Characterization of initial events in bacterial surface colonization by two Pseudomonas species using image analysis

The processes leading to bacterial colonization on solidwater interfaces are adsorption, desorption, growth, and erosion. These processes have been measured individually in situ in a flowing system in real time using image analysis. Four different substrata (copper, silicon, 316 stainless-steel and glass) and 2 different bacterial species (Pseudomonas aeruginosa and Pseudomonas fluorescens) were used in the experiments. The flow was laminar (Re = 1.4) and the shear stress was kept constant during all experiments at 0.75 N m(-2). The surface roughness varied among the substrata from 0.002 mum (for silicon) to 0.015 mum (for copper). Surface free energies varied from 25.1 dynes cm(-1) for silicon to 31.2 dynes cm(-1) for copper. Cell curface hydrophobicity, reported as hydrocarbon partitioning values, ranged from 0.67 for Ps. fluorescens to 0.97 for Ps. aeruginosa.The adsorption rate coefficient varried by as much as a factor of 10 among the combinations of bacterial strain and substratum material, and was positively correlated with surface free energy, the surface roughness of the substratum, and the hydrophobicity of the cells. The probability of desorption decreased with increasing surface free energy and surface roughness of the substratum. Cell growth was inhibited on copper, but replication of cells overlying an initial cell layer was observed with increased exposure time to the cell-containing bulk water. A mathematical model describing cell accumulation on a substratum is presented.     

In vivo analysis of plant RNA structure: soybean 18S ribosomal and ribulose-1,5-bisphosphate carboxylase small subunit RNAs

A method to investigate the structure of RNA molecules within intact plant tissues has been developed. The RNA structures are analyzed using dimethyl sulfate (DMS), which modifies substituents of adenine and cytosine residues within single-stranded regions of RNA molecules. Reactive sites are identified by primer extension analysis. Using this procedure, an analysis of the secondary structure of the cytoplasmic 18S ribosomal RNA in soybean seedling leaves has been completed. DMS modification data are in good agreement with the phylogenetic structure predicted for soybean 18S rRNA. However, there are a few notable exceptions where residues thought to be involved in double-stranded regions in all 18S rRNAs are strongly modified in soybean leaf samples. These data taken together with the phylogenetic structure suggest that alternate structures may exist in vivo.The further applicability of this technique is demonstrated by comparing the modification pattern obtained in vivo to that obtained in vitro for a particular mRNA molecule encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. The results obtained are compared to a predicted minimum energy secondary structure. The data indicate that the conformation of RNA molecules within the cell may not be reflected in a structural analysis of purified mRNA molecules.     

A rapid and efficient method for the extraction of total DNA from the sweet potato and its related species

Secondary metabolites, latex/mucilagenous secretions, polysaccharides, and proteins interfere with the extraction of high-quality, restrictable total cellular DNA from sweet potato [Ipomoea batatas (L.) Lamk.] and related species. A method for the DNA extraction is described which overcomes these problems.     

Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities

The profile method, for detecting distantly related proteins by sequence comparison, has been extended to incorporate secondary structure information from known X-ray structures. The sequence of a known structure is aligned to sequences of other members of a given folding class. From the known structure, the secondary structure (alpha-helix, beta-strand or "other") is assigned to each position of the aligned sequences. As in the standard profile method, a position-dependent scoring table, termed a profile, is calculated from the aligned sequences. However, rather than using the standard Dayhoff mutation table in calculating the profile, we use distinct amino acid mutation tables for residues in alpha-helices, beta-strands or other secondary structures to calculate the profile. In addition, we also distinguish between internal and external residues. With this new secondary structure-based profile method, we created a profile for eight-stranded, antiparallel beta barrels of the insecticyanin folding class. It is based on the sequences of retinol-binding protein, insecticyanin and beta-lactoglobulin. Scanning the sequence database with this profile, it was possible to detect the sequence of avidin. The structure of streptavidin is known, and it appears to be distantly related to the antiparallel beta barrels. Also detected is the sequence of complement component C8, which we therefore predict to be a member of this folding class.     

Physical reasons for secondary structure stability: alpha-helices in short peptides

It was recently found that some short peptides (including C- and S-peptide fragments of RNase A) can have considerable helicity in solution, ^1–12 which was considered to be surprising. Does the observed helicity require a new explanation, or is it consistent with previous understanding? In this work we show that this helicity is consistent with the physical theory of secondary structure^12–19 based on an extension of the conventional Zimm-Bragg model.²⁰ Without any special modifications, this theory explains reasonably well almost all the experimentally observed dependencies of helicity on pH, temperature, and amino acid replacements. We conclude that the observed “general level” of helicity of C- and S-peptides (5–30% at room temperature and 10–50% near 0°C) is “normal” for short peptides consisting mainly of helix-forming and helix-indifferent residues. The helicity is modified by a multitude of weak specific side chain interactions, many of which are taken into account by the present theory;^13–19 some discrepancies between the theory and experiment can be explained by weak side-chain-side chain interactions that were neglected. A reasonable coincidence of the theory with experiment suggests that it had been used to investigate the role of local interactions in the formation of α-helical “embryos” in unfolded protein chains.     

The circular dichroism of tumor necrosis factor-α: Measurement into the vacuum UV and analysis for secondary structure

The circular dichroism (CD) spectrum of tumor necrosis factor-α has been measured into the vacuum UV to 168 nm. Analysis of the CD for secondary structure is in good agreement with X-ray diffraction results, but the analysis is somewhat unstable. Adding the CD of this protein together with its X-ray determined secondary structure to the basis set should improve subsequent analyses of CD spectra for other all-β proteins.     

Continuous culture of suspended plant cells

Summary Continuous culture is an attractive research tool in physiologic and growth and production kinetics research. However, fulfillment of the basic assumptions of continuous culture in the experimental set-up may cause problems. The homogeneity of plant cell cultures and effluent, particularly, may cause problems. This paper presents an experimental set-up which solves these problems and describes the use of this equipment in a study of the growth kinetics of plant cells. Industrial application of the continuous culture of plant cells in the production of secondary metabolites seems to be profitable when compared with batch or fed-batch cultures. However, various problems such as uncoupled product formation and strain instability make fed-batch culture a better choice. Presented in the Session-in-Depth Batch Production and Fermentation at the 1991 World Congress on Cell and Tissue Culture, Anaheim, California, June 16–20, 1991.     

Cannibalism in prehistoric Europe

The key argument for the identification of prehistoric cannibalism is provided by analysis of close similarities in the treatment of human and animal remains. Such analysis requires precise data on depositional context, meticulous excavation records, detailed bone modification studies, a relatively large sample of human and animal postcranial bones, and data on local mortuary practices. With the exception of Fontbrégoua Cave, these necessary conditions are lacking at all Stone Age European sites where it has been hypothesized that cannibalism occurred. The alternative hypothesis of secondary burial practices has been proposed informally for some sites and, in a more formal and detailed way, for Krapina and Fontbrégoua. However, this hypothesis does not have a higher probability, is not justified by current data, and uses ethnographic analogies to prop up interpretations of materials for which contextual data are missing or have been neglected. At Fontbrégoua, cannibalism remains the simplest and most plausible explanation of the evidence; at Krapina and other sites the available evidence is insufficient to prove either secondary burial or cannibalism.     

Life cycle and production ofCladopelma virescens (Mg.) (Diptera: Chironomidae) in Lake Banyoles (NE Spain)

Life cycles and annual production of the chironomidCladopelma virescens are studied at two different depths in the sublittoral (5m) and the profundal (12m) zones of the karstic Lake Banyoles (NE Spain). Two generations were completed by this chironomid in the two sampling stations studied. Production was estimated with two different methods: increment-summation (IS) and size-frequency (SF). In the IS method the smoothed survivorship curves were estimated because of the absence of the smaller instars in the samples. The mean annual production varied from 44 to 70 mg m^–2y^–1 in the deeper station and from 215 to 270 mg m^–2y^–1 in the shallower, depending on whether the size-frequency or increment summation method was used. Annual P/B varied between 5.07 and 5.67, and 6.14 and 4.11 respectively. Due to the many assumptions to be made with the IS method, we suggest the SF method in this case, because the values given by the two methods are of the same order of magnitude.     

Lignicolous marine fungi in the Straits of Messina,Italy

The occurrence and distribution of lignicolous marine fungi in the Straits of Messina has been studied. Using submerged panels of pine, beech and poplar, twenty fungal species were identified. The lignicolous mycoflora of the Messina Straits was not significantly different from that reported in the literature for other temperate marine coastal environments, Ascomycotina being frequent, while Basidiomycotina were rare.