Age-dependent regulation of glucocorticoid receptors in the liver of male rats

Specific binding of [3H]dexamethasone to cytosol and the activation of bound hormone-receptor complexes were studied in the liver of immature (3 weeks old) and mature (26 weeks old) Long-Evans male rats. The concentration of specific binding sites was significantly higher (33%) in the liver of immature rats as compared to mature, while dissociation constants (Kd) remain unaltered at both ages. Heat activation (for 45 min at 25 degrees C) significantly enhances the binding of [3H]dexamethasone-receptor complexes to DNA-cellulose and purified nuclei at both the ages, with a greater magnitude in mature rats. Cross mixing experiments (i.e., binding of activated cytosol from mature rats to nuclei of immature and vice-versa) show receptor specificity. Ca2+ activation (20 mM Ca2+ for 45 min at 0 degree C) also enhances the nuclear and DNA-cellulose binding at both the ages, but to a similar extent. Differences in the number of specific binding sites and some of the physiochemical properties of glucocorticoid receptors presented here between immature and mature rats may underlie the functional changes in tissue response with age.     

Choline acetyltransferase activity and total protein content in selected optic areas of the rat after complete light-deprivation during CNS development

Choline acetyltransferase (acetyl-CoA: choline O-acetyltransferase, I.U.B. 2.3.1.6) activity and total protein content in visual and extra-visual areas were compared in normal Long-Evans rats and in rats subjected to complete light-deprivation for 21 days from birth. The enzyme activity and the protein content in the superior colliculi, lateral geniculate bodies and visual cortex, as well as in the sensory-motor cortex, hypothalamus, brain stem and cerebellum, were measured in both mothers and progeny. By means of a radiochemical technique modified in this laboratory, a significant decline of ChAc activity was observed in the lateral geniculate bodies and superior colliculi, with no significant decline in the visual cortex of the experimental progeny. Total protein content, measured colorimetrically, was significantly decreased in the superior colliculi of the progeny. The biochemical data obtained from all other brain areas in the experimental animals (progeny and mothers) and controls demonstrated no marked differences. The enzymic alterations observed in the cholinergic system of progeny after complete light-deprivation during this critical period of CNS development can be specifically correlated with decreased functional maturation of the visual system. If it is accepted that ACh is a neuro-transmitter in some parts of the visual pathway, the data presented here suggest that complete light-deprivation from birth to 21 days of age in the rat has an effect on a biochemical system involved in synaptic transmission.     

Enhancement of seminiferous tubular growth and spermatogenesis in testes of rats recovering from early hypothyroidism: a quantitative study

Testicular weight and DNA content were markedly reduced (63 and 69%) in weanling Long-Evans rat pups rendered hypothyroid from birth by administration of propylthiouracil (PTU), a reversible goitrogen. These growth deficits worsened to >80% by continuing hypothyroidism beyond weaning, to days 50 and 90. Recovery of thyroid function, brought about by discontinuing PTU at weaning, resulted in a paradoxical stimulation of testis growth, amounting to increased weight (40%), DNA content (60%) and size by 90 days, compared to age-matched controls. In the 25-day or older hypothyroid rats, testicular structure was immature and spermatogenesis markedly delayed, as evident by closed lumen and significantly reduced diameter of seminiferous tubules (38%), thickness of germinal layer (70%), and number of primary spermatocytes (86%), compared to control. Hypothyroidism did not alter the number of tubules per testis cross section. In the 90-day recovery rats, numbers of seminiferous tubules were unchanged but tubular diameter was significantly (20%) larger than in controls and spermatogenesis appeared very active as indicated by significantly increased germinal layer thickness (22%) and total number and density of primary spermatocytes (55% and 40%). The results show that although postnatal hypothyroidism is deleterious for testicular growth and spermatogenesis, recovery from this condition leads to enhanced seminiferous tubular growth and spermatogenesis.     

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/.     

Properties of triiodothyronine binding sites in cerebral cortical cytosol

Some properties of brain cytosol components that specifically bind L-triiodothyronine (T3) were examined in order to resolve their relevance and relationship to nuclear receptors. A marked variation in T3 binding activity was apparent among different brain areas. Binding exhibited temperature dependence and was maximal at 0 degrees C. The binding component was shown to be a protein that migrated as a single included peak on Sephadex G-100 columns at a position corresponding to a Stokes radium of 30A degrees and a M.W. of 54,000. On a linear glycerol gradient the T3-macromolecular complex was estimated to have a sedimentation constant of .4.2S. By combining sedimentation and gel filtration data the calculated M.W. was 53,000. With DEAE-cellulose chromatography the T3 complex eluted as a single peak at 115mM KH2PO4. The results indicate that the properties of the cytosol thyronine-binding protein are similar in many respects to those reported for nuclear receptors. In addition, the regional and developmental binding parameters parallel those for nuclei. We conclude that cytosolic recognition sites may function in the modulation of nuclear receptors and in addition serve to distinguish target from non-target tissue.     

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.