Protistan microbial observatory in the Cariaco Basin,Caribbean. I. Pyrosequencing vs Sanger insights into species richness

Microbial diversity and distribution are topics of intensive research. In two companion papers in this issue, we describe the results of the Cariaco Microbial Observatory (Caribbean Sea, Venezuela). The Basin contains the largest body of marine anoxic water, and presents an opportunity to study protistan communities across biogeochemical gradients. In the first paper, we survey 18S ribosomal RNA (rRNA) gene sequence diversity using both Sanger- and pyrosequencing-based approaches, employing multiple PCR primers, and state-of-the-art statistical analyses to estimate microbial richness missed by the survey. Sampling the Basin at three stations, in two seasons, and at four depths with distinct biogeochemical regimes, we obtained the largest, and arguably the least biased collection of over 6000 nearly full-length protistan rRNA gene sequences from a given oceanographic regime to date, and over 80 000 pyrosequencing tags. These represent all major and many minor protistan taxa, at frequencies globally similar between the two sequence collections. This large data set provided, via the recently developed parametric modeling, the first statistically sound prediction of the total size of protistan richness in a large and varied environment, such as the Cariaco Basin: over 36 000 species, defined as almost full-length 18S rRNA gene sequence clusters sharing over 99% sequence homology. This richness is a small fraction of the grand total of known protists (over 100 000–500 000 species), suggesting a degree of protistan endemism.     

Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)

The series Staphyliniformia is one of the mega‐diverse groups of Coleoptera, but the relationships among the main families are still poorly understood. In this paper we address the interrelationships of staphyliniform groups, with special emphasis on Hydrophiloidea and Hydraenidae, based on partial sequences of the ribosomal genes 18S rDNA and 28S rDNA. Sequence data were analysed with parsimony and Bayesian posterior probabilities, in an attempt to overcome the likely effect of some branches longer than the 95% cumulative probability of the estimated normal distribution of the path lengths of the species. The inter‐family relationships in the trees obtained with both methods were in general poorly supported, although most of the results based on the sequence data are in good agreement with morphological studies. In none of our analyses a close relationship between Hydraenidae and Hydrophiloidea was supported, contrary to the traditional view but in agreement with recent morphological investigations. Hydraenidae form a clade with Ptiliidae and Scydmaenidae in the tree obtained with Bayesian probabilities, but are placed as basal group of Staphyliniformia (with Silphidae as subordinate group) in the parsimony tree. Based on the analysed data with a limited set of outgroups Scarabaeoidea are nested within Staphyliniformia. However, this needs further support. Hydrophiloidea s.str., Sphaeridiinae, Histeroidea (Histeridae + Sphaeritidae), and all staphylinoid families included are confirmed as monophyletic, with the exception of Hydraenidae in the parsimony tree. Spercheidae are not a basal group within Hydrophiloidea, as has been previously suggested, but included in a polytomy with other Hydrophilidae in the Bayesian analyses, or its sistergroup (with the inclusion of Epimetopidae) in the parsimony tree. Helophorus is placed at the base of Hydrophiloidea in the parsimony tree. The monophyly of Hydrophiloidea s.l. (including the histeroid families) and Staphylinoidea could not be confirmed by the analysed data. Some results, such as a placement of Silphidae as subordinate group of Hydraenidae (parsimony tree), or a sistergroup relationship between Ptiliidae and Scydmaenidae, appear unlikely from a morphological point of view.     

The monoclonal antibody 22/18 recognizes a conformational change in an intermediate filament of the newt,Notophthalmus viridescens,during limb regeneration

Summary Previous work has shown that the monoclonal antibody 22/18 identifies progenitor cells (blastemal cells) which depend on the nerve for their division in the early stages of limb regeneration in the newt,Notophthalmus viridescens. This antibody also reacts with cultured cells derived from the newt limb, and the intensity of immunoreactivity appears related to cell density and differentiation into myotubes. We report here that the monoclonal antibody 22/18 recognizes a polypeptide (22/18 antigen) which is intracellular and filamentous. Double staining of cells with 22/18 monoclonal antibody and antibodies against various cytoskeletal components indicates that the epitope is expressed on an intermediate filament component. Although this antibody is specific for blastemal cells in cryostat sections of the regenerating limb, its reactivity on immunoblots is not confined to this tissue. The 22/18 antigen is differentially affected by aldehyde fixatives distinguished by the spacing of their reactive groups. While formaldehyde fixation impairs detection of the antigen, ethylene glycol-bis[succinic acid n-hydroxysuccinimide ester] reveals the antigen in sections of normal and regenerating limbs in a distribution that is consistent with the one obtained from immunoblots. We suggest that the 22/18 monoclonal antibody detects a change in protein conformation, probably related to changes in the physiological state of the cell, that occurs transiently during regeneration and possibly during development.     

Photosynthetic gas exchange and the stable isotope composition of leaf water: comparison of a xylem-tapping mistletoe and its host

Photosynthetic gas exchange and the stable isotopic composition of foliage water were measured for a xylem tapping mistletoe, Phoradendron juniperinum, and its host tree, Juniperus osteosperma, growing in southern Utah. The observed isotopic composition of water extracted from foliage was compared to predictions of the Craig-Gordon model of isotopic enrichment at evaporative sites within leaves. Assimilation rates of juniper were higher and stomatal conductance was lower than the values observed for the mistletoe. This resulted in lower intercellular/ ambient CO₂ values in the juniper tree relative to its mistletoe parasite. For mistletoe, the observed foliage water hydrogen and oxygen isotopic enrichment was less than that predicted by the model. In juniper, foliage water hydrogen isotopic enrichment was also lower than that predicted by the evaporative enrichment model. In contrast, the oxygen isotopic enrichment in juniper foliage water was slightly greater than that predicted for the evaporative sites within leaves. Hydrogen isotopic enrichment in mistletoe foliage shows systematic variation with stem segment, being highest near the tips of the youngest stems and decreasing toward the base of the mistletoe, where isotopic composition is close to that of stem water in the host tree. In a correlated pattern, mid-day stomatal conductance declined abruptly in mistletoe foliage of increasing age.     

Isolation of the RAD18 gene of Saccharomyces cerevisiae and construction of rad18 deletion mutants

Summary The RAD18 gene of Saccharomyces cerevisiae is involved in mutagenic DNA repair. We describe its isolation from a yeast library introduced into the centromeric YCp50 vector, a low copy number plasmid. The insert was sublconed into YCp50 and into the multicopy YRp7 plasmid. RAD18 is not toxic when present in multiple copies but the UV survival response indicates an heterogeneity in the cell population, a fraction of it being more sensitive. A DNA segment, close to RAD18, is toxic on the multicopy plasmid and may correspond to the tRAN sup61 known to be tightly linked to RAD18. Chromosomal deletions of RAD18 were constructed. The gene is not essential and the deleted strains have the properties of single site mutants. Thus, RAD18 appears to be essentially involved in DNA repair metabolism.     

Localization of the α2-macroglobulin gene and Lpm gene family on mink chromosome 9

Summary Using cloned cDNA for human ₂-macroglobulin (A2M) as a probe, mink-Chinese hamster hybrid cells were analysed. The results allowed us to assign a gene for A2M to mink chromosome 9. Breeding tests demonstrated that the Lpm-locus coding for other related -macroglobulin protein and the gene for peptidase B (PEPB) are linked 11±3 cm apart. The PEPB gene is located on mink chromosome 9, and hence, the Lpw-locus is on the same mink chromosome. The relationship of the genetic systems controlling the isotypically different -macroglobulins in mink serum are discussed.     

Keratin and vimentin expression in early organogenesis of the rabbit embryo

Summary The expression of vimentin and keratins is analysed in the early postimplantation embryo of the rabbit at 11 days post conceptionem (d.p.c.) using a panel of monoclonal antibodies specific for single intermediate filament polypeptides (keratins 7, 8, 18, 19 and vimentin) and a pan-epithelial monoclonal keratin antibody. Electrophoretic separation of cytoskeletal preparations obtained from embryonic tissues, in combination with immunoblotting of the resulting polypeptide bands, demonstrates the presence of the rabbit equivalents of human keratins 8, 18, and vimentin in 11-day-old rabbit embryonic tissues. Immunohistochemical staining shows that several embryonic epithelia such as notochord, surface ectoderm, primitive intestinal tube, and mesonephric duct, express keratins, while others (neural tube, dermomyotome) express vimentin, and a third group (coelomic epithelia) can express both. Similarly, of the mesenchymal tissues sclerotomal mesenchyme expresses vimentin, while somatopleuric mesenchyme (abdominal wall) expresses keratins, and splanchnopleuric mesenchyme (dorsal mesentery) expresses both keratins and vimentin. While these results are in accordance with most results of keratin and vimentin expression in embryos of other species, they stand against the common concept of keratin and vimentin specificity in adult vertebrate tissues. Furthermore, keratin and vimentin are not expressed in accordance with germ layer origin of tissues in the mammalian embryo; rather the expression of these proteins seems to be related to cellular function during embryonic development.Supported by the Deutsche Forschungsgemeinschaft and by the Netherlands Cancer Foundation     

Thiosulfate production from cystine by the keratinolytic prokaryote Streptomyces fradiae

In cultures of Streptomyces fradiae on wool as the only source of nutrition inorganic thiosulfate (in amounts up to 0.5 mg of Na₂S₂O₃·5 H₂O/ml) was formed as the final product of metabolization of sulfur from cystine of keratin proteins. The presence of thiosulfate was proved by qualitative tests and thin-layer chromatography and estimated quantitatively by spectrophotometry, titrimetry, and capillary isotachophoresis. Metabolization of organic sulfur to thiosulfate excreted into the medium is a process not yet described in microorganisms.     

Endogenous cholesterol synthesis is sufficient for ACTH-induced differentiation of rat adrenocortical cells in primary culture

Summary To define the role of endogenously synthesized cholesterol in the differentiation of adrenocortical cells in primary culture, fetal rat adrenal cells were cultured in the presence of exogenous cholesterol (serum-supplemented medium) or in the absence of it (serum-free medium or lipoprotein-free medium). Ultrastructurally the cells had features of glomerulosa cells: mitochondria were oval or rod shaped with lamellar inner membranes. The amount of smooth endoplasmic reticulum was small, and lipid droplets were few. When the cells were cultured in serum-free medium some intracytoplasmic vacuoles were seen. The undifferentiated zona glomerulosa-like cells secreted low amounts of corticosterone and 18-OH-deoxycorticosterone (18-OH-DOC) in all three media (serum-supplemented medium, serum-free medium, and lipoprotein-free medium). Stimulation of the adrenocortical cells with ACTH induced the ultrastructural features of differentiated zona fasciculata-like cells. Mitochondrial inner membranes were well developed in lipoprotein-free medium, but not in serum-free medium. The amount of intracellular lipids was increased in both media devoid of cholesterol. In the ACTH stimulated cultures the presence of exogenous cholesterol resulted in increased secretions of corticosterone and 18-OH-DOC. In the absence of an exogenous source of cholesterol, the amounts of steroids secreted were only half of that secreted in the presence of serum-supplemented medium. Endogenously synthesized cholesterol is sufficient for the morphologic differentiation of fetal rat adrenocortical cells under ACTH stimulation. However, without exogenously provided cholesterol, the steroid production accounts only for half of the maximal output achieved using serum-supplemented medium. This work was supported by Finnish Culture Foundation.     

Immunohistochemical localization of keratin in bull,goat, and sheep anterior pituitary glands

Summary Immunohistochemical localization of keratin, an intermediate filament protein, was studied in bull, goat, and sheep anterior pituitary glands, i.e., in animals of the order Artiodactyla. Strong immunoreactivity was detected in the cells of the marginal layer of bull and goat, as well as in cysts or large follicles in the anterior lobe of all 3 species. In addition, a number of stellateshape cells were immunoreactive for keratin and were distributed throughout the anterior lobe. The localization of keratin-positive cells in light-microscopic preparations correlated precisely with the localization of folliculo-stellate cells in adjacent ultrathin sections. In ultrastructural studies, many slender and elliptical membranous components which were different from smooth endoplasmic reticulum were observed in the cytoplasm of the some keratin-positive cells. Some of the folliculostellate cells in the 3 species were also immunoreactive for the subunit of S-100 protein, which exists in some epithelial cells. On the other hand, immunolocalization of glial fibrillary acidic protein, a glial cell marker, could not be demonstrated in the anterior pituitary glands of the 3 species studied. These results suggest that keratin-positive folliculo-stellate cells express epithelial-like characteristics.