Future trends in bacterial taxonomy

World Journal of Microbiology and Biotechnology -     

Future trends in pain research

In the future we shall need to modify the classical view that nerve impulses which signal the presence of injury are reliably transmitted by specified and automatic relay cells. We must investigate at least four different modifying mechanisms that are likely to generate chronic intractable pains. With a latency of milliseconds, combinations of afferent signals and of descending controls operate a rapid and powerful gate control. With a latency of minutes, impulses in C fibres change the excitability of peripheral endings and of spinal cord circuits. With a latency of days, chemical transport in C fibres from areas of damage further modifies cord connectivity with a disappearance of inhibitions and an expansion of receptive fields. With a latency of weeks and months, anatomical degeneration produces secondary changes in deafferented cells with atrophy, sprouting and abnormal firing patterns.     

Future trends in nitrogen research

N research effort has undergone major changes over recent decades with changing emphasis because of environmental problems and issues. This driving force, coupled with a universal desire to improve N-use efficiency, appreciation of the importance of maintaining soil resource quality and a need to provide integrated landscape managements, will continue to prompt new research areas and issues for study. Already, much information has been provided and new approaches and needs defined. It will be essential in future research to take full note of the many interactions that occur and to provide a mechanistic basis so that scaling of effects can be undertaken with the appropriate simplification without being superficial. Examples of interactions, as well as fundamental gaps in the basic processes are discussed and needs for future research identified.     

Functional taxonomy of bacterial hyperstructures.

The levels of organization that exist in bacteria extend from macromolecules to populations. Evidence that there is also a level of organization intermediate between the macromolecule and the bacterial cell is accumulating. This is the level of hyperstructures. Here, we review a variety of spatially extended structures, complexes, and assemblies that might be termed hyperstructures. These include ribosomal or "nucleolar" hyperstructures; transertion hyperstructures; putative phosphotransferase system and glycolytic hyperstructures; chemosignaling and flagellar hyperstructures; DNA repair hyperstructures; cytoskeletal hyperstructures based on EF-Tu, FtsZ, and MreB; and cell cycle hyperstructures responsible for DNA replication, sequestration of newly replicated origins, segregation, compaction, and division. We propose principles for classifying these hyperstructures and finally illustrate how thinking in terms of hyperstructures may lead to a different vision of the bacterial cell.     

Some applications of deoxyribonucleic acid base composition in bacterial taxonomy

The melting pointT _m, the mean molar (guanine+cytosine) composition and the compositional distribution of purified DNA from several strains ofXanthomonas, Chromobacterium and yellow-pigmented marine bacteria have been determined. These groups were selected because they had been analyzed adansonially. Ten strains ofXanthomonas had an average molar (guanine+cytosine) composition within the range 66.0–68.2%, which was very close to that ofPseudomonas (60–68%), as expected. All strains ofChromobacterium (six of theviolaceum biotype and three of thelividum biotype) had mean molar (guanine+cytosine) compositions within the range 63.4–71.4%. The yellow-pigmented marine flavobacteria had mean molar (guanine+cytosine) compositions of 35.6–40.6%. This suggests that they would not be genetically related to the yellow-pigmentedXanthomonas, nor to facultative aerobic organisms, such asAeromonas and theEnterobacteriaceae. The yellow-pigmented marine swarming bacteria, which resembleCytophaga, fell into two separate groups: some had a mean molar (guanine+cytosine) composition of about 34%, others were around 63%. This suggests genetic heterogeneity. The compositional distribution of DNA molecules was on the whole more narrow in polarly flagellated than in peritrichous organisms.     

Future trends in the treatment of urinary incontinence

Anticholinergic drugs act on efferent nerves to counteract overactive bladder (OAB) after it occurs. To prevent the occurrence of OAB, therapies should be directed at blocking the afferent nerves that control the bladder. Tachykinin-receptor antagonists hold great promise in this regard, since they can be administered orally and do not increase the risk of urinary retention that occurs with anticholinergics. Advanced drug delivery systems, such as controlled-release oral oxybutynin (oxybutynin-XL) can reduce the incidence of anticholinergic side effects. In a similar manner intravesical therapy for OAB is site specific, and thus also reduces the occurrence of adverse events. Moreover, the difficulties of intravesical therapy may now be overcome with advanced delivery techniques such as an implantable, long-acting drug-delivery pump. Another intravesical therapy that has met with great acceptance and success is the administration of chili pepper extracts, especially resiniferitoxin, which may be effective for up to 3 months with one application. Finally, gene therapy holds great promise for OAB, because it is possible to access all of the genitourinary organs via endoscopy and other minimally invasive techniques that are ideally suited for gene therapy.     

Lipid analysis in bacterial taxonomy: proposal for a standardized method

To increase the application of lipid analysis for taxonomic purposes, a standardized method would be useful. This method has to be simple enough to be used routinely. Such a method, based on thin-layer and gas chromatography, is proposed. It can be applied to any kind of bacteria when a few milligrams of cells are available. Comparison of the results provided by this analysis with data found in the literature (given in a schematic form in six tables) allows the identification of the studied strain in the most favorable cases, or gives information for the choice of conclusive complementary tests in the other cases.     

Numerical taxonomy of bacterial communities associated with a subantarctic mussel bed

A large mussel bed occurs in one of the largest fjords in Kerguelen archipelago. In January 1986, seawater and bivalves were collected at four tidal levels to determine whether a specific heterotrophic bacterial community could be observed in the mussels, especially in the stomach and in the fecal pellets, and to compare these microflora to seawater bacterial communities. The investigation was carried out using morphological and biochemical tests. Test results were analysed by a numerical taxonomic method. Almost all the heterotrophic mesophile isolates, grown on Zobell medium, were non-fermentative Gram-negative rods. The bacterial communities in the mussel fecal pellets were clearly different from the other communities studied. This specific bacterial microflora was characterized by the existence of Vibrionaceae.     

Analysis of bacterial RM-systems through genome-scale analysis and related taxonomy issues

Recognition sites for type II restriction and modification enzymes in genomes of several bacteria are recognized as semi-palindromic motifs and are avoided at a significant degree. The key idea of contrast word analysis with respect to RMS recognition sites, is that under-represented words are likely to be selected against. Starting from over- or underrepresented words corresponding to RMS recognition sites in specific clades, the specificity of unknown R-M systems can be highlighted. Among the known restriction enzymes, that are described in the REBASE database of restriction and modification systems, many of their recognition sites are still uncharacterized. Eventually, this motivates studies aimed at assessing horizontal transferring events of RMS in micro-organisms through the analysis of word usage biases in well-determined genomic regions. A probabilistic model is built on a first-order Markovian chain. Statistics on the k-neighborhood of a word is carried out to assess the biological significance of a genomic motif. Efficient word counting procedures have been implemented and statistics are used for the assessment of the significance of individual words in large sequences. On the basis of the set of most avoided words, and in accordance to the IUPAC coding standards, suggestions are made regarding potential recognition sequences. In certain cases, a comparison of avoided palindromic words in taxonomically related bacteria shows a pattern of relatedness of their R-M systems. For strengthening this analysis, the primary protein structure of all type II R-M systems known in REBASE have been blasted against the nr-GENBANK database. The combination of these analyses has revealed some interesting examples of possible horizontal transfer events of R-M systems.