Histochemical detection of horseradish peroxidase activity in the rat by the vibratome-paraplast method

A method is described for the histochemical detection of horseradish peroxidase in Paraplast Plus embedded brain sections. The procedure uses 150-micron-thick Vibratome-cut slices of glutaraldehyde-paraformaldehyde-fixed brain tissue. Tetramethylbenzidine stabilized by diaminobenzidine/cobalt/H2O2 is used as chromogen. The Vibratome-cut slices are dehydrated through a graded series of acetone, cleared in toluol and flat-embedded in Paraplast Plus embedding medium. Serial sections can be cut as thin as 5-7 micron. The method is universal in its application and permits optimal visualization of labeled neurons with great morphological detail at the light-microscopic level.     

Intracellular distribution of mammalian stress proteins. Effects of cytoskeletal-specific agents

Following a brief period of heat stress, the two highly conserved mammalian stress proteins, hsp68 and 70, were examined with respect to their intracellular locations. In four independent cell lines, hsp68 and 70 were found to partition into both Triton X-100-soluble and insoluble fractions as assessed by two-dimensional gel analysis of newly synthesized polypeptides, whereas a fifth cell line showed these proteins only in the Triton X-100-insoluble fraction. In addition, a previously described cell fractionation technique was utilized to gain information regarding the segregation of the two major mammalian stress proteins, hsp68 and 70, into distinct biochemically and morphologically characterized subcellular compartments of PtK2-epithelial cells. Two cytoskeletal-specific agents, taxol and colchicine, were also probed for their effects on the disposition of these polypeptides. Under our conditions of acute heat exposure, hsp68, 70 and their isoforms were globally distributed in all subcellular fractions examined, with a few notable exceptions in drug-treated cells. Colchicine, a microtubule-depolymerizing drug, inhibited the association of hsp68 and its variants with the double-detergent-extractable labile "cytoskeleton," whereas taxol, a microtubule-stabilizing agent, in some manner, facilitated the transit of hsp68 and its isovariants from a cytoplasmic to nuclear domain. Degree of cell density is a factor which influences the synthesis of various cytoskeletal proteins; therefore, we studied the effect of cell confluency on the disposition of mammalian stress proteins hsp68 and 70 in human FS-4 fibroblasts. In confluent cultures, where cell-cell contact was maximal, we observed the appearance of a previously undetected polypeptide which was not found in sparsely populated cultures. This protein may represent a post-translationally modified isoform of a preexisting heat shock protein, or perhaps, a novel stress protein.     

The strong hepatocarcinogenicity of the electrophilic and mutagenic metabolite 6-sulfooxymethylbenzo[a]pyrene and its formation of benzylic DNA adducts in the livers of infant male B6C3F1 mice

6-Hydroxymethylbenzo[a]pyrene was activated to an electrophilic and mutagenic sulfuric acid ester metabolite by rat and mouse liver sulfotransferase activity. The intrinsic mutagenicity of this reactive ester, 6-sulfooxymethylbenzo[a]pyrene, was inhibited by glutathione and glutathione S-transferase. A single i.p. dose of 2.5 nmol/g body wt of 6-sulfooxymethylbenzo[a]pyrene in infant male B6C3F1 mice induced liver tumors in 35 of 36 mice at 10 months with an average multiplicity of 4.4. A comparable dose of the parent hydrocarbon, 6-hydroxymethylbenzo[a]pyrene, was only a tenth as active. The electrophilic sulfuric acid ester produced high levels of benzylic DNA adducts in the livers of these mice that accounted for about 80% of the total DNA adducts. These results strongly suggest that this sulfuric acid ester is an important ultimate electrophilic and carcinogenic metabolite in carcinogenesis by 6-hydroxymethylbenzo[a]pyrene and possibly even by 6-methylbenzo[a]pyrene and benzo[a]pyrene in mouse liver.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.     

Sour taste preferences of children relate to preference for novel and intense stimuli

Previous research has suggested that some children have a preference for sour tastes. The origin of this preference remains unclear. We investigated whether preference for sour tastes is related to a difference in rated sour intensity due to physiological properties of saliva, or to an overall preference for intense and new stimuli. Eighty-nine children 7-12 years old carried out a rank-order procedure for preference and category scale for perceived intensity for four gelatins (i.e. 0.0 M, 0.02 M, 0.08 M, 0.25 M added citric acid) and four yellow cards that differed in brightness. In addition, we measured their willingness to try a novel candy and their flow and buffering capacity of their saliva. Fifty-eight percent of the children tested preferred one of the two most sour gelatins. These children had a higher preference for the brightest color (P < 0.05) and were more likely to try the candy with the unknown flavor (P < 0.001) than children who did not prefer the most sour gelatins. Preference for sour taste was not related with differences in rated sour intensity, however those who preferred sour taste had a higher salivary flow (P < 0.05). These findings show that a substantial proportion of young children have a preference for extreme sour taste. This appears to be related to the willingness to try unknown foods and preference for intense visual stimuli. Further research is needed to investigate how these findings can be implemented in the promotion of sour-tasting food such as fruit.     

Plakins in development and disease

Plakins are large multi-domain molecules that have various functions to link cytoskeletal elements together and to connect them to junctional complexes. Plakins were first identified in epithelial cells where they were found to connect the intermediate filaments to desmosomes and hemidesmosomes [Ruhrberg, C., and Watt, F.M. (1997). The plakin family: versatile organizers of cytoskeletal architecture. Curr Opin Genet Dev 7, 392-397.]. They were subsequently found to be important for the integrity of muscle cells. Most recently, they have been found in the nervous system, where their functions appear to be more complex, including cross-linking of microtubules (MTs) and actin filaments [Leung, C.L., Zheng, M., Prater, S.M., and Liem, R.K. (2001). The BPAG1 locus: Alternative splicing produces multiple isoforms with distinct cytoskeletal linker domains, including predominant isoforms in neurons and muscles. J Cell Biol 154, 691-697., Leung, C.L., Sun, D., Zheng, M., Knowles, D.R., and Liem, R.K. (1999). Microtubule actin cross-linking factor (MACF): a hybrid of dystonin and dystrophin that can interact with the actin and microtubule cytoskeletons. J Cell Biol 147, 1275-1286.]. These plakins have also indicated their relationship to the spectrin superfamily of proteins and the plakins appear to be evolutionarily related to the spectrins, but have diverged to perform different specialized functions. In invertebrates, a single plakin is present in both Drosophila melanogaster and Caenorhabditis elegans, which resemble the more complex plakins found in mammals [Roper, K., Gregory, S.L., and Brown, N.H. (2002). The 'spectraplakins': cytoskeletal giants with characteristics of both spectrin and plakin families. J Cell Sci 115, 4215-4225.]. In contrast, there are seven plakins found in mammals and most of them have alternatively spliced forms leading to a very complex group of proteins with potential tissue specific functions [Jefferson, J.J., Leung, C.L., and Liem, R.K. (2004). Plakins: goliaths that link cell junctions and the cytoskeleton. Nat Rev Mol Cell Biol 5, 542-553.]. In this review, we will first describe the plakins, desmoplakin, plectin, envoplakin and periplakin and then describe two other mammalian plakins, Bullous pemphigoid antigen 1 (BPAG1) and microtubule actin cross-linking factor 1 (MACF1), that are expressed in multiple isoforms in different tissues. We will also describe the relationship of these two proteins to the invertebrate plakins, shortstop (shot) in Drosophila and VAB-10 in C. elegans. Finally, we will describe an unusual mammalian plakin, called epiplakin.     

beta-Internexin, a ubiquitous intermediate filament-associated protein

In this article we show a Triton-insoluble, intermediate filament-associated protein of approximately 70 kD to be expressed ubiquitously in diverse mammalian cell types. This protein, assigned the name beta-internexin, exhibits extreme homology in each of the various cell lines as demonstrated by identical limited peptide maps, similar mobilities on two-dimensional gels, and detection in Triton-soluble and -insoluble extracts. beta-Internexin also shares some degree of homology with alpha-internexin, an intermediate filament-associated protein isolated and purified from rat spinal cord, which accounts for the immunologic cross-reactivity displayed by these polypeptides. Light microscopic immunolocalization of beta-internexin with a monoclonal antibody (mAb-IN30) reveals it to be closely associated with the vimentin network in fibroblasts. The antigen is also observed to collapse with the vimentin reticulum during the formation of a juxtanuclear cap induced by colchicine treatment. Ultrastructural localization, using colloidal gold, substantiates the affinity of beta-internexin for cytoplasmic filaments and, in addition, demonstrates its apparent exclusion from the intranuclear filament network. We examine also the resemblance of beta-internexin to a microtubule-associated polypeptide and the constitutively synthesized mammalian heat shock protein (HSP 68/70).     

Tissue factor expression in newt iris coincides with thrombin activation and lens regeneration

Lens regeneration in adult salamanders occurs at the pupillary margin of the mid-dorsal iris where pigmented epithelial cells (PEC) re-enter the cell cycle and transdifferentiate into lens. It is not understood how the injury caused by removal of the lens (lentectomy) in one location is linked to initiating the response in a different spatial location (dorsal iris) and to this particular sector. We propose that the blood provides a link between the localised coagulation and signal transduction pathways that lead to regeneration. A transmembrane protein (tissue factor) is expressed in a striking patch-like domain in the dorsal iris of the newt that localises coagulation specifically to this location, but is not expressed in the axolotl, a related species that does not show thrombin activation after lentectomy and cannot regenerate its lens. Our hypothesis is that tissue factor expression localises the initiation of regeneration through the activation of thrombin and the recruitment of blood cells, leading to local growth factor release. This is the first example of gene expression in a patch of cells that prefigures the location of a regenerative response, and links the immune system with the initiation of a regenerative program.