Generalized conjugate priors for Bayesian analysis of risk and survival regressions

Conjugate priors for Bayesian analyses of relative risks can be quite restrictive, because their shape depends on their location. By introducing a separate location parameter, however, these priors generalize to allow modeling of a broad range of prior opinions, while still preserving the computational simplicity of conjugate analyses. The present article illustrates the resulting generalized conjugate analyses using examples from case-control studies of the association of residential wire codes and magnetic fields with childhood leukemia.     

Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example

Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes.     

On the origin of Metazoan adhesion receptors: cloning of integrin alpha subunit from the sponge Geodia cydonium

Integrins are prominent receptors known from vertebrates and the higher phyla of invertebrates. Until now, no evidence has been provided for the existence of integrins in the lowest Metazoa, the sponges (Porifera). We have isolated and characterized a cDNA clone encoding the alpha subunit of integrin from the marine sponge Geodia cydonium (GCINTEG). The open reading frame encodes a polypeptide of 1,086 residues (118 kDa). The intracellular domain features the sequence Tyr- Phe-x-Gly-Phe-Phe-x-Arg, which is different in one residue from the characteristic consensus pattern for integrin alpha subunits. We conclude that sponges, the oldest multicellular animal phylum, already utilize the structural elements which are required for a tuned and controlled interaction among cells, and between cells and the extracellular matrix.      

An Economic Study of the Biological Control of the Spiny Blackfly, Aleurocanthus spiniferus (Hemiptera: Aleyrodidae), in a Citrus Orchard in Swaziland

Control costs and direct crop losses due to infestations by the spiny blackfly, Aleurocanthus spiniferus Quaintance, were studied in orchards of a 667 ha citrus estate, Inyoni Yami Irrigation Scheme at Tshaneni, Swaziland. In the 1995/96 season the control costs and direct losses at this estate amounted to R 476 000 (= US$ 86 500). This excludes the reduction in growth, the additional costs of sorting sooty mould-stained fruit and the potential reduction in crop production of the next season. To import, rear and establish the spiny blackfly parasitoid, Encarsia cf. smithi (Silvestri), including the project overheads, amounted to R 169 750 (= US$ 30 900). Because of the classical biological control that was achieved, no chemical control of this pest was necessary during the following two seasons and no further losses of fruit were incurred due to sooty mould. The amount spent to establish biological control of the spiny blackfly in parts of Southern Africa, even if compared to the direct losses and control costs of a single season on one citrus estate, was exceptionally cost effective. A benefit ratio was calculated at 2.8.     

Sulfation of fucoidin in focus embryos: III. Required for localization in the rhizoid wall

Zygotes of the brown alga Fucus distichus L. Powell accumulate a sulfated polysaccharide (fucoidin) in the cell wall at the site of rhizoid formation. Previous work indicated that zygotes grown in seawater minus sulfate do not sulfate the preformed fucan (an unsulfated fucoidin) but form rhizoids. Under these conditions, we determined whether sulfation of the fucan is required for its localization in the rhizoid wall. This was accomplished by developing a specific stain for both the fucan and fucoidin. Using a precipitin assay, we demonstrated in vitro that the lectin ricin (RCA(I)) specifically complexes with both the sulfated and desulfated polysaccharide. No precipitate is observed when either is incubated in 0.1 M D-galactose or when RCA(I) is mixed with laminarin or alginic acid, the other major polysaccharides in Fucus. RCA(I) conjugated with fluorescein isothiocyanate (FITC) is also shown to bind specifically to fucoidin using a filter paper (DE81) assay. When added to zygotes, RCA(I)-FITC binds only to the site of fucoidin localization, i.e., the rhizoid cell wall. However, RCA(I)-FITC is not observed in the rhizoid wall of zygotes grown in the absence of sulfate. This observation is not due to inability of RCA(I)-FITC to bind to the fucan in vivo. Chemically desulfated cell walls that contained fucoidin in the rhizoid wall bind RCA(I)-FITC only in the rhizoid region. Also, the concentration of fucose-containing polymers and polysaccharides that form precipitates with RCA(I) is the same in embryos grown in the presence or absence of sulfate. If sulfate is added back to cultures of zygotes grown without sulfate, fucoidin is detected at the rhizoid tip by RCA(I)-FITC several hours later. These results support the conclusion that the enzymatic sulfation of the fucan is a modification of the polysaccharide required for its localization and/or assembly into a specific region of the cell wall.     

Mammary transmission of caprine arthritis encephalitis virus: a 3D model for in vitro study

Transmission of Caprine Arthritis Encephalitis virus (CAEV) from the mother to offspring is principally mediated by infected cells from colostrum and milk. The infection of the dam is often sub-clinical, and results in increased cellularity of milk, sometimes exacerbated by bacterial co-infections. Although monocytes are the major viral host cells, several other cell types, including epithelial mammary cells, fibroblasts and endothelial cells show low levels of in vivo infection. In vitro, however, all phenotypes of mammary gland cells are individually highly sensitive to CAEV infection. This suggests that local mechanisms act to control viral expression. Our goal is to analyse the mechanisms regulating local virus infection, including the physiological status of the mammary gland and bacterial co-infections. In this work, we present the development of a model for the in vitro reconstitution of mammary gland tissue using 3D cultures in Matrigel. Mononuclear cells from the blood are added to the 3D cultures in vitro. In these experimental conditions, the mammary cells spontaneously organize into mammospheres. Blood leucocytes migrate into the culture gel, and localize particularly at the periphery of the mammospheres. Mammospheres were susceptible to infection in vitro by CAEV, as shown by a cytopathic effect and expression of late CAEV antigen p30. This model will allow the in vitro study of virus expression, transfer of infection to mammary gland cells and interactions between the mammary gland cells, infected monocytes and immunocompetent cells. It will allow the study of mechanisms participating in the control of passage of pathogens into milk, according to the physiological and CAEV-infection status of the animal, microenvironment and the presence of bacterial co-infections.     

Regulation of S-adenosyl methionine synthesis in the mouse embryo

In early embryos, methylation is involved in "gamete imprinting" and inactivation of artificially introduced foreign genes. We studied the biosynthesis of the universal methylation cofactor: S-Adenosyl methionine (SAM). In the mouse, SAM conversion from methionine is limited by saturation of the methionine endogenous pool. SAM is present at a practically unchanged level from the unfertilized oocyte to early morula. SAM synthesis is increased at the time of compaction. In blastocysts, although methionine uptake is increased, the conversion rate from methionine is lowered. We observed no differences between C57 Black and Swiss albino random bred strains. In few experiments with human unfertilized oocytes and spared embryos, we observed higher methionine incorporation, and higher conversion to SAM. Next, the effect of two methylation inhibitors was tested, on early mouse embryonic development, at the one-cell and the two-cell stage. We found that ethionine is very toxic, even at the lowest tested concentration of 25 microM. Homocysteine is more potent at the one-cell stage than at the 2-cell stage, and it only partially blocks blastocyst formation from the 2-cell stage even at a concentration of 500 microM. It clearly acts as a methylation inhibitor; it lowers the SAM pool and the methylation index, SAH/SAM ratio (SAH: S-Adenosyl Homocysteine). We also found that homocysteine is an unexpected competitor for methionine influx and efflux.     

d‐glufosinate as a male sterility agent for hybrid seed production

A chemical male sterility system based on anther‐localized conversion of the inactive d ‐enantiomer of the herbicide, glufosinate (2‐amino‐4‐(methylphosphinyl)‐butanoate) to the phytotoxic l is described. Highly pure d ‐glufosinate was isolated in >98% enantiomeric excess from the racemate via fermentation with a strain of Escherichia coli expressing the PAT (l ‐glufosinate N‐acetyl transferase) gene and purification of the unreacted d ‐enantiomer from the broth by ion exchange. A modified (F58K, M213S) form of the d ‐amino acid oxidase (DAAO) (EC 1.4.3.3) from Rhodosporidium toruloides was designed, tested in vitro and found to efficiently oxidize d ‐glufosinate to its 2‐oxo derivative [2‐oxo‐4‐(methylphosphinyl)‐butanoic acid]. Tobacco (Nicotiana tabacum) plants were transformed to express this modified oxidase under control of the TAP1 tapetum‐specific promoter. A number of the resultant transgenic lines exhibited complete male sterility that persisted for two or more weeks immediately following foliar treatment with 75 or 200 g/ha of d ‐glufosinate without exhibiting obvious phytotoxic symptoms or any measurable decline in female fertility. Similarly, plants containing the same construct and, additionally, a PAT gene expressed from a plastocyanin promoter exhibited significantly reduced male fertility and no reduction in female fertility following foliar application of racemic glufosinate. Thus, foliar application of d ‐glufosinate either purified or as the commercial herbicide, combined with anther expression of a modified DAAO promises to provide a cost‐effective conditional chemical male sterility system with the characteristics necessary for practical F₁ hybrid seed production.