Coefficients of distribution of cyclic polyether macrotetrolide antibiotics between hydrophobic and hydrophilic solvents

Dependence of distribution of 14C-macrotetrolide antibiotics between water and chloroform on the presence of various additives in the aqueous phase was studied with the radioindicator procedure. It was shown that in comparison to distilled water aqueous solutions of chlorine salts of ammonium, potassium and sodium increased the content of macrotetrolides in chloroform as a result of forming strong hydrophobic complexes. This is especially applied to the ions of ammonium whose addition to the aqueous phase led to an increase of macrotetrolide level in chloroform up to 98.4 per cent. Addition of weak hydrochloric acid or alkaline agents resulted in marked transfer of the ionophores into the aqueous phase at the expense of hydrolysis of the antibiotic cyclic molecules. The highest hydrolysis levels were induced by potassium hydroxide, the content of the ionophores in the hydrophobic phase decreasing up to 90.6 per cent. The effect of picric acid on distribution of the macrotetrolides between water and chloroform was different and depended on its concentration.     

Carbon dioxide fixation by the mycelium of the actinomycete Streptomyces chrysomallus var. macrotetrolidi

The mycelium of Streptomyces chryzomallus var. macrotetrolidi producing the macrotetrolide antibiotic nonactin was shown to be capable of carbon dioxide fixation. Carbon was found to be incorporated into nonactin and macromolecular compounds in the biomass. Carbon was incorporated within 20 to 40 min of the mycelium incubation with NaH14CO3. Pyruvic and propionic acids stimulated carbon incorporation.     

Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation

The signal produced by fluorescence in situ hybridization (FISH) often is inconsistent among cells and sensitivity is low. Small DNA targets on the chromatin are difficult to detect. We report here an improved nick translation procedure for Texas red and Alexa Fluor 488 direct labeling of FISH probes. Brighter probes can be obtained by adding excess DNA polymerase I. Using such probes, a 30?kb yeast transgene, and the rp1, rp3 and zein multigene clusters were clearly detected.     

Biodeterioration of Mayan buildings at uxmal and tulum,Mexico

Uxmal and Tulum are two important Mayan sites in the Yucatan peninsula. The buildings are mainly composed of limestone and grey/black discoloration is seen on exposed walls and copious greenish biofilms on inner walls. The principal microorganisms detected on interior walls at both Uxmal and Tulum were cyanobacteria; heterotrophic bacteria and filamentous fungi were also present. A dark‐pigmented mitosporic fungus and Bacillus cereus, both isolated from Uxmal, were shown to be acidogenic in laboratory cultures. Cyanobacteria belonging to rock‐degrading genera Synechocystis and Gloeocapsa were identified at both sites. Surface analysis previously showed that calcium ions were present in the biofilms on buildings at Uxmal and Tulum, suggesting the deposition of biosolubilized stone. Apart from their potential to degrade the substrate, the coccoid cyanobacteria supply organic nutrients for bacteria and fungi, which can produce organic acids, further increasing stone degradation.     

Identification of conformational B-cell Epitopes in an antigen from its primary sequence

Background

One of the major challenges in the field of vaccine design is to predict conformational B-cell epitopes in an antigen. In the past, several methods have been developed for predicting conformational B-cell epitopes in an antigen from its tertiary structure. This is the first attempt in this area to predict conformational B-cell epitope in an antigen from its amino acid sequence.

Results

All Support vector machine (SVM) models were trained and tested on 187 non-redundant protein chains consisting of 2261 antibody interacting residues of B-cell epitopes. Models have been developed using binary profile of pattern (BPP) and physiochemical profile of patterns (PPP) and achieved a maximum MCC of 0.22 and 0.17 respectively. In this study, for the first time SVM model has been developed using composition profile of patterns (CPP) and achieved a maximum MCC of 0.73 with accuracy 86.59%. We compare our CPP based model with existing structure based methods and observed that our sequence based model is as good as structure based methods.

Conclusion

This study demonstrates that prediction of conformational B-cell epitope in an antigen is possible from is primary sequence. This study will be very useful in predicting conformational B-cell epitopes in antigens whose tertiary structures are not available. A web server CBTOPE has been developed for predicting B-cell epitope http://www.imtech.res.in/raghava/cbtope/.     

The dependence of the distribution of ionophoric macrotetrolide antibiotics on the composition of their immiscible phases

Influence of various solvents on the content of macrotetrolides during their prolonged storage in solution was shown. Under the conditions of room temperature 90 per cent acetone induced hydrolysis of polyether antibiotics. 90 per cent ethanol and dry chloroform induced respectively slight and intensive cyclization of linear precursors (oxyacids). The study on distribution of macrotetrolides between immiscible phases of various composition revealed that addition of ethanol or acetone to the water-chloroform system of organic solvents induced the antibiotic liberation into the water phase which increased with increasing concentration of the substances being added. Inorganic cations intensified the process during either the oxyacid cyclization or the antibiotic hydrolysis and liberated the reaction products from the equilibrium mixture. Under such conditions the value of the ion radius or selectivity of the macrotetrolides to definite cations was in principle of no importance.     

Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs

Background

Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO) sequence database (GOSeqLite). This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences.

Results

We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006) at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS) had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS) had an estimated error rate of 49%.

Conclusion

While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.     

Tensile trabeculae--myth or reality?

Understanding of the functional role of the trabecular bone is very important for the analysis and computer-aided simulations of bone remodelling processes. The aspired wide clinical applications remain a remote future despite a great number of developed up-to-date approaches and theories and collected data on both material properties of the trabecular bone and its reaction to various stimuli. It is widely accepted that the mechanical loading plays the major role for the structure of the cancellous bone. The in vivo loading conditions of the cancellous bone are not known. Hence, for the computer-aided analysis and modelling of the trabecular bone specimens, simplified loading conditions are used. Also for the analysis of the cancellous bone as a part of a whole bone simplified loading conditions are assumed based on previous research without questioning its accuracy or relevance to the real in vivo conditions. In particular, the bending loading of the bone, which originates from the well-known observations made more than a century ago that have evolved in the trajectorial theory or "tensile trabeculae tradition", is often assumed to reflect the physiological loading conditions of bones. Some studies show that the bending or tensile-compressive orthogonal loading conditions for the cancellous bone may lead to plausible results. However, some other research works suggest that the presence of the tensile trabecular structures (particularly in the proximal femur) is doubtful and the bending loading conditions in bone should be treated with caution. Moreover, the loading conditions with compensated (or minimised) bending also produce results that correlate with the material distribution in the bone. The purpose of this review is to analyse some of the data and ideas available in the literature and to discuss the question of the major factors that define the shape and structure of the trabecular bone during the process of functional adaptation.     

Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein

Background  

A large number of papers have been published on analysis of microarray data with particular emphasis on normalization of data, detection of differentially expressed genes, clustering of genes and regulatory network. On other hand there are only few studies on relation between expression level and composition of nucleotide/protein sequence, using expression data. There is a need to understand why particular genes/proteins express more in particular conditions. In this study, we analyze 3468 genes of Saccharomyces cerevisiae obtained from Holstege et al., (1998) to understand the relationship between expression level and amino acid composition.