A multivariate analysis of fine-scale species density in the plant communities of a saltwater lagoon – the importance of disturbance intensity

Several factors might influence an organism's tendency or willingness to leave a given patch. One such factor is conspecific density, which may affect the per capita emigration rate. Some previous field studies on butterflies have reported positively density-dependent dispersal (emigration increases with population density) whereas the opposite, negatively density-dependent dispersal, has been found in other species. We investigated the effect of conspecific density on both the tendency to cross a patch boundary and within-patch mobility in Melitaea cinxia , by experimentally manipulating density in large outdoor cages divided into two habitat patches, separated by a barrier of unsuitable habitat. In contrast to previous results for M. cinxia , we found that the butterflies moved away from a patch at higher rates in high conspecific density (positively density-dependent emigration). The within-patch mobility, measured as the distance travelled per time unit, was however unaffected by butterfly density. A possible explanation for the seeming discrepancy with previous results could be that we used higher butterfly densities. For species with fluctuating population dynamics, such as M. cinxia , dispersal activity both at low and at high local density will be important for population phenomena such as fluctuations in distributional range over good and bad years.     

Sister kinetochore recapture in fission yeast occurs by two distinct mechanisms, both requiring Dam1 and Klp2

In eukaryotic cells, proper formation of the spindle is necessary for successful cell division. We have studied chromosome recapture in the fission yeast Schizosaccharomyces pombe. We show by live cell analysis that lost kinetochores interact laterally with intranuclear microtubules (INMs) and that both microtubule depolymerization (end-on pulling) and minus-end-directed movement (microtubule sliding) contribute to chromosome retrieval to the spindle pole body (SPB). We find that the minus-end-directed motor Klp2 colocalizes with the kinetochore during its transport to the SPB and contributes to the effectiveness of retrieval by affecting both end-on pulling and lateral sliding. Furthermore, we provide in vivo evidence that Dam1, a component of the DASH complex, also colocalizes with the kinetochore during its transport and is essential for its retrieval by either of these mechanisms. Finally, we find that the position of the unattached kinetochore correlates with the size and orientation of the INMs, suggesting that chromosome recapture may not be a random process.     

Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster

Mitochondrial DNA (mtDNA) variants are widely used in evolutionary genetics as markers for population history and to estimate divergence times among taxa. Inferences of species history are generally based on phylogenetic comparisons, which assume that molecular evolution is clock-like. Between-species comparisons have also been used to estimate the mutation rate, using sites that are thought to evolve neutrally. We directly estimated the mtDNA mutation rate by scanning the mitochondrial genome of Drosophila melanogaster lines that had undergone approximately 200 generations of spontaneous mutation accumulation (MA). We detected a total of 28 point mutations and eight insertion-deletion (indel) mutations, yielding an estimate for the single-nucleotide mutation rate of 6.2 × 10⁻⁸ per site per fly generation. Most mutations were heteroplasmic within a line, and their frequency distribution suggests that the effective number of mitochondrial genomes transmitted per female per generation is about 30. We observed repeated occurrences of some indel mutations, suggesting that indel mutational hotspots are common. Among the point mutations, there is a large excess of G→A mutations on the major strand (the sense strand for the majority of mitochondrial genes). These mutations tend to occur at nonsynonymous sites of protein-coding genes, and they are expected to be deleterious, so do not become fixed between species. The overall mtDNA mutation rate per base pair per fly generation in Drosophila is estimated to be about 10× higher than the nuclear mutation rate, but the mitochondrial major strand G→A mutation rate is about 70× higher than the nuclear rate. Silent sites are substantially more strongly biased towards A and T than nonsynonymous sites, consistent with the extreme mutation bias towards A+T. Strand-asymmetric mutation bias, coupled with selection to maintain specific nonsynonymous bases, therefore provides an explanation for the extreme base composition of the mitochondrial genome of Drosophila.     

Rationally designed PKA inhibitors for positron emission tomography: Synthesis and cerebral biodistribution of N-(2-(4-bromocinnamylamino)ethyl)-N-[11C]methyl-isoquinoline-5-sulfonamide

Protein kinase A (PKA) is an important signal transduction target for drug development because it influences critical cellular processes implicated in neuropsychiatric illnesses such as major depressive disorder. The goal of the present study was to develop the first imaging agent for measuring the levels of PKA with positron emission tomography (PET). By rational derivatization of 5-isoquinoline sulfonamides, it was found that the introduction of a methyl group to the sulphonamidic nitrogen on the known PKA inhibitors N-(2-aminoethyl)isoquinoline-5-sulfonamide (H-9, 1) and N-(2-(4-bromocinnamylamino)ethyl)isoquinoline-5-sulfonamide (H-89, 2), (yielding N-(2-aminoethyl)-N-methyl-isoquinoline-5-sulfonamide (4) and N-(2-(4-bromocinnamylamino)ethyl)-N-methyl-isoquinoline-5-sulfonamide (5), respectively) does not appreciably reduce in vitro potency toward PKA. We have facilitated the synthesis of 4 by reacting isoquinoline-5-sulfonyl chloride with N-methylethylenediamine (20% yield). Several techniques were used to thoroughly characterize 4 including multi (¹H, ¹³C and ¹⁵N) NMR spectroscopy and X-ray crystallography. Compound 4 and 1-(4-bromophenyl)-1-propen-3-yl bromide were reacted to produce 5 in 16% yield. Compound 2 was reacted with [¹¹C]CH₃I to prepare N-(2-(4-bromocinnamylamino) ethyl)-N-[¹¹C]methyl-isoquinoline-5-sulfonamide ([¹¹C]5), with a decay-corrected radiochemical yield of 32%, based on [¹¹C]CO₂. [¹¹C]5 was produced with >98% radiochemical purity and 1130 mCi/μmol specific activity after 40 min (end of synthesis). Conscious rats were administered [¹¹C] 5 and sacrificed at 5, 15, 30 and 60 min after injection. Radioactivity from all excised brain regions was <0.2%ID/g at all time points. The modest brain penetration of [¹¹C]5 may limit its use for studying PKA in the central nervous system.     

Mantel and partial Mantel tests suggest some factors that may control the local distribution of Aster laurentianus at Îles de la Madeleine,Québec

Spatial heterogeneity is a significant aspect of ecosystem structure andfunction. Because ecological variables often are spatially autocorrelated,standard statistics frequently are not appropriate to analyze ecological data.In this paper, we use Mantel and partial Mantel tests to explore the spatialstructure of and relationships between several variables –micro-topography, substrate salinity, wrack cover and the density ofAster laurentianus – at two sites at the peripheryofa shallow lagoon at Îles de la Madeleine, Québec.A. laurentianus is an annual halophyte endemic tothe Gulf of St. Lawrence. It typically occurs in a narrow band (from ca. 50 to200 cm wide) at the periphery of shallow lagoons. In this habitat,plants are exposed to frequent deposition of plant debris (wrack) and to thelimiting effects of substrate salinity.Our analyses show that substrate salinity, wrack cover and density ofA. laurentianus are significantly correlated withtopography, and that wrack cover affects substrate salinity at both sites. Atthe first site, the abundance of A. laurentianus increasesprogressively with distance from the waterline, while at the second site,density increases initially, but then diminishes with distance from thewaterline. At the first site, the most important structuring variable is wrackdeposition, the effect of salinity on plant density being indirect. At thesecond site, which is somewhat sheltered, wrack deposition is far lessimportantand substrate salinity predominates over wrack deposition as structuringvariable. We suggest that A. laurentianus distributionalong the shores of shallow lagoons is limited both by substrate salinity andwrack deposition, but that the relative importance of these structuringvariables changes with the physical characteristics of the site.     

Combining Peripheral Nerve Grafting and Matrix Modulation to Repair the Injured Rat Spinal Cord

Traumatic injury to the spinal cord (SCI) causes death of neurons, disruption of motor and sensory nerve fiber (axon) pathways and disruption of communication with the brain. One of the goals of our research is to promote axon regeneration to restore connectivity across the lesion site. To accomplish this we developed a peripheral nerve (PN) grafting technique where segments of sciatic nerve are either placed directly between the damaged ends of the spinal cord or are used to form a bridge across the lesion. There are several advantages to this approach compared to transplantation of other neural tissues; regenerating axons can be directed towards a specific target area, the number and source of regenerating axons is easily determined by tracing techniques, the graft can be used for electrophysiological experiments to measure functional recovery associated with axons in the graft, and it is possible to use an autologous nerve to reduce the possibility of graft rejection. In our lab we have performed both autologous (donor and recipient are the same animal) and heterologous (donor and recipient are different animals) grafts with comparable results. This approach has been used successfully in both acute and chronic injury situations. Regenerated axons that reach the distal end of the PN graft often fail to extend back into the spinal cord, so we use microinjections of chondroitinase to degrade inhibitory molecules associated with the scar tissue surrounding the area of SCI. At the same time we have found that providing exogenous growth and trophic molecules encourages longer distance axonal regrowth into the spinal cord. Several months after transplantation we perform a variety of anatomical, behavioral and electrophysiological tests to evaluate the recovery of function in our spinal cord injured animals. This experimental approach has been used successfully in several spinal cord injury models, at different levels of injury and in different species (mouse, rat and cat). Importantly, the peripheral nerve grafting approach is effective in promoting regeneration by acute and chronically injured neurons.Download video file.^{(224M, mp4)}     

Primary Cell Cultures for Understanding Rat Epididymal Inflammation

Treatment‐induced epididymal inflammation and granuloma formation is only an occasional problem in preclinical drug development, but it can effectively terminate the development of that candidate molecule. Screening for backup molecules without that toxicity must be performed in animals (generally rats) that requires at least 2 to 3 weeks of in vivo exposure, a great deal of specially synthesized candidate compound, and histologic examination of the target tissues. We instead hypothesized that these treatments induced proinflammatory gene expression, and so used mixed‐cell cultures from the rat epididymal tubule to monitor the induction of proinflammatory cytokines. Cells were exposed for 24 hr and then cytotoxicity was evaluated with the MTS assay and mRNA levels of Interleukin‐6 (IL‐6) and growth‐related oncogene (GRO) were measured. We found that compounds that were more toxic in vivo stimulated a greater induction of IL‐6 and GRO mRNA levels in vitro. By relating effective concentrations in vitro with the predicted C_eff, we could rank compounds by their propensity to induce inflammation in rats in vivo. This method allowed the identification of several compounds with very low inflammatory induction in vitro. When tested in rats, the compounds produced small degrees of inflammation at an acceptable margin (approximately 20×), and have progressed into further development     

Validation,Replication, and Sensitivity Testing of Heckman-Type Selection Models to Adjust Estimates of HIV Prevalence

A recent study using Heckman-type selection models to adjust for non-response in the Zambia 2007 Demographic and Health Survey (DHS) found a large correction in HIV prevalence for males. We aim to validate this finding, replicate the adjustment approach in other DHSs, apply the adjustment approach in an external empirical context, and assess the robustness of the technique to different adjustment approaches. We used 6 DHSs, and an HIV prevalence study from rural South Africa to validate and replicate the adjustment approach. We also developed an alternative, systematic model of selection processes and applied it to all surveys. We decomposed corrections from both approaches into rate change and age-structure change components. We are able to reproduce the adjustment approach for the 2007 Zambia DHS and derive results comparable with the original findings. We are able to replicate applying the approach in several other DHSs. The approach also yields reasonable adjustments for a survey in rural South Africa. The technique is relatively robust to how the adjustment approach is specified. The Heckman selection model is a useful tool for assessing the possibility and extent of selection bias in HIV prevalence estimates from sample surveys.