DNA-antibody complex can be removed while the color precipitate remains stably bound at its place on the filter. This allows several repeated hybridizations with other digoxigenin-labeled probes followed by antibody detection and color reaction with other naphthol AS phosphate-diazonium salt combinations. Aside from the ability to simultaneously visualize different target DNAs on a single filter, this new method provides several important features that are more powerful than the conventional 5-bromo-4-chloro-3-indolyl phosphate-nitro blue tetrazolium (BCIP-NBT) color reaction for alkaline phosphatase. The colors are more stable and brilliant than BCIP-NBT; their development is faster, the resolution of closely spaced bands is greater, and the background is much lower. The detection limit for alkaline phosphates is as good as with BCIP-NBT (0.1 pg of DNA). One major advantage is the simplicity of removing the colors by ethanol incubation. In this paper, the method is described using the example of Southern blotted DNA fragments.(ABSTRACT TRUNCATED AT 250 WORDS)

The structure of DNA in a nucleosome

We describe the application of the hydroxyl radical footprinting technique to examine the histone-DNA interactions of a nucleosome that includes part of the 5S ribosomal RNA gene of Xenopus borealis. We establish that two distinct regions of DNA with different helical periodicities exist within the nucleosome and demonstrate a change in the helical periodicity of this DNA upon nucleosome formation. In particular, we find that on average the helical periodicity of DNA in this nucleosome is 10.18 +/- 0.05 base pairs per turn. The same DNA, when bound to a calcium phosphate surface, has a periodicity of 10.49 +/- 0.05 base pairs per turn, similar to that of random sequence DNA. Modulations in minor groove width within the naked DNA detected by the hydroxyl radical are maintained and exaggerated in nucleosomal DNA. These features correlate with regions in the DNA previously suggested to be important for nucleosome positioning.

DNA restriction digest and ribosomal RNA gene patterns of Campylobacter jejuni: a comparison with bio-, sero-, and bacteriophage-types of United Kingdom outbreak strains

DNA restriction endonuclease (Hae III and Hind III) total digest and 16S and 23S ribosomal (r)RNA gene patterns (ribopatterns) were determined for 18 isolates of Campylobacter jejuni from three separate outbreaks of diarrhoea in the north of England. Strains were also characterized by biotyping, serotyping and phage typing. Comparisons of the DNA patterns by visual and numerical methods revealed five distinct strain groupings with clear differences between isolates from different outbreaks as well as some heterogeneity between strains within the community outbreak and one of the school outbreaks. An excellent correlation was observed between the genomic DNA fingerprints data and the Preston bacteriophage group, both of which gave better discrimination than biotyping and serotyping alone or in combination. Only one phage group (PG 37) was not confirmed by the DNA data. DNA fingerprints therefore provide additional information of value in studying the epidemiology of outbreaks of C. jejuni.

The phylogenetic position of Peptococcus niger based on 16S rRNA sequence studies

A 1330 base-pair fragment of a 16S rRNA gene has been amplified, cloned and sequenced. Comparison to other 16S rRNA sequences of eubacteria showed that P. niger represents a deep branch within the subdivision "Gram-positive with Gram-negative cell walls". It is not related to peptostreptococci, representatives of this genus studied so far are more closely related to clostridia.

Plasmodium falciparum infection rates in Anopheles gambiae, An. arabiensis, and An. funestus in western Kenya

Mosquitoes collected monthly for 1 year from human habitations in the Kisumu area of western Kenya were identified by morphological characters as Anopheles gambiae Giles sensu lato (An. gambiae s.l.) or An. funestus. Of the mosquitoes collected, 7,244 (67%) of the An. gambiae s.l. and 8,511 (87%) of the An. funestus were tested by enzyme-linked immunosorbent assay (ELISA) for the presence of Plasmodium falciparum circumsporozoite (CS) protein. ELISA positivity rates were 8.2% for An. gambiae s.l. and 6.1% for An. funestus. Both An. gambiae and An. arabiensis were detected among 432 ELISA-positive and 668 ELISA-negative An. gambiae s.l. identified to species with a ribosomal DNA probe. The species-specific infection rates were calculated to be 9.6% for An. gambiae and 0.4% for An. arabiensis. These results confirm that An. gambiae and An. funestus are the primary malaria vectors in western Kenya and that An. arabiensis is a relatively minor vector.

Eimeria species: studies using rRNA and rDNA probes

rRNA and a heterologous cloned rDNA probe have been used to detect the rRNA genes of Eimeria species which infect the chicken, and has allowed the isolation and preliminary characterization of cloned rDNA sequences from a genomic DNA library of Eimeria tenella. It is demonstrated that rRNA and rDNA probes can be used to identify individual Eimeria species by the restriction fragment patterns detected after Southern hybridization. In addition, studies have shown that the large and small subunit rRNAs are expressed throughout sporulation.

Primary structure of the non-transcribed spacer region and flanking sequences of the ribosomal DNA of Neurospora crassa and comparison with other organisms

The non-transcribed spacer (NTS) region of the rDNA of Neurospora crassa contains the transcription regulatory sequences. We isolated a 3.4 kb EcoRI fragment from wild type N.crassa rDNA and cloned in the plasmid pBR325 at the EcoRI site. The insert contains the entire NTS region along with the flanking sequences. Nucleotide sequencing of 3592 nt shows many interesting features like: the NTS region is rich in G+C content (65% G+C); it contains the conserved rRNA processing site 6 (with the nucleotide sequence motif GGTGCGAGAACCCGG, from nt residue 226 to 240, a characteristic feature of most eukaryotic rDNA nontranscribed spacer region); and the NTS region also contains the transcription termination site with the representative Sal I box (from nt residue 1469 to 1477). The potential sequences of transcription termination site are located 288 nt downstream from the end of 26S rRNA gene, and another sequence motif CTTCCT (from nt residue 512 to 517) shows similarity with the human transcription termination site T-2 of its pre-rRNA. Nucleotide sequence homology matrix analysis suggests its relatedness to Saccharomyces cerevisiae and not to human, mouse, rat, Drosophila, Xenopus, wheat, rice and cucumber NTS region. The phylogenetic implication of the NTS region and exploitation of N.crassa NTS rDNA clone to correlate the otherwise indistinguishable species of Neurospora and the correlation with other organisms has been discussed. To the best of our knowledge this is the first report where the nucleotide sequence of the entire NTS region of a filamentous fungus has been determined.

Primary and secondary structure of the 25S rRNA from the dimorphic fungus Mucor racemosus

A 9.76 Kb ribosomal DNA repeat unit from the nuclear genome of the dimorphic fungus Mucor racemosus (Zygomycetes) was identified using a hybridization probe from the yeast Saccharomyces cerevisiae (Ascomycetes). This material was cloned in Escherichia coli plasmids as four overlapping pieces and mapped with respect to cleavage sites for 12 restriction endonucleases. The nucleotide sequence of the complete 25S rRNA gene and flanking regions was determined. The 5' and 3' ends of the structural gene were identified by comparison with the published sequence for the S. cerevisiae gene. The Mucor gene was found to possess 3469 bp and have a GC content of 42.8%. It was compared with the homologous gene from several other eukaryotes and found to be most similar to that from Saccharomyces. A potential secondary structure of the putative RNA transcript consistent with the structures proposed for the E. coli and Saccharomyces molecules was constructed by computer modelling.

DNA analysis in the diagnosis of infection and in the speciation of nematode parasites

DNA analysis is playing an increasingly important role in characterising and classifying nematode parasites. Though less emphasis has been placed on utilising DNA elements to study nematodes of veterinary importance, correct diagnosis is, nevertheless, critical to proper treatment and control. The genus Trichinella presents a particularly interesting problem since the level of classification within this genus remains unclear. Herein we discuss the application of DNA analysis to the diagnosis and speciation of the parasitic nematode Trichinella spiralis, where the study of cloned repetitive DNA elements and ribosomal RNA genes has led to significant advances in the understanding of the species-level systematics of this nematode. Despite advances in the recognition of multiple gene pools within the genus Trichinella, their taxonomic level is still uncertain because of insufficient knowledge regarding intraspecific variation within this genus. The utility of mitochondrial DNA and ribosomal DNA sequence analysis in studying the phylogeny and evolutionary history of parasites within this genus is also discussed.

Comparison of rDNA and mtDNA in the sibling species Anopheles freeborni and A. hermsi

Comparison of the ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) of Anopheles freeborni and A. hermsi, 2 morphologically indistinguishable mosquito species in the North American A. maculipennis complex, revealed restriction enzyme site variation in both DNA families. Diagnostically useful interspecific differences in the rDNA were observed in the external transcribed spacer (ETS) and internal transcribed spacer (ITS) regions. The regions encoding rRNA, however, were indistinguishable with respect to the enzymes used. Intraspecific site and genome length variations were present in the mtDNA of 5 colonies of A. freeborni and 3 colonies of A. hermsi, but no species-specific differences were observed.

Electron microscopic in situ hybridization and autoradiography: localization and transcription of rDNA in human lymphocyte nucleoli

The distribution of ribosomal DNA (rDNA) in the nucleoli of human lymphocytes was revealed by in situ hybridization with a nonautoradiographic procedure at the electron microscopic level. rDNA is located in the dense fibrillar component of the nucleolus but not in the fibrillar centers. In the same cells the incorporation of tritiated uridine takes place in the dense fibrillar component of the nucleolus as seen by autoradiography followed by gold latensification. From these findings it can be concluded that the transcription of ribosomal DNA takes place in the dense fibrillar component of the nucleolus.

Identification of two isolates of Trichinella recovered from humans in France

Two Trichinella isolates from humans in France were characterized using reproductive capacity indices and a combination of molecular methods. The isolate TRLL hybridized with the pig type-specific probe pPra and had pig type restriction profiles and rDNA patterns. It was therefore identified as a domestic or pig type isolate. The isolate CTRD-85 had similarities and differences in restriction profiles and rDNA patterns with both AF1 and Trichinella nelsoni and was identified as a sylvatic type. Pattern comparisons also show that T. nelsoni is similar to variants of the North American sylvatic type.

Localization of ribosomal and telomeric DNA sequences in intact plant nuclei by in-situ hybridization and three-dimensional optical microscopy

We have combined the use of three-dimensional (3-D) fluorescence microscopy and computer image processing of images with in-situ hybridization to analyse the 3-D organization of interphase nuclei in plants. In sections of root tips of Pisum sativum, using cDNA probes, we have shown that telomeres are arranged around the nuclear periphery and that the ribosomal genes in this species appear to exist in discrete, 3-D domains.

Characterization of chromosomes and localization of the rDNA locus in the aye-aye (Daubentonia madagascariensis)

The karyotype of a prosimian primate, the aye-aye (Daubentonia madagascariensis), is described. Results from a variety of staining methods (Q-, R-, G-, and C-banding, distamycin A/DAPI and methyl-green/DAPI) are reported. Sites of methylation were visualized using antibodies against 5-methylcytosine. Digestion of aye-aye fixed metaphase chromosomes with the restriction endonuclease HaeIII produced G-banding. No other restriction enzymes tested produced clear G- or C-banding patterns. Ag-staining of the nucleolar organizer regions (NORs) revealed the location of rDNA sites on the short arms of the smallest pairs of acrocentric chromosomes, 13p and 14p.

Immunolocalization of DNA at nucleolar structural components in onion cells

Intranucleolar DNA, including ribosomal DNA (rDNA), was localized in situ in proliferating onion cells under the electron microscope using an anti-DNA monoclonal antibody and a postembedding indirect immunogold procedure. In the interphase nucleolus of this species, characterized by a very high amount of rRNA genes, we found DNA concentrated mostly in fibrillar centres (FCs) and in the region of the dense fibrillar component (DFC) immediately surrounding them. Clusters of gold particles were frequently seen covering both of these structural components of the nucleolus at the same time. Moreover, the same technique, applied to transcriptionally arrested quiescent onion cells, showed the nucleolar DFC devoid of DNA. Also, in mitotic cells at telophase, the prenucleolar material, which has the same morphological and cytochemical features as the DFC, does not contain DNA. These data suggest the existence of at least two subcomponents of the DFC in the onion cell nucleolus, one associated with pre-rRNA synthesis, and the other, with further processing of transcripts, already released from the rDNA template. We conclude that the first subcomponent forms part of the "transition between FC and DFC", which is the in situ structural counterpart of pre-rRNA synthesis. This transition is morphologicaly sizeable in onion cells, because of their high number of rRNA genes and the large size of the DFC mass; however, it would be largely detectable in situ in other cell systems, where the whole DFC comprises only a thin layer and the amount of rDNA is considerably reduced.

Restriction enzyme mapping of ribosomal DNA can distinguish between fasciolid (liver fluke) species

Recognition sites for nine different restriction endonucleases were mapped on rDNA genes of fasciolid species. Southern blots of digested DNA from individual worms were probed sequentially with three different probes derived from rDNA of Schistosoma mansoni and known to span between them the entire rDNA repeat unit in that species. Eighteen recognition sites were mapped for Fasciola hepatica, and seventeen for Fasciola gigantica and Fascioloides magna. Each fasciolid species had no more than two unique recognition sites, the remainder being common to one or both of the other two species. No intraspecific variation in restriction sites was noted in F. hepatica (individuals from 11 samples studied; hosts were sheep, cattle and laboratory animals; geographical origins. Australia, New Zealand, Mexico, U.K., Hungary and Spain), or in F. gigantica (two samples; Indonesia and Malaysia). Only one sample of F. magna was available. One specimen of Fasciola sp. from Japan (specific identity regarded in the literature as uncertain) yielded a restriction map identical to that of F. gigantica. Almost all recognition sites occurred in or near the putative rRNA coding regions. The non-transcribed spacer region had few or no cut sites despite the fact that this region is up to about one half of the entire repeat unit in length. Length heterogeneity was noted in the non-transcribed spacer, even within individual worms.

Ag-NOR staining and in situ hybridization of rDNA in the chromosomes of the South American camelids

The location and frequency of Ag-stained NORs and sites of rDNA hybridization were studied in the chromosomes of the South American camelids. In the four camelids these regions occur distally on chromosomes 18, 21, and 27 and the smallest biarmed elements. Quantitative analysis of NOR distribution showed variations between both cells and species. In llama, guanaco and alpaca the NORs number averaged 6 per cell, this being higher than in vicuña where the average was 3. Relative frequencies of NOR-bearing chromosomes in the four camelids were similar. Yet, in vicuña virtual absence of NOR sites on one of the smallest biarmed pairs was observed. The rDNA sites assessed in llama and vicuña by in situ hybridization with cloned 18S DNA were coincident with the NOR locations and with the frequencies characteristics for each species. Moreover, varying the exposure time of the autoradiographs, labeling patterns specific for each camelid were observed. Grain counts on individual chromosomes indicated that under our conditions one month exposure is enough to demonstrate all the rDNA sites available in the complement of llama. Conversely, at least two months are necessary to show the total sites existing in vicuña. Most probably this finding reflects the presence of variations in the amount of copies of the ribosomal genes per chromosome.

In situ hybridization at the electron microscope level: an improved method for precise localization of ribosomal DNA and RNA

In situ hybridization using biotinylated rDNA probes and secondary antibody coupled to gold particles was developed on ultrathin sections of Lowicryl-embedded Ehrlich tumor cells for precise localization of ribosomal RNA (rRNA) and ribosomal DNA (rDNA). For the detection of rDNA, an immunocytochemical approach involving an antibody against single-stranded DNA was used in order to determine the more efficient denaturation procedure. Using this technique, rDNA can be visualized in the fibrillar centers of nucleoli, especially in their peripheral regions at the proximity of both the dense fibrils and the nucleolar interstices as well as within the latter. rDNA was occasionally detected in some clumps of dense nucleolus-associated chromatin. Besides the presence of rRNA in the ribosome-rich cytoplasmic areas and in the dense fibrillar component and the granular component of the nucleolus, rRNA was also found in the fibrillar center areas close to the boundary region to the dense fibrillar component. These results are discussed in the light of the present knowledge on the functional organization of the nucleolus.

The genetics of abnormal abdomen, incomplete abdomen, and bobbed in Drosophila buzzatii

Five stocks of Drosophila buzzatii with superficially similar abdominal disruptions including partial tergite and sternite loss were isolated by inbreeding. Three of the stocks have indistinguishable phenotypes, the inheritance of which is maternally influenced. This phenotype and its mode of inheritance bear similarities with those of Abnormal abdomen in D. melanogaster. The phenotype in the fourth stock is slightly different and is due to a single autosomal recessive gene, which we denote incomplete abdomen. In the fifth stock the trait is limited to females, and in appearance and mode of inheritance resembles bobbed in D. melanogaster. Furthermore, only in this stock are rDNA deletions evident. The combined frequencies of the three types of abdominal aberration were found to be around 1% in several samples from wild and laboratory populations of D. buzzatii.

Circular DNA of Entamoeba histolytica encodes ribosomal RNA

The presence of repeated DNA sequences encoding RNA in Entamoeba histolytica has been reported. In the present study we demonstrate by agarose gel electrophoresis. DNase digestion and electron microscopic analysis that these genes are located on extrachromosomal circular DNA molecules with an approximate size of 26 kb. Detection of replication intermediates suggests the episomal nature of these molecules. Amplified, extrachromosomal rRNA genes appear to be a common feature among the lower eukaryotes, occurring more commonly as linear molecules and less commonly as circles. Entamoeba histolytica is 1 of the few organisms studied in which rRNA genes are located predominantly on extrachromosomal circles.

Schistosoma mansoni: chromosomal localization of DNA repeat elements by in situ hybridization using biotinylated DNA probes

Localization of the SM alpha family of repeated DNA and the rDNA repeat on the chromosomes of Schistosoma mansoni by in situ hybridization is presented. Biotinylated DNA was hybridized to target chromosomes and hybridization was detected using either alkaline phosphatase-labeled avidin or fluorescein-labeled avidin and biotinylated anti-avidin antibody. Hybridization detection using a fluorescein conjugate was more specific and sensitive with less background noise than detection with alkaline phosphatase conjugates. SM alpha hybridizing sequences were found dispersed throughout the genome, hybridizing to the sex chromosomes and autosomes. The SM alpha probe showed specific hybridization to the euchromatic gap region within the large heterochromatic block of the short arm of the W chromosome. This specific hybridization coupled with the lack of chiasma formation in this region of the ZW bivalent (presumably due to the heterochromatinization of this region) may explain the pattern of sex-specific hybridization reported for the SM alpha family. The rDNA repeat was localized to the secondary constriction of the short arm of chromosome 3. Specifically, the rDNA probe hybridized with the stalk of the secondary constriction and with parts of both side regions, the satellite and the short arm proper.

Evaluation and practical aspects of the use of a commercial DNA probe for detection of mycoplasma infections in cell cultures

Cell cultures have been analyzed for mycoplasma infections by using a commercial DNA-probe based on rRNA genes from mycoplasmas. Both the original version, Mycoplasma T.C. Detection Kit, and the improved version of the kit, Mycoplasma T.C. II Rapid Detection System, were used. The sensitivities of the two tests were found to be adequate in most cases and the improved version of the kit was 10-100 times more sensitive than the original one. A batch variation was observed with the improved version, which is not satisfactory. This batch variation can, however, be checked and the performance of the method with a properly working lot was found to be good.

Ribosomal RNA gene restriction patterns provide increased sensitivity for typing Salmonella typhi strains

To date, epidemiologic associations among strains of Salmonella typhi are based exclusively on phage typing, which may be of limited value if a common phage type is involved. Analysis of ribosomal RNA gene restriction patterns allows separation of most independently isolated strains of identical phage types. The sensitivity of the method is dependent on the restriction enzymes used to digest chromosomal DNA. It was highest for PstI, which separated 16 of 20 strains that belonged to 8 phage types including 3 untypable strains. Three strains differed in their phage types but had identical ribosomal RNA gene restriction patterns. Also, two pairs of strains indistinguishable by phage typing exhibited identical patterns; however, two of these strains were expected to be identical because they were isolated from two patients who were likely exposed to the same source. Ribosomal RNA gene restriction patterns appear to be stable. Thus, the method may complement phage typing and aid in further differentiation of strains.

Study on mechanism of micronucleoli formation by laser microirradiation

In the male rat kangaroo cell line PTK2, argon laser (514.5 nm) microirradiation of both nucleoli in interphase cells 30, 23, and 12 h before mitosis, and nucleoli in early prophase cells resulted in the formation of micronucleoli, i.e., several small nucleolus-like bodies, in daughter cells. The irradiated cells were stained with methylene blue, which indicated that the nucleolar RNA was destroyed by laser microirradiation. Feulgen staining was applied to the irradiated cells in combination with the measurements of an MPV-II model microphotometer. Irradiated nucleoli were negative for DNA-Feulgen stain, which indicated that nucleolar DNA was destroyed by laser irradiation, so the nucleolar organizer gene was destroyed. After the nucleoli had been irradiated, the cells were continuously incubated at 37 degrees C for 12 and/or 24 h, then fixed and stained with AgNO3. Most of the nucleoli irradiated silver-stained negative that demonstrated that when the nucleoli were irradiated, rDNA was destroyed and transcription stopped. However, some silver grains were found in the nucleoplasm, whereas the nucleoli were silver-stained negative. The results suggest that subsidiary nucleolar organizer loci might exist scattered throughout the genome.

Evaluation of evolutionary divergence in the genus Naegleria by analysis of ribosomal DNA plasmid restriction patterns

Ribosomal DNA (rDNA) plasmid restriction maps of 10 strains and rDNA hybridisation patterns of 61 additional strains have been used to assess inter- and intra-specific diversity and phylogenetic relationships in the genus Naegleria. The results obtained by this method largely confirm those of previous studies based on a variety of other criteria. They indicate that very little variation exists within the pathogenic species Naegleria fowleri despite its worldwide distribution and that it is closely related to the nonpathogenic Naegleria lovaniensis. Naegleria gruberi is most likely a polyphyletic grouping and care should be taken when using one strain as a reference point for this species. In addition, the two subspecies of the pathogenic Naegleria australiensis arose separately from within the range of variability encompassed by N. gruberi, as did the species Adelphamoeba galeacystis which should probably be assigned to the genus Naegleria. The species Naegleria jadini and Naegleria andersoni are not closely related to any other in the genus based on their rDNA patterns.

Combined immuno- and non-radioactive hybridocytochemistry on cells and tissue sections: influence of fixation, enzyme pre-treatment, and choice of chromogen on detection of antigen and DNA sequences

Conditions for combination of DNA in situ hybridization, using biotinylated DNA probes, with immunohistochemistry were investigated on cryostat sections, cytological preparations, and paraffin sections. We found that cryostat sections and cytological preparations are suitable for in situ hybridization of target DNA after fixation in acetone, methanol, ethanol, or Carnoy without further proteinase pretreatment. Acetone is also very suitable for immunostaining of cell surface or cytoskeleton antigens. We therefore performed combined immunoenzyme and in situ hybridization staining using this fixative. The best results were obtained when immunoperoxidase staining with diaminobenzidine/H2O2 was followed directly by in situ hybridization. In addition to immunoperoxidase, alkaline phosphatase-antialkaline phosphatase (APAAP) staining with naphthol ASBI phosphate and New Fuchsin as a substrate could be used. In most instances, detection of the biotinylated hybrid with a streptavidin-biotinylated polyalkaline phosphatase method using nitroblue tetrazolium and 5-bromo-4-chloro-3-indolylphosphate as the substrate was preferable. The double stainings were studied on the following test models: (a) frozen tonsil sections: cell surface antigens (pan T) and ribosomal DNA; (b) frozen genital condyloma sections; cytokeratins and human papillomavirus type 6 + 11 (HPV-6/11) DNA; (c) CaSKi cells: cytokeratins and HPV-16 DNA; (d) infected fetal lung fibroblasts: vimentin and cytomegalovirus (CMV) DNA. An adapted procedure was followed on routinely formaldehye-fixed and paraffin-embedded condyloma tissue. Immunoperoxidase staining for papilloma virus capsid antigen could be combined with DNA in situ hybridization with HPV-6/11 DNA. In this model, however, the accessibility of the target DNA had to be improved by enzyme treatment after the immunostaining and before starting the in situ hybridization.

Restriction mapping of rDNA and the taxonomy of Kluyveromyces van der Walt emend. van der Walt

Ribosomal DNA from the type strains of 13 nomenspecies of Kluyveromyces and from other strains were mapped with 11 restriction endonucleases. The length of the repeating unit ranged from ca. 8.4 kb (in K. aestuarii) to ca. 10.9 kb (in K. phaffii). The length variation resided as expected in the nontranscribed spacer. The patterns confirmed some of the inferences articulated by various students of the genus. The closely related species K. marxianus and K. lactis constituted a core to which could be linked first K. wickerhamii and K. dobzhanskii and then K. aestuarii. The presumed relatedness between K. waltii and K. thermotolerans was endorsed by rDNA mapping as well, but evidence linking these two species to the rest of the genus is wanting. The restriction patterns suggest that the multispored species together with K. delphensis form a loose assemblage acting as a bridge between the "core" species and the species K. phaffii and K. lodderi.

Relationship between interphasic nucleolar organizer regions and growth rate in two neuroblastoma cell lines

The relationship between the quantity of silver-stained interphasic nucleolar organizer regions (NORs) and nuclear synthetic activity, caryotype, and growth rate was studied in two established neuroblastoma cell lines (CHP 212 and HTB 10). Statistical analysis of silver-stained NORs revealed four times as many in CHP 212 cells compared with HTB 10 cells. No difference was observed in the ribosomal RNA synthesis between the two cell lines. The caryotype index was 1.2 for CHP 212 and 1.0 for HTB 10 cells. The number of chromosomes carrying NORs and the quantity of ribosomal genes was found to be the same for the two cell lines. Doubling time of CHP 212 cells was 20 hours compared with 54 hours for HTB 10 cells. In CHP 212 cells bindering of cell duplication by serum deprivation induced a progressive lowering (calculated at 48, 72, and 96 hours) of the quantity of silver-stained interphasic NORs. Recovery of duplication by new serum addition induced, after 24 hours, an increase of the quantity of silver-stained interphasic NORs up to control levels. In the light of available data, these results indicate that the quantity of interphasic NORs is strictly correlated only to the growth rate of the cell.

A simple, sensitive method of analyzing bacterial ribosomal DNA polymorphism

A rapid DNA extraction procedure and random primer labelling of Escherichia coli ribosomal RNA with cloned reverse transcriptase have been used to establish a simple and highly sensitive method for studying ribosomal DNA polymorphism in bacteria. Examples of inter- and intraspecies differentiation of bacteria are given and potential applications in bacterial epidemiology and taxonomy are discussed.

Ultrastructural changes in nucleoli and fibrillar centers under the effect of local ultraviolet microbeam irradiation of interphase culture cells

As shown previously, ultraviolet (uv) microbeam irradiation of one of the two mature nucleoli within an interphase cell nucleus causes significant diminution and inactivation of the irradiated nucleolus and compensatory growth and activation of the nonirradiated one. In the present work we describe the results of an ultrastructural study of this phenomenon. The changes in the nucleoli were examined by means of complete series of ultrathin sections obtained from seven irradiated pig kidney cells. The compensatory hypertrophy of the nonirradiated nucleoli is shown to be accompanied by a nearly twofold increase in the number of fibrillar centers (FCs) and by a decrease in their linear dimensions compared with the control cells of the same ploidy. In the degraded nucleoli the number of FCs decreases, but their dimensions increase. Ultraviolet microbeam irradiation causes dramatic diminution of the dense fibrillar component within the irradiated nucleoli as well. The nucleolar capacity for compensatory hypertrophy indicates that in addition to active ribosomal genes, mature nucleoli also contain "silent" genes capable of being activated under extreme conditions to sustain the required level of rRNA synthesis. It is assumed that activation of latent ribosomal genes is accompanied by FC "fragmentation" without a considerable increase in their total volume per cell.

Variation of electrophoretic karyotypes among Naegleria spp

All species and subspecies of the genus Naegleria were subjected to karyotype analysis by contour-clamped homogeneous electric field and transverse alternating-field electrophoresis. The former technique proved to be superior in detecting differences in karyotype. The chromosome pattern of each species and subspecies was found to be distinct. Between 15 and 23 bands were resolved, with chromosome sizes ranging from a few hundred kilobases to about 1.5 Mb. Hybridisation with cloned rDNA identified one band in all species, corresponding to the rDNA plasmid that does not migrate according to its molecular weight because it is circular. In Willaertia magna a similar size distribution was found, in contrast to Giardia and Entamoeba, which have only very large chromosomes. Within the pathogenic N. fowleri some strains showed slight differences in chromosome pattern. The karyotype differed more between strains within the subspecies N. and andersoni than between the two species N. fowleri and N. lovaniensis. The results suggest that karyotype analysis cannot be used to identify a Naegleria species but is useful for stock identification, gene localisation, genetic exchange studies and epidemiological investigation of the pathogenic N. fowleri.

The molecular-cytogenetic analysis of grasses and its application to studying relationships among species of the Triticeae

An analysis of four species from the genus Secale, including the study of different accessions, has shown that the properties of DNA clones of monomer units from three repeated sequence loci, namely, Ter, Nor, and 5S DNA, proved to be representative of the entire loci from which they were isolated. This finding in Secale species, including the discovery of a new locus for 5S DNA on chromosome 5R, has been used to interpret information on the Ter, Nor, and 5S DNA loci from 15 species in the Triticeae complex. The evolutionary relationship among species suggested by the DNA sequence data has shown many consistencies with a number of other characters such as those used in classical systematics, as well as geographical distribution data and isozyme and chromosome-pairing studies. Apparent inconsistencies such as a close relationship between the R and P genomes at the Ter loci are interpreted in terms of amplification-deletion phenomena known to occur at repetitive sequence loci. In addition, this study included species endemic to Australia and thus provided a broad time span in which to consider some features of repeated sequence family evolution, such as the conservation of certain parts of 5S DNA spacer regions.

An overhanging 3' terminus is a conserved feature of telomeres

The reactivity of single-stranded thymidines with osmium tetraoxide was used to demonstrate the existence of a terminal overhang of the G-rich strand of telomeres from two distantly related eucaryotes, the ciliated protozoan Tetrahymena spp. and the acellular slime mold Didymium spp. Conservation of a G-strand overhang at the molecular terminus of telomeres is consistent with our suggestion that an unusual DNA structure formed by the G-strand overhang is important for telomere function (E. Henderson, C. C. Hardin, S. K. Wolk, I. Tinoco Jr., and E. H. Blackburn, Cell 51:899-908, 1987).

Structural determinant of the species-specific transcription of the mouse rRNA gene promoter

Mammalian ribosomal DNA (rDNA) transcription has a certain species specificity such that, both in vivo and in vitro, human rDNA cannot be transcribed by mouse machinery and vice versa. This is due to a species-dependent transcription factor, TFID (Y. Mishima, I. Financsek, R. Kominami, and M. Muramatsu, Nucleic Acids Res. 10:6659-6670, 1982). On the basis of the information obtained from 5' and 3' substitution mutants, we prepared a chimeric gene in which the mouse sequence from positions -32 to -14 was inserted into the corresponding location of the human rDNA promoter. The chimeric gene could be transcribed by mouse extracts nearly as efficiently as the wild-type mouse promoter. The chimeric gene could also sequester transcription factor TFID at an efficiency similar to that for the mouse promoter. Partially purified mouse TFID that could not protect the human rDNA promoter against DNase I produced a clear footprint on this chimeric gene that was similar to that on mouse rDNA promoter. The basic structure of the mouse rDNA core promoter is discussed in relation to the interaction with TFID.

A replication fork barrier at the 3' end of yeast ribosomal RNA genes

Replication of the approximately 200 tandem copies of yeast ribosomal RNA genes (rDNA) is known to be initiated within a subset of the repeats, with transcription continuing during the replication process. To examine replication fork movement in this gene cluster, we used a two-dimensional (2D) agarose gel electrophoresis procedure that distinguishes molecules with different branched structures. Replication forks move through most of the rDNA in the same direction in which RNA polymerase I transcribes the 35S rRNA precursor: the 3' end of this transcription unit acts as a barrier to replication forks moving in the direction opposite to RNA polymerase I. The replication fork barrier (RFB) is observed as the accumulation of branched intermediates of specific size. We propose that the act of transcription may influence the movement of replication forks, creating barriers at the 3' ends of actively transcribed genes.

Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm

A fraction of the 28S ribosomal genes in certain insect species is interrupted by the insertion elements R1 and R2. These two elements from the silkworm Bombyx mori (R1Bm and R2Bm) are retrotransposons capable of transposing in a highly sequence-specific manner. We report here the functional expression in E. coli of the entire single open reading frame of R2Bm and show that it encodes a double-stranded endo-nuclease (integrase) that can specifically cleave the 28S gene at the R2 insertion site. The resulting cleavage is a 4 bp staggered 5' overhang. Deletion analysis of the 28S gene revealed that the DNA sequence required for specific cleavage is asymmetric with respect to the actual insertion (cleavage) site, with fewer than 10 bp required at one side and at least 24 bp at the other side of the site. A model is proposed based on these and previous data to account for the sequence-specific integration of the R2 retrotransposon.

Detection of genomic variation in Providencia stuartii clinical isolates by analysis of DNA restriction fragment length polymorphisms containing rRNA cistrons

Chromosomal DNA from 26 strains of Providencia stuartii isolated mainly in hospitals in the United Kingdom and reference strains of P. stuartii, P. rustigianii, and Proteus vulgaris were digested with the restriction endonucleases EcoRI and HindIII. After electrophoresis in agarose gels, the fragments were subjected to Southern blot hybridization analysis with a biotin-labeled cDNA probe transcribed from a mixture of 16S and 23S rRNA from P. stuartii NCTC 11800T. The pattern of bands (the rDNA fingerprint), which depended on restriction fragment length polymorphisms containing rRNA genes, was used as a measure of minor genomic variation within and between species. The P. stuartii clinical isolates had similar total digest patterns, but the rDNA fingerprints revealed some heterogeneity between strains, with EcoRI digests providing better strain discrimination than HindIII. Such rDNA fingerprints comprised between five and seven bands with sizes in the range of 5 to 28 kilobases. The 11 different EcoRI patterns were compared by numerical analysis, and several groups or subgroups of strains were identified. Over half (15 of 26) of the urease-negative isolates (subgroups Aa and Ab) had patterns that differed only by the presence or absence of a 25-kilobase band. Urease-negative strains from other clinical material were more heterogeneous in their patterns. No correlation was apparent between strain pattern group and urease production or geographic location of isolate. The P. stuartii rDNA fingerprints were quite distinct from those of allied Providencia and Proteus species and provided a more sensitive measure of minor genomic differences than total DNA digests did.

Biochemical, genetic, and epidemiologic characterization of Haemophilus influenzae biogroup aegyptius (Haemophilus aegyptius) strains associated with Brazilian purpuric fever

Brazilian purpuric fever (BPF) is a recently recognized fulminant pediatric disease characterized by fever, with rapid progression to purpura, hypotensive shock, and death. BPF is usually preceded by purulent conjunctivitis that has resolved before the onset of fever. Both the conjunctivitis and BPF are caused by Haemophilus influenzae biogroup aegyptius (formerly called H. aegyptius). Isolates from 15 BPF cases, mainly from blood or hemorrhagic cerebrospinal fluid, case-associated isolates from 42 persons in towns where BPF cases occurred, and control strains from 32 persons in towns without BPF cases were characterized biochemically, genetically, and epidemiologically. Results indicated that a single clone was responsible for all BPF cases identified in six Brazilian towns from 1984 through 1986. All of 15 (100%) case strains were the same clone as was 1 of 32 (3%) control strains (P = less than 10(-8). Isolates of the clone were preferentially intrarelated by DNA hybridization (99% relatedness, hydroxyapatite method at 60 and 75 degrees C) and were separable from other H. influenzae biogroup aegyptius strains (approximately 90% relatedness at 60 degrees C and 82% relatedness at 75 degrees C). All isolates of the BPF clone and no other strains contained a 24-megadalton plasmid of restriction endonuclease type 3031, were of a single multilocus enzyme mobility type, were of a single sodium dodecyl sulfate-polyacrylamide gel electrophoresis type, and were in one of two ribosomal DNA restriction patterns. All BPF clone isolates reacted with monoclonal antibodies produced from a case strain; only 3 of 62 (5%) other strains reacted with this monoclonal antibody. Ninety percent of BPF clone strains and 27% of other strains were relatively resistant to sulfamethoxazole-trimethoprim.

Ribosomal DNA-probes differentiate five cryptic species in the Anopheles gambiae complex

This study describes the use of ribosomal DNA probes to identify the species of individual mosquitoes in the Anopheles gambiae complex, a group of six morphologically identical mosquito species among which are two of the principal vectors of malaria in Africa. The DNA probes are sequences of DNA derived from the ribosomal genes of An. gambiae. Each probe reveals a different sized restriction enzyme fragment specific to each of the five species in the complex that were examined in this study: An. gambiae, An. arabiensis, An. quadriannulatus, An. melas and An. merus. The probes detect highly repeated sequences of DNA, thus the method is sufficiently sensitive to be applied to a small portion of a mosquito. Furthermore, because the DNA can be extracted from desiccated or alcohol preserved specimens, the test is compatible with other mosquito assays performed on dried specimens such as blood meal and malaria sporozoite antigen ELISAs. Determination of the nucleotide sequences that underlie the species-specific restriction enzyme site differences detected by these probes will lead to the development of synthetic DNA probes that can be used to identify an individual mosquito to species on the basis of a simple dot-blot or squash-blot.

[Structure of nucleosomes and organization of inter-nucleosomal DNA in chromatin]

We have compared mononucleosomes that were obtained by hydrolysis of chromatin micrococcal nuclease from a number of sources with the length of a nucleosomal repeat 185--245 b. p. long. For hydrolysis of chromatin isolated from nuclei, a series of nucleosomes was formed: MN145 (core particle), MN165, MN175...MN205, MN215, the lengths of their DNAs differing (by approximately 10.n b.p. where n = 1, 2, 3...) by a factor of 10. A feature of hydrolysis of chromatin in nuclei was the appearance of an additional H1-depleted MN155 particle. It is suggested that upon isolation of chromatin from nuclei, its partial decompactization takes place. This decompactization changes the character of nuclease splitting and seems to be connected with rearrangement of histone H1. These observations demonstrate that besides core particles MN145 and chromatosomes MN165, the major particles of digest of nuclei appear to be MN155, and for isolated chromatin--MN175. Unlike this standard picture, mainly MN145, MN155, MN235 and MN245 are formed upon hydrolysis of sea urchin sperm nuclei.

Differential ribosomal gene responsiveness to human growth hormone is visualized by selective silver staining

Differential activity of rRNA gene clusters following growth-hormone administration has been demonstrated in cultured lymphocytes from subjects with different genetic backgrounds, i.e., with or without in vivo peripheral responsiveness to the hormone. The influence of different culture conditions on ribosomal gene responsiveness was also tested. Ribosomal gene activity was evaluated by selective silver staining of nucleolus organizing regions. The results show that hormone-induced enhancement of transcriptional activity requires both genetically determined cell responsiveness and environmentally determined permissive factors.

Production of monoclonal antibodies against RNA polymerase I from nonimmunized autoimmune MRL/lpr mice and their use in rDNA transcription analysis

A hybridoma secreting monoclonal antibodies against RNA polymerase I was produced by the fusion of myeloma cells with spleen cells from a nonimmunized MRL/lpr mouse which is known to produce autoantibodies to RNA polymerase I. The antibodies (McAb-2D11) belong to the IgG2b subclass, reacted specifically with the second largest (120 kDa) subunit of RNA polymerase I, and inhibited accurate transcription of cloned rat rDNA in a fractionated cell extract following immunoprecipitation of RNA polymerase I. McAb-2D11 did not inhibit RNA polymerase II-mediated transcription of the mouse metallothionein-I gene. Immunocytochemical procedures with biotinylated second antibody demonstrated specific immunolocalization of RNA polymerase I in the nucleus. These studies have (a) presented direct evidence that autoantibodies to functional RNA polymerase I are produced in a murine model of systemic lupus erythematosus, (b) demonstrated specificity of the monoclonal antibody for RNA polymerase I, and (c) provided a useful tool for the purification of RNA polymerase I and/or transcription factor(s) associated with RNA polymerase I.

A ribosomal RNA gene probe differentiates member species of the Anopheles gambiae complex

A 0.59 kilobase DNA fragment cloned from an rDNA cistron of the mosquito Anopheles gambiae can be used as a probe to differentiate between A. gambiae, A. arabiensis, and A. melas, three morphologically identical sibling species in the A. gambiae complex which otherwise can be reliably distinguished only by polytene chromosome banding patterns. Although all are important (and often sympatric) African malaria vectors, their relative roles in malaria transmission have thus far been difficult to assess. The probe, an EcoRI-SalI fragment from the 3' end of the 28S beta coding region of the cistron, is present in all three species, but the species differ uniquely with respect to the location of an EcoRI site in the nontranscribed spacer (NTS) downstream of the fragment. We have routinely used the probe to identify A. gambiae complex mosquitoes to species on the basis of genomic DNA extracted from individual air dried specimens. A single mosquito abdomen provides more than sufficient DNA for the assay, and neither eggs nor a bloodmeal in the abdomen interfere with DNA yield. Moreover, the DNA extraction procedure does not degrade the bloodmeal IgG, so the residual protein pellet can be used to identify the mosquito bloodmeal source. Since the rDNA cistron organization as detected by the probe does not differ between male and female mosquitoes, the probe can be used for either sex. Preliminary experiments show that the probe is equally useful for mosquito larvae and pupae.

Quantitation of genes and transcripts by saturation hybridization in urea solutions using strand-selected probes

This report describes methods for quantifying specific sequences in preparations of single-stranded or double-stranded nucleic acids. We use saturating amounts of hybrid-selected, strand-specific probes and perform hybridizations in urea solutions. Hybrids (RNA-DNA or DNA-DNA) are then analyzed by either of two methods. The first employs standard S1 nuclease digestion, precipitation of resistant material on glass fiber filters, and assay by liquid scintillation counting. This method is generally chosen in the assay of rare transcripts in total nucleic acid extracts as well as preparations of polyadenylated RNA. The second employs the separation of excess probe from probe-target hybrids by gel electrophoresis, recovery of hybrids on ion-exchange paper, and determination of cpm bound by liquid scintillation counting. This method is of particular value in the assay of double-stranded sequences and the quantitation of restriction fragment length polymorphisms. Whereas both methods are accurate over ranges of target abundance representing at least several orders of magnitude, the latter ("NA45 assay") is most sensitive, and the selection of M13-bound or unbound DNA fragments by this method can be exploited in a variety of other applications.

The ribosomal gene spacer as a tool for the taxonomy of Leishmania

A recombinant DNA ribosomal gene spacer of Leishmania braziliensis Y was used as probe to test different Leishmania species. Based on the similarity of their restriction patterns, three groups were distinguished with respect to international Leishmania references: first a group with a similar restriction pattern to L. braziliensis Y and the reference organism L. mexicana garnhami JAP78; a second group with restriction patterns similar to the reference organism L. mexicana mexicana M379; and finally a group where all the restriction patterns were related to the reference organism L. braziliensis braziliensis M2903. These results support the existence of L. garnhami as an independent Leishmania species; they confirm previous studies on L. mexicana and L. braziliensis and open the way for the more exact diagnosis of New World Leishmaniasis.

On the position of nucleolus organizer regions (NORs) in interphase nuclei. Studies with a new, non-autoradiographic in situ hybridization method

The distribution of 18S and 28S ribosomal RNA (rRNA), i.e. the chromosomal nucleolus organizer regions (NORs) was visualized in interphases and metaphases of non-stimulated and phytohemagglutinin (PHA)-stimulated human lymphocytes with a recently developed non-autoradiographic in situ hybridization method. This procedure involves mercurated RNA as a probe and a sulfhydryl-trinitrophenyl-mercury binding ligand and FITC-labelled antibodies as detection system. Silver staining was used to visualize nucleoli in interphase. In the secondary constriction of all ten acrocentric chromosomes, varying amounts of rDNA were detected. In the interphase nuclei of most of the non-stimulated human lymphocytes, only one small nucleolus could be seen. The in situ hybridization, however, revealed several agglomerations of rDNA scattered over the whole nuclear area, clearly outnumbering the number of nucleoli in these cells. This means that not all of the NORs are transcriptionally active in non-stimulated lymphocytes and that these inactive NORs lie at a distinct distance from the active ones. With PHA stimulation (transforming the small lymphocytes from peripheral blood into large, lymphoblast-like cells) the number of nucleoli increased slightly, whereas the number of separable rDNA spots decreased. This means that in the course of PHA-induced cellular activation, formerly inactive NORs become transcriptionally active and tend to associate with one another. This indicates the occurrence of movements of the NORs within the nucleus, depending on their transcriptional activity.

The core promoter of mouse rDNA consists of two functionally distinct domains

We have determined the sequences constituting the minimal promoter of mouse rDNA. A very small region immediately upstream of the transcription start site (from -1 to -39) is sufficient to direct correct transcription initiation. Sequences immediately downstream of the transcription start site (+1 to +11) increase the efficiency of transcription initiation. Point mutations within the core promoter have been generated and assayed for their effects on template activity and on interaction with the pol I specific transcription factor TIF-IB. The core promoter element appears to consist of two functionally different domains. The distal sequence motif from position -22 to -16 is recognized by factor TIF-IB. Mutations within this region lead to similar changes of both template activity and binding of TIF-IB. Two point mutations within the proximal sequence motif from -15 to -1 do not affect TIF-IB binding although they severely impair transcription initiation. It is suggested, that this proximal region plays a role in the assembly of functional transcription initiation complexes rather than in the primary binding of TIF-IB.

Spheroplastic phase of mycobacteria isolated from patients with Crohn's disease

Two strains of an unclassified Mycobacterium species were isolated after 18 and 30 months of incubation of media inoculated with resected intestinal tissues from patients with Crohn's disease. These strains represented the third and fourth isolates of this organism from Crohn's disease patients. Ultrastructural examination of this strain and two previously isolated strains revealed the presence of spheroplasts which eventually transformed into the bacillary form of a previously unrecognized Mycobacterium species. These cell wall-deficient forms did not stain with conventional dyes and failed to grow on hypertonic media. Restriction polymorphism of the ribosomal DNA genes was used to determine the relationship between the cell wall-deficient and bacillary forms. Identical restriction patterns of the ribosomal DNA genes were found between the spheroplasts and Mycobacterium sp. isolates with EcoRI, BamHI, and XhoI restriction endonucleases, thus providing definitive evidence of their origin. Unidentified spheroplasts were isolated from an additional 12 patients with Crohn's disease, of which 7 of 10 seroagglutinated with antiserum prepared against the Mycobacterium sp. Spheroplasts were isolated from 16 of 26 (61%) patients with Crohn's disease but not from tissues of 13 patients with ulcerative colitis or 13 patients with other diseases of the bowel. These findings support the role of mycobacteria as etiologic agents in some cases of Crohn's disease.