Mechanistic Studies of ABCR, the ABC Transporter in Photoreceptor Outer Segments Responsible for Autosomal Recessive Stargardt Disease

ABCR is an ABC transporter that is found exclusively in vertebrate photoreceptor outer segments. Mutations in the human ABCR gene are responsible for autosomal recessive Stargardt disease, the most common cause of early onset macular degeneration. In this paper we review our recent work with purified and reconstituted ABCR derived from bovine retina and from cultured cells expressing wild type or site-directed mutants of human ABCR. These experiments implicate all-trans-retinal (or Schiff base adducts between all-trans-retinal and phosphatidylethanolamine) as the transport substrate, and they reveal asymmetric roles for the two nucleotide binding domains in the transport reaction. A model for the retinal transport reaction is presented which accounts for these experimental observations.     

Astronomical Sources of Circularly Polarized Light and the Origin of Homochirality

Possible astronomical sources of ultraviolet circularly polarized light(UVCPL) which might be responsible for enantiomeric selection in interstellarorganic molecules are considered, Synchrotron radiation from magnetic neutronstars has been suggested as a possible source of UVCPL. However, synchrotronradiation in these situations is not predicted to be strongly circularlypolarized. Very few such sources show optical synchrotron radiation and in thefew that do circular polarization has not been observed. Magnetic white dwarfsand white dwarf binaries (Polars) can be highly circularly polarized but anyeffect on molecular clouds and star formation regions must rely on rare chance encounters. Recent observations show that substantial levels of circularpolarization are present in reflection nebulae in star formation regions. Thismechanism produces polarized light exactly when and where it is needed inregions where star formation is occurring and organic molecules are known to be present.     

Improved Understanding of the Bacterial Vaginal Microbiota of Women before and after Probiotic Instillation

The vaginal bacterial microbiota of 19 premenopausal women was examined by PCR-denaturing gradient gel electrophoresis (DGGE) and sequencing of the V2-V3 region of the 16S rRNA gene. Ten of the women were studied further to investigate the effect and persistence of vaginally inserted capsules containing viable lactobacilli. PCR-DGGE indicated that most subjects had a microbiota represented by one to three dominant DNA fragments. Analysis of these fragments revealed that 79% of the women possessed sequences with high levels of similarity to Lactobacillus species sequences. Sequences homologous to Lactobacillus iners sequences were the most common and were detected in 42% of the women tested. Alteration of the vaginal microbiota could be detected by PCR-DGGE in several women after the instillation of lactobacilli. Additionally, randomly amplified polymorphic DNA analysis of lactobacilli isolated from selective media demonstrated that the exogenous strains could be detected for up to 21 days in some subjects. This study demonstrates that non-culture-based techniques, such as PCR-DGGE, are useful adjuncts for studies of the vaginal microbiota.     

Mobility of Stichodactyla Gigantea Sea Anemones and Implications for Resident False Clown Anemonefish, Amphiprion Ocellaris

For reef fishes that do not move between habitat patches following settlement, habitat selection is expected during settlement. Although false clown anemonefish, Amphiprion ocellaris, are sedentary following settlement, they are not especially discriminating during settlement, and are commonly found occupying anemones at which no apparent nest site exists. In this study I report on mobility of Stichodactyla gigantea sea anemones, including anemones with resident false clowns. I argue that anemone mobility can help explain why settling false clowns are not more discriminating: although the per annum probability of an anemone moving is low, the probability of that anemone moving over the course of a resident's life is considerably higher. Therefore, an anemone's current microhabitat may not be a good predictor of its microhabitat and suitability as a host in the future.     

Relationships between spatial environmental heterogeneity and plant species diversity on a limestone pavement

No empirical studies have examined the relationship between diversity and spatial heterogeneity across unimodal species richness gradients. We determined the relationships between diversity and environmental factors for 144 0.18 m² plots in a limestone pavement alvar in southern Ontario, Canada, including within-plot spatial heterogeneity in soil depth, microtopography and microsite composition. Species richness was unimodally related to mean soil depth and relative elevation. Microsite heterogeneity and soil depth heterogeneity were positively correlated with species richness, and the richness peaks of the unimodal gradients correspond to the maximally spatially heterogeneous plots. The best predictive models of species richness and evenness, however, showed that other factors, such as ramet density and flooding, are the major determinants of diversity in this system. The findings that soil depth heterogeneity had effects on diversity when the effects of mean soil depth were factored out, and that unimodal richness peaks were associated with high spatial heterogeneity in environmental factors represent significant contributions to our understanding of how spatial heterogeneity might contribute to diversity maintenance in plant communities.     

An Analysis of Single Clutch Paternity in the Burrower Bug Sehirus cinctus Using Microsatellites

Recent studies of the burrower bug, Sehirus cinctus, have examined the genetic basis of parental care. An understanding of the burrower bug mating system, and the subsequent pattern of offspring relatedness that this system generates, is critical to further interpret genetic data. To this end, we developed three consistently amplifiable highly polymorphic microsatellite loci and used them to determine genotypic patterns at the level of both the population and the single clutch. We found that all clutches were sired by single males. Further, we find no evidence for inbreeding. We hypothesize that single paternity within a clutch may play an important role in reducing the potential for sibling rivalry, by increasing the relatedness among clutchmates.     

Use of mutants to study long-distance signalling in response to compacted soil.

When plants encounter compacted soil, stomatal closure occurs and shoot growth slows. These responses occur in the absence of detectable changes in foliar water status. The use of genotypes with a reduced capacity to synthesize either ABA or ethylene has provided convincing evidence that ABA is responsible for providing the signal that regulates stomatal aperture, whereas increased ethylene production leads to an inhibition of shoot growth. Compaction results in an elevated export of ABA from the roots while enhanced ethylene synthesis is associated with increased expression of ACC oxidase in the aerial parts of the plant. Future work will explore the mechanisms responsible for regulating these events and the contribution of anaerobiosis to the stresses experienced by roots growing under compacted conditions.     

Generation of diversity in the innate immune system: macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes.

Microbial products such as LPS stimulate macrophages to produce a wide diversity of inducible gene products needed for immediate host defense and priming of an appropriate acquired immune response. In this study, we have examined LPS-inducible gene expression in subclones of a mouse macrophage cell line, RAW264, using cDNA microarrays. Even archetypal target genes such as TNF-alpha were not induced in all subclones, and there was no absolute correlation between expression of pairs of genes. Nevertheless, the array analysis revealed clusters of genes that were more likely to be coexpressed. RAW264 cells stably transfected with luciferase reporter genes driven by LPS-responsive promoters revealed the same kind of clonal heterogeneity. The results indicate that each LPS-inducible gene has its own inherent probability of activation in response to LPS.     

Microarray data quality analysis: lessons from the AFGC project

Genome-wide expression profiling with DNA microarrays has and will provide a great deal of data to the plant scientific community. However, reliability concerns have required the development data quality tests for common systematic biases. Fortunately, most large-scale systematic biases are detectable and some are correctable by normalization. Technical replication experiments and statistical surveys indicate that these biases vary widely in severity and appearance. As a result, no single normalization or correction method currently available is able to address all the issues. However, careful sequence selection, array design, experimental design and experimental annotation can substantially improve the quality and biological of microarray data. In this review, we discuss these issues with reference to examples from the Arabidopsis Functional Genomics Consortium (AFGC) microarray project.