Characterization of a naturally occurring trans-splicing intein from Synechocystis sp. PCC6803

A naturally occurring trans-splicing intein from the dnaE gene of Synechocystis sp. PCC6803 (Ssp DnaE intein) was used to characterize the intein-catalyzed splicing reaction. Trans-splicing/cleavage reactions were initiated by combining the N-terminal splicing domain of the Ssp DnaE intein containing five native N-extein residues and maltose binding protein as the N-extein with the C-terminal Ssp DnaE intein splicing domain (E(C)) with or without thioredoxin fused in-frame to its carboxy terminus. Observed rate constants (k(obs)) for dithiothreitol-induced N-terminal cleavage, C-terminal cleavage, and trans-splicing were (1.0 +/- 0.5) x 10(-3), (1.9 +/- 0.9) x 10(-4), and (6.6 +/- 1.3) x 10(-5) s(-1), respectively. Preincubation of the intein fragments showed no change in k(obs), indicating association of the two splicing domains is rapid relative to the subsequent steps. Interestingly, when E(C) concentrations were substoichiometric with respect to the N-terminal splicing domain, the levels of N-terminal cleavage were equivalent to the amount of E(C), even over a 24 h period. Activation energies for N-terminal cleavage and trans-splicing were determined by Arrhenius plots to be 12.5 and 8.9 kcal/mol, respectively. Trans-splicing occurred maximally at pH 7.0, while a slight increase in the extent of N-terminal cleavage was observed at higher pH values. This work describes an in-depth kinetic analysis of the splicing and cleavage activity of an intein, and provides insight for the use of the split intein as an affinity domain.     

Structure and synthesis of naturally occurring anhydrovitamin A2.

The structure of naturally occurring anhydrovitamin A2 was elucidated as 3-hydroxyanhydroretinol from study of its u.v.--visible, i.r., n.m.r. and mass spectra. The structure has been confirmed by a chemical synthesis. Saccobranchus fossils, a freshwater fish, can convert 3-hydroxyretinol into 3-hydroxyanhydroretinol, which in turn is converted into-3-dehydroretinol. Chemical conversion of 3-hydroxyretinol into 3-dehydroretinol was also carried out.     

A virus of tobacco rattle group naturally occurring inPlantago sp. in Czechoslovakia

The Czechoslovak isolate produced symptoms characteristic for viruses belonging to the rattle group. A virus variant comparable to Köhler's “Wintertyp” appeared to be present. Two predominant particle lengths of 90 and 191 nm were found in purified preparations. The virus reacted with Dutch TRV antiserum.     

杉木人工林种子雨组成和季节动态

杉木人工林已成为亚热带森林的重要组成部分,它具有可持续的自然更新能力,是决定杉木林群落演替方向和维持杉木林大面积存在的基础.本文以杉阔混交林和杉木纯林为研究对象,分析其种子雨的物种组成、数量大小和季节动态,以及林分优势物种种子雨数量特征和季节变化,揭示种源条件是否是制约杉木人工林天然更新的主要因素.结果表明:杉阔混交林和杉木纯林分别收集到13科18属21种和12科16属19种的种子.混交林和纯林的所有物种种子雨强度分别为3797和3300粒·m^-2.乔木物种种子数量在种子雨中占绝对优势,混交林占89.1%,纯林占86.2%,其中杉木种子数量最多,其完整种子雨强度分别为825和345粒·m^-2.两林分种子雨各类型种子所占比例均为完整种子>干瘪或腐烂种子>被取食种子.两林分种子雨均具有明显的季节动态,均在秋季到达高峰,且在落种高峰期种子雨以完整种子为主.无论是杉阔混交林还是杉木纯林都有充足的种源,种源(种子雨)条件不是制约杉木林天然更新的主要因素.     

Structure of a naturally occurring plasmid with genes for enterotoxin production and drug resistance.

A physical map of the 117-kilobase conjugative plasmid pCG86 was constructed using electron microscope heteroduplex analysis. This plasmid carries the genes elt, for heat-labile enterotoxin, and estA, for heat-stable enterotoxin, as well as the genes for resistance to tetracycline, streptomycin, sulfonamides, and mercury. These genes were mapped using deletions and Tn5 insertions as physical markers. Analysis of a heteroduplex between pCG86 and a previously described enterotoxin plasmid (EntP307) showed a 48-kilobase region of complete homology which included the genes elt and estA. An 8.8-kilobase BamHI fragment of EntP307 carrying elt, cloned by others, was also shown to be completely homologous with pCG86. The position of elt on the fragment was verified, and it was shown to carry estA as well. A 44-kilobase region of pCG86 showed partial homology with the region of EntP307 previously shown to contain conjugal transfer genes. The gene for tetracycline resistance is carried on a stem-loop structure with the dimensions of Tn10, and the genes for the other drug resistance markers are carried on a 14.6-kilobase segment that forms an insertion loop in heteroduplexes with EntP307. These studies suggest that pCG86 arose either by recombination between an enterotoxin plasmid of incompatibility group FI, like EntP307, and a multiple resistance factor of incompatibility group FII, or by transposition into EntP307 of two transposons.     

Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes

A versatile software tool, VIRTUALMSLAB, is presented that can perform advanced complex virtual proteomic experiments with mass spectrometric analyses to assist in the characterization of proteins. The virtual experimental results allow rapid, flexible and convenient exploration of sample preparation strategies and are used to generate MS reference databases that can be matched with the real MS data obtained from the equivalent real experiments. Matches between virtual and acquired data reveal the identity and nature of reaction products that may lead to characterization of post-translational modification patterns, disulfide bond structures, and cross-linking in proteins or protein complexes. The most important unique feature of this program is the ability to perform multistage experiments in any user-defined order, thus allowing the researcher to vary experimental approaches that can be conducted in the laboratory. Several features of VIRTUALMSLAB are demonstrated by mapping both disulfide bonds and artificially introduced protein cross-links. It is shown that chemical cleavage at aspartate residues in the protease resistant RNase A, followed by tryptic digestion can be optimized so that the rigid protein breaks up into MALDI-MS detectable fragments, leaving the disulfide bonds intact. We also show the mapping of a number of chemically introduced cross-links in the NK1 domain of hepatocyte growth factor/scatter factor. The VIRTUALMSLAB program was used to explore the limitation and potential of mass spectrometry for cross-link studies of more complex biological assemblies, showing the value of high performance instruments such as a Fourier transform mass spectrometer. The program is freely available upon request.     

Wavelike distributions of infections by an introduced and naturally occurring root pathogen along wheat roots

Previously, we showed that copiotrophic and oligotrophic bacteria fluctuate as moving waves along roots. These waves probably originate as a result of growth and death cycles at any location where a moving nutrient source passed. In this study, we placed sclerotia of Rhizoctonia solani AG8 along growing roots of wheat and showed that the proportions of root sections from which R. solani was isolated fluctuated with distance from the root tip. Similarly, proportions of root sections from which naturally occurring Pythium spp. were isolated fluctuated with distance from the root tip. Fourier analysis showed that these fluctuations constituted significant waves. Cross-correlation analyses demonstrated that there were negative correlations between R. solani infections and colony forming units of copiotrophic bacteria at the time of inoculation at the same locations on the root (lag = 0 cm), indicating that infection by R. solani could have been inhibited by these bacteria. There was a positive correlation between Pythium infections and copiotrophic bacteria at a lag of 6 cm along the roots. It therefore appears that Pythium infection took place shortly after the initial peak in copiotrophic bacteria following the passage of the root tip.     

Ecological physiology of Synechococcus sp. strain SH-94-5, a naturally occurring cyanobacterium deficient in nitrate assimilation.

Synechococcus sp. strain SH-94-5 is a nitrate assimilation-deficient cyanobacterium which was isolated from an ammonium-replete hot spring in central Oregon. While this clone could grow on ammonium and some forms of organic nitrogen as sole nitrogen sources, it could not grow on either nitrate or nitrite, even under conditions favoring passive diffusion. It was determined that this clone does not express functional nitrate reductase or nitrite reductase and that the lack of activity of either enzyme is not due to inactivation of the cyanobacterial nitrogen control protein NtcA. A few other naturally occurring cyanobacterial strains are also nitrate assimilation deficient, and phylogenetic analyses indicated that the ability to utilize nitrate has been independently lost at least four times during the evolutionary history of the cyanobacteria. This phenotype is associated with the presence of environmental ammonium, a negative regulator of nitrate assimilation gene expression, which may indicate that natural selection to maintain functional copies of nitrate assimilation genes has been relaxed in these habitats. These results suggest how the evolutionary fates of conditionally expressed genes might differ between environments and thereby effect ecological divergence and biogeographical structure in the microbial world.     

Structure,composition and properties of naturally occurring non-calcified crustacean cuticle

Crustaceans are known for their hard, calcified exoskeleton; however some regions appear different in colour and opacity. These include leg and cheliped tips in the grapsid crab, Metopograpsus frontalis. The chelipeds and leg tips contain only trace levels of calcium but a significant mass of the halogens, chlorine (Cl) and bromine (Br). In contrast, the carapace is heavily calcified and contains only a trace mass of Cl and no Br. In transverse section across the non-calcified tip regions of cheliped and leg the mass percent of halogens varies with position. As such, the exoskeleton of M. frontalis provides a useful model to examine a possible correlation of halogen concentration with the physical properties of hardness (H) and reduced elastic modulus (E_r), within a chitin-based matrix. Previously published work suggests a correlation exists between Cl concentration and hardness in similar tissues that contain a metal (e.g. zinc). However, in M. frontalis H and E_r did not vary significantly across cheliped or leg tip despite differences in halogen concentration. The non-calcified regions of M. frontalis are less hard and less stiff than the carapace but equivalent to values found for insect cuticle lacking metals. Cheliped tips showed a complex morphological layering that differed from leg tips.     

Interactions among phytophagous mites, and introduced and naturally occurring predatory mites, on strawberry in the UK

In choice test experiments on strawberry leaf disc arenas the phytoseiid mites Neoseiulus californicus and N. cucumeris were more effective than Typhlodromus pyri as predators of the phytophagous mites Tetranychus urticae and Phytonemus pallidus. There were no preferences shown for either prey by any of these predators. In multiple predator leaf disc experiments both Phytoseiulus persimilis and N. cucumeris significantly reduced numbers of T. urticae eggs and active stages; this effect was seen when the two species were present alone or in combination with other predator species. Neoseiulus californicus was less effective at reducing T. urticae numbers, and T. pyri was not effective; no interaction between predator species was detected in these experiments. When T. urticae alone was present as prey on potted plants, P. persimilis and N. californicus were the only phytoseiids to significantly reduce T. urticae numbers. These two predator species provided effective control of T. urticae when P. pallidus was also present; however, none of the predators reduced numbers of P. pallidus. There were no significant negative interactions when different species of predators were present together on these potted plants. In field experiments, releases of both P. persimilis and N. cucumeris significantly reduced T. urticae numbers. However, there was a significant interaction between these predator species, leading to poorer control of T. urticae when both species were released together. These results show the importance of conducting predator/prey feeding tests at different spatial scales.     

Characterization of a naturally occurring diamine auxotroph of Veillonella alcalescens.

Veillonella alcalescens strain ATCC 17745 was shown to require putrescine or cadaverine for growth. None of the other compounds tried, including magnesium and spermidine, were able to substitute for the diamines. Studies with labeled diamines showed that spermidine was made from putrescine in this organism. A polyamine analogous to spermidine, but made from cadaverine, was not found. A combination of growth experiments and chemical assays suggested that protein synthesis was limited in diamine-starved cells. Protein synthesis occurred prior to nucleic acid synthesis when putrescine was added to starved cells.     

Maintenance and stability of introduced genotypes in groundwater aquifer material.

Three indigenous groundwater bacterial strains and Pseudomonas putida harboring plasmids TOL (pWWO) and RK2 were introduced into experimentally contaminated groundwater aquifer microcosms. Maintenance of the introduced genotypes was measured over time by colony hybridization with gene probes of various specificity. On the basis of the results of colony hybridization quantitation of the introduced organisms and genes, all introduced genotypes were stably maintained at approximately 10(5) positive hybrid colonies g-1 of aquifer microcosm material throughout an 8-week incubation period. Concomitant removal of the environmental contaminants, viz., toluene, chlorobenzene, and styrene, in both natural (uninoculated) and inoculated aquifer microcosms was also demonstrated. The results indicate that introduced catabolic plasmids, as well as indigenous organisms, can be stably maintained in groundwater aquifer material without specific selective pressure for the introduced genotypes. These results have positive implications for in situ treatment and biodegradation in contaminated aerobic groundwater aquifers.