Identification and analysis of cis-regulatory elements in development using comparative genomics with the pufferfish, Fugu rubripes

The control of vertebrate development is facilitated by cis-regulatory sequences hardwired into the genome. Given that many developmental processes are strikingly similar across all backboned animals, it is reasonable to expect these sequences to be conserved at the nucleotide level, their potential for mutation being constrained by their function. Comparison between the genomes of highly divergent organisms allows such sequences to be identified and some of the most successful approaches have compared regions from the pufferfish, Fugu rubripes, with its distant mammalian relatives, rodents and humans. This review describes progress made in this kind of comparison, from small regions of individual genes, to whole genome alignments.     

Cell types of the endocrine pancreas in the shark Scyliorhinus stellaris as revealed by correlative light and electron microscopy

Summary In the pancreas of Scyliorhinus stellaris large islets are usually found around small ducts, the inner surface of which is covered by elongated epithelial cells; thus the endocrine cells are never exposed directly to the lumen of the duct. Sometimes, single islet cells or small groups of endocrine elements are also incorporated into acini. Using correlative light and electron microscopy, eight islet cell types were identified:Only B-cells (type I) display a positive reaction with pseudoisocyanin and aldehyde-fuchsin staining. This cell type contains numerous small secretory granules (Ø280 nm). Type II- and III-cells possess large granules stainable with orange G and azocarmine and show strong luminescence with dark-field microscopy. Type II-cells have spherical (Ø700 nm), type III-cells spherical to elongated granules (Ø450 × 750 nm). Type II-cells are possibly analogous to A-cells, while type III-cells resemble mammalian enterochromaffin cells. Type IV- cells contain granules (Ø540 nm) of high electron density showing a positive reaction to the Hellman-Hellerström silver impregnation and a negative reaction to Grimelius' silver impregnation; they are most probably analogous to D-cells of other species. Type VI-cells exhibit smaller granules (Ø250 × 500 nm), oval to elongated in shape. Type VI-cells contain small spherical granules (Ø310 nm). Type VII-cells possess two kinds of large granules interspersed in the cytoplasm; one type is spherical and electron dense (Ø650 nm), the other spherical and less electron dense (Ø900 nm). Type VIII-cells have small granules curved in shape and show moderate electron density (Ø100 nm). Grimelius-positive secretory granules were not only found in cell types II and III, but also in types V, VI, and VII. B-cells (type I) and the cell types II to IV were the most frequent cells; types V to VII occurred occasionally, whereas type VIII-cells were very rare.This work was supported by a fellowship from the Ministry of Education of Japan and the Deutsche Forschungsgemeinschaft, Bonn-Bad Godesberg (La 229/8)     

Identification of novel tropomyosin 1 genes of pufferfish (Fugu rubripes) on genomic sequences and tissue distribution of their transcripts

Fugu genome database enabled us to identify two novel tropomyosin 1 (TPM1) genes through in silico data mining and isolation of their corresponding cDNAs in vivo. The duplicate TPM1 genes in Japanese pufferfish Fugu rubripes suggest that additional an ancient segmental duplication or whole genome duplication occurred in fish lineage, which, like many other reported Fugu genes, showed reduction in genomic size in comparison with their human homologue. Computer analysis predicted that the coiled-coil probabilities, that were thought to be the most major function of TPM, were the same between the two TPM1 isoforms. We confirmed that the tissue expression profiles of the two TPM1 genes differed from each other, which implied that changes in expression pattern could fix duplicated TPM1 genes although the two TPM1 isoforms appear to have similar function.     

Immunocytochemical study of the endocrine pancreas in the grey kangaroo (Macropus fuliginosus)

Summary The endocrine pancreas of the grey kangaroo,Macropus fuliginosus, was investigated by means of immunocytochemistry using the PAP method on the same section at the light- and electron-microscopic levels. Semithin plastic sections were stained individually with primary antibodies for insulin, glucagon, somatostatin and pancreatic polypeptide (PP), and then photographed. Sections were osmicated, re-embedded in BEEM capsules, and ultrathin sections made and examined. The same labelled cells as in the semithin sections were localised in the thin sections, photographs taken and the morphology of secretory granules studied. The insulin cells were pleomorphic; their secretory granules displayed an electron-dense core surrounded by an empty halo. The glucagon cells possessed granules with an electron-dense core usually surrounded by a halo of less dense granular material. Somatostatin cells had larger, less dense secretory granules. The PP cells showed small, dense secretory granules. In order for an ultrastructural study to be considered reliable for the definite identification of endocrine cell types, it is essential that it be corroborted by correlated immunocytochemical data at the light-and electron-microscopic levels.     

The pancreatic islets of the teleost Scorpaena scropha

Summary The principal pancreatic islets of the teleost Scorpaena scropha are found ultrastructurally to contain four different kinds of parenchymal cells, viz. ₁-(= D), ₂-, -and agranular cells. The -cells show considerable variations in the shape of the secretory granules. A peculiar feature is that many of these granules are composed of fibrillar subunits, often in parallel arrangement. All -granules are surrounded by membranes and between the membrane and the granule core there is a moderately wide electron lucent space. The electron density of the cytoplasm in the -cells varies somewhat. The ₂-cells possess typical secretory granules with an electron dense core and a closely applied membrane. The secretory granules in the ₁-cells show also a closely applied membrane but a less dense core. Also in the -cells the electron opacity of the cytoplasm varies. The agranular cells are mainly characterized by low cytoplasmic electron density, narrow cisterns of endoplasmic reticulum and sometimes a laminated Golgi complex. Small immature secretory granules are occasionally seen in the cytoplasm of these cells. The significance of the fibrillar -granules remains obscure.This work was supported by grants from the Nordic Insulin Fund, the Town of Umeå, the Swedish Medical Research Council (Project No. B69-12X-718-04A), and by a postdoctoral fellowship from the United States Public Health Service.     

A light- and electron-microscopic study on the migration of primordial germ cells in the teleost,Oryzias latipes

Summary The primordial germ cells (PGCs) of Oryzias latipes in migration to the gonadal anlage have been investigated by light and electron microscopy. The ultrastructure of the PGCs, which occur in the subendodermal space on the syncytial periblast, differ conspicuously from that of the surrounding endodermal cells. After the PGCs move to the cavity between lateral plate and ectoderm, they are taken into the somatomesodermal layer and transferred to the dorsal mesentery where they form gonadal anlage with mesodermal cells. During their translocation to the dorsal mesentery through the somatic mesoderm, apparently without formation of pseudopods, the PGCs are completely surrounded by mesodermal cells. Since these conditions seem unfavorable to the active translocation of the PGCs to the dorsal mesentery, it is more likely that the PGCs are transferred passively by the morphogenic activity of the lateral-plate mesoderm.Counts of the number of the PGCs revealed that they are mitotically dormant during the migratory period. After the completion of the migration, they regain their proliferative activity. The PGCs in the female proliferate more actively than those in the male, which provides the first morphological indication of sex differentiation in this species of fish.     

New cell types of the pancreatic islets in the crucian carp,Carassius carassius

Summary The pancreatic islets ofCarassius carassius have been studied by electron microscopy. 1. Besides A-, B- and D-cells, two new cell types, the fourth and the fifth, have been identified. The fourth cell type is numerous; it occurs interposed among the other types of islet cells or in small clusters. The secretory granules (90–280 mg in diameter) are round or oval and usually with much lower electron density than α- and δ-granules. The secretory granules of the fifth type of cell (approximately 140–240 mμ in diameter) contain finely granular material and an electron dense core that is round or often tetra- or hexagonal. 2. The islet cells with clear cytoplasmic matrix generally contain large numbers of fine, agranular and cored vesicles 400–680 ? in diameter. They appear, in bead-like chains, or randomly scattered throughout the cytoplasm, or often clustered in aggregates close to the secretory granules and show evidence of incorporation into the secretory granules. The two types of vesicles may be formed by constriction or pinching-off of the tubular smooth endoplasmic reticulum.     

<Emphasis Type="Italic"> Fugu rubripes</Emphasis> possesses genes for the entire set of the ITAM-bearing transmembrane signal subunits

The transmembrane signaling subunits (TSSs) bearing the immunoreceptor tyrosine-based activation motif (ITAM) play a crucial role in triggering the effector functions of mammalian leukocytes. The involvement in key immune reactions and obvious extension through duplication events make TSSs valuable markers of the evolution of the immune system. We surveyed the genomic sequences of the teleostean fish Fugu rubripes for the presence of genes encoding these accessory molecules. Automatic gene prediction was not efficient because of the poor ability of the programs used to recognize the short exons encoding the intracellular regions of TSSs. However, the unique compactness of the Fugu genome and the conservation of the exon/intron arrangements of the TSS genes facilitated their recognition by visual inspection of the candidate genomic sequences. Evidence for the presence of the CD3, CD3/, CD79a, CD79b, TCR, FcR, DAP12 and DAP10 genes in the Fugu genome was obtained. Furthermore, conserved synteny for the short regions including the TSS genes was revealed by comparison of the Fugu and human genomes. The data demonstrate that the set of TSSs arose before the teleost–tetrapod split and provide a starting point for experimental investigation of the molecular evolution of the leukocyte-activating receptor complexes from fish species to mammals.Abbreviations TSS Transmembrane signal subunit - ITAM Immunoreceptor tyrosine-based activation motif     

Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage

A whole-genome duplication in the ray-finned fish lineage has been supported by the analyses of the genome sequence of the Japanese pufferfish, Fugu rubripes. Recently, genome sequence of a second teleost fish, the freshwater pufferfish, Tetraodon nigroviridis, was completed. Comparisons of long-range synteny between the Tetraodon and human genomes provided additional evidence for the whole-genome duplication in the ray-finned fish lineage. In the present study, we conducted phylogenetic analysis of the Tetraodon and human proteins to identify ray-finned fish lineage-specific (‘fish-specific’) duplicate genes in the Tetraodon genome. Our analyses provide evidence for 1087 well defined fish-specific duplicate genes in Tetraodon. We also analyzed the Fugu proteome that was predicted in the recent Fugu genome assembly, and identified 346 duplicate genes in addition to the 425 duplicates previously identified. We estimated the ages of duplicate genes using the molecular clock. The ages of duplicate genes in the two pufferfishes independently support a large-scale gene duplication around 380–400 Myr ago. In addition, a burst of recent gene duplications was evident in the Tetraodon lineage. These findings provide further evidence for a whole-genome duplication early in the evolution of ray-finned fishes, and suggest that independent gene duplications have occurred recently in the Tetraodon lineage.     

Characterization of the novel human transmembrane protein 9 (TMEM9) that localizes to lysosomes and late endosomes

We report the isolation and characterization of a cDNA coding for Fugu rubripes prion protein (PrP)-like of 180 amino acids which includes the PrP-conserved hydrophobic region homologous to that of Xenopus PrP. In addition to the hydrophobic region, Fugu PrP-like has several features common to PrPs, such as a signal sequence, a basic nature (pI 9.7) and a single intron in the 5' untranslated region. A possible glycosyl phosphatidylinositol (GPI) anchor site also exists in PrP-like. In expression analysis, PrP-like mRNA was detected in retina, skin, and brain, all of which express PrP mRNA in mammals. In a genome fragment clone (T002589, 31945 bp) sequenced by the Fugu Genomics Project, PrP-like located between KIAA0168 and SLC231A homologues. In human chromosome 20p13, PrP, Doppel, KIAA0168, and SLC231A align in this order. The close gene arrangement between the Fugu and human genomes suggests that Fugu PrP-like is a real orthologue of human PrP. However, Fugu PrP-like does not possess tandem repeats or a region with two glycosylation sites and a disulphide bridge. We do not declare that the cloned Fugu PrP-like represents fish PrP due to structural inconsistency, but believe that it will offer new insights into the evolution of PrPs from fish to tetrapods.     

Light and electron microscopic study of the bacterial adhesion to termite flagellates applying lectin cytochemistry

Summary Many of the flagellates inhabiting the hindgut of lower termites are associated with ectobiotic, rod-like bacteria or spirochetes. Different types of attachment sites are present. Electron dense material underlies, e.g., the plasma membrane ofJoenia annectens at the contact site, whereas other attachment sites do not show any visible specializations. The host cell's glycocalyx may, however, be reduced at the attachment sites as it is the case inDevescovina glabra. The thick glycocalyx ofStephanonympha nelumbium is not changed at the sites where bacterial rods attach, but spirochetes penetrate to a certain extent. Bacteria which colonize the extracellular surface structures ofMicrorhopalodina multinucleata express their own glycocalyx to mediate a contact. In this study we focussed on the examination of one common mode of interaction between bacteria and their host cells, i.e., adhesion via lectins and sugars. The sugar composition was analysed by light and electron microscopic labelling experiments using the lectins Con A, WGA and SBA. In general, only the posterior body surface ofJoenia which is colonized with bacteria is labelled. The demonstrated sugars are found in fibrous glycocalyx portions surrounding the attachment sites of the bacteria. Such glycocalyx fibres in combination with the electron dense material supporting the attachment sites seem to be the prerequisites for bacterial attachment. InD. glabra, however, a role for sugars in mediating the attachment could not be demonstrated. Removal of the ectobiotes using antibiotics revealed that the specialized contact sites ofJoenia are present in the absence of bacteria and thus possibly serve to attract bacteria. Nothing, however, remains of the former attachment sites in bacteria-freeDevescovina cells. Attachment sites in this case could be induced by bacterial contact. There is not one general mechanism for bacterial attachment to termite flagellates; rather, adhesion seems to follow different strategies.Abbreviations Con A concanavalin A - DAB 3,3-diaminobenzidine tetrahydrochloride - DAPI 4,6-diamidino-2-phenylindole - DIC differential interference contrast - FA formaldehyde - FITC fluorescein isothiocyanate - GA glutaraldehyde - PB Soerensen's phosphate buffer - PC phase contrast - pen/strep penicillin and streptomycin - SBA soybean agglutinin - SEM scanning electron microscope - TBS Tris buffer saline - TEM transmission electron microscope - WGA wheat germ agglutinin Dedicated to Prof. Dr. Dr. h.c. Eberhard Schnepf on the occasion of his retirement     

Ultrastructure of the neurohypophysis of the teleost Poecilia latipinna in relation to neural control of the adenohypophysial cells

Summary The structure of the neurohypophysis of Poecilia latipinna (green molly, sailfin molly) was studied with the electron microscope. Profile diameters of neurosecretory granules in the non-myelinated neurohypophysial nerve fibres were measured and mathematically corrected for error due to section thickness. Six different types of nerve fibres could be distinguished by statistical classification of their granules and by other ultrastructural features. One fibre-type (type B) contained granules with a mean diameter of 85 nm, and the other five types (types Ala, Alb, A2, A3 and A4) all contained granules with mean diameters greater than 100 nm. Synaptic contacts were observed between type B fibres and all the adenohypophysial cell-types, although in the case of the ACTH cells the synapses were separated from the cell membrane by a continuous double basement membrane. Type A fibres were observed to contact the cells of the proximal pars distalis and pars intermedia, but did not form synapses. However, synapses occurred between type A fibres and pituicytes, and between type A fibres and the pericapillary basement membrane in the interior of the neurohypophysis. The possible roles of the different types of nerve fibres in controlling the adenohypophysial cells are discussed in the context of evidence from other teleosts.We thank Mr. W.A. Thomson and Mr. D.I. Hollingworth for technical assistance, and Dr. D.I.C. Pearson (Department of Physics, University of Nancy, Nancy, France) for advice on mathematical analysis and computer programs. The work was carried out during the tenure of an S.R.C. Research Studentship by T.F.C.B.     

Light and electron microscopic investigations of six types of glandular cells of the bovine adenohypophysis

Summary Twelve bovine adenohypophyses were prepared for light and electron microscopy of the cell types of pars distalis. Correlation between the light and electron microscopy was effected by use of alternate thin and thick sections. Cytological changes in the experimental animals were used as criteria for the identification of six different types of secretory cells.Two types of acidophils, alpha and epsilon cells, are recognized in peripheral area of the pars distalis by light and electron microscopy. The alpha cells contain orangeophilic secretory granules of a maximum diameter of 400–450 m and correspond to ordinary acidophils (STH cells). The second type, epsilon cells, contains larger, fuchsinophilic granules of 600 to 900 m in diameter, increase in number and granulation after pregnancy and thyroidectomy, and are thought to be prolactin cells (LTH cells).Two types of amphophils, zeta and delta 1 cells, were found in the central area of the pars distalis. The zeta cells contain smaller numbers of amphophilic, cored granules (200 m maximum diameter) and based on the comparison with literature on other species of animals, are designated as ACTH cells. The delta 1 cells are round or oval and contain very dense, spherical granules (250–300 m) which are stained red or reddish purple with PAS, aldehyde thionin and PAS-methyl blue methods. They show extreme enlargement and bizarre cytoplasmic appearance after castration and are designated tentatively as LH gonadotrophs or LH cells.Two types of basophils, beta and delta 2 cells, were also identified by correlative light and electron microscopy. The beta cells are polygonal in outline, distributed exclusively in the zona tuberalis and contain large, less dense secretory granules (300–400 m) which are stained selectively with Gomori's aldehyde fuchsin. After thyroidectomy, they lose their secretory granules and are transformed into large, vacuolated thyroidectomy cells. They are therefore, identified as thyrotrophs or TSH cells. The delta 2 cells are round, oval or polygonal in shape and contain basophilic granules ranging from 220 to 300 m in diameter. They show extreme enlargement and vacuolization due to the dilation of endoplasmic reticulum, after castration, and are designated tentatively as FSH gonadotrophs or FSH cells.The investigation reported herein was supported by a Scientific Research Grant (No. 291049) from the Ministry of Education of Japan.     

Rhinosporidium seeberi: Light,phase contrast,fluorescent and scanning electron microscopic study

Phase contrast microscopic study indicated the multilayered structure of the sporangial wall of R. seeberi while the scanning electronmicroscopic study revealed a trilaminated wall compared to a thick double walled light microscopic structure. The scanning electronmicroscopy revealed the spores of varying sizes which were found either discretely or in groups interconnected and seen attached to the inner aspect of the sporangial wall. Autofluorescence of sporangia and spores was observed under microscope. Acridine orange staining revealed the presence of DNA materials in the spore and sporangia.     

Use of immunocytochemical staining of somatostatin for correlative light and electron microscopic investigation of D cells in the pancreatic islet of Xiphophorus helleri H. (Teleostei)

Summary Somatostatin-containing cells have been demonstrated by immunocytochemistry in semithin sections of the pancreatic islet of the teleost fish, Xiphophorus helleri. These cells were shown by correlative light and electron microscopy to be identical with D cells previously defined in this species by the silver impregnation method of Hellman and Hellerström.Supported in part by grants from the British Council and from the Medical Research Council of Great Britain     

Principal cell types in the pancreatic islet of a teleost fish,Xiphophorus helleri H.

Summary By means of correlative light and electron microscopy, five pancreatic islet cell categories are described in the teleost fish, Xiphophorus helleri, each of which has specific light microscopic appearance and fine structure. Different histochemical techniques have been used, including immunofluorescence with antiporcine insulin and glucagon sera. In addition to B- and A₁-cells, two categories of A₂-cells have been observed, both reacting with antiporcine glucagon serum: A₂-cells with round granules gave a positive reaction for tryptophan; A₂-cells with crystalline granules gave a negative reaction with the same staining technique on the same section. The clear cells, the last category, were not specifically stained by any of the staining methods carried out in this investigation. The influence of fixation on staining affinities and on ultrastructure was shown to be considerable.Supported in part by the Deutsche Forschungsgemeinschaft, Bonn-Bad Godesberg (grant La 229/4) and by the Deutscher Akademischer Austauschdienst, Bonn-Bad Godesberg.     

Electron microscopy of the skin of the teleost,Hippoglossoides elassodon

Summary The normal skin of the pleuronectid fish, Hippoglossoides elassodon, is described by light and electron microscopy. The epidermis consists of 5 to 9 layers of cells, the majority of which are squamous cells and the minority mucous cells. The squamous cells are characterized by numerous desmosomes and associated cytoplasmic filaments. The mucous cells accumulate mucous droplets in vacuoles of Golgi origin and are observed apparently in the process of releasing their content at the free surface. The dermis consists of alternating lamellae composed of typical collagen fibers. Pigment cells are of three types: melanophores, iridophores (guanophores), and lipophores.This work was supported by Public Health Service Research Grant CA-08158 from the National Cancer Institute.     

An immunocytochemical and electron-microscopical study of endocrine cells in the gut and pancreas of a stomachless teleost fish,Barbus conchonius (Cyprinidae)

Summary Four immunoreactive endocrine cell types can be distinguished in the pancreatic islets of B. conchonius: insulin-producing B cells, somatostatin-producing A₁ (= D) cells, glucagon-producing A₂ cells and pancreatic poly-peptide-producing PP cells. The principal islet of this species contains only a few PP cells, while many PP cells are present in the smaller islets. Except for the B cell all pancreatic endocrine cell types are also present in the pancreatic duct.At least six enteroendocrine cell types are present in the gut of B. conchonius: 1. a cell type (I) with small secretory granules, present throughout the intestine, and possibly involved in the regulation of gut motility; 2. a C-terminal gastrin immunoreactive cell, probably producing a caerulein-like peptide; these cells are located at the upper parts of the folds, especially in the proximal part of the intestinal bulb; 3. a met-enkephalin-immunoreactive cell, present throughout the first segment; 4. a glucagon-immunoreactive cell, which is rare in the first segment; 5. a PP-immunoreactive cell, mainly present in the first half of the first segment; 6. an immunoreactive cell, which cannot at present be specified, located in the intestinal bulb. The latter four cell types are mostly located in the basal parts of the folds, although some PP-immunoreactive cells can also be found in the upper parts.Most if not all enteroendocrine cells are of the open type. The possible functions of all enteroendocrine cell types are discussed.Abbreviations BPP bovine pancreatic polypeptide - CCK cholecystokinin - GEP gastro-entero-pancreatic - GIP gastric inhibitory peptide or glucose-dependent insulin releasing peptide - PPP pig pancreatic polypeptide - VIP vasoactive intestinal polypeptide     

Thin section and freeze fracture studies of the hypophyseal proximal pars distalis in a teleost (Rhamdia hilarii Val.) during different stages of the reproductive cycle

Summary Chromophilic cells in the proximal pars distalis of the adenohypophysis of Rhamdia hilarii were studied in thin section and freeze fracture preparations. The gonadotropic cells (GTH-cells) exhibit a diversity of form, the frequency of which can be related to stages (maturation, mature and spent) in the sexual cycle. GTH-cells showing a cytoplasm filled with electron dense polymorphic secretory granules and small rough endoplasmic reticulum (RER) vesicles, have been termed non-vacuolated. During the mature gonadal stage, such cells become increasingly vacuolated. The small RER vesicles become dilated and/or fuse, forming a single enormous cisternum (4–11 m diameter), the contents of which show direct contact with the inner nuclear membrane. These morphological aspects support the idea that Rhamdia hilarii possesses only one GTH-cell type. Evidence from freeze fracture replicas suggests that membrane-associated events precursory to exocytosis take place in regions where the cell and secretory granule membranes are in close apposition. Thin section analysis of secretory granule formation revealed their derivation from the dilated extremities of the inner Golgi saccule which appears to resemble the rigid lamella described in other cells. After detachment of the inner saccule, the immature secretory granules appear to enlarge by microvesicular transport. Freeze fracture and ultrastructural data on the morphology of the cells that presumably synthetise growth hormone are also presented.This work was aided by the Fundação de Amparo à Pesquisa do Estado de São Paulo (75/1282)