Radiation hybrid mapping of 70 rat genes from a data set of differentially expressed genes

The spontaneously hypertensive rat (SHR) is a model of human essential hypertension. Increased blood pressure in SHR is associated with other risk factors associated with cardiovascular disease, including insulin resistance and dyslipidemia. DNA microarray studies identified over 200 differentially expressed genes and ESTs between SHR and normotensive control rats. These clones represent candidate genes that may underlie previously detected QTLs in SHR. This study made use of the publication of two whole-genome maps to identify positional QTL candidates. Radiation hybrid (RH) mapping was used to determine the chromosomal locations of 70 rat genes and ESTs from this dataset. Most of the locations are novel, but in five cases we identified a definitive map location for genes previously mapped by somatic cell hybrids and/or linkage analysis. Genes for which the mouse genome map location was already determined mapped to syntenic segments in the rat genome map, except for two rat genes whose map locations confirmed previous findings. Where synteny comparisons could be made only with the human, 74% of the genes mapped in this study lay in a conserved syntenic segment. Chromosomal localisation of these mouse and human orthologs to syntenic segments produces a high level of confidence in the data presented in this study. The data provide new map locations for rat genes and will aid efforts to advance the rat genome map. The data may also be used to prioritize candidate QTL genes in SHR and other rat strains on the basis of their map location.     

Trade-offs between reproductive and somatic (storage) investments in animals: a comparative test of the Van Noordwijk and De Jong model

Classical life-history theory predicts ‘trade-offs’ between reproductive and somatic investments. However, empirical studies have shown that intraspecific phenotypic correlations between these two resource investments are often positive or nonsignificant, rather than negative as predicted. The model of Van Noordwijk and De Jong (1986) was proposed to explain these unexpected results. According to their model, positive correlations between reproductive and somatic investments will result if individual variation in resource acquisition exceeds that of resource allocation, whereas negative correlations will result if individual variation in resource allocation exceeds that of resource acquisition. To test this model, I used body storage/condition as an index of somatic investment because it is usually strongly related to level of resource acquisition. I predicted that laboratory studies should more often show negative correlations between reproductive and somatic investments than field studies, because individual variation in resource acquisition is expected to be lower in controlled laboratory environments than in variable natural environments. A literature review revealed that correlations between somatic (storage) investment and reproductive investment (estimated as clutch/litter mass, number of offspring per clutch/litter, or number of clutches/litters) among conspecific breeding female animals are more often positive (15 species) or nonsignificant (17 species) than negative (6 species). Moreover, as expected, five of six negative correlations were observed in laboratory studies, whereas 13 of 15 positive correlations were observed in field studies. It is concluded that future empirical and theoretical work on life histories should consider individual variation in both resource acquisition and allocation and the interaction between the two. This revised version was published online in July 2006 with corrections to the Cover Date.     

Temperature,resources and predation interact to shape phytoplankton size–abundance relationships at a continental scale

Aim

Communities contain more individuals of small species and fewer individuals of large species. According to the ‘metabolic theory of ecology’, the relationship of log mean abundance with log mean body size across communities should exhibit a slope of −3/4 that is invariant across environmental conditions. Here, we investigate whether this slope is indeed invariant or changes systematically across gradients in temperature, resource availability and predation pressure.

Location

1048 lakes across the USA.

Time Period

2012.

Major Taxa Studied

Phytoplankton.

Results

We found that the size–abundance relationship across all sampled phytoplankton communities was significantly lower than −3/4 and near −1 overall. More importantly, we found strong evidence that the environment affects the slope: it varies between −0.33 and −0.93 across interacting gradients of temperature, resource (phosphorus) supply and zooplankton predation pressure. Therefore, phytoplankton communities have orders of magnitude more small or large cells depending on environmental conditions across geographical locations.

Conclusion

Our results emphasise the importance of the environmental factors' effect on macroecological patterns that arise through physiological and ecological processes. An investigation of the mechanisms underlying the link between individual energetics constrain and macroecological patterns would allow to predict how global warming and changes in nutrients will alter large-scale ecological patterns in the future.     

Success of maximum likelihood phylogeny inference in the four-taxon case

We used simulated data to investigate a number of properties of maximum- likelihood (ML) phylogenetic tree estimation for the case of four taxa. Simulated data were generated under a broad range of conditions, including wide variation in branch lengths, differences in the ratio of transition and transversion substitutions, and the absence of presence of gamma-distributed site-to-site rate variation. Data were analyzed in the ML framework with two different substitution models, and we compared the ability of the two models to reconstruct the correct topology. Although both models were inconsistent for some branch-length combinations in the presence of site-to-site variation, the models were efficient predictors of topology under most simulation conditions. We also examined the performance of the likelihood ratio (LR) test for significant positive interior branch length. This test was found to be misleading under many simulation conditions, rejecting too often under some simulation conditions. Under the null hypothesis of zero length internal branch, LR statistics are assumed to be asymptotically distributed chi 2(1); with limited data, the distribution of LR statistics under the null hypothesis varies from chi 2(1).      

Energy allocation rules inDaphnia magna: clonal and age differences in the effects of food limitation

Summary The allocation of energy to carapace formation, respiration, growth, and reproduction were examined in two parthenogenetic clones ofDaphnia magna (Cladocera) cultured at two levels of food (Chlorella) concentration. Clonal differences in energy allocation were more apparent at high ration (1.5 g C mL^-1) than at low ration (0.3 g C mL^-1). These differences included respiratory and molting costs, and the timing of energy allocation to growth and reproduction. A comparison of active vs. anesthetized animals revealed that the interclonal difference in respiration rate was the result of a difference in activity level. In both clones mass-specific rates of respiration, growth, and brood production all decreased at low vs. high ration levels, whereas mass-specific molt-loss rate increased. Lowered food concentration decreased the relative allocation of energy to growth and reproduction, but increased allocation to maintenance (respiration and carapace formation). These allocation responses to food limitation indicated that for both clones the highest energy priority was carapace formation. However, the relative priority of respiration, growth and reproduction varied with age and clone. In juveniles (instars 1–4) the priority ranking of growth was essentially equal to that of respiration, whereas respiration always had higher priority in adults (instars 5–9). All three possibilities for the relative ranking of growth and reproduction (i.e., growth>reproduction, growth=reproduction, and reproduction>growth), as specified by different models in the literature, were observed depending on age and clone. The energy allocation rules were also shown to vary between other daphniid species. Furthermore, metabolic responses to chronic food limitation may be different from responses to acute food deprivation. In this study, one clone showed a greater decrease in respiration rate as a result of lifetime food limitation than did the other, but the opposite was true when these clones were exposed to 48 h of starvation. These differences in allocation rules and in acute vs. chronic responses may have to be considered when using physiological data to modelDaphnia populations.     

Magic Spot Metabolism in an Escherichia coli Mutant Temperature Sensitive in Elongation Factor Ts

A temperature-sensitive mutant of Escherichia coli HAK88 which has been shown to have a lesion in elongation factor Ts (EFTs) was studied with repsect to its metabolism of guanosine 5′-diphosphate, 2′(3′)-diphosphate (ppGpp) and the associated failure of ribosomal ribonucleic acid (rRNA) accumulation at the nonpermissive temperature. Results reported here show that (i) when EFTs is nonfunctional, a full complement of charged transfer RNA (tRNA) cannot prevent accumulation of ppGpp (magic spot) and the stringent failure of rRNA accumulation; (ii) chloramphenicol prevents magic spot (MS) formation and the stringent response not by increasing the percentage of charged tRNA, but possibly by somehow interfering directly with the synthesis of MS; and (iii) tetracycline can lead to MS disappearance without resumption of RNA synthesis. Thus, the absence of MS and the presence of a functional RNA polymerase and charged tRNA are not sufficient to support rRNA accumulation in vivo. An additional element in the regulatory system is suggested.     

Establishment of a doxycycline-regulated cell line with inducible,doubly-stable expression of the wild-type p53 gene from p53-deleted hepatocellular carcinoma cells

p53 is important in the development of hepatocellular carcinoma (HCC) and in therapeutic approaches, but the mechanism whereby it inhibits HCC growth is still unclear. The aim of the present study was to establish a HCC cell system in which p53 levels can be regulated. Full-length wild-type p53 cDNA obtained by PCR was cloned into a retroviral response vector controlled by the tetracycline responsive element (RevTRE-p53). The regulatory vectors RevTet-Off and RevTRE-p53 were transfected into a packaging cell line, PT67. Hep3B cells in which the p53 gene was deleted were infected with RevTet-Off viral particles from the PT67. Three G418-resistant cell clones with high luciferase expression and low background were infected with RevTRE-p53. By screening dozens of RevTRE-p53-infected clones with hygromycin we identified the one with the highest expression of p53 and the lowest background after doxycycline treatment. The results showed that p53 expression in this cell clone could be simply turned on or off by removing or adding doxycycline. Furthermore, it was found that the level of p53 protein was negatively and sensitively related to the doxycycline concentration. In conclusion, we have established a HCC cell line in which p53 expression can be switched on or off and regulated in a dose- and time-dependent manner.     

High-resolution circular dichroism of N-acetyl-L-phenylalaninamide: solvent effects

Biological membranes consist mainly of lipids and proteins. At present, the structure of the lipid phase appears to be established, but hypotheses on the molecular organization of the protein are difficult to support. Thus the deformation behavior of whole human erythrocyte ghosts, ghosts after the selective removal of lipids and ghosts stripped of lipids as well as nonlipid components have been examined in the hope of securing indirect information on the organization of the protein. It has been found that large localized deformations result in partial membrane failure and long uniformly wide fibrils, frequently in excess of 3000 Å, are drawn across the rupture. These data are interpreted in terms of currently favored membrane models and the possibility of a fibrous membrane framework consisting predominantly of protein is reviewed. The behavior of the membrane in its various stages of extraction is compared and contrasted to that of synthetic polymer films of known organization.     

Detecting substitution-rate heterogeneity among regions of a nucleotide sequence

Likelihood-ratio statistics are proposed to test for heterogeneity in nucleotide substitution rate among regions of a DNA sequence. The tests examine three-sequence phylogenies, and two specific tests are proposed: a test to detect rate heterogeneity among genic regions within a sequence, over all evolutionary lineages; and a test to detect rate heterogeneity among regions in a specific evolutionary lineage. Simulations examine the ability of tests to detect a single region that varies in nucleotide substitution rate relative to the remainder of the sequence. A 50-bp region with a fivefold substitution-rate increase can be detected > or = 90% of the time when it is found in all three lineages of the phylogeny, and a 50-bp region of fivefold rate increase can be detected with approximately 70% power when it is found in only one evolutionary lineage. Simulation also examines the effect of transition- and transversion-rate differences. The tests are applied to published DNA sequences. While the tests are powerful, significant results can be difficult to interpret biologically.