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.      

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.     

Cosegregation of novel mitochondrial 16S rRNA gene mutations with the age-associated T414G variant in human cybrids

Ever increasing evidence has been provided on the accumulation of mutations in the mitochondrial DNA (mtDNA) during the aging process. However, the lack of direct functional consequences of the mutant mtDNA load on the mitochondria-dependent cell metabolism has raised many questions on the physiological importance of the age-related mtDNA variations. In the present work, we have analyzed the bioenergetic properties associated with the age-related T414G mutation of the mtDNA control region in transmitochondrial cybrids. The results show that the T414G mutation does not cause per se any detectable bioenergetic change. Moreover, three mtDNA mutations clustered in the 16S ribosomal RNA gene cosegregated together with the T414G in the same cybrid cell line. Two of them, namely T1843C and A1940G, are novel and associate with a negative bioenergetic phenotype. The results are discussed in the more general context of the complex heterogeneity and the dramatic instability of the mitochondrial genome during cell culture of transmitochondrial cybrids.     

A new species of Heth Cobb, 1898 (Nematoda: Rhigonematida: Hethidae) from an Australian millipede (Myriapoda: Diplopoda: Spirostreptida)

Abstract

A new species of nematode, Heth baudini sp. n. from a diplopod (Spirostreptida: Iulomorphidae Verhoeff, 1924) collected in Queensland, Australia, is described and illustrated. The cephalic and cervical cuticular ornamentation of females of H. baudini sp. n. is similar to those of South-East Asian and Australasian Heth species. Heth baudini sp. n. females are particularly close to Heth taynguyeni from Vietnam but can be distinguished by the shape of the lateral lappets, which in H. taynguyeni limit the trapezium-shaped region of smooth cuticle unlike the elliptical region in H. baudini sp. n., and by the presence of lateral spines only half the size. The cuticle of the H. baudini sp. n. is finely annulated along the entire body, whereas H. taynguyeni has broader rings behind the first pair of lateral spines, each consisting of five or six narrower rings separated from each other by deeper furrows. Males of H. baudini sp. n. are characterised by the presence of a bursa-like fold on the tail and can be distinguished from other species of the genus by the presence of somatic papillae embedded into the bursal fold.     

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.     

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.     

Effects of Irbesartan on the Growth and Differentiation of Adipocytes in Obese Zucker Rats

Objective: The aim of this study was to evaluate the effects of the selective angiotensin receptor 1 antagonist irbesartan on the growth and differentiation of the adipocytes in obese Zucker fa/fa rats. Research Methods and Procedures: Obese Zucker fa/fa rats were treated by oral route for 3 weeks with irbesartan at doses of 3–10‐30 mg/kg per day. The adipocyte differentiation was evaluated by analyzing tissue samples of white (retroperitoneal) or brown (interscapular) adipose tissue for the presence of peroxisome proliferator activated receptor γ, leptin, and the activity of glycerol‐3‐phosphate dehydrogenase. Results: This study showed that the treatment of obese Zucker fa/fa with irbesartan effectively reduced the differentiation of adipocytes within brown (interscapular) and white (retroperitoneal) adipose tissue. In fact, irbesartan significantly (p < 0.01) and dose‐dependently reduced the tissue levels of leptin, peroxisome proliferator activated receptor γ, and the activity of the enzyme glycerol‐3‐phoshate dehydrogenase accepted markers of adipocyte differentiation. None of the tested doses of irbesartan affected these markers in non‐obese rats. Discussion: The antagonism of the angiotensin receptor 1 receptors with irbesartan reduces the adipogenic activity of angiotensin II in obese Zucker rats, with the endpoint being reduction of the growth and differentiation of the adipocytes within the adipose tissue.