DNA Data Support a Rapid Radiation of Pocket Gopher Genera (Rodentia: Geomyidae)

In this study, we address the question of phylogenetic relationships in the Geomyidae, focusing primarily on intergeneric relationships within the tribe Geomyini. Our study makes use of DNA sequences from two mitochondrial and two nuclear genes, and we use model-based methods of phylogenetic analysis to infer relationships and determine the level of support for each proposed relationship. Relationships among geomyine pocket gopher genera remain only partially resolved despite a number of earlier attempts to reconstruct their phylogenetic history and despite the newly generated sequence data analyzed in this study. This lack of resolution does not appear to result from insufficient or inappropriate DNA data, nor is it caused by inadequate sampling of taxa. Rather, molecular data and fossil data together lead to the conclusion that diversification within the Geomyini likely occurred during a geologically brief period in the Blancan. Rapid climate change during the Blancan, the origin of patchily distributed grasslands, and the evolution of hypsodonty may have triggered the rapid diversification that eventually produced the five extant genera of the Geomyini.     

DNA amplification fingerprinting: A strategy for genome analysis

A novel strategy to detect genetic differences among organisms, DNA amplification fingerprinting (DAF), uses a thermostable DNA polymerase directed by usually one short (≥5 bp) oligonucleotide primer of arbitrary sequence to amplify short segments of genomic DNA and generate a range of DNA extension products. These products can be analyzed by polyacrylamide gel electrophoresis and silver staining. DAF is rapid and sensitive and is independent of cloning and prior genetic characterization. Here we describe this new methodology, its application to plant genotyping, and its perspectives in DNA fingerprinting and genome mapping.     

Poly(ethylene oxide), a new slowing agent for protozoa.

The water-soluble, viscoelastic resin Polyox WSR 301), a poly(ethylene oxide) of high molecular weight (approximately 4 million) is introduces as a new slowing agent for protozoa. Generally, as the kinetic viscosity of the resin increased from 0.25% to 1% (w/v), the swimming velocity of Euglena gracilis, Didnium nasutum, Paramecium aurelia, Blepharisma undulans, and Prorodon platyodon decreased. The 1.0% solution had the highest viscosity and decreased velocity more effectively than 1.0% methyl cellulose and Protoslo solutions. The Polyox solutions differed from those of methyl cellulose and Protoslo by having, in addition to viscous drag, an elastic recoil that pulled the protozoa backwards when their swimming efforts stopped. The toxicity of these slowing agents was determined using 10 P. aurelia/test slide preparation. Paramecium numbers decreased in 1.0% methyl cellulose and Protoslo to nearly zero by 24 hr; in Polyox, not only were most these ciliates alive after 24 hr, but many survived for 96 hr and divisions occurred in 0.25% and 0.50% solutions.     

Effect of viscosity on instilled perfluorocarbon distribution in rabbit lungs

The effect of viscosity on the distribution of perfluorocarbon instilled into the lungs for liquid ventilation was investigated. Perfluorocarbon (either perfluorodecalin or FC-3283) was instilled into the trachea during ventilation at a constant infusion rate of 40 ml/min and radiographic images were obtained at 30 frames/s. Image analysis was performed and the homogeneity index of the distribution was computed for images at the end of inspiration of each breath to evaluate the evolution of perfluorocarbon distribution during filling. The higher viscosity perfluorocarbon (perfluorodecalin) resulted in a more homogeneous distribution. This was attributed to perfluorodecalin's higher propensity to form liquid plugs in large airways and to those plugs leaving behind a thicker liquid layer as they propagated through the lungs.     

Efficient delivery of siRNA into cytokine-stimulated insulinoma cells silences Fas expression and inhibits Fas-mediated apoptosis

Fas/FasL interactions have been proposed as a potentially important mechanism mediating beta-cell death in type 1 diabetes. Recent investigations suggest RNA interference, afforded by small interfering RNAs (siRNA), can provide specific and robust gene silencing in mammalian cells. The current study attempted to investigate the effects of silencing Fas expression with siRNA on Fas-mediated apoptosis in mouse insulinoma cells following cytokine incubation. Our results indicate that siRNA is capable of rapid inhibition of cytokine-induced Fas mRNA production and cell surface Fas protein. A complete suppression of the total Fas protein was only observed after prolonged incubation with siRNA, suggesting a slow turn-over of Fas protein. Moreover, siRNA significantly inhibited Fas-mediated beta-cell apoptosis assessed by Caspase-3 and terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling assays, the extent of which positively correlated with the level of cell surface Fas. These observations provide additional evidence supporting a role for the Fas-mediated pathway in beta-cell destruction, and suggest that siRNA targeting Fas may be of therapeutic value in preventing type 1 diabetes and improving islet cell viability in transplantation.     

Identification of genetic loci for basal cell nevus syndrome and inflammatory bowel disease in a single large pedigree

Basal Cell Nevus Syndrome (BCNS) is an autosomal dominant disease. PTCH1 gene mutations have been found responsible in many but not all pedigrees. Inflammatory Bowel Disease (IBD) is a complex genetic disorder, disproportionate in Ashkenazim, and characterized by chronic intestinal inflammation. We revisited a large Ashkenazim pedigree, first reported in 1968, with multiple diagnoses of BCNS and IBD, and with a common genetic cause for both disorders proposed. We expanded the pedigree to four generations and performed a genome-wide linkage study for BCNS and IBD traits. Twelve members with BCNS, seven with IBD, five with both diagnoses and eight unaffected were genotyped. Both non-parametric (GENEHUNTER 2.1) and parametric (FASTLINK) linkage analyses were performed and a validation through simulation was performed. BCNS linked to chromosome 9q22 (D9S1120) just proximal to the PTCH1 gene (NPL=3.26, P=0.003; parametric two-point LOD=2.4, parametric multipoint LOD=3.7). Novel IBD linkage evidence was observed at chromosome 1p13 (D1S420, NPL 3.92, P=0.0047; parametric two-point LOD=1.9). Linkage evidence was also observed to previously reported IBD loci on 4q, (D4S2623, NPL 3.02, P=0.012; parametric two-point LOD=2.15), 10q23 (D10S1225 near DLG5, NPL 3.33, P=0.0085; parametric two-point LOD=1.3), 12 overlapping the IBD2 locus (D12S313, NPL 2.6, P=0.018; parametric two-point LOD=1.52), and 7q (D7S510 and D7S3046, NPL 4.06, P=0.0035; parametric two-point LOD=2.18). In this pedigree affected by both BCNS and IBD, the two traits and their respective candidate genetic loci segregate independently; BCNS maps to the PTCH1 gene and IBD maps to several candidate regions, mostly overlapping previously observed IBD loci.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.Carolien I. Panhuysen and Amir Karban contributed equally to this work     

Effects of temperature and nitrate on phosphomonoesterase activities between carbon source and sink tissues in Zostera marina L.

Inorganic phosphorus (P_i) is important in the regulation of many carbon and nitrogen metabolic processes of plants. In this study, we examined alterations of phosphomonoesterase activity (PA; both alkaline and acid) in a submersed marine angiosperm, Zostera marina, grown in P_i non-limiting conditions under elevated temperature and/or nitrate enrichment. Control plants (ambient water-column NO₃⁻ < 2.5 μM, with weekly mean water temperatures between 26.5-27.0 °C based on a 20-yr data set in a local embayment) were compared to treated plants that were exposed to increased water-column nitrate (8 μM NO₃⁻ above ambient, pulsed daily at 0900 h), and/or increased temperature (ca. 3 °C above weekly means) over eight weeks in late summer-fall. Under both nitrate regimes, increased temperature resulted in periodic increased leaf and root-rhizome tissue carbon content, and increased acid and alkaline PA activities (AcPAs and AlPAs, respectively). There was a positive correlation between AlPA and AcPA activities and sucrose synthase activities in belowground structures, and a negative correlation between AlPA activities and sucrose concentrations. There were also periodic changes in PA partitioning between carbon source and sink tissues. In high-temperature and high-nitrate treatments, AcPAs significantly increased in leaves relative to activities in root-rhizome tissues (up to 12-fold higher in aboveground than belowground tissues in as little as 3 weeks after initiation of treatments). These responses were not observed in control plants, which maintained comparable AcPA activities in above- and belowground tissues. In addition, AlPA activity was significantly higher in leaf than in root-rhizome tissues of plants in high-temperature (weeks 3 and 6) and high temperature combined with high nitrate treatments (week 8), relative to AlPA activities in control plants. The observed changes in PAs were not related to P_i growth limitation, and may allow Z. marina to alter its carbon metabolism during periods of increased carbon demand/mobilization. This response would make it possible for Z. marina to meet short-term P requirements to maximize carbon production/allocation. Such a mechanism could help to explain the variability in PA activities that has been observed for many plant species during periods when environmental P_i exceeds requirements for optimal growth.     

Genetic determinants of hyaloid and retinal vasculature in zebrafish

Background

The retinal vasculature is a capillary network of blood vessels that nourishes the inner retina of most mammals. Developmental abnormalities or microvascular complications in the retinal vasculature result in severe human eye diseases that lead to blindness. To exploit the advantages of zebrafish for genetic, developmental and pharmacological studies of retinal vasculature, we characterised the intraocular vasculature in zebrafish.

Results

We show a detailed morphological and developmental analysis of the retinal blood supply in zebrafish. Similar to the transient hyaloid vasculature in mammalian embryos, vessels are first found attached to the zebrafish lens at 2.5 days post fertilisation. These vessels progressively lose contact with the lens and by 30 days post fertilisation adhere to the inner limiting membrane of the juvenile retina. Ultrastructure analysis shows these vessels to exhibit distinctive hallmarks of mammalian retinal vasculature. For example, smooth muscle actin-expressing pericytes are ensheathed by the basal lamina of the blood vessel, and vesicle vacuolar organelles (VVO), subcellular mediators of vessel-retinal nourishment, are present. Finally, we identify 9 genes with cell membrane, extracellular matrix and unknown identity that are necessary for zebrafish hyaloid and retinal vasculature development.

Conclusion

Zebrafish have a retinal blood supply with a characteristic developmental and adult morphology. Abnormalities of these intraocular vessels are easily observed, enabling application of genetic and chemical approaches in zebrafish to identify molecular regulators of hyaloid and retinal vasculature in development and disease.