Studies on the mechanism for entry of vesicular stomatitis virus glycoprotein g mRNA into membrane-bound polyribosome complexes

Glycoprotein mRNA (G mRNA) of vesicular stomatitis virus is synthesized in the cytosol fraction of infected HeLa cells. Shortly after synthesis, this mRNA associates with 40S ribosomal subunits and subsequently forms 80S monosomes in the cytosol fraction. The bulk of labeled G mRNA is then found in polysomes associated with the membrane, without first appearing in the subunit or monomer pool of the membrane-bound fraction. Inhibition of the initiation of protein synthesis by pactamycin or muconomycin A blocks entry of newly synthesized G m RNA into membrane-bound polysomes. Under these circumstances, labeled G mRNA accumulates into the cytosol. Inhibition of the elongation of protein synthesis by cucloheximide, however, allows entry of 60 percent of newly synthesized G mRNA into membrane-bound polysomes. Furthermore, prelabeled G mRNA associated with membrane-bound polysomes is released from the membrane fraction in vivo by pactamycin or mucomycon A and in vitro by 1mM puromycin - 0.5 M KCI. This release is not due to nonspecific effects of the drugs. These results demonstrate that association of G mRNA with membrane-bound polysomes is dependent upon polysome formation and initiation of protein synthesis. Therefore, direct association of the 3' end of G mRNA with the membrane does not appear to be the initial event in the formation of membrane-bound polysomes.     

MMP-9, TIMP-1 and inflammatory cells in sputum from COPD patients during exacerbation

Background

Irreversible airflow obstruction in Chronic Obstructive Pulmonary Disease (COPD) is thought to result from airway remodelling associated with aberrant inflammation. Patients who experience frequent episodes of acute deterioration in symptoms and lung function, termed exacerbations, experience a faster decline in their lung function, and thus over time greater disease severity However the mechanisms by which these episodes may contribute to decreased lung function are poorly understood.This study has prospectively examined changes in sputum levels of inflammatory cells, MMP-9 and TIMP-1 during exacerbations comparing with paired samples taken prior to exacerbation.

Methods

Nineteen COPD patients ((median, [IQR]) age 69 [63 to 74], forced expiratory volume in one second (FEV1) 1.0 [0.9 to1.2], FEV1% predicted 37.6 [27.3 to 46.2]) provided sputa at exacerbation. Of these, 12 were paired with a samples collected when the patient was stable, a median 4 months [2 to 8 months] beforehand.

Results

MMP-9 levels increased from 10.5 μg/g [1.2 to 21.1] prior to exacerbation to 17.1 μg/g [9.3 to 48.7] during exacerbation (P < 0.01). TIMP-1 levels decreased from 3.5 μg/g [0.6 to 7.8] to 1.5 μg/g [0.3 to 4.9] (P = 0.16). MMP-9/TIMP-1 Molar ratio significantly increased from 0.6 [0.2 to 1.1] to 3.6 [2.0 to 25.3] (P < 0.05). Neutrophil, eosinophil and lymphocyte counts all showed significant increase during exacerbation compared to before (P < 0.05). Macrophage numbers remained level. MMP-9 levels during exacerbation showed highly significant correlation with both neutrophil and lymphocyte counts (Rho = 0.7, P < 0.01).

Conclusion

During exacerbation, increased inflammatory burden coincides with an imbalance of the proteinase MMP-9 and its cognate inhibitor TIMP-1. This may suggest a pathway connecting frequent exacerbations with lung function decline.     

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics     

Phylogenetic inference: how much evolutionary history is knowable?

In order to reconstruct phylogenetic trees from extremely dissimilar sequences it is necessary to estimate accurately the extent of sequence divergence. In this paper a new method of sequence analysis, Markov triple analysis, is developed for determining the relative frequencies of nucleotide substitutions within the three branches of a three-taxon dendrogram. Assuming that nucleotide sites are independently and identically distributed and assuming a Markov model for nucleotide (or protein) evolution, it is shown that the unique Markov matrices can be reconstructed given only the joint probability distribution relating three taxa. (In the much simpler case involving only two taxa and two character states, Markov matrices can also be reconstructed, provided symmetry assumptions are placed on the elements of the matrices.) The method is illustrated using sequence data from the combined first and second codon positions derived from complete human, mouse, and cow mitochondrial sequences.      

DNA hybridization evidence for the principal lineages of hummingbirds (Aves:Trochilidae)

The spectacular evolutionary radiation of hummingbirds (Trochilidae) has served as a model system for many biological studies. To begin to provide a historical context for these investigations, we generated a complete matrix of DNA hybridization distances among 26 hummingbirds and an outgroup swift (Chaetura pelagica) to determine the principal hummingbird lineages. FITCH topologies estimated from symmetrized delta TmH-C values and subjected to various validation methods (bootstrapping, weighted jackknifing, branch length significance) indicated a fundamental split between hermit (Eutoxeres aquila, Threnetes ruckeri; Phaethornithinae) and nonhermit (Trochilinae) hummingbirds, and provided strong support for six principal nonhermit clades with the following branching order: (1) a predominantly lowland group comprising caribs (Eulampis holosericeus) and relatives (Androdon aequatorialis and Heliothryx barroti) with violet-ears (Colibri coruscans) and relatives (Doryfera ludovicae); (2) an Andean-associated clade of highly polytypic taxa (Eriocnemis, Heliodoxa, and Coeligena); (3) a second endemic Andean clade (Oreotrochilus chimborazo, Aglaiocercus coelestis, and Lesbia victoriae) paired with thorntails (Popelairia conversii); (4) emeralds and relatives (Chlorostilbon mellisugus, Amazilia tzacatl, Thalurania colombica, Orthorhyncus cristatus and Campylopterus villaviscensio); (5) mountain-gems (Lampornis clemenciae and Eugenes fulgens); and (6) tiny bee-like forms (Archilochus colubris, Myrtis fanny, Acestrura mulsant, and Philodice mitchellii). Corresponding analyses on a matrix of unsymmetrized delta values gave similar support for these relationships except that the branching order of the two Andean clades (2, 3 above) was unresolved. In general, subsidiary relationships were consistent and well supported by both matrices, sometimes revealing surprising associations between forms that differ dramatically in plumage and bill morphology. Our results also reveal some basic aspects of hummingbird ecologic and morphologic evolution. For example, most of the diverse endemic Andean assemblage apparently comprises two genetically divergent clades, whereas the majority of North American hummingbirds belong a single third clade. Genetic distances separating some morphologically distinct genera (Oreotrochilus, Aglaiocercus, Lesbia; Myrtis, Acestrura, Philodice) were no greater than among congeneric (Coeligena) species, indicating that, in hummingbirds, morphological divergence does not necessarily reflect level of genetic divergence.      

Somatic embryogenesis from leaf callus derived from mature trees of the cycad Ceratozamia hildae (Gymnospermae)

A friable and transient embryogenic callus was initiated from pinnae removed from leaves in new vegetative flushes of mature Ceratozamia hildae Landry & Wilson, a cycad. Somatic proembryos developed from the callus approximately 3 months after explanting onto plant growth medium consisting of a modified B5 formulation with 60 g l^-1 sucrose, 400 mg l^-1 glutamine, 100 mg l^-1 arginine, 100 mg l^-1 asparagine, 4.5 M 2,4-dichlorophenoxyacetic acid with either 1.2 M or 4.6 M kinetin and 1.75 g l^-1 gellan gum. Following subculture of somatic proembryos at this time onto medium without plant growth regulators, they continued to proliferate by a process resembling cleavage embryony or polyembryogenesis for several months. Proliferating embryogenic cultures consisted of hyperhydric somatic proembryos. Some 15 months after explanting, the somatic proembryos began to change in appearance; the suspensors became white and opaque, but were usually highly branched due to cleavage embryony. A single cotyledonary somatic embryo usually developed from the tip of each of the suspensors. Somatic embryos were primarily dicotyledonous, and less frequently monocotyledonous. Fewer than 10% of the somatic embryos appeared to be morphologically abnormal. Germination occurred in vitro whereby the coleorhiza elongated and a tap root emerged; however, plantlet recovery has not been demonstrated because the shoot axis failed to elongate.Abbreviations 2,4-d 2,-4-dichlorophenoxyacetic acid     

Control of hyperhydricity of mango somatic embryos

Hyperhydricity of immature somatic embryos has been a limiting factor for the development of highly embryogenic suspension cultures of many important mango cultivars. Reversion of hyperhydricity was achieved in two ways: 1) heart-stage somatic embryos (2–3 mm length) were partially dehydrated under controlled conditions at high relative humidity (RH) for 24–48 h and 2) the gelling agent (Gel-Gro) concentration of the plant growth medium was increased from 2.0 to 6.0 g l^-1. Partially dehydrated immature somatic embryos were normal in appearance. Somatic embryos that were partially dehydrated germinated precociously when cultured on maturation medium. Although abscisic acid (ABA) did not reverse hyperhydricity of primary somatic embryos, ABA did stimulate the reversal of this abnormal pattern of development among secondary embryos. ABA (500 M) inhibited precocious germination and permitted somatic embryo maturation. Partially dehydrated, immature somatic embryos (4–7 mm long) remained viable for up to 32 days in the absence of maturation medium under high RH.Abbreviations 2,4-d 2,4-dichlorophenoxyacetic acid - ABA abscisic acid - BA 6-benzyladenine - RH relative humidity     

Induction of embryogenic mango cultures as affected by genotype,explanting, 2,4-D and embryogenic nurse culture

The nucellus was removed from immature seeds of 4 mango genotypes, andcultured under different induction conditions. The mango genotypes includedpolyembryonic ‘Hindi’ and ‘Nam Doc Mai’ and monoembryonic ‘Lippens’ and’Tommy Atkins‘. Nucellar explants were cultured on modified B5 basal mediumunder the following inductive conditions: 1) 4.52 μM 2,4-D; 2) nogrowth regulator (control); 3) 4.52 μM 2,4-D + embryogenic ‘Parris‘nurse culture; 4) no growth regulator + embryogenic ‘Parris’ nurse culture.Induction of embryogenic competence was mediated by 4 factors: genotype,explanting, 2,4-D and the presence of a highly embryogenic nurse culture,although there was considerable difference in genotype response. ‘Hindi’ hadthe greatest embryogenic potential, followed by ‘Lippens’, ‘Tommy Atkins‘and ‘Nam Doc Mai’, respectively. Induction of embryogenic cultures of allgenotypes at low frequency occurred as a result of explanting excisednucellus onto control medium. The most effective treatment for inducingembryogenic cultures was 2,4-D + embryogenic ‘Parris’ nurse culture with’Hindi’, ‘Lippens’ and ‘Nam doc Mai’, with the exception of ‘Tommy Atkins’,in which the treatment with 2,4-D alone was most effective. This revised version was published online in June 2006 with corrections to the Cover Date.