Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species,Robinia pseudoacacia

Wood is of critical importance to humans as a primary feedstock for biofuel, fiber, solid wood products, and various natural compounds including pharmaceuticals. The trunk wood of most tree species has two distinctly different regions: sapwood and heartwood. In addition to the major constituents, wood contains extraneous chemicals that can be removed by extraction with various solvents. The composition and the content of the extractives vary depending on such factors as, species, growth conditions, and time of year when the tree is cut. Despite the great commercial and keen scientific interest, little is known about the tree-specific biology of the formation of heartwood and its extractives. In order to gain insight on the molecular regulations of heartwood and its extractive formation, we carried out global examination of gene expression profiles across the trunk wood of black locust (Robinia pseudoacacia L.) trees. Of the 2,915 expressed sequenced tags (ESTs) that were generated and analyzed in the current study, 55.3% showed no match to known sequences. Cluster analysis of the ESTs identified a total of 2278 unigene sets, which were used to construct cDNA microarrays. Microarray hybridization analyses were then performed to survey the changes in gene expression profiles of trunk wood. The gene expression profiles of wood formation differ according to the region of trunk wood sampled, with highly expressed genes defining the metabolic and physiological processes characteristic of each region. For example, the gene encoding sugar transport had the highest expression in the sapwood, while the structural genes for flavonoid biosynthesis were up-regulated in the sapwood-heartwood transition zone. This analysis also established the expression patterns of 341 previously unknown genes.     

Emperipolesis in a common breast malignancy. A case report

BACKGROUND: Emperipolesis is a phenomenon characterized by the presence of leukocytes/lymphocytes within the cytoplasm of other cells. The present report describes this unusual observation within epithelial cancer cells of the breast. CASE: A 52-year-old female presented with a hard, adherent lump over the right breast for one year. Fine needle aspiration and histopathologic examination of the tumor showed features of infiltrating duct carcinoma with emperipolesis as a striking feature of the tumor cells. The tumor showed a near-total response to neoadjuvant chemotherapy. CONCLUSION: The mechanism and biologic significance of emperipolesis in producing a near-total response to neoadjuvant chemotherapy in the present case suggest its role in inducing a tumoricidal effect, possibly involving a cascade of chemokines.     

Fragmentation and dispersal of the pericentriolar Golgi complex is required for entry into mitosis in mammalian cells

The pericentriolar Golgi stacks are fragmented and found dispersed in mitotic mammalian cells. Addition of an antibody to the Golgi-associated protein GRASP65 inhibited Golgi fragmentation by mitotic cytosol in permeabilized cells. Microinjecting this antibody or the C-terminal fragment of GRASP65, which contains the antibody binding site, into normal rat kidney cells prevented entry into mitosis. Under these conditions the cells had completed S phase but were not in the prophase stage of mitosis. Fragmentation of the Golgi apparatus by nocodazole or Brefeldin A treatment prior to or post microinjection of the anti-GRASP65 antibody alleviated the block in mitotic entry. Based on our findings, we suggest that the pericentriolar Golgi organization is a sensor for controlling entry into mitosis in mammalian cells.     

MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal-sulfur cluster biosynthesis proteins including Molybdenum cofactor sulfurases

Using computational analysis, a novel superfamily of beta-strand-rich domains was identified in the Molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms such as the bacterial YiiM proteins, or fused to other domains such as a NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters. The identification of this domain may clarify the mechanism of biogenesis of various metallo-enzymes including Molybdenum cofactor-containing enzymes that are compromised in human type II xanthinuria.     

Characterization and expression analysis of Staphylococcus aureus pathogenicity island 3. Implications for the evolution of staphylococcal pathogenicity islands

We describe the complete sequence of the 15.9-kb staphylococcal pathogenicity island 3 encoding staphylococcal enterotoxin serotypes B, K, and Q. The island, which meets the generally accepted definition of pathogenicity islands, contains 24 open reading frames potentially encoding proteins of more than 50 amino acids, including an apparently functional integrase. The element is bordered by two 17-bp direct repeats identical to those found flanking staphylococcal pathogenicity island 1. The island has extensive regions of homology to previously described pathogenicity islands, particularly staphylococcal pathogenicity islands 1 and bov. The expression of 22 of the 24 open reading frames contained on staphylococcal pathogenicity island 3 was detected either in vitro during growth in a laboratory medium or serum or in vivo in a rabbit model of toxic shock syndrome using DNA microarrays. The effect of oxygen tension on staphylococcal pathogenicity island 3 gene expression was also examined. By comparison with the known staphylococcal pathogenicity islands in the context of gene expression described here, we propose a model of pathogenicity island origin and evolution involving specialized transduction events and addition, deletion, or recombination of pathogenicity island "modules."     

Monophyly of class I aminoacyl tRNA synthetase,USPA, ETFP,photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA

Protein sequence and structure comparisons show that the catalytic domains of Class I aminoacyl-tRNA synthetases, a related family of nucleotidyltransferases involved primarily in coenzyme biosynthesis, nucleotide-binding domains related to the UspA protein (USPA domains), photolyases, electron transport flavoproteins, and PP-loop-containing ATPases together comprise a distinct class of alpha/beta domains designated the HUP domain after HIGH-signature proteins, UspA, and PP-ATPase. Several lines of evidence are presented to support the monophyly of the HUP domains, to the exclusion of other three-layered alpha/beta folds with the generic "Rossmann-like" topology. Cladistic analysis, with patterns of structural and sequence similarity used as discrete characters, identified three major evolutionary lineages within the HUP domain class: the PP-ATPases; the HIGH superfamily, which includes class I aaRS and related nucleotidyltransferases containing the HIGH signature in their nucleotide-binding loop; and a previously unrecognized USPA-like group, which includes USPA domains, electron transport flavoproteins, and photolyases. Examination of the patterns of phyletic distribution of distinct families within these three major lineages suggests that the Last Universal Common Ancestor of all modern life forms encoded 15-18 distinct alpha/beta ATPases and nucleotide-binding proteins of the HUP class. This points to an extensive radiation of HUP domains before the last universal common ancestor (LUCA), during which the multiple class I aminoacyl-tRNA synthetases emerged only at a late stage. Thus, substantial evolutionary diversification of protein domains occurred well before the modern version of the protein-dependent translation machinery was established, i.e., still in the RNA world.     

Effect of experimental oxidative stress on steroidogenesis and DNA damage in mouse testis

The objective of the present study was to evaluate the effect of oxidative stress induced by feeding various levels of selenium on steroidogenesis and DNA damage in mouse testes. To create various levels of oxidative stress in mice, diets with three different Se levels were fed to separate groups for 8 weeks. Group 1 animals were fed a yeast-based diet, which was considered a Se-deficient diet (0.02 ppm). Group 2 and 3 animals were fed a Sedeficient diet supplemented with 0.2 and 1 ppm Se as sodium selenite, respectively. After completion of the diet feeding, estimations were carried out, and results were compared with those of group 2. A significant decrease in Se levels was observed in group 1 animals, whereas they were greatly enhanced in group 3. Glutathione peroxidase (GSH-Px) activity was greatly reduced in both the liver and testes in group 1, whereas no significant changes were found in GSH-Px activity in group 3. Serum luteinizing hormone, follicle-stimulating hormone (FSH), and testosterone levels were reduced in group 1. Significant decreases of sperm number and motility were observed in group 1 when compared to group 2 male mice. No changes in these parameters were observed in group 3. DNA fragmentation was observed in both groups 1 and 3; however, the damage was more prevalent in group 1. The results clearly demonstrate the effect of oxidative stress generated by feeding various Se levels on the steroidogenesis and DNA fragmentation in mice testes.     

Image segmentation for automatic particle identification in electron micrographs based on hidden Markov random field models and expectation maximization

Three-dimensional reconstruction of large macromolecules like viruses at resolutions below 10 A requires a large set of projection images. Several automatic and semi-automatic particle detection algorithms have been developed along the years. Here we present a general technique designed to automatically identify the projection images of particles. The method is based on Markov random field modelling of the projected images and involves a pre-processing of electron micrographs followed by image segmentation and post-processing. The image is modelled as a coupling of two fields--a Markovian and a non-Markovian. The Markovian field represents the segmented image. The micrograph is the non-Markovian field. The image segmentation step involves an estimation of coupling parameters and the maximum á posteriori estimate of the realization of the Markovian field i.e, segmented image. Unlike most current methods, no bootstrapping with an initial selection of particles is required.