Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS)     

Chloroflexus-like organisms from marine and hypersaline environments: Distribution and diversity

We report the presence of a diverse number ofChloroflexus-like organisms in intertidal marine and submerged hypersaline microbial mats using light, infrared fluorescence, and electron microscopy. The intertidal organisms appear morphologically very similar to thermophilicC. aurantiacus while the 2 hypersaline strains are larger and have a more complex ultrastructure composed of chlorosome-bearing internal membranes that appear to arise as invaginations of the cell membrane. By comparing spectroradiometry of microbial mat layers with microscopic observations, we have confirmed that theChloroflexus-like organisms are major constituents of the hypersaline microbial mat communities. In situ studies on mat layers dominated byChloroflexus-like organisms showed that sulfide-dependent photoautotrophic activity sustained by near infrared radiation prevailed. Autoradiographic analyses revealed that autotrophy was sustained in the filaments by 750 nm radiation. Three morphologically distinct strains are now maintained in mixed culture. One of these appears to be growing photoautotrophically.     

Simultaneous detection of neuropeptides and messenger RNA in the magnocellular hypothalamo-neurohypophysial system by a combination of non-radioactive in situ hybridization histochemistry and immunohistochemistry

A protocol was developed combining non-radioactive in situ hybridization histochemistry with enzyme based immunohistochemistry, detect the expression of mRNA in phenotypically defined neurons. Freefloating brain sections were hybridized with the oligonucleotide probes which have been 3-end labelled with biotin-11-dUTP. The hybridized probe was visualized by a combined avidin-biotin bridge method, anti-avidin immunohistochemistry, and horseradish peroxidase detection using diaminobenzidine as a substrate. The in situ hybridization step yielded a very stable reaction product enabling subsequent immunohistochemical reactions using horseradish peroxidase and benzidine dihydrochloride as a chromogen. Magnocellular neurons of the hypothalamo-neurophypophysial system synthesize either vasopressin or oxytocin; water deprivation and chronic saline ingestion are potent stimuli for the expression of both of the genes encoding these neuropeptides. A number of other neuropeptides with putative transmitter action are synthesized in magnocellular neurons during such stimulation. Experiments were performed to explore whether neuropeptide Y immunoreactivity is present within magnocellular vasopressin mRNA-expressing neurons of the hypothalamo-neurophypophysial system. The results clearly demonstrated that neuropeptide Y-immunoreactive elements were present within a number of magnocellular vasopressin mRNA-containing cells. In addition, immunohistochemical detection of the neuropeptides ocytocin and cholecystokinin was carried out on sections hybridized non-radioactively for vasopressin; as expected vasopressin mRNA did not co-exist with cholecystokinin, whereas a few oxytocin immunoreactive neurons in osmotically stimulated animals also contained vasopressin mRNA. The developed method makes possible the immunohistochemical detection of intracellular antigens with concomitant detection of intracellular mRNA.     

Determination of the overall volumetric mass transfer coefficient kLa,by a temperature dependent change of gas solubility

Summary The solubility of oxygen in the liquid phase of a bioreactor was changed by a ramp change of temperature, and k_La was determined from the resulting return to equilibrium of dissolved oxygen activity. The maximum k_La that can be measured by this method in a standard laboratory scale bioreactor is 145 h^–1 corresponding to a temperature change rate of 320°C h^–1.Nomenclature p Difference between p_G and p_L (% saturation) - T Ramp change of temperature (°C) - E Temperature-compensated output from the oxygen electrode (A) - E_u Uncompensated output from the oxygen electrode (A) - k_La Overall volumetric mass transfer coefficient (h^–1) - k_La_Tm Overall volumetric mass transfer coefficient at temperature T_m (h^–1) - P_G Dissolved oxygen activity in equilibrium with the gas phase (% saturation) - p_L Dissolved oxygen activity (% saturation) - p_Lm Dissolved oxygen activity at time t_m (% saturation) - t Time (h) - t_m Time of maximum p (h) - T Temperature (°C) - T_cal Calibration temperature of the oxygen electrode (°C) - T_m Final temperature after a temperature shift (°C) - T_n Temperature at time t_n     

Biomarker indications for microbial contribution to Recent and Late Jurassic carbonate deposits

Summary Biomarker investigations were applied to the hydrocarbon fractions of three Recent (cyanobacterial mat, Lake Van microbialite and Lake Satonda microbialite) and two Late Jurassic carbonate samples obtained from sponge bioherms. The relative concentrations ofn-alkanes, monomethyl alkanes, acyclic isoprenoids, steroids and hopanoids in these samples are studied and their probable biological precursors are discussed. Normal alkanes with carbon chain lengths ranging from C₁₅ to C₃₄ and monomethyl alkanes ranging from C₁₇ to C₂₁ with a varying methyl branching pattern are found. The major hydrocarbons are low molecular weight (LMW)n-alkanes (C₁₅–C₂₁) with a slight to strong predominance ofn-heptadecane (C₁₇). High molecular weight (HMW)n-alkanes occur in low to moderate relative concentrations showing a preference of odd-carbon numbered compounds with a maximum at C₂₉. Within the acyclic isoprenoids, pristane, phytane/phytene, pentamethyl-eicosane, squalane and lycopane could be identified. Polycyclic terpenoids of the sterane and/or hopane type are present in all carbonate samples. The carbon numbers of these components range from 27 to 29 and 27 to 32, respectively. These organic compounds identified can be attributed to various source organisms such as cyanobacteria, archaebacteria, algae and vascular plants. All hydrocarbon fractions of the samples are characterized by moderate to high relative concentrations of compounds derived from cyanobacteria, signifying the role of these organisms as contributors to the Recent as well as to the Late Jurassic carbonate deposits.     

Note on the nomenclature of Cassieae (Leguminosae-Caesalpinioideae) in Malaysia

As a precursor for the treatment of Caesalpiniaceae in Flora Malesiana the following new combinations are proposed: Cassia javanica ssp. pubiflora stat. nov., C. javanica ssp. agnes stat. nov., C. javanica ssp. microcalyx stat. nov. C. javanica ssp. renigera stat. nov., C. javanica ssp. bartonii stat. nov., Senna divaricata comb. nov., Chamae-christa pumila comb. nov. and Chamaechrista mindanaensis comb. nov.     

ANTIVIRAL ACTIVITY OF CULTURED BLUE-GREEN ALGAE (CYANOPHYTA)1

Lipophilic and hydrophilic extracts from approximately 600 strains of cultured cyanophytes, representing some 300 species, were examined for antiviral activity against three pathogenic viruses. Approximately 10% of the cultures produced substances that caused significant reduction in cytopathic effect normally associated with viral infection. The screening program identified the order Chroococcales as commonly producing antiviral agents.     

Bacterial Disproportionation of Elemental Sulfur Coupled to Chemical Reduction of Iron or Manganese

A new chemolithotrophic bacterial metabolism was discovered in anaerobic marine enrichment cultures. Cultures in defined medium with elemental sulfur (S⁰) and amorphous ferric hydroxide (FeOOH) as sole substrates showed intense formation of sulfate. Furthermore, precipitation of ferrous sulfide and pyrite was observed. The transformations were accompanied by growth of slightly curved, rod-shaped bacteria. The quantification of the products revealed that S⁰ was microbially disproportionated to sulfate and sulfide, as follows: 4S⁰ + 4H₂O → SO₄^2- + 3H₂S + 2H⁺. Subsequent chemical reactions between the formed sulfide and the added FeOOH led to the observed precipitation of iron sulfides. Sulfate and iron sulfides were also produced when FeOOH was replaced by FeCO₃. Further enrichment with manganese oxide, MnO₂, instead of FeOOH yielded stable cultures which formed sulfate during concomitant reduction of MnO₂ to Mn²⁺. Growth of small rod-shaped bacteria was observed. When incubated without MnO₂, the culture did not grow but produced small amounts of SO₄^2- and H₂S at a ratio of 1:3, indicating again a disproportionation of S⁰. The observed microbial disproportionation of S⁰ only proceeds significantly in the presence of sulfide-scavenging agents such as iron and manganese compounds. The population density of bacteria capable of S⁰ disproportionation in the presence of FeOOH or MnO₂ was high, > 10⁴ cm^-3 in coastal sediments. The metabolism offers an explanation for recent observations of anaerobic sulfide oxidation to sulfate in anoxic sediments.     

Molecular cut-off values of dialysis membranes for alginate and kappa-carrageenan oligosaccharides

The effective molecular weight cut-off values of dialysis membranes for carrageenan and alginate oligosaccharides were evaluated by gel permeation chromatography and nuclear magnetic resonance spectroscopy. For the different membranes tested, i.e. Medicell, Spectra Por 1000D and 3500D, the porous sizes are analogous to tri- and tetrasaccharides. A simple dialysis can be used to recover the majority of the oligosaccharides produced by a carrageenase or an alginate lyase digestion.