Broad host range fluorescence and bioluminescence expression vectors for Gram-negative bacteria

Tagging of bacteria with living colors and living light allows increasingly valuable new imaging and detection technologies to be accessible to researchers. In this study, we aimed to create stable broad host range expression vectors for tagging Gram-negative bacteria with fluorescence and bioluminescence. To accomplish this, a mutated form of promoterless green fluorescent protein (gfp) gene, gfpmut3a, from Aequorea victoria and promoterless bacterial luciferase genes, luxCDABE, from Photorhabdus luminescens were inserted into broad host range plasmid pBBR1MCS4. Expression of gfp and luxCDABE genes was driven by lacZ promoter. In addition, dual versions with both gfpmut3a and luxCDABE genes and inducible versions carrying lacI(q) gene were also constructed. These new broad host range vectors containing a stable broad host range origin of replication and mobility genes can be transferred to Gram-negative bacteria by either electroporation or conjugal mating and maintained stably. Availability of these expression vectors should be useful in developing new approaches to study a broad variety of Gram-negative bacteria, particularly for applications investigating host-pathogen interactions in vivo and in vitro.     

Systematic analysis of intrinsic factors affecting differential display

Differential display (DD) is a widely used method for identifying differentially expressed genes. To improve further the efficiency and reproducibility of the method, this report systematically examines four critical parameters of standard DD-PCR. Specifically, the study determined the optimal annealing temperature, elongation time, dNTP concentration, and arbitrary primer concentration. By using a thermal cycler that was capable of displaying a temperature gradient across a PCR plate, it was possible to determine (in a single experiment) the effect of different annealing temperatures. The optimal annealing temperaturefor a 13-mer arbitrary primer fell within a broad range of 40 degrees C-50 degrees C. Elongation times over a range of 30-120 s worked best. The optimal concentration for dNTPs was within a very broad range of 2-50 microM, with higher amounts allowing for greater pipetting accuracy. The most favorable concentration for the arbitrary primer was also within a broad range of 0.1-2.0 microM. A primer concentration below this range greatly reduced the efficiency of the amplification process. In conclusion, the experimental findings delineated the best possible DD conditions for a more reliable assessment of differential gene expression.     

Regional‐scale directional changes in abundance of tree species along a temperature gradient in Japan

Climate changes are assumed to shift the ranges of tree species and forest biomes. Such range shifts result from changes in abundances of tree species or functional types. Owing to global warming, the abundance of a tree species or functional type is expected to increase near the colder edge of its range and decrease near the warmer edge. This study examined directional changes in abundance and demographic parameters of forest trees along a temperature gradient, as well as a successional gradient, in Japan. Changes in the relative abundance of each of four functional types (evergreen broad‐leaved, deciduous broad‐leaved, evergreen temperate conifer, and evergreen boreal conifer) and the demography of each species (recruitment rate, mortality, and population growth rate) were analyzed in 39 permanent forest plots across the Japanese archipelago. Directional changes in the relative abundance of functional types were detected along the temperature gradient. Relative abundance of evergreen broad‐leaved trees increased near their colder range boundaries, especially in secondary forests, coinciding with the decrease in deciduous broad‐leaved trees. Similarly, relative abundance of deciduous broad‐leaved trees increased near their colder range boundaries, coinciding with the decrease in boreal conifers. These functional‐type‐level changes were mainly due to higher recruitment rates and partly to the lower mortality of individual species at colder sites. This is the first report to show that tree species abundances in temperate forests are changing directionally along a temperature gradient, which might be due to current or past climate changes as well as recovery from past disturbances.     

Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro‐evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host–parasite cophylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro‐evolutionary regime showed a low diversification rate, high frequency of duplication events and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.     

Monitoring the spread of broad host and narrow host range plasmids in soil microcosms

Abstract: Escherichia coli recipient and E. coli donor strains carrying streptothricin-resistance genes were inoculated together into different soil microcosms. These genes were localized on the narrow host range plasmids of incompatibility (Inc) groups FII, Il, and on the broad host range plasmids of IncP1, IncN, IncW3, and IncQ. The experiments were intended to study the transfer of these plasmids in sterile and non-sterile soil with and without antibiotic selective pressure and in planted soil microcosms. Transfer of all broad host range plasmids from the introduced E. coli donor into the recipient was observed in all microcosm experiments. These results indicate that broad host range plasmids encoding short and rigid pili might spread in soil environments by conjugative transfer. In contrast, transfer of the narrow host range plasmids of IncFII and IncI1, into E. coli recipients was not found in sterile or non-sterile soil. These plasmids encoded flexible pili or flexible and rigid pili, respectively. In all experiments highest numbers of transconjugants were detected for the IncP1-plasmid (pTH16). There was evidence with plasmids belonging to IncP group transferred by conjugation into a variety of indigenous soil bacteria at detectable frequencies. Significantly higher numbers of indigenous transconjugants were obtained for the IncP-plasmid under antibiotic selection pressure, and a greater diversity of transconjugants was detected. Availability of nutrients and rhizosphere exudates stimulated transfer in soil. Furthermore, transfer of the IncN-plasmid (pIE1037) into indigenous bacteria of the rhizosphere community could be detected. The transconjugants were determined by BIOLOG as Serratia liquefaciens . Despite the known broad host range of IncW3 and IncQ-plasmids, transfer into indigenous soil bacteria could not be detected.     

<Emphasis Type="Italic">Bacillus pumilus</Emphasis>laccase: a heat stable enzyme with a wide substrate spectrum

Background  

Laccases are multi-copper oxidases that catalyze the one electron oxidation of a broad range of compounds. Laccase substrates include substituted phenols, arylamines and aromatic thiols. Such compounds are activated by the enzyme to the corresponding radicals. Owing to their broad substrate range laccases are considered to be versatile biocatalysts which are capable of oxidizing natural and non-natural industrial compounds, with water as sole by-product.     

Parameters important in tuning the response of monolayer enzyme electrodes fabricated using self-assembled monolayers of alkanethiols

Enzyme electrodes were observed experimentally to have a broad dynamic range, high sensitivity and excellent reproducibility. The theoretically predicted response of the monolayer enzyme electrodes was in good agreement with that observed experimentally over the broad range of experimental conditions tested. The response is limited by the rate of enzyme turnover by a mediating species rather than mass transport. As a consequence of this limitation, the response was very sensitive to the enzyme loading and the concentration of mediator in the sample solution but insensitive to mass transport variables such as solution stirring or the diffusion coefficients of the substrate or cosubstrate.     

Replication of derivatives of the broad host range plasmid RK2 in two distantly related bacteria

A 0.7-kb segment of the broad host range plasmid RK2 containing the replication origin of this plasmid will replicate in Escherichia coli and Pseudomonas putida when this segment is joined to a 1.8-kb region of RK2 designated traA*. The presence of another region of RK2, designated trfB, that previously was implicated in RK2 replication had no effect on the maintenance of the RK2 trfA*-oriV replicon in these two organisms. These observations indicate a requirement for a minimal account of information for replication of this broad host range plasmid in two distantly related bacteria.     

It's all GO for plant scientists

The Gene Ontology project (http://www.geneontology.org/) produces structured, controlled vocabularies and gene product annotations. Gene products are classified according to the cellular locations and biological process in which they act, and the molecular functions that they carry out. We annotate gene products from a broad range of model species and provide support for those groups that wish to contribute annotation of further model species. The Gene Ontology facilitates the exchange of information between groups of scientists studying similar processes in different model organisms, and so provides a broad range of opportunities for plant scientists.     

Optimization of MALDI-TOF MS detection for enhanced sensitivity of affinity-captured proteins spanning a 100 kDa mass range

Analysis of complex biological samples by MALDI-TOF mass spectrometry has been generally limited to the detection of low-mass protein (or protein fragment) peaks. We have extended the mass range of MALDI-TOF high-sensitivity detection by an order of magnitude through the combined optimization of instrument parameters, data processing, and sample preparation procedures for affinity capture. WCX, C3, and IMAC magnetic beads were determined to be complementary and most favorable for broad mass range protein profiling. Key instrument parameters for extending mass range included adjustment of the ADC offset and preamplifier filter values of the TOF detector. Data processing was improved by a combination of constant and quadratic down-sampling, preceded by exponential baseline subtraction, to increase sensitivity of signal peaks. This enhancement in broad mass range detection of protein signals will be of direct benefit in MS expression profiling studies requiring full linear range mass detection.     

Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry (UPLC-HRMS)

Here we present a workflow to analyze the metabolic profiles for biological samples of interest including; cells, serum, or tissue. The sample is first separated into polar and non-polar fractions by a liquid-liquid phase extraction, and partially purified to facilitate downstream analysis. Both aqueous (polar metabolites) and organic (non-polar metabolites) phases of the initial extraction are processed to survey a broad range of metabolites. Metabolites are separated by different liquid chromatography methods based upon their partition properties. In this method, we present microflow ultra-performance (UP)LC methods, but the protocol is scalable to higher flows and lower pressures. Introduction into the mass spectrometer can be through either general or compound optimized source conditions. Detection of a broad range of ions is carried out in full scan mode in both positive and negative mode over a broad m/z range using high resolution on a recently calibrated instrument. Label-free differential analysis is carried out on bioinformatics platforms. Applications of this approach include metabolic pathway screening, biomarker discovery, and drug development.     

Broad bean wrinkly seed caused by artichoke yellow ringspot nepovirus

Artichoke yellow ringspot nepovirus (AYRV) was isolated from stunted broad bean plants in Crete showing leaf mottling and deformation and wrinkling of seed testas. AYRV identification was based on host range, behaviour during purification, electron microscopy and serology. AYRV-broad bean isolate was seed-transmitted in broad bean, and embryo infection appeared to be a prerequisite for virus transmission to seedlings. Transmission through pollen was not detected in broad bean plants, although pollen grains were externally contaminated by the virus. Ovule infection occurred in a high proportion of seed and was independent of pollination.     

Isolation and characteristics of a recombinant pOV13 plasmid as a vector for DNA cloning in a broad range of bacterial hosts

The hybrid plasmid pOV13 proposed as a potential vector for DNA cloning in a broad bacterial host range has been constructed on the basis of the broad host range plasmid RSF1010 and a shortened derivative of RP4, the plasmid pVZ115 serving a marker DNA fragment. The plasmid pOV13 contains the genes for streptomycin, kanamycin and tetracycline resistance and single cleavage sites for restriction endonucleases BamHI, BgIII, SalI, SmaI, PvuII, XhoI, as well as double cleavage sites for restriction endonucleases PstI and HindIII permitting one to clone DNA with insertional inactivation of genes. The physicogenetical map of the birepliconed plasmid pOV13 is presented.     

Genome organization of the plasmid of IncQ/P4 group and its vector derivatives

The genome organization and functioning of IncQ/P4 plasmids are reviewed. Based on these plasmids, cloning vectors have been constructed for broad host range of gram-negative bacteria. Together with one- and two-replicon vectors for cloning via insertion inactivation of markers, specialized plasmid vectors are described: cosmids, promoter-probe vectors, vectors for direct selection of recombinant molecules. Examples of using broad host range vectors for gene cloning and expression in non-enteric gram-negative bacteria are presented.     

Motor activity of protozoa: Position of motor activity in the hierarchy of environmental bioassay criteria

Stable dose-independent behavioral modification in the infusorium Spirostomum ambiguum immediately after the exposure to γ-radiation in a broad dosage range has been shown in model experiments. Negative effect is observed already at a dose of 0.01 Gy and is inherited through several generations of spirostoma. Decreased motor activity is accompanied by morphological pathology, the manifestation of which is also dose-independent in a broad range of low doses. The possibility of express evaluation of changes in the motor activity of protozoa for the biotesting of radioactive contamination of the environment, as well as the prognostic character of this study, is under discussion.     

Reticuloendotheliosis type C and primate type D oncoretroviruses are members of the same receptor interference group.

The reticuloendotheliosis viruses (REVs), originally isolated from avian species, constitute a group of retroviruses which are more closely related to mammalian retroviruses than to other avian retroviruses. The envelope glycoproteins of members of the REV group display a striking amino acid sequence identity with a group of primate oncoretroviruses which belong to a single receptor interference group and include all of the type D and some type C primate oncoretroviruses. Members of the REV group also have a broad host range which covers most avian cells and some mammalian cells, including those of simian and human origin. In view of this broad host range and the envelope sequence similarities, we investigated the cross-interference pattern between REV and primate virus groups to determine whether they utilized the same receptor. Superinfection experiments using a vector virus containing an Escherichia coli lacZ gene showed that reticuloendotheliosis and simian oncoretroviruses constitute a single receptor interference group on both human and canine cells and indicate that the viruses bind to the same receptor to initiate infection. These results suggest that this receptor binding specificity has been maintained over a wide range of retroviruses and may be responsible for the broad spread of these retroviruses between different orders of vertebrates.     

Tobacco mitochondrial small heat shock protein NtHSP24.6 adopts a dimeric configuration and has a broad range of substrates

There is a broad range of different small heat shock proteins (sHSPs) that have diverse structural and functional characteristics. To better understand the functional role of mitochondrial sHSP, NtHSP24.6 was expressed in Escherichia coli with a hexahistidine tag and purified. The protein was analyzed by non-denaturing PAGE, chemical cross-linking and size exclusion chromatography and the H6NtHSP24.6 protein was found to form a dimer in solution. The in vitro functional analysis of H6NtHSP24.6 using firefly luciferase and citrate synthase demonstrated that this protein displays typical molecular chaperone activity. When cell lysates of E. coli were heated after the addition of H6NtHSP24.6, a broad range of proteins from 10 to 160 kD in size remained in the soluble state. These results suggest that NtHSP24.6 forms a dimer and can function as a molecular chaperone to protect a diverse range of proteins from thermal aggregation.     

A coarse-grained framework for spiking neuronal networks: between homogeneity and synchrony

Homogeneously structured networks of neurons driven by noise can exhibit a broad range of dynamic behavior. This dynamic behavior can range from homogeneity to synchrony, and often incorporates brief spurts of collaborative activity which we call multiple-firing-events (MFEs). These multiple-firing-events depend on neither structured architecture nor structured input, and are an emergent property of the system. Although these MFEs likely play a major role in the neuronal avalanches observed in culture and in vivo, the mechanisms underlying these MFEs cannot easily be captured using current population-dynamics models. In this work we introduce a coarse-grained framework which illustrates certain dynamics responsible for the generation of MFEs. By using a new kind of ensemble-average, this coarse-grained framework can not only address the nucleation of MFEs, but can also faithfully capture a broad range of dynamic regimes ranging from homogeneity to synchrony.     

Plasmid pBS195 with a wide range of hosts, isolated from lactobacilli

The nonconjugative 4.4 kb plasmid pBS195 has been found in Lactobacillus sp. 195 strain resistant to kanamycin and streptomycin. The plasmid pBS195 determining the resistance to kanamycin has a broad host range. It is inherited by the Gram-positive microorganisms (Bacillus subtilis) as well as by Escherichia coli cells, has the cleavage sites for the restriction endonucleases BamHI, EcoRI, HindIII, PstI, KpnI. The restriction map of the plasmid for these enzymes is constructed. The broad host range, efficiently expressed marker, the presence of the unique restriction sites, small size make the plasmid pBS195 promising for the genetic engineering research.