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High sensitivity immunolocalization of double and single-stranded DNA by a monoclonal antibody
(1987)
A monoclonal antibody (AK 30-10) is described which specifically reacts with DNA both in double and single-stranded forms but not with other molecules and structures, including deoxyribonucleotides and RNAs. When used in immunocytochemical experiments on tissue sections and permeabilized cultured cells, this antibody detects DNA-containing structures, even when the DNA is present in very small amounts. Examples of high resolution detection include the DNA present in amplified extrachromosomal nucleoli, chromomeres of lampbrush chromosomes, mitochondria, chloroplasts and mycoplasmal particles. In immunoelectron microscopy using the immunogold technique, the DNA was localized in distinct substructures such as the "fibrillar centers" of nucleoli and certain stromal centers in chloroplasts. The antibody also reacts with DNA of chromatin of living cells, as shown by microinjection into cultured mitotic cells and into nuclei of amphibian oocytes. The potential value and the limitations of immunocytochemical DNA detection are discussed.
Some decades ago it was noted by cytologists that within the interphase nucleus large portions of the transcriptionally ("genetically," in their terms) inactive chromosomal material are contained in aggregates of condensed chromatin, the "chromocenters," whereas transcriptionally active regions of chromosomes appear in a more dispersed form and are less intensely stained with DNA-directed staining procedures (Heitz 1929, 1932, 1956; Bauer 1933). The hypothesis that condensed chromatin is usually characterized by very low or no transcriptional activity, and that transcription occurs in loosely packed forms of chromatin (including, in most cells, the nucleolar chromatin) has received support from studies of ultrathin sections in the electron microscope and from the numerous attempts to separate transcriptionally active from inactive chromatin biochemically (for references, see Anderson et al. 1975; Berkowitz and Doty 1975; Krieg and Wells 1976; Rickwood and Birnie 1976; Gottesfeld 1977). Electron microscopic autoradiography has revealed that sites of RNA synthesis are enriched in dispersed chromatin regions located at the margins of condensed chromatin (Fakan and Bernhard 1971, 1973; Bouteille et al. 1974; Bachellerie et al. 1975) and are characterized by the occurrence of distinct granular and fibrillar ribonucleoprotein (RNP) structures, such as perichromatin granules and fibrils. The discovery that, in most eukaryotic nuclei, major parts of the chromatin are organized in the form of nucleosomes (Olins and Olins 1974; Kornberg 1974; Baldwin et al. 1975) has raised the question whether the same nucleosomal packing of DNA is also present in transcriptionally active chromatin strands. Recent detailed examination of the morphology of active and inactive chromatin involving a diversity of electron microscopic methods, particularly the spreading technique by Miller and coworkers (Miller and Beatty 1969; Miller and Bakken 1972), has indicated that the DNA of some actively transcribed regions is not packed into nucleosomal particles but is present in a rather extended form within a relatively thin (4-7 nm) chromatin fiber.
Using a monoclonal antibody (No-194) we have identified, in Xenopus laevis and other amphibia, an acidic protein of M, 40,000 (ribocharin) which is specifically associated with the granular component of the nucleolus and nucleoplasmic 65S particles. These particles contain the nuclear 28S rRNA and apparently represent the precursor to the large ribosomal subunit in nucleocytoplasmic transit. By immunoelectron microscopy ribocharin has been localized in the granular component of the nucleolus and in interchromatin granules. During mitosis ribocharin-containing particles are associated with surfaces of chromosomes and are recollected in the reconstituting nucleoli in late telophase. We suggest that ribocharin is a specific component of precursor particles of the large ribosomal subunit, which dissociates from the 65S particle before passage through the nuclear envelope, and is reutilized in ribosome biogenesis.
A non-radioactive in situ hybridization method is described for the localization of transcription units of defined genes to lateral loops of Xenopus laevis lampbrush chromosomes. Two Xenopus cONA probes were used encoding the nucleolar protein N038/ B23 and cytokeratin 1(8). Both proteins are known to be synthesized in Xenopus oocytes, and Northern blot analysis revealed the presence of the corresponding mRNAs in different oogenic stages. The probes were enzymatically labeled with biotin-dCTP and hybridized to lampbrush chromosomes. The sites of hybridization were detected either by indirect immunofluorescence microscopy using rabbit antibodies against biotin and fluorescein-conjugated antirabbit IgG or enzymatically using peroxidase-conjugated streptavi din. The probe encoding the nucleolar protein hybridized to two sets of lateral loops on different bivalents, the cytokeratin probe to at least four. Our finding that each probe hybridized to more than one chromosomal locus may reflect the tetraploid nature of the Xenopus laevis genome or results from cross-hybridization to other transcriptionally active members of the N038/ B23-nucleoplasmin or the cytokeratin-Iamin gene families. The method described should facilitate further in situ hybridization studies with appropriate genomic clones in order to map specific DNA sequences to defined loop regions and to come to a better understanding of the relationship between loop organization and gene transcription unit.
Many nuclear proteins are released into the cytoplasm at prometaphase and are transported back into the daughter nuclei at the end of mitosis. To determine the role of this reentry in nuclear remodelling during early interphase, we experimentally manipulated nuclear protein uptake in dividing cells. Recently we and others have shown that signal-dependent, pore complex-mediated uptake of nuclear protein is blocked in living cells on microinjection of the lectin wheat germ agglutinin (WGA), or of antibodies such as PI1 that are directed against WGA-binding pore complex glycoproteins. In the present study, we microinjected mitotic PtKz cells with WGA or antibody PIt and followed nuclear reorganization of the daughter cells by immunofluorescence and electron microscopy. The inhibitory effect on nuclear protein uptake was monitored by co-injection of the karyophilic protein nucleoplasmin. When injected by itself early in mitosis, nucleoplasmin became sequestered into the daughter nuclei as they entered telophase. In contrast, nucleoplasmin was excluded from the daughter nuclei in the presence of WGA or antibody PI1 . Although PtKz cells with blocked nuclear protein uptake completed cytokinesis, their nuclei showed a telophaselike organization characterized by highly condensed chromatin surrounded by a nuclear envelope containing a few pore complexes. These findings suggest that pore complexes become functional as early as telophase, in close coincidence with nuclear envelope reformation. They further indicate that the extensive structural rearrangement of the nucleus during the telophase-G1 transition is dependent on the influx of karyophilic proteins from the cytoplasm through the pore complexes, and is not due solely to chromosome- associated components.
In order to investigate the DNA localization within Ehrlich tumor cell nucleoli during mitosis, two recent immunocytochemical methods using either an anti-DNA or an anti-bromodeoxyuridine (BrdU) monoclonal antibody have been applied. In both cases, the immunogold labeling has been performed on ultrathin sections of cells embedded either in Lowicryl K4M or in Epon, respectively. Identical results are observed with both immunocytochemical approaches. In the interphase nucleolus, besides the labeling of the perinucleolar chromatin shell and of its intranucleolar invaginations which penetrate into the nucleolar body and often terminate at the fibrillar centers, a few gold particles are also preferentially found towards the peripheral region of the fibrillar centers. In contrast, the dense fibrillar component and the granular component are never labeled. During mitosis, the fibrillar centers persist at the chromosomal nucleolus organizing regions (NOR's) and can be selectively stained by the silver method. However, these metaphase fibrillar centers are no longer decorated by the DNA- or BrdU antibodies. These results indicate that until the end of prophase, rRNA genes are present inside the fibrillar center material, disappear during metaphase and reappear in reconstituting nucleoli during telophase. Thus, fibrillar centers appear to represent structures sui generis, which are populated by rRNA genes only when the nucleolus is functionally active. In segregated nucleoli after actinomycin D treatment, the DNA labeling is exclusively restricted to the perinucleolar chromatin blocks. These findings also suggest that the DNA content of the fibrillar center material varies according to the rRNA transcription level of the cells. The results are discussed in the light of the present knowledge of the functional organization of the nucleolus.
After microinjection of antibodies against RNA polymerase I into the nuclei of cultured rat kangaroo (PtKz) and rat (RVF-SMC) cells alterations in nucleolar structure and composition were observed. These were detected by electron microscopy and double-label immunofluorescence microscopy using antibodies to proteins representative of the three major components of the nucleolus. The microinjected antibodies produced a progressive loss of the material of the dense fibrillar component (DFC) from the nucleoli which, at 4 h after injection, were transformed into bodies with purely granular component (GC) structure with attached fibrillar centers (FCs). Concomitantly, numerous extranucleolar aggregates appeared in the nucleoplasm which morphologically resembled fragments of the DFC and contained a protein (fibrillarin) diagnostic for this nucleolar structure. These observations indicate that the topological distribution of the material constituting the DFC can be experimentally influenced in interphase cells, apparently by modulating the transcriptional activity of the rRNA genes. These effects are different from nucleolar lesions induced by inhibitory drugs such as actinomycin D-dependent "nucleolar segregation". The structural alterations induced by antibodies to RNA polymerase I resemble, however, the initial events of nucleolar disintegration during mitotic prophase.
The ultrastructure of twO kinds of transcription ally active chromatin, the lampbrush chromosome loops and the nucleoli from amphibian oocytes and primary nuclei of the green alga Acetabularia, has been examined after manual isolation and dispersion in low salt media of slightly alkaline pH using various electron microscopic staining techniques (positive staining, metal shadowing, negative staining, preparation on positively charged films, etc.) and compared with the appearance of chromatin from various somatic cells (hen erythrocytes, rat hepatocytes, ClIltured murine sarcoma cells) prepared in parallel. While typical nucleosomes were revealed with all the techniques for chromatin from the latter three cell system, no nucleosomes were identified in either the lampbrush chromosome structures or the nucleolar chromatin. Nucleosomal arrays were absent not only in maximally fibril-covered matrix units but also in fibril-free regions between transcriptional complexes, including the apparent spacer intercepts between different transcriptional units. Moreover, comparisons of the length of the repeating units of rDNA in the transcribed state with those determined in the isolated rDNA and with the lengths of the first stable product of rDNA transcription, the pre-rRNA, demonstrated that the transcribed rDNA was not significantly shortened and/or condensed but rather extended in the transcriptional units. Distinct granules of about nucleosomal size which were sometimes found in apparent spacer regions as well as within matrix units of reduced fibril density were shown not to represent nucleosomes since their number per spacer unit was not inversely correlated with the length of the specific unit and also on the basis of their resistance to treatment with the detergent Sarkosyl NL-30. It is possible to structurally distinguish between transcriptionally active chromatin in which the DNA is extended in a non-nucleosomal form of chromatin and condensed, inactive chromatin within the typical nucleosomal package. The characteristic extended structure of transcriptionally active chromatin is found not only in the transcribed genes but also in non-transcribed regions within or between ("spacer") transcriptional units as well as in transcriptional units that are untranscribed amidst transcribed ones and/or have been inactivated for relatively short time. It is hypothesized that activation of transcription involves a transition from a nucleosomal to an extended chromatin organisation and that this structural transition is not specific for single "activated" genes but may involve larger chromatin regions, including adjacent untranscribed intercepts.
Thin section electron microscopy of Actinomycin D treated Tetrahymena cells and amphibian oocytes (Xenopus laevis, Triturus aZpestris) reveal no reduction in the central granules in the nuclear pore complexes. Possible reasons for the diversity between these results and earlier observations using negatively stained isolated nuclear envelopes from the same objects are discussed. The results clearly show that the presence of central granules within the nuclear pores does neither depend on nuclear RNA synthesis nor does indicate nucleocytoplasmic RNA transport. This conclusion leads to a reconsideration of the nature of the central granule. The functioning of the central granule of the nuclear pore complexes is further discussed in connection with recent studies on the ultrastructure of various types of cisternal pores.
A small fraction of HeLa cells within an exponentially growing culture showed cisternal differentiations, such as cytoplasmic as well as intranuclear annulate lamellae and special smooth surfaced endoplasmic reticulum aggregates with a typical "Cotte de maillet" appearance. Additionally, clusters of dense granules were observed in the cytoplasm which were often associated with polysomes and strongly resembled the so-called "heavy bodies" known in particular in diverse oocytes. The functional meaning of these structures is discussed. Moreover, it is deduced from the ultrastructural identity of the pore complexes in the nuclear envelope and the cytoplasmic and intranuclear annulate lamellae that the pore complex material with its highly ordered arrangement is not a structure characteristic for nucleocytoplasmically migrating material, but rather is a general structural expression of a tight binding of ribonucleoprotein (RNP) to cisternal membranes. The pore complexes are thought of as representing sites of a RNP-storage. A similar functioning is hypothesized for the "heavy body"like aggregates. To the current hypotheses on the formation of annulate lamellae and the nuclear envelope, which are based on the concept of membrane continuities and constancies, the alternative view of a self assembly mechanism of membrane constituents on nucleoprotein structures is added.
Primary (giant) nuclei of the green algae Acetabularia mediterranea and A. major were studied by light and electron microscopy using in situ fixed material as well as manually isolated nuclear components. In addition, cytochemical reactions of nuclear structures and biochemical determinations of nuclear and cytoplasmic RNA and of genome DNA content were performed. The data obtained and the structures observed are interpreted as demonstralions of transcriptional activities of different gene classes. The most prominent class is the nucleolar cistrons of precursors of ribosomal RNA which occur highly repeated in clusters in the form of regularly alternating intercepts on deoxyribonucleoprotein axes of transcribed rDNA, the fibril-covered matrix units, and the fibril-free "spacer" segments. A description and a classification of the various structural complexes which seem to represent transcriptional activities is given. Quantitative evaluations of these arrangements are presented. The morphology and the dimensions of such structures are compared with the RNA molecular weight determinations and with the corresponding data reported from various animal cell systems. It is suggested that the formation of the giant nucleus is correlated with, and probably due to, an enormous amplification of transcriptionally active rDNA and packing of the extrachromosomal copies into the large nucleolar aggregate bodies.
Electron-opaque material is shown in the perinuclear cisternae of various cell types to connect the inner and outer nuclear membrane faces. Similar bridges were observed between the outer nuclear membrane and the outer mitochondrial membrane. The intracisternal bridges of the nuclear envelope appear to be important for the structural stability of the perinuclear cisterna. Stable structural linkage of mitochondria to the outer nuclear membrane might be relevant to the understanding of the characteristic juxtanuclear accumulation of mitochondria and also provide arguments for the discussions of certain biochemical activities found in nuclear and nuclear membrane fractions.
In this work, a behavioural analysis of different mutants of the fruit fly Drosophila melanogaster has been carried out. Primarily, the gap climbing behaviour (Pick & Strauss, 2005) has been assayed as it lends itself for the investigation of decision making processes and the neuronal basis of adaptive behaviour. Furthermore it shows how basic motor actions can be combined into a complex motor behaviour. Thanks to the neurogenetic methods, Drosophila melanogaster has become an ideal study object for neurobiological questions. Two different modules of climbing control have been examined in detail. For the decision making, the mutant climbing sisyphus was analysed. While wild-type flies adapt the initiation of climbing behaviour to the width of the gap and the probability for a successful transition. climbing sisyphus flies initiate climbing behaviour even at clearly insurmountable gap widths. The climbing success itself is not improved in comparison to the wild-type siblings. The mutant climbing sisyphus is a rare example of a hyperactive mutant besides many mutants that show a reduced activity. Basic capabilities in vision have been tested in an optomotor and a distance-estimation paradigm. Since they are not affected, a defect in decision making is most probably the cause of this behavioural aberration. A second module of climbing control is keeping up orientation towards the opposite side of the gap during the execution of climbing behaviour. Mutants with a structural defect in the protocerebral bridge show abnormal climbing behaviour. During the climbing attempt, the longitudinal body axis does not necessarily point into the direction of the opposite side. Instead, many climbing events are initiated at the side edge of the walking block into the void and have no chance to ever succeed. The analysed mutants are not blind. In one of the mutants, tay bridge1 (tay1) a partial rescue attempt used to map the function in the brain succeeded such that the state of the bridge was restored. That way, a visual targeting mechanism has been activated, allowing the flies to target the opposite side. When the visibility of the opposing side was reduced, the rescued flies went back to a tay1 level of directional scatter. The results are in accord with the idea that the bridge is a central constituent of the visual targeting mechanism. The tay1 mutant was also analysed in other behavioural paradigms. A reduction in walking speed and walking activity in this mutant could be rescued by the expression of UAS-tay under the control of the 007Y-GAL4 driver line, which concomitantly restores the structure of the protocerebral bridge. The separation of bridge functions from functions of other parts of the brain of tay1 was accomplished by rescuing the reduced optomotor compensation in tay1 by the mb247-GAL4>UAS-tay driver. While still having a tay1-like protocerebral bridge, mb247-GAL4 rescue flies are able to compensate at wild-type levels. An intact compensation is not depended on the tay expression in the mushroom bodies, as mushroom body ablated flies with a tay1 background and expression of UAS-tay under the control of mb247-GAL4 show wild-type behaviour as well. The most likely substrate for the function are currently unidentified neurons in the fan-shaped body, that can be stained with 007Y-GAL4 and mb247-GAL4 as well.
So me species of the paleotropical tree genus Macaranga (Euphorbiaceae) live in elose association with ants. Thc genus comprises the full range of species from those not regularly inhabited by ants to obligate myrmecophytes. In Malaysia (peninsular and Borneo) 23 ofthe 52 species areknown to be ant-associated (44%). The simplest structural adaptation of plants to attract ants are extrafloral nectaries. We studied the distribution of extraflural nectaries in the genus Macaranga to assess the significance of this character as a possible predisposition for the evolution of obligate myrmecophytism. All species have marginal glands on the leaves. However, only the glands of nonmyrmecophytic species function as nectaries, whereas liquids secreted by these glands in myrmecophytic species did not contain sugar. Some non-myrmecophytic Macaranga and transitional Macaranga species in addition have extrafloral nectaries on the leaf blade near the petiole insertion. All obligatorily myrmecophytic Macaranga species, however, lack additional glands on the lamina. The non-myrmecophytic species are visited by a variety of different ant species, whereas myrmecophytic Macaranga are associated only with one specific ant-partner. Since these ants keep scale insects in the hollow sterns, reduction of nectary production in ant-inhabited Macaranga seems to be biologically significant. We interpret this as a means of (a) saving the assimilates and (b) stabilization of maintenance of the association's specificity. Competition with other ant species for food rewards is avoided and thereby danger ofweakening the protective function ofthe obligate antpartner for the plant is reduced. A comparison with other euphorb species living in the same habitats as Macaranga showed that in genera in which extrafloral nectaries are widespread, no myrmecophytes have evolved. Possession of extrafloral nectaries does not appear to be essential for the development of symbiotic ant-plant interactions. Other predispositions such as nesting space might have played a more important role.
Zanthoxylum myriacanthum, a small Rutaceous tree growing mainly in secondary hill forests in SE Asia, is a true myrmecophyte. It possesses stem domatia in the form of hollow branches with slitlike openings. Branch hollows and entrance slits are produced by the plant itself through pith degene~.tion ?u.d growth proceSses. If the entrance is not kept open by ants it closes again by growth ol the surrounding tissue after some time. The domatia are colonized opportunistic ally by different arboreous ants, e.g. Crematogaster and Campono tus. Additionally many small extrafloral nectaries are found on the leaflets of Zanthoxylum myriacanthum. Judging from herbarium studies and literature records at least four more true ant trees are found in the genus Zanthoxylum namely Z. rhetsa in SE Asia, Z. conspersipunctatum, Z. pluviatile and Z. vinkii in New Guinea. We could not confirm ant inhabitation in Drypetes pendula (Euphorbiaceae) on the Malay Peninsula, which has also been recorded to be an anttree.
The human genome has been sequenced since 2001. Most proteins have been characterized now and with everyday more bioinformatical predictions are experimentally verified. A project is underway to sequence thousand humans. But still, little is known about the evolution of the human proteome itself. Domains and their combinations are analysed in detail but not all of the human domain architectures at once. Like no one before, we have large datasets of high quality human protein-protein-protein interactions and complexes available which allow us to characterize the human proteome with unmatched accuracy. Advanced clustering algorithms and computing power enable us to gain new information about protein interactions without touching a pipette. In this work, the human proteome is analysed at three different levels. First, the origin of the different types of proteins was analysed based on their domain architectures. The second part focuses on the protein-protein interactions. Finally, in the third part, proteins are clustered based on their interactions and non-interactions. Most proteins are built of domains and their function is the sum of their domain functions. Proteins that share the same domain architecture, the linear order of domains are homologues and should have originated from one common ancestral protein. This ancestor was calculated for roughly 750 000 proteins from 1313 species. The relations between the species are based on the NCBI Taxonomy and additional molecular data. The resulting data set of 5817 domains and 32868 domain architectures was used to estimate the origin of these proteins based on their architectures. It could be observed, that new domain architectures are only in a small fraction composed of domains arisen at the same taxon. It was also found that domain architectures increase in length and complexity in the course of evolution and that different organisms like worm, and human share nearly the same amount of proteins but differ in their number of distinct domain architectures. The second part of this thesis focuses on protein-protein interactions. This chapter addresses the question how new evolved proteins form connections within the existing network. The network built of protein-protein interactions was shown to be scale free. Scale free networks, like the internet, consist of few hubs with many connections and many nodes with few connections. They are thought to arise by two mechanisms. First, newly emerged proteins interact with proteins of the network. Second, according to the theory of preferential attachment, new proteins have a higher chance to interact with already interaction rich proteins. The Human Protein Reference Database provides an on in-vivo interaction data based network for human. With the data obtained from chapter one, proteins were marked with their taxon of origin based on their domain architectures. The interaction ratio of proteins of the same taxa compared to all interactions was calculated and higher values than the random model showed for nearly every taxa. On the other hand, there was no enrichment of proteins originated at the taxon of cellular organisms for the node degree found. The node degree is the number of links for this node. According to the theorie of preferential attachment the oldest nodes should have the most interactions and newly arisen proteins should be preferably attached to them not together. Both could not be shown in this analysis, preferential attachment could therefore not be the only explanation for the forming of the human protein interaction network. Finally in part three, proteins and all their interactions in the network are analysed. Protein networks can be divided into smaller highly interacting parts carrying out specific functions. This can be done with high statistical significance but still, it does not reflect the biological significance. Proteins were clustered based on their interactions and non-interactions with other proteins. A version with eleven clusters showed high gene ontology based ratings and clusters related to specific cell parts. One cluster consists of proteins having very few interactions together but many to proteins of two other clusters. This first cluster is significantly enriched with transport proteins and the two others are enriched with extracellular and cytoplasm/membrane located proteins. The algorithm seems therefore well suited to reflect the biological importance behind functional modules. Although we are still far from understanding the origin of species, this work has significantly contributed to a better understanding of evolution at the protein level and has, in particular, shown the relation of protein domains and protein architectures and their preferences for binding partners within interaction networks.
The production of extrafloral nectar and food bodies plays an important role in many tropical ant-plant mutualisms. In Malaysia, a close association exists between ants and some species of the pioneer tree genus Macaranga (Euphorbiaccac). Macaranga is a very diverse genus which exhibits all stages ofintcraction with ants, from facultative to obligatory associations. The ants nest inside the hollow inlcrnodes and reed mainly on food budies provided by the plants. Food body production had previously been reported only in myrrnecophytic Macaranga species, where it is usually coneentrated on protected parts or the plants such as recurved stipules. We found that non-myrmecophytic Macaranga species also produce food bodies on leaves and stems, where they are collected by a variety or ants. Levels of food body production differ between facultatively and obligatorily ant-associated species but also among the various non-myrmecophytes. This may he rdated to the degree of interaction with ants. Food body production starts at a younger age in the myrmccophytic species than in the transitional or non-myrmcccophytic Macaranga. Although food bodies of the non-inhabited Macaranga species are collected by a variety of ants, there is nu evidence of association with specific ant species. Our observations suggest that food bodies enhance the evolution of ant-plant interactions. Production of food bodies alone, however, does not appear to be the most important factor for the development of obligate myrmccopllytism in Macaranga.
Nucleoli provide the fascinating possibility of linking morphologically distinct structures such as those seen in the electron microscope with biochemical f eatures of the formation and step wise maturation of ribosomes. Localization of proteins by immunocytochemistry and of rRNA genes and their transcripts by in situ hybridization has greatly improved our understanding of the structural-functional relationships of the nucleolus. The present review describes some recent results obtained by electron microscopic in situ hybridization and argues that this approach has the potential to correlate each step of the complex pre-rRNA maturation pathway with nucleolar structures. Evidence is accumulating that the nucleolus-specific U3 snRNPs (small nuclear ribonucleoprotein particles) participate in rRNA processing events, similar to the role played by the nucleoplasmic snRNPs in mRNA maturation. The intranucleolar distribution of U3 snRNA is consistent with the view that it is involved in both early and late stages of pre-rRNA processing.
Lampbrush chromosomes of amphibian oocytes were isolated in the presence of near-physiological salt concentrations, to preserve their native state, and studied by electron microscopy of ultrathin s~dions. The transcriptional state of the lampbrush chromosomes was experimentally modulated by incubating the oocytes for various time periods in medium containing actinomycin D. The observations show that the structure of the lateral loops changes rapidly in response to alterations in transcriptional activity. During decreasing transcriptional activity and reduced packing density of transcripts, the chromatin axis first condensed into nucleosomes and then into an approximately 30 nm thick higher order chromatin fiber. Packaging of the loop axis into supranucleosomal structures may contribute to the foreshortening and retraction of the loops observed during inhibition of transcription and in later stages of meiotic prophase. The increasing packing density of the DNA during the retraction process of the loops could also be visualized by immunofluorescence microscopy using antibodies to DNA. The dependence of the loop chromatin structure on transcriptional activity is discussed in relation to current views of mechanisms involved in gene activation.
The distribution of DNA in Ehrlich tumour cell nucleoli was investigated by means of an immunocytochemical approach , involving a monoclonal antibody directed against double- and single-stranded DNA. Immunolabelling was performed . either before or after the embedding process. The postembedding labelling method allows better ultrastructural preservation than the preembedding labelling method. In particular, the various nucleolar components are well preserved and identifiable. In the nucleolus, labelling is particularly concentrated over the perinucleolar chromatin and over its intranucleolar invaginations, which penetrate the nucleolar body and often terminate at the fibrillar centres. In addition, aggregates of gold particles are found in the fibrillar centres, preferentially towards the peripheral regions. By contrast, the dense fibrillar component is completely devoid of labelling. The results seem to indicate that DNA containing the rDNA genes is located in the fibrillar centres, with a preference for the peripheral regions. This finding suggests that transcription of the rDNA genes should occur within the confines of the fibrillar centre, probably close to the boundary region of the surrounding dense fibrillar component. The results are discussed in the light of present knowledge of the functional organization of the nucleolus.
Small nucleolus-related bodies which occur in the nUcleoplasm of " micronuclei" lacking nucleolar organizers have been studied by immunofluorescence microscopy. These bodies stained specifically with three different antibodies directed against proteins that are normally associated with the dense fibrillar component of functional nucleoli, but not with antibodies specific for certain proteins of the granular component or the fibrillar centers. Our data show that, in the absence of rRNA genes, the various constituent proteins characteristic of the dense fibrillar component spontaneously assemble into spherical entities but that the subsequent fusion of these bodies into larger structures is prevented in these micronuclei. The similarity between these nucleolus-related bodies of micronuclei and the prenucleolar bodies characteristic of early stages of nucleologenesis during mitotic telophase is discussed.
Nucleoli are the sites of ribosome biogenesis. Transcription of the ribosomal RNA genes as well as processing and initial packaging of their transcripts with ribosomal and non-ribosomal proteins all occur within the nucleolus in an ordered manner and under defined topological conditions. Components of the nucleolus have been localized by immunocytochemistry and their functional aspects investigated by microinjection of antibodies directed against the enzyme responsible for rDNA transcription, RNA polymerase I. The role of nascent transcripts in postmitotic formation of nucleoli will be discussed.
A significant contribution to the understanding of chromatin organization was the d iscovery of the nucleosome as a globular repeating unit of the package of DNA (Hewish and Burgoyne, 1973; Woodcock, 1973; Kornberg, 1974; Olins and Olins, 1974; for review see Oudet et al., 1978 a) . In accord with the original definition and in ag reement with most workers in this field of research we identify a nucleosome as a spheric alor slightly oblate gr anular particle 10-13 nm in diameter, containing about 200 base pairs of DNA and two of each of the four his tones H2a, H2b, H3 and H4. It is this structure in which the bulk of the nuclear chroma tin is organized in most eukaryotic cells, with the exception of the dinofl age llates (Rae and Steele, 1977; dinofl agellate DNA, however, c an be packed into nucleosoma l structures in vitro by addition of the appropriate amounts of histones;the same reference). Although it seems clear from the work reported that condensed and transcriptiona lly inactive chroma tin is contained in nucleosomes as the principle for first order p acking of DNA there are two important questions onto which we are focusing in the present study: ( i ) What is the higher order of p a cking present in - and perhaps typical-of - the condensed sta te of chromatin, and (ii) what is the specific form of arrangement of transcriptionally a ctive chromatin?
The present article had originally been conceived as a review on endomembranes, the plasma membrane, and the major product of membrane-bound activities, the cell wall material. However, limitations of space and the cascading number of pertinent literature articles made it necessary to confine this to one group of membranes and one type of cell wall components. Therefore, we shall begin our survey on the biochemical and cytological aspects of membranes by a review of the class of the pore complex bearing endomembranes, i.e. the nuclear envelope and the annulate lamellae (AL). Next year the membranes of the endoplasmic reticulum and the dictyosomes will be dealt with in conjunction with a discussion of the various intracellular vesicles, the tonoplast and the plasmalemma.
In order to investigate the chemical composition of the nuclear pore complexes isolated nuclei from mature Xenopus laevis oocytes were manually fractioned into nucleo· plasmic aggregates and the nuclear envelopes. The whole isolation procedure takes no more than 60- 90 sec, and the pore complexes of the isolated envelopes are well preserved as demonstrated by electron microscopy. Minor nucleoplasmic and cytoplasmic contaminations associated with the isolated nuclear envelopes were determined with electron microscopic morphometry and were found to be quantitatively negligible as far as their mass and nucleic acid content is concerned. The RNA content of the fractions was determined by direct phosphorus analysis after differential alkaline hydrolysis. Approximately 9% of the total nuclear RNA of the mature Xenopus egg was found to be attached to the nuclear envelope. The nonmembranous elements of one pore complex contain 0.41 X 10- 16 g RNA. This value agrees well with the content estimated from morphometric data. The RNA package density in the pore complexes (270 X 10- 15 g/fJ-3) is compared with the nucleolar, nucleoplasmic and cytoplasmic RNA concentration and is discussed in context with the importance of the pore complexes for the nucleo-cytoplasmic transport of RNA-containing macromolecules. Additionally, the results of the chemical analyses as well as of the 3H-actinomycin D autoradiography and of the nucleoprotein staining method of Bernhard (1969) speak against the occurence of considerable amounts of DNA in the nuclear pore complex structures.
Electron opaque cross-bridge structures span the inter- and intracisternal spaces and provide membrane-to-membrane connections between adjacent cisternae of dictyosomes of pollen tubes of Clivia and Lilium. Additionally, the classic intercisternal rods, characteristic of intercisternal regions near the maturing face of dictyosomes, are connected with the adjacent membranes through similar cross-bridge elements. We suggest that these structural links are responsible for maintaining the flattened appearance of the central parts of Golgi apparatus cisternae as well as for the coherence of cisternae within the stack. Observations on other plant (e.g. microsporocytes of Canna) and animal cells (e.g. rodent liver and hepatoma cells, newt spermatocytes) show that such an array of membrane cross-links is a universal feature of Golgi apparatus architecture. The cross-bridges appear as part of the complex "zone of exclusion" which surrounds dictyosomes, entire Golgi apparatus and Golgi apparatus equivalents in a variety of cell types.
The disintegration of the nuclear envelope has been examined in nuclei and nuclear envelopes isolated from amphibian oocytes and rat liver tissue, using different electron microscope techniques (ultrathin sections and negatively or positively stained spread preparations). Various treatments were studied, including disruption by surface tension forces, very low salt concentrations, and non ionic detergents such as Triton X-lOO and Nonidet P-40. The high local stability of the cylinders of nonmembranous pore complex material is emphasized. As progressive disintegration occurred in the membrane regions, a network of fibrils became apparent which interconnects the pore complexes and is distinguished from the pore complexassociated intranuclear fibrils. This network might correspond to an indistinct lamella, about 15 - 20 nm thick, located at the level of the inner nuclear membrane, which is recognized in thin sections to bridge the interpore distances. With all disintegration treatments a somewhat higher susceptibility of the outer nuclear membrane is notable, but a selective removal does not take place. Final stages of disintegration are generally characterized by the absence of identifiable, membrane- like structures. Analysis of detergent-treated nuclei and nuclear membrane fractions shows almost complete absence of lipid components but retention of significant amount of glycoproteins with a typical endomembrane-type carbohydrate pattern. Various alternative interpretations of these observations are discussed. From the present observations and those of Aaronson and Blobel (1,2), we favor the notion that threadlike intrinsic membrane components are stabilized by their attachment to the pore complexes, and perhaps also to peripheral nuclear structures, and constitute a detergent-resistant, interpore skeleton meshwork.
In somatic cells DNA topoisomerase II (topo II) is thought to be involved in the domain Organization of the genome by anchoring the basis of chromatin loops to a chromosomal scafFold. Lampbrush chromosomes of am-phibian oocytes directly display this radial loop Organization in cytological preparations. In order to find out whether topo II may play a role in the Organization of these meiotic chromosomes, we performed immunofluorescence studies using antibodies against Xenopus topo II. Our results indicate that topo II is apparently absent from lampbrush chromosomes and is hence unlikely to act as a "fastener" of the numerous lateral chromosomal loops. Topo II was, however, enriched in the amplified nucleoli of Xenopus oocytes.
Structural details of the dictyosomal pores in several plant cell types are described from tangential and cross sections of Golgi cisternae. Frequency distributions of the sizes of such Golgi pores are given and compared with the corresponding values of nuclear pores in the same cells. Golgi pore inner diameters are less homogeneously distributed and can be as small as 100 A or less. They are not simply cisterna I holes, but are often associated with centrally located electron dense granules or rods and with inner pore filaments. This organization, which is very common in dictyosomal pores in plant and animal cells, has some similarities with the structural architecture of nuclear envelope and annulate lamellar pore complexes. The particulate material associated with the dictyosomal pores shows spatial and structural relationship to cytoplasmic ribosomes. Possible modes of Golgi pore formation and some consequences of these observations for interpretation of nuclear pore structures are discussed.
Several types of "irregular" structures in the arrangement of lateral fibrils were noted in electron microscopic preparations of transcriptionally active nucleolar chromatin from various plant and animal cells. Such forms include: I. Disproportionately long lateral fibrils which occur either as individual fibrils or in groups; 2. "Prelude complexes" and other arrangements of lateral fibrils in apparent spacer intercepts; 3. Thickening of the rDNA chromatin axis at the starting end of pre-rRNA matrix units; 4. Extremely long matrix units , the length of which exceeds that of the rDNA (double-strand) sequence complementary to the specific pre-rRN A (for abbreviations see text). In addition, the stability of high molecular weight RNAs contained in the nucleolar ribonucleoproteins during the preparation for electron microscopy was demonstrated by gel electrophoresis. The observations indicate that the morphological starting point of a pre-rRNA matrix unit is not necessarily identical with the initiation site for synthesis of pre-rRNA, but they rather suggest that the start of the transcriptional unit is located at least O.2-D.8 JLm before the matrix unit and that parts of the "apparent spacer" are transcribed. It is proposed that the pre-rRN A molecules do not represent the primary product of rDNA transcription but rather relatively stable intermediate products that have already been processed during transcription.
The assembly of DNA into nucleosomal and supranucleosomal chromatin structures has been studied (i) by injection of circular DNA molecules (plasmids) into nuclei of Pleurodeles waltlii oocytes; and (ii) by in vitro incubation of plasmid molecules with the supernatant fraction from oocyte nuclei of Pleurodeles and Xenopus laevis, followed by purification of nucleoprotein structures formed with sucrose gradient centrifugation. [n both types of experiments , spread preparations of the newly assembled and transcriptionally inactive chromatin , examined by electron microscopy , show dense globular higher order (supranucleosomal) packing forms. Under partially relaxing (low salt) preparation conditions granular chromatin subunits of about 30 nm diameter can be seen either as widely spaced particles or in closely packed aggregates. The transcriptionally inactive endogenous chromatin of chromomeres of lampbrush chromosomes is arranged in similar higher order chromatin units. A correlation is found between the sizes of the DN A molecule probes used and the numbers of nucleosomes and higher order globules in the assembled chromatin structures. After prolonged dispersion in low salt buffers , these globular chromatin units unfold into chains of7-12 nucleosomes. The results support the concept that chromatin is arranged , under physiological ion concentrations as they are present in the nucleus , in supranucleosomal units of globular morphology.
Using antibodies to various nucleolar and ribosomal proteins, we define, by immunolocalization in situ, the distribution of nucleolar proteins in the different morphological nucleolar subcompartments. In the present study we describe the nucleolar localization of a specific ribosomal protein (51) by immunofluorescence and immunoelectron microscopy using a monoclonal antibody (R5 1-105). In immunoblotting experiments, this antibody reacts specifically with the largest and most acidic protein of the small ribosomal subunit (51) and shows wide interspecies cross-reactivity from amphibia to man. Beside its localization in cytoplasmic ribosomes, this protein is found to be specifically localized in the granular component of the nucleolus and in distinct granular aggregates scattered over the nucleoplasm. This indicates that ribosomal protein 51, in contrast to reports on other ribosomal proteins, is not bound to nascent pre-rRNA transcripts but attaches to preribosomes at later stages of rRNA processing and maturation. This protein is not detected in the residual nucleolar structures of cells inactive in rRNA synthesis such as amphibian and avian erythrocytes. During mitosis, the nucleolar material containing ribosomal protein 51 undergoes a remarkable transition and shows a distribution distinct from that of several other nucleolar proteins. In prophase, the nucleolus disintegrates and protein 51 appears in numerous small granules scattered throughout the prophase nucleus. During metaphase and anaphase, a considerable amount of this protein is found in association with the surfaces of all chromosomes and finely dispersed in the cell plasm. In telophase, protein 51-containing material reaccumulates in granular particles in the nucleoplasm of the newly formed nuclei and, finally, in the re-forming nucleoli. These observations indicate that the nucleolus-derived particles containing ribosomal protein 51 are different from cytoplasmic ribosomes and, in the living cell, are selectively recollected after mitosis into the newly formed nuclei and translocated into a specific nucleolar subcompartment, i.e ., the granular component. The nucleolar location of ribosomal protein 51 and its rearrangement du'ring mitosis is discussed in relation to the distribution of other nucleolar proteins.
Nuclei of amphibian oocytes contain large amounts of actin, mostly in unpolymerized or short-polymer form. When antibodies to actin or actin-binding proteins (fragmin and the actin modulator from mammalian smooth muscle) are injected into nuclei of living oocytes of Pleurodeles waltlii, transcription of the lampbrush chromosomes, but not of the rRNA genes, is inhibited. When transcription is repressed by drugs or RNA is digested by microinjection of RNAase into oocyte nuclei, an extensive meshwork of actin filament bundles is seen in association with the isolated lampbrush chromosomes. These observations indicate a close relationship between the state of nuclear actin and transcriptional activity and suggest that nuclear actin may be involved in transcriptional events concerning protein-coding genes.
Ultrastructural localization of DNA in two Cryptomonas species by use of a monoclonal DNA-antibody
(1986)
Immunogold cytochemistry - DNA localization - Cryptomonas nucleomorph The distribution and subcellular localization of DNA in the unicellular alga Cryptomonas has been investigated electron-microscopically by indirect immunocytochemistry, using a monoclonal DNA antibody and a gold-Iabeled secondary antibody. This technique proved to be very sensitive and entirely specific. DNA could be demonstrated in four different compartments (nucleus, nucleomorph, plastid, and mitochondrion). Within the plastid, DNA is concentrated in stroma regions that are localized preferentially around the center of the organelle. The mitochondrion contains several isolated DNA-containing regions (nucleoids). Within the nucleus, most of the DNA is localized in the 'condensed' chromatin. DNA was also detectable in small areas of the nucleolus, whereas the interchromatin space of the nucleus appeared almost devoid of DNA. Within the nucleomorph, DNA is distributed inhomogeneously in the matrix. DNA could furthermore be detected in restricted areas of the 'fibrillogranular body' of the nucleomorph, resembling the situation encountered in the nucleol us. The presence of DNA and its characteristic distribution in the nucleomorph provide additional, strong evidence in favour of the interpretation of that organelle as the residual nucleus of a eukaryotic endosymbiont in Cryptomonas.
The morphology of nucleolar and non-nucleolar (Iampbrush chromosome loops) chromatin was studied in the electron microscope during states of reduced transcriptional activity in amphibian oocytes (Xenopus laevis, Triturus alpestris, T. cristatus). Reduced transcriptional activity was observed in maturing stages of oocyte development and after treatment with an inhibitor, actinomycin D. Strands of nucleolar chromatin appear smooth and thin, and contain only few, if any, nucleosomal particles in the transcribed units. This is true whether they are densely or only sparsely covered with lateral ribonucleoprotein fibrils. This smooth and non-nucleosomal character is also predominant in the interspersed, apparently nontranscribed rDNA spacer regions. During inactivation, however, nucleolar chromatin frequently and progressively assumes a beaded appearance in extended fibril-free-that is, apparently nontranscribed - regions. I n either fUll-grown 00- cytes or late after drug treatment, most of the nucleolar chromatin is no longer smooth and thin, but rather shows a beaded configuration indistinguishable from inactive non - nucleolar chromatin. In many chromatin strands, transitions of fibril-associated regions of smooth character into beaded regions wihout lateral fibrils are seen. Similarly, in the non-nucleolar chromatin of the retracting lampbrush chromosome loops, reduced transcriptional activity is correlated with a change from smooth to beaded morphology. Here, however, beaded regions are also commonly found interspersed between the more or less distant bases of the lateral fibrils, the putative transcriptional complexes. I n both sorts of chromatin, detergents (in particular Sarkosyl) that remove most of the chromatin proteins including histones from the DNA axis but leave the RNA polymerases of the transcriptional complexes attached were used to discriminate between polymerases and nucleosomal particles. The results suggest that nucleosomes are absent in heavily transcribed chromatin regions but are reformed after inactivation. In contrast to the findings with inactivated nucleolar genes, in lampbrush chromosome loops the beaded nucleosomal configuration appears to be assumed also in regions within transcriptional units that, perhaps temporarily, are not involved in transcription.
Comparisons ofrelative lengths oflampbrush loops, nascent RNP transcripts and hnRNA molecules from oocytes of amphibia with different C-values show that there is an increasing trend in loop, and transcriptional unit, length with increase in genome size but no increasing trend with respect to RN A contour length.The formation of duplex regions and circles in RNP fibrils indicates that RNA processing may occur within the nascent fibrils. The hnRNA molecules from oocytes of the various amphibia readily form intermolecular duplex structures. These complementary sequences have a low kinetic complexity and are transcribed from highly repetitive sequences distributed throughout the genome. Their possible function is considered.
A monoclonal murine antibody (No-I 14) is described which reacts specifically with a polypeptide of molecular weight (M,) 180000 present in low-speed nuclear pellets from oocytes and somatic cells of Xenopus laevis and X. borealis and in isolated amplified nucleoli. Two-dimensional gel electrophoresis has revealed the acidic nature of this polypeptide (isoelectric at pH of ca 4.2 in the presence of 9.5 M urea). A relatively large proportion of the protein is extracted at elevated ionic strength( i.e., at 0.4-0.5 M alkali salt) in a form sedimenting at approx. 7-8S , compatible with a monomeric state. It is also extracted by digestion with RNase but not with DNase. In immunofluorescence microscopy, antibody No-114 stains intensely nucleoli of oocytes and all somatic cells examined , including the residual nucleolar structure of Xenopus erythrocytes which are transcriptionally inactive. During mitosis the antigen does not remain associated with the nucleolar organizer regions (NOR) of chromosomes but is released and dispersed over the cytoplasm until telophase when it re-associates with the reforming interphase nucleoli. At higher resolution the immunofluorescent region is often resolved into a number of distinct subnucleolar components of varied size and shape. Immunoelectron microscopy using colloidal gold-coupled secondary antibodies reveals that the M, 180000 protein is confined to the dense fibrillar component of the nucleolus. This conclusion is also supported by its localization in the fibrillar part of segregated nucleoli of cells treated with actinomycin D. We conclude that nucleoli contain a prominent protein of M, 180000 which contributes to the general structure of the dense fibrillar component of the interphase nucleolus , independent of its specific transcriptional activity.
Nucleoli are the morphological expression of the activity of a defined set of chromosomal segments bearing rRNA genes. The topological distribution and composition of the intranucleolar chromatin as well as the definition of nucleolar structures in which enzymes of the rDNA transcription machinery reside have been investigated in mammalian cells by various immunogold labelling approaches at the ultrastructural level. The precise intranucleolar location of rRNA genes has been further specified by electron microscopic in situ hybridization with a non-autoradiographic procedure. Our results indicate that the fibrillar centers are the sole nucleolar structures where rDNA, core histones, RNA polymerase I and DNA to po isomerase I are located together. Taking into account the potential value and limitations of immunoelectron microscopic techniques, we propose that transcription of the rRNA genes takes place within the confines of the fibrillar centers, probably close to the boundary regions to the surrounding dense fibrillar component.
Homozygous deletions in Wilms' tumor DNA have been a key step in the identification and isolation of the WTI gene. Several additional loci are also postulated to contribute to Wilms' tumor formation. To assess the frequency of WTI alterations we have analyzed the WTI locus in a panel of 77 Wilms' tumors. Eight tumors showed evidence for large deletions of several hundred or thousand kilobasepairs of DNA, some of which were also cytogenetically detected. Additional intragenic mutations were detected using more sensitive SSCP analyses to scan all 10 WTI exons. Most of these result in premature stop codons or missense mutations that inactivate the remaining WTI allele. The overall frequency of WTI alterations detected with these methods is less than 15%. While some mutations may not be detectable with the methods employed, our results suggest that direct alterations of the WTI gene are present in only a small fraction of Wilms' tumors. Thus, mutations at other Wilms' tumor loci or disturbance of interactions between these genes likely play an important role in Wilms' tumor development.
Recent progresses and developments in molecular biology provide a wealth of new but insufficiently characterised data. This fund comprises amongst others biological data of genomic DNA, protein sequences, 3-dimensional protein structures as well as profiles of gene expression. In the present work, this information is used to develop new methods for the characterisation and classification of organisms and whole groups of organisms as well as to enhance the automated gain and transfer of information. The first two presented approaches (chapters 4 und 5) focus on the medically and scientifically important enterobacteria. Its impact in medicine and molecular biology is founded in versatile mechanisms of infection, their fundamental function as a commensal inhabitant of the intestinal tract and their use as model organisms as they are easy to cultivate. Despite many studies on single pathogroups with clinical distinguishable pathologies, the genotypic factors that contribute to their diversity are still partially unknown. The comprehensive genome comparison described in Chapter 4 was conducted with numerous enterobacterial strains, which cover nearly the whole range of clinically relevant diversity. The genome comparison constitutes the basis of a characterisation of the enterobacterial gene pool, of a reconstruction of evolutionary processes and of comprehensive analysis of specific protein families in enterobacterial subgroups. Correspondence analysis, which is applied for the first time in this context, yields qualitative statements to bacterial subgroups and the respective, exclusively present protein families. Specific protein families were identified for the three major subgroups of enterobacteria namely the genera Yersinia and Salmonella as well as to the group of Shigella and E. coli by applying statistical tests. In conclusion, the genome comparison-based methods provide new starting points to infer specific genotypic traits of bacterial groups from the transfer of functional annotation. Due to the high medical importance of enterobacterial isolates their classification according to pathogenicity has been in focus of many studies. The microarray technology offers a fast, reproducible and standardisable means of bacterial typing and has been proved in bacterial diagnostics, risk assessment and surveillance. The design of the diagnostic microarray of enterobacteria described in chapter 5 is based on the availability of numerous enterobacterial genome sequences. A novel probe selection strategy based on the highly efficient algorithm of string search, which considers both coding and non-coding regions of genomic DNA, enhances pathogroup detection. This principle reduces the risk of incorrect typing due to restrictions to virulence-associated capture probes. Additional capture probes extend the spectrum of applications of the microarray to simultaneous diagnostic or surveillance of antimicrobial resistance. Comprehensive test hybridisations largely confirm the reliability of the selected capture probes and its ability to robustly classify enterobacterial strains according to pathogenicity. Moreover, the tests constitute the basis of the training of a regression model for the classification of pathogroups and hybridised amounts of DNA. The regression model features a continuous learning capacity leading to an enhancement of the prediction accuracy in the process of its application. A fraction of the capture probes represents intergenic DNA and hence confirms the relevance of the underlying strategy. Interestingly, a large part of the capture probes represents poorly annotated genes suggesting the existence of yet unconsidered factors with importance to the formation of respective virulence phenotypes. Another major field of microarray applications is gene expression analysis. The size of gene expression databases rapidly increased in recent years. Although they provide a wealth of expression data, it remains challenging to integrate results from different studies. In chapter 6 the methodology of an unsupervised meta-analysis of genome-wide A. thaliana gene expression data sets is presented, which yields novel insights in function and regulation of genes. The application of kernel-based principal component analysis in combination with hierarchical clustering identified three major groups of contrasts each sharing overlapping expression profiles. Genes associated with two groups are known to play important roles in Indol-3 acetic acid (IAA) mediated plant growth and development as well as in pathogen defence. Yet uncharacterised serine-threonine kinases could be assigned to novel functions in pathogen defence by meta-analysis. In general, hidden interrelation between genes regulated under different conditions could be unravelled by the described approach. HMMs are applied to the functional characterisation of proteins or the detection of genes in genome sequences. Although HMMs are technically mature and widely applied in computational biology, I demonstrate the methodical optimisation with respect to the modelling accuracy on biological data with various distributions of sequence lengths. The subunits of these models, the states, are associated with a certain holding time being the link to length distributions of represented sequences. An adaptation of simple HMM topologies to bell-shaped length distributions described in chapter 7 was achieved by serial chain-linking of single states, while residing in the class of conventional HMMs. The impact of an optimisation of HMM topologies was underlined by performance evaluations with differently adjusted HMM topologies. In summary, a general methodology was introduced to improve the modelling behaviour of HMMs by topological optimisation with maximum likelihood and a fast and easily implementable moment estimator. Chapter 8 describes the application of HMMs to the prediction of interaction sites in protein domains. As previously demonstrated, these sites are not trivial to predict because of varying degree in conservation of their location and type within the domain family. The prediction of interaction sites in protein domains is achieved by a newly defined HMM topology, which incorporates both sequence and structure information. Posterior decoding is applied to the prediction of interaction sites providing additional information of the probability of an interaction for all sequence positions. The implementation of interaction profile HMMs (ipHMMs) is based on the well established profile HMMs and inherits its known efficiency and sensitivity. The large-scale prediction of interaction sites by ipHMMs explained protein dysfunctions caused by mutations that are associated to inheritable diseases like different types of cancer or muscular dystrophy. As already demonstrated by profile HMMs, the ipHMMs are suitable for large-scale applications. Overall, the HMM-based method enhances the prediction quality of interaction sites and improves the understanding of the molecular background of inheritable diseases. With respect to current and future requirements I provide large-scale solutions for the characterisation of biological data in this work. All described methods feature a highly portable character, which allows for the transfer to related topics or organisms, respectively. Special emphasis was put on the knowledge transfer facilitated by a steadily increasing wealth of biological information. The applied and developed statistical methods largely provide learning capacities and hence benefit from the gain of knowledge resulting in increased prediction accuracies and reliability.
Like many other social insect societies, honeybees collectively share the resources they gather by feeding each other. These feeding contacts, known as trophallaxis, are regarded as the fundamental basis for social behavior in honeybees and other social insects for assuring the survival of the individual and the welfare of the group. In honeybees, where most of the trophallactic contacts are formed in the total darkness of the hive, the antennae play a decisive role in initiation and maintenance of the feeding contact, because they are sensitive to gustatory stimuli. The sequences of behaviors performed by the receiver bees at the beginning of a feeding contact includes the contact of one antenna with the mouthparts of a donor bee where the regurgitated food is located. The antennal motor action is characterized by behavioral asymmetry, which is novel among communicative motor actions in invertebrates. This preference of right over left antenna is without exception even after removal of the antennal flagellum. This case of laterality in basic social interaction might have its reason in the gustatory asymmetry in the antennae, because the right antenna turns out to be significantly more sensitive to stimulation with sugar water of various concentrations than the left one. Trophallactic contacts which guarantee a constant access to food for every individual in the hive are vitally important to the honeybee society, because honeybees are heterothermic insects which actively regulate their thoracic temperature. Even though the individual can regulate its body temperature, its heating performance is strictly limited by the amount of sugar ingested. The reason for this is that honeybees use mostly the glucose in their hemolymph as the energy substrate for muscular activity, and the heat producing flight muscles are among the metabolically most active tissues known. The fuel for their activity is honey; processed nectar with a sugar content of ~80% stored in the honeycomb. The results show that the sugar content of the ingested food correlates positively with the thoracic temperature of the honeybees even if they are caged and show no actual heating-related behavior as in brood warming or heating in the centre of the winter cluster. Honeybees actively regulate their brood temperature by heating to keep the temperature between 33 °C to 36 °C if ambient temperatures are lower. Heating rapidly depletes the worker’s internal energy; therefore the heating performance is limited by the honey that is ingested before the heating process. This study focused on the behavior and the thoracic temperature of the participants in trophallactic food exchanges on the brood comb. The brood area is the centre of heating activity in the hive, and therefore the region of highest energy demand. The results show that the recipients in a trophallactic food exchange have a higher thoracic temperature during feeding contacts than donors, and after the feeding contact the former engage in brood heating more often. The donor bees have lower thoracic temperature and shuttle constantly between honey stores and the brood comb, where they transfer the stored honey to heating bees. In addition, the results show a heat-triggered mechanism that enables donor and recipient to accomplish trophallactic contacts without delay in the total darkness of the hive in the brood area as the most energy consuming part of the hive. Providing heat-emitting workers with small doses of high performance fuel contributes to an economic distribution of resources consistent with the physiological conditions of the bees and the ecological requirements of the hive, resulting in a highly economical resource management system which might be one of the factors favouring the evolution of perennial bee colonies in temperate regions. The conclusion of these findings suggests a resource management strategy that has evolved from submissive placation behavior as it is seen in honeybees, bumblebees and other hymenopterans. The heat-triggered feedback mechanism behind the resource management of the honeybee´s thermoregulatory behavior reveals a new aspect of the division of labor and a new aspect of communication, and sheds new light on sociality in honeybees.
Around 10.000 – 150.000 endogenous DNA damage-induced lesions occur in a human body per day and cell. Accumulation of unrepaired lesions can lead to aneuploidy and the loss of genomic integrity which in turn contributes to tumor formation. Therefore, an efficient DNA damage response has to be initiated, in the end leading to cell cycle inhibition and induction of repair. Since it is known that a recently characterized human multiprotein complex named LINC (or human dREAM) together with B-MYB is involved in the regulation of G2/M gene expression (Plk1, cyclin B1, cdc2 etc.), its function in the DNA damage response was analyzed in this study. In growing cells B-MYB is associated to the LIN core complex which consists of 5 different proteins named LIN-9, LIN-54, LIN-52, LIN-37 and RbAp48. After induction of DNA damage B-MYB leaves the complex and binding of E2F4 and p130 to LINC is induced. Importantly, the upstream pathway leading to LINC rearrangement is dependent on the activation of p53 and p21. Interestingly, p53 -/- cells solely have the potential to block in the G2 phase of the cell cycle, thereby making them vulnerable for errors during G2 arrest induction or maintenance. Here I demonstrate that LINC rearrangement is absent in p53 -/- cells and that B-MYB/LINC binding to target gene promoters is increased. This in turn leads to an increased G2/M gene expression after DNA damage induction and triggers premature cell cycle re-entry (checkpoint adaptation). Significantly, B-MYB expression is increased in p53 mutated primary breast cancer tumors and correlates with poor prognosis and reoccurrence probably due to its function in checkpoint adaptation. This study gives evidence that inhibition of B-MYB gene expression or B-MYB function in p53 mutant tumors could be a good choice for adjuvant therapy.
1 n order to review the contradictory statements on the ultrast ructure of the nuclear envelope, a study was undertaken combining section and negat ive stai ning electron microscopy on manually isolated oocyte nuclei and nuclear envelopes from six amphibian species including Anura as well as Urodela. The a ppeara nce of the negatively stained iso lated nuclear envelopes is described in deta il and the dependence on the preparation co nditions used is emphas ized . Pore complex structures such as pore perimeter, central granule, an nul ar components, interna l fibrils, and annu lus-attached fibrils could be identified by both techniques, negat ive staining and sect ions. Comparative studies show that no marked diffe rences ex ist in the structural data of the nuclear envelope among the investigated amphibians and the significance of the structural components is discussed. A model of the nuclea r pore complex based on the findings of the present investigation is prese nted.
Regulated progression through the cell cycle is essential for ordered cell proliferation. One of the best characterized tumor suppressors is the retinoblastoma protein pRB, which together with the E2F transcription factors regulates cell cycle progression. In the model organisms Drosophila melanogaster and Caenorhabditis elegans, RB/E2F containing multiprotein complexes have been described as transcriptional regulators of gene expression. This work first describes a homologous complex in human cells named LINC (for LIN complex). It consists of a stable core complex containing LIN-9, LIN-37, LIN-52, LIN-54 and RbAp48. This core complex interacts cell cycle-dependently with different pocket proteins and transcription factors. In quiescent cells, LINC associates with p130 and E2F4. In S-phase cells these interactions are lost and LINC binds to B-MYB and p107. The transient knock-down of LIN-54 in primary fibroblasts, as the depletion of LIN-9, leads to cell cycle defects. The cells are delayed before the entry into mitosis. This effect is due to the fact that the knock-down of LINC components leads to the downregulation of cell cycle genes responsible for the entry into and exit from mitosis as well as for checkpoints during mitosis. These LINC target genes are known E2F G2/M target genes, which are expressed later than the classical G1/S E2F target genes. The transcriptional regulation by LINC is a direct effect as LINC binds to the promoters of its target genes throughout the cell cycle. LINC contains three DNA-binding proteins. E2F4 and B-MYB, which cell cycle-dependently bind to LINC, are known DNA-binding transcription factors. Additionally, it is show here that the LINC core complex member LIN-54 also directly binds to the promoter of a LINC target gene. Although the exact molecular mechanism of LINC function needs to be analyzed further, data in this work provide a model for the delayed activation of G2/M target genes. B-MYB, a G1/S E2F target gene, binds to LINC upon its expression in S-phase. Then only LINC is a transcriptional activator that induces the expression of the G2/M genes. This provides an explanation for the delayed expression of these E2F G2/M target genes.
Eine der größten Herausforderungen in der Neurobiologie ist es, die neuronalen Prozesse zu verstehen, die Lernen und Gedächtnis zugrundeliegen. Welche biochemischen Pfade liegen z.B. der Koinzidenzdetektion von Reizen (klassische Konditionierung) oder einer Handlung und ihren Konsequenzen (operante Konditionierung) zugrunde? In welchen neuronalen Unterstrukturen werden diese Informationen gespeichert? Wie ähnlich sind die Stoffwechselwege, die diese beiden Arten des assoziativen Lernens vermitteln und auf welchem Niveau divergieren sie? Drosophila melanogaster ist wegen der Verfügbarkeit von Lern-Paradigmen und neurogenetischen Werkzeugen ein geeigneter Modell-Organismus, zum diese Fragen zu adressieren. Er ermöglicht eine umfangreiche Studie der Funktion des Gens S6KII, das in der Taufliege in klassischer und operanter Konditionierung unterschiedlich involviert ist (Bertolucci, 2002; Putz et al., 2004). Rettungsexperimenten zeigen, dass die olfaktorische Konditionierung in der Tully Maschine (ein klassisches, Pawlow’sches Konditionierungsparadigma) von dem Vorhandensein eines intakten S6KII Gens abhängt. Die Rettung war sowohl mit einer vollständigen, als auch einer partiellen Deletion erfolgreich und dies zeigt, dass der Verlust der phosphorylierenden Untereinheit der Kinase die Hauptursache des Funktionsdefektes war. Das GAL4/UAS System wurde benutzt, um die S6KII Expression zeitlich und räumlich zu steuern. Es wurde gezeigt, dass die Expression der Kinase während des adulten Stadiums für die Rettung hinreichend war. Dieser Befund schließt eine Entwicklungsstörung als Ursache für den mutanten Phänotyp aus. Außerdem zeigte die gezielte räumliche Rettung von S6KII die Notwendigkeit der Pilzkörper und schloss Strukturen wie das mediane Bündel, die Antennalloben und den Zentralkomplex aus. Dieses Muster ist dem vorher mit der rutabaga Mutation identifizierten sehr ähnlich (Zars et al., 2000). Experimente mit der Doppelmutante rut, ign58-1 deuten an, dass rutabaga und S6KII im gleichen Signalweg aktiv sind. Vorhergehende Studien hatten bereits gezeigt, dass die unterschiedlichen Ergebnisse bei operanter und klassischer Konditionierung auf verschiedenen Rollen für S6KII in den zwei Arten des Lernens hindeuten (Bertolucci, 2002; Putz, 2002). Diese Schlussfolgerung wurde durch den mutanten Phänotyp der transgenen Linien in der Positionskonditionierung und ihr wildtypisches Verhalten in der klassischen Konditionierung zusätzlich bekräftigt. Eine neue Art von Lern-Experiment, genannt „Idle Experiment“, wurde entworfen. Es basiert auf der Konditionierung der Laufaktivität, stellt eine operante Aufgabenstellung dar und überwindet einige der Limitationen des „Standard“ Heat-Box Experimentes. Die neue Art des Idle Experimentes erlaubt es, „gelernte Hilflosigkeit“ in Fliegen zu erforschen, dabei zeigte sich eine erstaunliche Ähnlichkeit zu den Vorgängen in komplizierteren Organismen wie Ratten, Mäusen oder Menschen. Gelernte Hilflosigkeit in der Taufliege wurde nur in den Weibchen beobachtet und wird von Antidepressiva beeinflusst.
Certain autoimmune sera contain antibodies against a nucleolar ribonucleoprotein particle associated with 7-2-RNA (R. Reddy et al. (1983) J. Bioi. Chem . 258, 1383; C. Hashimoto and J. A. Steitz (1983) J. Bioi. Chem. 258, 1379). In this study, we showed by immunofluorescence microscopy that antibodies reactive with 7-2-ribonucleoprotein immunolocalized in the granular regions of actinomycin D and 5,6-dichloro-I-j3-D-ribofuranosylbenzimidazole (DRB)-segregated nucleoli from Vero cells. By electron microscopic immunocytochemistry, antigen-antibody complexes were located in the granular component of transcriptionally active nucleoli from rat liver hepatocytes and HeLa cells. Anti-7- 2-RNP antibodies from two autoimmune sera immunoprecipitated a major protein of Mr 40,000 from e5S] methionine-Iabeled HeLa cell extract. The immunolocalization data suggest that 7-2-ribonucleoprotein may be involved in stages of ribosome biogenesis which take place in the granular component of the nucleolus, i.e., assembly, maturation, and/or transport of preribosomes
Repeat sequences are transcribed in the germinal vesicles of amphibian oocytes. In the hnRNA population both complements of the repeats are found and can be readily detected because they form intermolecular duplex structures. The structure and formation of duplex regions have been studied in the hnRNA of Xenopus laevis, Triturus cristatus, Amphiuma means and Necturus maculosus, a series of amphibians of increasing genome size (C-value). In T. cristatus, the duplex structures are mostly 600- 1200 bp in length, whereas in X. laevis they are shorter and in N. maculosus they tend to be longer. Although the proportion of RNA sequence capable of rapidly forming duplex structures is different in different organisms, this property bears no relationship to C-value. However the sequence complexity of complementary repeats, as estimated from the rate of duplex formation, does show an increasing trend with C-value. The complementary repeats found in oocyte hnRNA are transcribed from families of DNA sequence that are each represented in the genome by thousands of copies. The extent of cross-species hybridization is low, indicating that the repeat sequences transcribed in different amphibian genera are not the same. In situ hybridization experiments indicate that the repeat sequences are spread throughout the genome. The evolution and possible function of complementary repeats are considered.
The formation of daughter nuclei and the reformation of nucleolar structures was studied after microinjection of antibodies to RNA polymerase I into dividing cultured cells (PtK2). The fate of several nucleolar proteins representing the three main structural subcomponents of the nucleolus was examined by immunofluorescence and electron microscopy. The results show that the RNA polymerase I antibodies do not interfere with normal mitotic progression or the early steps of nucleologenesis, i.e. , the aggregation of nucleolar material into prenucleolar bodies. However,they inhibit the telophasic coalescence of the prenucleolar bodies into the chromosomal nucleolar organizer regions, thus preventing the formation of new nucleoli. These prenucleolar bodies show a fibrillar organization that also compositionally resembles the dense fibrillar component of interphase nucleoli . We conclude that during normal nucleologenesis the dense fibrillar component forms from preformed entities around nucleolar organizer regions, and that this association seems to be dependent on the presence of an active form of RNA polymerase I.
The ultrastructure of th e growin g and ma turing primary nucleus of Acetabularia medite rranea and Acetabularia major has been studied with the use of various fi xation procedures. Particular interest has been focused on the deta ils of the nuclear periphery and the perinuclear region. It is demonstrated that early in nuclear grow th a characteristic perinucl ear structura l complex is formed which is, among the eukaryotic cells, unique to Acetabularia and re lated genera. This perinuclear system consists essentially of a) the nuclear envelope with a very hi gh pore frequency and various pore complex assoc iat ion s w ith granular and/or threadlike structures some of which are continuous with the nucleolus; b) an approx imate ly 100 nm thick intermediate zone densely filled with a filam entOus material and occasional sma ll membraneous structures from which the typical cytOplasmic and nuclear organe lles and particles are excl ud ed ; c) an adjacent Iacunar labyrinthum which is interrupted by many plasmatic junction channels between the intermed iate zone and the free cytOplasm; d) numerous dense perinuclear bodies in the juxtanuclear cytOplasm which a re especia lly frequent at the junction channels and reveal a composition of aggregated fibrillar and granul ar structures; e) very dense exclusively fibrill ar agg regates which occur either in assoc iation with t he perinuclear region of the lacunar labyrinthum or, somewhat further out, in the cytOplasmic strands between the bra nches of the lacun ar labyrinthum in the form of slender, characteristic rods or "sausages".
The number of ribosomal RNA molecules which are transferred through an average nuclear pore complex per minute into the cytoplasm (nuclear pore flow rate, NPFR) during oocyte growth of Xenopus laevis is estimated. The NPFR calculations are based on determinations of the increase of cytoplasmic rRNA content during defined time intervals and of the total number of pore complexes in the respective oogenesis stages. In the mid-la mpbrush stage (500:"700 I'm oocyte diameter) the NPFR is maximal with 2.62 rRNA molecules/ pore/ minute. Then it decreases to zero at the end of oogenesis. The nucleocytoplasmic RNA f10w rates determined are compared with corresponding values of other cell types. The molecular weight of the rRNA precursor transcribed in the extrachromosomal nucleoli of Xenopus lampbrush stage oocytes is determined by acrylamide gel electrophoresis to be 2.5 x 10· daltons. From the temporal increase of cytoplasmic rRNA (3.8 I'g per oocyte in 38 days) and the known number of simultaneously growing precursor molecules in the nucleus the chain growth rate of the 40 S precursor RNA is estimated to be 34 nucleotides per second.
Semi -iso la ted annul a te lamellae were prepared from single newt oocy tes (Triturus alpestris) by a modified Call a n-T omlin technique. Such preparations were examined with the electron mi croscope, and the negative sta ining a ppearance of th e a nnulate lamellae is described . The annul a te lamellae can be de tected either adhering to the nuclear envelope or being detached from it. Sometimes they a re obse rved to be connected with slender tubular-like structures interpreted as pa rts of the endoplasmic reti culum. The results obta ined from negativ e sta ining a re combined with those from sections. Especially, the structural data on th e a nnula te lamellae and the nuclear envelope of the very same cell were compa red . Evidence is presented th a t in the oocytes studied the two kinds of porous cisternae, n amely a nnul a te lamellae and nuclear envelope, a re markedly distinguished in that the annul a te lamellae ex hibit a much higher pore frequency (generally about twice tha t found for the corresponding nuclear envelope) and have al so a rela tive pore area occupying as much as 32 % to 55 % of th e cistern al surface (compa red with 13 % to 22 % in the nuclear envelopes). T he pore di ame ter a nd all other ultras tructural details of the pore complexes, however, a re equi valent in both kinds of porous cisternae. Like the annuli of the nuclear pore complexes of various a nimal and pl ant cells, the a nnuli of the a nnula te lamellae pores reveal al so an eightfold symmetry of their subunits in negatively stained as well as in ectioned ma teria l. Furthermore, th e a nnul a te lamellae a re shown to be a site of activity of the Mg-Na-Kstimul a ted ATPase.
RNA polymerase I preparations purified from a rat hepatoma contained DNA topoisomerase activity. The DNA topoisomerase associated with the polymerase had an Mr of 110000, required Mg2+ but not ATP, and was recognized by anti-topoisomerase I antibodies. When added to RNA polymerase I preparations containing topoisomerase activity, anti-topoisomerase I antibodies were able to inhibit the DNA relaxing activity of the preparation as well as RNA synthesis in vitro. RNA polymerase II prepared by analogous procedures did not contain topoisomerase activity and was not recognized by the antibodies. The topoisomerase I: polymerase I complex was reversibly dissociated by column chromatography on Sephacryl S200 in the presence of 0.25 M (NH4hS04. Topoisomerase I was immunolocalized in the transcriptionally active ribosomal gene complex containing RNA polymerase I in situ. These data indicate that topoisomerase I and RNA polymerase I are tightly complexed both in vivo and in vitro, and suggest a role for DNA topoisomerase I in the transcription of ribosomal genes.
The karyotype of D. elongatus was investigated by means of C-banding, silver staining, and mithramycinand quinacrine fluorescent staining. The diploid chromosome number is 2n = 50. C-banding shows pericentromerically localized constitutive heterochromatin in every chromosome. Two of the chromosome pairs carry two telomeric nucleolus organizer regions each. No heteromorphic sex chromosomes were found.
Behavioural adaptations have made the desert isopod Hemilepistus reaumuri the most successful herbivore and detritivore of the macrofauna of many arid areas in North Africa and Asia Minor. For survival and reproduction Hemilepistus is dependent on burrows. New burrows can only be dug during spring. With the time-consuming digging of a burrow, Hemilepistus has only made the first step towards solving its ecological problems. The burrows are vital and have to be continuously defended against competitors. This requirement is met by co-operation of individuals within the framework of a highly developed social behaviour. In spring adults form monogamous pairs in which partners recognize each other individually and later form, with their progeny, strictly closed family communities. Hemilepistus is compared with a Porcellio' sp. which has developed, convergently, a social behaviour which resembles that of Hemilepistus in many respects, but differs essentially in some aspects, partly reflecting differences in ecological requirements. This and a few other Porcellio species demonstrate some possible steps in the evolution of the social behaviour of Hemilepistus. The female Hemilepistus is-in contrast to Porcellio sp. - semelparous and the selective advantages of monogamy in its environment are not difficult to recognize. This chapter discusses how this mating system could have evolved and especially why monogamous behaviour is also the best method for the Hemilepistus male to maximize its reproductive success. The cohesion of pairs and of family communities in Hemilepistus is based on a highly developed chemical communication system. Individual- and family-specific badges owe their specificity to genetically determined discriminating substances. The nature of the badges raises a series of questions: e.g. since alien badges release aggression, how do parents avoid cannibalizing their young? Similar problems arise from the fact that family badges are mixtures of chemical compounds of very low volatility with the consequence that they can only be transferred by direct contact and that during moulting all substances are lost which an individual does not produce itself. It is shown that in solving these problems inhibiting properties (presumably substances) and learning play a dominant role.
Individual recogmtlon in the non-eusocial arthropods is, according to our present knowledge, predominantly found in the frame of permanent or temporary monogamy. In some cases, e. g. in stomatopods and possibly other marine crustaceans too, individual recognition may serve to allow identification of (i) individuals within dominance hierarchies or (ii) neighbours in territorial species thus helping to avoid the repetition of unnecessary and costly fights. Kin recognition is experimentally proven only in some isopod species (genera Hemilepistus and Porcel/io) and in the primitive cockroach (termite?) Cryptocercus. The «signatures» or «discriminators» used in the arthropods are chemical. It is assumed that the identifying substances are mainly genetically determined and in this paper I shall discuss possible evolutionary origins. The main part of this account is devoted to the presentation of some aspects of the highly developed individual and kin identification and recognition system in the desert isopod Hemilepistus reaumuri - a pure monogamous species in which pairs together with their progeny form strictly exclusive family units. Amongst other things problems of (i) mate choice, (ii) learning to recognize a partner, (iii) avoiding the un adaptive familiarization with aliens are treated. Monogamy under present conditions is for both sexes the only suitable way of maximizing reproductive success; an extremely strong selection pressure must act against every attempt to abandon monogamy under the given ecological conditions. The family «badges» which are certainly always blends of different discriminator substances are extremely variable. This variability is mainly due to genetical differences and is not environmentally caused. It is to be expected that intra-family variabiliry exists in respect of the production of discriminator substances. Since the common badge of a family is the result of exchanging and mixing individual substances, and since the chemical nature of these discriminators requires direct body contacts in order to acquire those substances which an individual does not produce itself, problems must arise with molting. These difficulties do indeed exist and they are aggravated by the fact that individuals may produce substances which do not show up in the common family badge. An efficient learning capability on the one hand and the use of inhibiting properties of newly molted isopods help to solve these problems. In the final discussion three questions are posed and - partly at least - answered; (i) why are families so strictly exclusive, (ii) how many discriminator substances have to be produced to provide a variability allowing families to remain exclusive under extreme conditions of very high population densities, (iii) what is the structure of the family badge and what does an individual have to learn apart from the badge in order not to mistake a family member for an alien or vice versa.
Observations on captive reed frogs Hyperolius viridijlavus ommatostictus showed that seven out of 24 females changed into males. Sex change occurred without any hormone treatment and resulted in completely functional males. The adaptive value is discussed in terms of maximizing life-time reproductive success. Hyperolius r. ommatostictus is the first amphibian known to show functional sex reversal.
The relationship between different degrees of intraspecific crowding of reedfrog tadpoles and their physiological responses to a deterioration of the natal pond water quality was examined under laboratory conditions. Tadpoles that were reared at a lower density metamorphosed significantly earlier than those raised at a higher density. As density increases, the average body length at metamorphosis decreases. However, at low tadpole density, a significantly higher diversity of body size classes among freshly metamorphosed froglets was observed than under more crowded conditions. Mortality increased during metamorphic climax and was inversely correlated with the tadpole density. In ephemeral ponds, an accumulation of nitrogenous wastes from metabolic processes and/or a concentration by evaporation in prolonged rainless periods can pose a considerable chemical stress to reedfrog tadpoles. Hyperolius viridiflavus ommatostictus responded to an increasing ammonia concentration with an activity increase of the ornithine cycle (intensified urea synthesis). hi contrast, Hyperolius marmoratus taeniatus exhibited a strong tolerance against high ammonia levels. A deterioration of the natal pond water quality caused H. v. ommatostictus and H. v. nitidulus tadpoles to adjust to harsher climatic conditions at the time of metamorphosis. This physiological preadjustment enabled the froglets to start feeding and growing immediately after metamorphosis even at low air humidity and rare precipitation events. In contrast, froglets that were raised in daily refreshed water exhibited high mortality rates if subjected to identical conditions. As one possible indicator of the actual climatic conditions prevailing in the surrounding terrestrial habitat, fluctuations in the water ammonia level are discussed.
Precipitating anti-PM-Sel antibodies are present in sera from patients with polymyositis. scleroderma. and polymyositis/scleroderma overlap syndromes. By indirect immunofluorescence microscopy. anti-PM-Scl antibodies stained the nucleolus in cells of different tissues and species. suggesting that the antigen is highly conserved. By electron microscopy, anti-PM-Scl antibodies reacted primarily with the granular component of the nuc1eolus. Drugs that inhibit rRNA synthesis had a marked effect on the expression of PM-Scl antigen. In actinomycin D-treated cells, immunofluorescence staining by anti-PM-Scl was signüicantly reduced with residual staining restricted to the granular regions of nuc1eoli. Treatment with 5,6-dichloro-beta-D- ribofuranosylbenzimidazole (DRB) also selectively reduced nuc1eolar staining. On a molecular level, anti-PM-Sel antibodies precipitated 11 polypeptides with molecular weights (Mr) ranging from 110,000 to 20,000. The Mr 80,000 and 20.000 polypeptides were phosphorylated. Evidence suggests that the PM-Scl antigen complex may be related to a prerlbosomal particle.
Antibodies to calf thymus histone H2B were purified by chromatography on DEAE-cellulose and injected into oocyte nuclei of Pleurodeles waltlii. As shown by indirect immunofluorescence these antibodies cross-reacted strongly with corresponding histones associated with lampbrush chromosomes. Shortly after injection the lateral loops of the chromosomes retracted into the chromomeres and by 3 h postinjection the 'lampbrush' appearance was completely lost and the chromosomes appeared in light-microscopic preparations as rod-like structures consisting of 10ngitudina11y coalesced chromomeres. In control oocytes injected with non-immune immunoglobulins or antibodies against a ubiquitous transcript-associated protein no morphological alterations of the lampbrush chromosomes could be observed. Electron microscopic spreads of chromosomes prepared at various times after injection of anti-H2B revealed a progressive loss of transcriptional complexes from the loop axes. Finally, higher-order chromatin configurations, like supranuc1eosomal globules (' superbeads ') or cable-like chromatin strands 50- 60 nm thick predominated, indicating complete transcriptional inactivation of a11 chromosomal regions. The results indicate that H2B antibodies react specifically with his tones associated with the transcribed DNA of lateral loops in their native state. The resulting antigenantibody complexes seem to inhibit progression of the R A polymerases along the template, thus causing the premature release of transcripts, a process analogous to the stripping effect of actinomycin D. The demonstration of histones associated with heavily transcribed regions, which are not compacted into nucleosomes but largely extended, supports the current concept that unfolding of nucleosomes to a110w transcription of the DNA does not involve dissociation of histones. In contrast, amplified ribosomal RNA genes are unaffected by injected HzB antibodies. This does not necessarily indicate absence of his tones from nucleolar chromatin, since we do not know whether it is accessible in vivo to antibodies or whether the histone antigenie determinants are masked by the presence of other proteins. The technique of injecting specific antibodies should be widely applicable when analysing the in vivo distribution of chromosomal components at the electron-microscopic level and when studying complex metabolie processes, like the cleavage and modification of RNA, by selective inhibition of defined enzymic steps.
Autoantibodies to components of the nucleolus are a unique serological feature of patients with scleroderma. There are autoantibodies of several specificities; one type produces a speckled pattern of nucleolar staining in immunofluorescence. In actinomycin D and 5,6-dichloro-{j-D-ribofuranosylbenzimidazoletreated Vero cells, staining was restricted to the fibrillar and not the granular regions. By double immunofluorescence, specific rabbit anti-RNA polymerase I antibodies stained the same fibrillar structures in drug-segregated nucleoli as scleroderma sera. Scleroderma sera immunoprecipitated 13 polypeptides from (35S)methionine-labeled HeLa cell extract with molecular weights ranging from 210,000 to 14,000. Similar polypeptides were precipitated by rabbit anti-RNA polymerase I antibodies, and their common identities were confirmed in immunoabsorption experiments. Microinjection of purified IgG from a patient with speckled nucleolar staining effectively inhibited ribosomal RNA transcription. Autoantibodies to RNA polymerase I were restricted to certain patients with scleroderma and were not found in other autoimmune diseases.
Nuclei assembled in Xenopus egg extract from purified DNA or chromatin resemble their natural counterparts in a number of structural and functional features. However, the most obvious structural element of normal interphase nuclei, the nucleolus, is absent from the in vitro reconstituted nuclei. By EM, cytological silver staining, and immunofluorescence microscopy employing antibodies directed against various nucleolar components we show that nuclei assembled in vitro contain numerous distinct aggregates that resemble prenucleolar bodies (PNBs) by several criteria. Formation of these PNB-like structures requires pore complex-mediated nuclear transport of proteins but is independent of the genetic content of the in vitro nuclei as well as transcriptional and translational events. Our data indicate that nuclei assembled in vitro are capable of initiating early steps of nucleologenesis but that the resulting PNBs are unable to fuse with each other, probably due to the absence of a functional nucleolus organizer. With appropriate modifications, this experimental system should be useful to define and analyze conditions promoting the site-specific assembly of PNBs into a coherent nucleolar body.
Electron microscope preparations of lampbrush chromosomes from oocytes of Pleurodeles waltl;; have revealed a new class of tandemly repeated genes. These genes are highly active, as judged by the close spacing of nascent transcripts. They occur in clusters of >100 copies and are transcribed in units containing roughly 940 base pairs of DNA that are separated by nontranscribed spacers of an estimated DNA content of 2,410 base pairs. The size and the pattern of arrangement of these transcription units can not be correlated with any of the repetitious genes so far described.
A nucleolar skeleton of protein filaments demonstrated in amplified nucleoli of Xenopus laevis
(1981)
The amplified, extrachromosomal nucleoli of Xenopus oocytes contain a meshwork of -4-nm-thick filaments, which are densely coiled into higher-order fibrils of diameter 30-40 nm and are resistant to treatment with high- and low-salt concentrations, nucleases (DNase I, pancreatic RNase, micrococcal nuclease), sulfhydryl agents, and various nonionic detergents. This filamentous "skeleton" has been prepared from manually isolated nuclear contents and nucleoli as weil as from nucleoli isolated by fluorescence-activated particle sorting. The nucleolar skeletons are observed in light and electron microscopy and are characterized by ravels of filaments that are especially densely packed in the nucleolar cortex. DNA as weil as RNA are not constituents of this structure, and precursors to ribosomal RNAs are completely removed from the extraction-resistant filaments by treatment with high-salt buffer or RN ase. Fractions of isolated nucleolar skeletons show specific enrichment of an acidic major protein of 145,000 mol wt and an apparent pi value of -6.15, accompanied in some preparations by various amounts of minor proteins. The demonstration of this skeletal structure in "free" extrachromosomal nucleoli excludes the problem of contaminations by nonnucleolar material such as perinucleolar heterochromatin normally encountered in studies of nucleoli from somatic cells. It is suggested that this insoluble protein filament complex forms a skeleton specific to the nucleolus proper that is different from other extraction-resistant components of the nucleus such as matrix and lamina and is involved in the spatial organization of the nucleolar chromatin and its transcriptional products. In studies of the organization of the interphase nucleus, considerable progress has been made in the elucidation of the arrangement of chromatin components and transcriptional products. However, relatively little is known about the composition and function of another category of nuclear structures, the nonnucleoproteinaceous architectural components that are insoluble in solutions of low and high ionic strength, despite numerous studies dedicated to this problem. Such structures include (a) the nuclear envelope and its pore complexes (I, 15, 18, 23, 37, 41), (b) a peripheral layer of insoluble protein ("lamina"; I, 15, 22, 23, 59), (e) certain skeletal proteins related to the chromosome "scaffold" described by Laemmli and coworkers (see references 2 and 3), and (d) ill-defined tangles of fibrillar structures of the nuclear interior that are collectively described as residual "matrix" (6, 21 ; for reviews, see references THE JOURNAL OF CEll BrOlOGY . VOlUME 90 AUGUST 1981 289-299 © The RockefeIler University Press · 0021 -9525/ 81 / 08/ 0289/ 11 $1 .00 4 and 12). The latter, preparatively
Antibodies directed against RNA polymerase II (B) from Drosophila melanogaster were obtained from rabbit sera and, as monoclonal immunoglobulins, from mouse hybridomas and shown to cross-react with the amphibian enzyme protein. Localization by indirect immunofluorescence microscopy revealed the association of this enzyme with chromatin of interphase nuclei of amphibian cells and its absence in nucleoli. Purified immunoglobulins were microinjected in to nuclei ofliving vitellogenic oocytes of Ple1lrodeles waltlii and X enopus laevis and their effects on transcriptional processes were monitored by biochemical and light and electron microscopic stud ies. RNA polymerase II antibodies from rabbit sera caused a rapid and almost complete release of nascent transcripts from the chromatin axis of the loops of lampbrush chromosomes, followed by collapse of the loops and their retraction on the main chromosome axis. Monoclonal murine antibodies to the Iarge RNA polymerase II subunits also inhibited transcription in chromosome Ioops but appeared to inhibit initiation rather than elongation events. Activities of class land III RNA polymerases were not significantly affected by injection of antibodies to polymerase II, indicating immunological differences between the three RNA polymerases. The potential value of the in vitro test system described , as a very sensitive assay for detecting proteins involved in transcription in living cells, is discussed. 1
The pioneer tree Macaranga in SE Asia has developed manyfold associations with ants. The genus comprises all stages of interaction with ants, from facultative relationships to obligate myrmecophytes. Only myrmecophytic Macaranga offer nesting space for ants and are associated with a specific ant partner. The nonmyrmecophytic species are visited by a variety of different ant species which are attracted by extrafloral nectaries (EFN) and food bodies. Transitional Macaranga species like M. hosei are colonized later in their development due to their stem structure. Before the colonization by their specific Crematogaster partner the young plants are visited by different ant species attracted by EFN. These nectaries are reduced and food body production starts as soon as colonization becomes possible. We demonstrated earlier that obligate ant partners can protect their Macaranga plants against herbivore damage and vine cover. In this study we focused on nonspecific interactions and studied M. tanarius and M. hosei, representing a non-myrmecophyte and a transitional species respectively. In ant exclusion experiments both M. tanarius and M. hosei suffered significantly higher mean leaf damage than controls, 37% versus 6% in M. hosei, 16% versus 7% in M. tanarius. M. tanarius offers both EFN and food bodies so that tests for different effects of these two food rewards could be conducted. Plants with food bodies removed but with EFN remaining had the lowest mean increase of herbivore damage of all experimental groups. Main herbivores on M. hosei were mites and caterpillars. Many M. tanarius plants were infested by a shootborer. Both Macaranga species were visited by various ant species. Crematogaster spp. being the most abundant. We found no evidence for any specific relationships. The results of this study strongly support the hypothesis that non-specific, facultative associations with ants can be advantageous for Macaranga plants. Food bodies appear to have lower attractive value for opportunistic ants than EFN and may require a specific dietary adaptation. This is also indicated by the fact that food body production in the transitional M. hosei does not start before stem structure allows a colonization by the obligate Crematogaster species. M. hosei thus benefits from facultative association with a variety of ants until it produces its first domatia and can be colonized by its obligate mutualist.
C. borneensis (Myrmicinae) lives in dose association with several myrmecophytic species of the South East Asian pioneer tree genus Macaranga (Euphorbiaceae). The ants are adapted to the plants so dosely that they do not survive away from it. The only food they utilize is provided as food bodies by the plant and honeydew from specific scale insects kept inside the hollow internodes. The anatomy of the digestive tract is also adapted to life on the host plant: the crop is very sm all and can store only minute food quantities. C. borneensis exdusively colonizes certain Macaranga species. Queens as weIl as workers are able to recognize their host plant species, probably by chemical cues. Colony founding queens swarm throughout the year, mostly during darkness. There is strong competition among queens for host plants. Queens do not carry scale insects on their nuptial flight. Worker ants are active day and night. Most of them patrol and collect food bodies on the younger parts of the host plant. An important characteristic is their deaning behaviour, which results in removal of aIl foreign objects. Even though they are rather smalI, workers respond very aggressively to certain kinds of disturbance of the host plant. The ants attack most phytophagous insects and are especially effective in killing and removing smalI, softbodied herbivores (e.g. caterpillars). They do not possess a functional sting, but apply defensive secretion and-once biting an intruder-will not let go. Their effective alarm system results in a mass attack, which provides adequate defence for the colony and the host plant. A comparison with another Crematogaster species further illustrated the special adaptations of C. borneensis to its host plant.
Nonnucleolar chromatin from interphase nuclei of Physarum polycephalum plasmodia occurs in two different structural configurations as seen in electron microscopic spread preparations. While the majority of the chromatin is devoid of nascent ribonucleoprotein (RNP) fibrils and compacted into nucleosomal particles, a minor proportion (10- 20%) is organized differently and reveals a smooth contour. It is this form of smooth chromatin which is rich in transcription units (mean length: 1.36±0.21 11m). Only occasionally are solitary nascent RNP fibrils observed which are associated with beaded strands of chromatin. In transcribed smooth chromatin nucleosomal particles are not only absent from the transcription units but also from their nontranscribed flan king regions, indicating that this special structural aspect is not merely a direct consequence of the transcriptional process. The existence of ca. 10- 20% of Physarum chromatin in the smoothly contoured form is discussed in relation to reports of a preferential digestibility of a similar proportion of Physarum chromatin by DNAse I (Jalouzot et al. , 1980) and to the altered configuration of "peak A" chromatin subunits after micrococcal nuclease digestion (Johnson et al., 1978a, b).
Oocytes of the water beetle, Dytiscus marginalis, contain large amounts of rDNA most of which is present in the form of rings containing one or several pre-rRNA genes. Electron microscopy of spread preparations of vitellogenic oocytes has shown that the rDNA is extended in chromatin rings with transcribed pre- rRNA genes and is not packed into nucleosomes (Trendelenburg eta!. , 1976). When similar preparations are made from previtellogenic ooytes in which a large proportion of the nuc1eolar chromatin is transcriptionally inactive, a different morphological form of this chromatin is recognized. In contrast to the transcribed chromatin rings the inactive nucleolar chromatin circles show the characteristic beaded configuration, indicative of nucleosomal packing. Nuc1eosomal packing is also indicated by the comparison of the lengths of these chromatin rings with both iso lated rDNA circ1es and transcribed chromatin rings. In addition, these inactive nuc1eofilaments often appear to be compacted into globular higher order structures of diameters from 21 to 34nm, each composed of an aggregate of 6-9 nuc1eosomes. While the estimated reduction of the overall length of rDNA, as seen in our preparations, is, on the average, only 2.2 - 2.4 fold in the nuc1eosomal state it is 10- 13 fold when supranuc1eosomal globules are present. These data show that the extrachromosomal rDNA of these oocytes goes through a cycle of condensation and extensio n, as a function of the specific transcriptional activity, and that the beaded state described here is exc1usively found in the non-transcribed state.
Lengths and patterns of transcriptional units in the amplified nucleoli of oocytes of Xenopus laevis
(1977)
Transcriptionally active chromatin from peripheral amplified nuc1eoli of lampbrush-chromosome stage oocytes of Xenopus laevis was dispersed and spread in various solutions of low salt concentrations (incIuding some with additions of detergents) and examined by electron microscopy. Nucleolar material from oocytes of animals with normal (2-nu) and mutant (I-nu) genetical constitution of nucleolus organizers was compared. Histograms showing the distributions of the lengths of matrix units, apparent spacer intercepts, and the total repeating units of the rDNA containing chromatin axes revealed a significant degree of heterogeneity, with indications of subclasses and predominant repeat unit size c1asses of 3.3 and 3.8 11m length. The correspondence of matrix unit length to the molecular weight of the first stable product of rDNA transcription was studied using gel electrophoresis of labelIed pre-rRNA under non-denaturing and denaturing conditions. Evaluations of individual strands of nucleolar chromatin furt her demonstrated the existence of both (i) strands with obviously homogeneous repeating units and (ii) strands with intra-axial heterogeneity of rDNA subunits. " Preludecomplexes ", i.e. groups of transcriptional complexes in apparent spacer intercepts, were not infrequently noted. The data are compared with the measurements of lengths of repeating units in fragments of rDNA obtained by digestion with EcoRI endonuclease as described by Morrow et al. (1974) and Wellauer et al. (1974, 1976a, b). The results are discussed in relation to problems of variations in the modes of arrangement of the pre-rRNA genes, the state of packing of rDNA during transcription, and possible mechanisms of the amplification process.
The paleotropical tree genus Macaranga (Euphorbiaceae) comprises all stages of interaction with ants, from facultative associations to obligate myrmecophytes. In SE.-Asia food availability does not seem to be the limiting factor for the development of a close relationship since all species provide food for ants in form of extrafloral nectar and/or food bodies. Only myrmecophytic Macaranga species offer nesting space for ants (domatia) inside intern odes which become hollow due to degeneration of the pith. Non-myrmecophytic species have a solid stem with a compact and wet pith and many resin ducts. The stem interior of some transitional species remains solid, but the soft pith can be excavated. The role of different ant-attracting attributes for the development of obligate ant-plant interactions is discussed. In the genus Macaranga, the provision of nesting space seems to be the most important factor for the evolution of obligate myrmecophytism.
Nuclear envelopes of maturing oocytes of various amphibia contain an unusually high number of pore complexes in very close packing. Consequently, nuclear envelopes , which can be manually isolated in great purity, provide a remarkable enrichment of nuclear pore complex material, relative to membranous and other interporous structures. When the polypeptides of nuclear envelopes isolated from oocytes of Xenopl/s la evis and Triturus alpestris are examined by gel electrophoresis, visualized either by staining with Coomassie blue or by radiotluorography after in vitro reaction with [3H]dansyl chloride , a characteristic pattern is obtained (10 major and 15 minor bands). This polypeptide pattern is radically different from that of the nuclear contents isolated from the same cell. Extraction of the nuclear envelope with high salt concentrations and moderateIy ac tive detergents such as Triton X- 100 results in the removal of membrane material but leaves most of the non-membranous structure of the pore complexes. The dry weight of the pore complex (about 0.2 femtograms) remains essentially unchanged during such extractions as measured by quantitative electron microscopy . The extracted preparations which are highly enriched in nuclear pore complex material contain only two major polypeptide components with apparent molecular weights of 150000 and 73000. Components of such an electrophoretic mobility are not present as major bands , if at all , in nuclear contents extracted in the same way. lt is concluded that these two polypeptides are the major constituent protein(s) of the oocyte nuclear pore complex and are specific for this structure. When nuclear envelopes are isolated from rat liver and extracted with high salt buffers and Triton X- 100 similar bands are predominant, but two additional major components of molecular weights of 78000 and 66000 are also recognized. When the rat liver nuclear membranes are further subfractionated material enriched in the 66000 molecular weight component can be separated from the membrane material, indicating that this is relatively loosely associated material , probably a part of the nuclear matrix . The results suggest that the nuclear pore complex is not only a characteristic ubiquitous structure but also contains similar, if not identical , skeletal proteins that are remarkably re sistant to drastic changes of ionic strength as weil as to treatments with detergents and thiol reagents.
Sizes of chromosome loops and hnRNA molecules in oocytes of amphibia of different genome sizes
(1982)
The lengths of lampbrush chromosome loops and their tran scription units show a positive correlation with genome size in oocytes of amphibia with different C values. However, there is no such correlation with contour lengths of hnRNA molecu les isolated from these oocytes. These results indi cate th at more ON A sequences are transcribed in amphibia of higher C value , but that processing of RNA transc ripts occurs while they are still attached to the chromosomes as nascent ribonucleoprotein fibrils.
Under the intluence of 5-tluoro-uridine, the ultrastructure of the rDNA transcription units in Xenopus oocytes is altered. Whereas part of the matrix units maintains anormal aspect or shows various degrees of inhibition, in a strong proportion of the transcription units the alternating pattern of matrix units and fibril-free spacer regions is no longer recognized. Transcriptional complexes are found along the entire DNP axis, including the regions of the spacers. These observations support biochemical data on transcription in rDNA spacer region.
Transcriptionally inactive chick erythrocyte nudei were reactivated by Sendai virusinduced fusion of erythrocytes with rat L6j1 myoblasts. We used antibodies to trace the appearance of a specific protein engaged in transcription of a defined dass of genes, those coding for rRNA, during reactivation. Using immunofluorescence microscopy, we found increasing amounts of rat RNA polymerase I to appear, during a certain period of time after fusion, in the reforming nudeoli of the chick nudei. Amounts of rat RNA polymerase I sufficient to be detected by immunofluorescence microscopy had accumulated in the newly developed chick nudeoli 72- 190 h after fusion was initiated. This time interval coincides with the time when chick rRNA synthesis can first be detected. The results raise the possibility that during these stages of the reactivation process chick rRNA genes are transcribed by heterologous RNA polymerase I moleeules of rat origin.
Upon incubation of cultured rat cells with the adenosine analogue 5,6-dichloro-l-β- D-ribofuranosylbenzimidazole (DRB), nucleoli reversibly dissociate into their substructures, disperse throughout the nuclear interior, and form nucleolar "necklaces". We have used this experimental system, which does not inhibit transcription of the rRNA genes, to study by immunocytochemistry the distribution of active rRNA genes and their transcriptional products during nucleolar dispersal and recovery to normal morphology. Antibodies to RNA polymerase I allow detection of template-engaged polymerase, and monoclonal antibodies to a ribosomal protein (S 1) of the small ribosomal subunit permit localization of nucleolar preribosomal particles. The results show that, under the action of DRB transcribed rRNA, genes spread throughout the nucleoplasm and finally appear in the form of several rows, each containing several (up to 30) granules positive for RNA polymerase land argyrophilic proteins. Nucleolar material containing preribosomal particles also appears in granular structures spread over the nucleoplasm but its distribution is distinct from that of rRNA gene-containing granules. We conclude that, although transcriptional units and preribosomal particles are both redistributed in response to DRB, these entities retain their individuality as functionally defined subunits. We further propose that each RNA polymerase-positive granular unit represents a single transcription unit and that each continuous array of granules ("string of nucleolar beads") reflects the linear distribution of rRNA genes along a nucleolar organizer region. Based on the total number of polymerase I-positive granules we estimate that a minimum of 60 rRNA genes are active during interphase of DRB-treated rat cells.
Purified mitochondrial DNA (mitDNA) from ovaries ofXenopus lae vis was injected into the nuclei (germinal vesicles) of large viteUogenic oocytes of the same organism and examined by electron microscopy ofthe spread nuclear contents. Normally located nuclei of untreated oocytes as weil as peripherally translocated nuclei of centrifuged oocytes were used. In addition, oocyte nuclei isolated and incubated under liquid paraffin oil were injected with DNA. The integrity oftranscriptional structures of endogenous chromosomal (Iampbrush chromosomes) and extrachromosomal (nucleoli) genes of the injected nuclei was demonstrated. Microinjected mitDN A was identified as circles of chromatin exhibiting polynucleosome-like organization and a me an contour length of 2.6 J.Lm, corresponding to a compaction ratio of the mitDN A of about 2 : I. This DNA packing ratio is similar to that observed after preparation of various kinds of native chromatin in low salt buffers. The chromatin circles formed from injected mitDNA only very rarely exhibited lateral fibrils suggestive of transcriptional activity. These results suggest that purified mitDNA can be transformed to normally structured chromatin when exposed to oocyte nuclear contents but is rarely , if at all , transcribed in this form and in this environment.
Rabbit antibodies to RNA polymerase I from a rat hepatoma have been used to localize the enzyme in a variety of cells at the light and electron microscopic level. In interphase cells the immunofluorescence pattern indicated that polymerase I is contained exclusively within the nucleolus. That this fluorescence, which appeared punctated rather than uniform, represented transcriptional complexes of RNA polymerase I and rRNA genes was suggested by the observation that it was enhanced in regenerating liver and in a hepatoma and was markedly diminished in cells treated with actinomycin D. Electron microscopic immunolocalization using gold-coupled second antibodies showed that transcribed rRNA genes are located in, and probably confined to, the fibrillar centers of the nucleolus. In contrast, the surrounding dense fibrillar component, previously thought to be the site of nascent prerRNA, did not contain detectable amounts of polymerase I. During mitosis, polymerase I molecules were detected by immunofluorescence microscopy at the chromosomal nucleolus organizer region, indicating that a considerable quantity of the enzyme remains bound to the rRNA genes. From this we conclude that rRNA genes loaded with polymerase I molecules are transmitted from one cell generation to the next one and that factors other than the polymerase itself are involved in the modulation of transcription of DNA containing rRNA genes during the cell cycle.