Estimating synonymous and nonsynonymous substitution rates

Partitioning the total substitution rate into synnonymous and nonsynonymous components is a key aspect of many analyses in molecular evolution. Numerous methods exist for estimating these rates. However, until recently none of the estimation procedures were based on a sound statistical footing. In this paper, the evolutionary model of Muse and Gaut (1994) is used as the basis for two sets of parameters quantifying silent and replacement substitution rates. The parameters are shown to be equal when the four nucleotides are equally frequent and unequal otherwise. Maximum-likelihood estimation of these parameters is described, and the performance of these estimates is compared to that of existing estimation procedures. It is shown that the estimates of Nei and Gojobori (1986) are not unbiased for either set of parameters, although they provide very good estimates for one set as long as sequence divergence is not too high. However, some disturbing properties are found for the Nei and Gojobori estimates. In particular, it is shown that the expected value of the Nei and Gojobori estimate of silent substitution rate is a function of both the silent and replacement substitution rates. The maximum-likelihood estimates have no such problems.      

Subdominant CD8+ T-cell responses are involved in durable control of AIDS virus replication

"Elite controllers" are individuals that durably control human immunodeficiency virus or simian immunodeficiency virus replication without therapeutic intervention. The study of these rare individuals may facilitate the definition of a successful immune response to immunodeficiency viruses. Here we describe six Indian-origin rhesus macaques that have controlled replication of the pathogenic virus SIVmac239 for 1 to 5 years. To determine which lymphocyte populations were responsible for this control, we transiently depleted the animals' CD8+ cells in vivo. This treatment resulted in 100- to 10,000-fold increases in viremia. When the CD8+ cells returned, control was reestablished and the levels of small subsets of previously subdominant CD8+ T cells expanded up to 2,500-fold above pre-depletion levels. This wave of CD8+ T cells was accompanied by robust Gag-specific CD4 responses. In contrast, CD8+ NK cell frequencies changed no more than threefold. Together, our data suggest that CD8+ T cells targeting a small number of epitopes, along with broad CD4+ T-cell responses, can successfully control the replication of the AIDS virus. It is likely that subdominant CD8+ T-cell populations play a key role in maintaining this control.     

Phycotoxin accumulation in zooplankton feeding on Alexandrium fundyense--vector or sink?

Zooplankton can consume toxic Alexandrium spp. dinoflagellatesin the Gulf of Maine and retain paralytic shellfish poisoning(PSP) toxins, potentially acting as toxin vectors. We performedexperiments to determine toxin budgets for common species ofcopepods (Acartia hudsonica, Eurytemora herdmani, Centropageshamatus) feeding on toxic Alexandrium fundyense, offered asmonocultures or in mixtures of algal prey, by comparing calculatedtoxin ingestion rates and toxin content of copepod body tissueand fecal pellets. When fed monocultures, both copepod tissueand fecal pellet fractions accounted for 5% each of the calculatedingested toxin, and thus by difference 90% was lost as a dissolvedfraction into the seawater medium. The presence of alternativefood did not significantly alter the efficiency of toxin retention.Sloppy feeding or regurgitation are probable mechanisms forrelease of toxin to sea water. Experiments using varying concentrationsof A. fundyense and alternativenon-toxic species did not showsignificant effects of cell concentration on toxin retentionefficiency. Total toxin retained and efficiency of retentionvaried among copepod species. Toxin profiles (% molar composition)of dinoflagellates, copepod tissues and fecal pellets differedslightly, suggesting some metabolic transformation. Becauseof their low retention efficiency, copepod grazers can effectivelydisperse PSP toxins produced by Alexandrium spp. into the environment,where they are much less likely to be harmful—zooplanktonact as a sink for PSP toxins. Nevertheless, sufficient toxinbody burdens are attained to contribute to propagation of PSPtoxins to other trophic levels.     

Power frequency fields promote cell differentiation coincident with an increase in transforming growth factor-beta(1) expression.

Recent information from several laboratories suggest that power frequency fields may stimulate cell differentiation in a number of model systems. In this way, they may be similar to pulsed electromagnetic fields, which have been used therapeutically. However, the effects of power frequency fields on phenotypic or genotypic expression have not been explained. This study describes the ability of power frequency fields to accelerate cell differentiation in vivo and describes dose relationships in terms of both amplitude and exposure duration. No change in proliferation or cell content were observed. A clear dose relationship, in terms of both amplitude and duration of exposure, was determined with the maximal biological response occurring at 0.1 mT and 7-9 h/day. Because this study was designed to explore biological activity at environmental exposure levels, this exposure range does not necessarily define optimal dosing conditions from the therapeutic point of view. This study reports the stimulation by power frequency fields of transforming growth factor-beta, an important signalling cytokine known to regulate cell differentiation. The hypothesis is raised that the stimulation of regulatory cytokines by electromagnetic fields may be an intermediary mechanism by which these fields have their biological activity.     

Cortistatin modulates calcitonin gene-related peptide release from neuronal tissues of rat. Comparison with somatostatin

Cortistatin (CST) is an endogenous neuropeptide bearing strong structural and functional analogies with somatostatin (SST). Gene expression of CST and its putative receptor MrgX2 in dorsal root ganglia (DRG) neurons in man suggests the involvement of CST in pain transmission. In this study we have investigated the effects of CST and SST on calcitonin gene-related peptide (CGRP, the main neuropeptide mediator of pain transmission) from primary cultures of rat trigeminal neurons. Moreover, here for the first time we used organotypic cultures of rat brainstem to investigate the release of CGRP form nucleus caudalis as a model of pre-synaptic peptide release. In both experimental paradigm CGRP release was evaluated in the presence of CST or SST, with or without the addition of known secretagogues (namely high KCl concentrations, veratridine and capsaicin). We found that CST and SST do not modify basal CGRP secretion from trigeminal neurons, but both peptides were able to inhibit in a concentration-dependent manner the release of CGRP stimulated by KCl, veratridine or capsaicin. Likewise, in brainstem organotypic cultures CST and SST did not modify baseline CGRP secretion. Of the secretagogues used, capsaicin proved to be most effective compared to KCl and veratridine (8-fold vs 2-fold increase, respectively). Thereafter, CST and SST were tested on capsaicin-stimulated CGPR release only. Under these conditions, CST but not SST was able to inhibit in a significant manner pre-synaptic CGRP release from the brainstem, providing further evidence in support of a role for CST in pain transmission.