Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans

Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we present sequence data for the ND3 and ND5 genes from 59 lines of Drosophila melanogaster and 29 lines of D. simulans. Of interest are the frequency spectra of silent and replacement polymorphisms, and potential variation among genes and taxa in the departures from neutral expectations. The Drosophila ND3 and ND5 data show no significant excess of replacement polymorphism using the McDonald-Kreitman test. These data are in contrast to significant departures from neutrality for the ND3 gene in mammals and other genes in Drosophila mtDNA (cytochrome b and ATPase 6). Pooled across genes, however, both Drosophila and human mtDNA show very significant excesses of amino acid polymorphism. Silent polymorphisms at ND5 show a significantly higher variance in frequency than replacement polymorphisms, and the latter show a significant skew toward low frequencies (Tajima's D = -1.954). These patterns are interpreted in light of the nearly neutral theory where mildly deleterious amino acid haplotypes are observed as ephemeral variants within species but do not contribute to divergence. The patterns of polymorphism and divergence at charge-altering amino acid sites are presented for the Drosophila ND5 gene to examine the evolution of functionally distinct mutations. Excess charge-altering polymorphism is observed at the carboxyl terminal and excess charge-altering divergence is detected at the amino terminal. While the mildly deleterious model fits as a net effect in the evolution of nonrecombining mitochondrial genomes, these data suggest that opposing evolutionary pressures may act on different regions of mitochondrial genes and genomes.      

The characteristics of 90Sr accumulation and elimination in residents of the Urals region in the period of 1957-1988

A number of radiation accidents occurred at the "Mayak" plutonium production complex (Southern Urals, Russia) in 1950-60s that resulted in environmental contamination of large territories in the Southern and Middle Urals with long-lived radionuclides (90Sr, 137Cs). The results of long-term radiological monitoring were compiled into special databases at the Urals Research Center for Radiation Medicine, which allow the study of 90Sr behaviour in the environment and its accumulation in the human body. Retrospective analysis of the data on postmortem measurements of 90Sr in bones performed on residents of the Urals region over 1957-1988 were conducted for the first time. A time-dependence of 90Sr accumulation in the human body upon its density in soils was observed. Age and gender characteristics of 90Sr retention in bones were studied. It was shown that the levels of 90Sr in residents of large territories north and north-east of Chelyabinsk region, and of bordering territories of Sverdlovsk region were several times higher than the average values for the Russian Federation. Based on the measurements the direct dependence of 90Sr content in the skeleton on 90Sr density in soils was observed 30 years after the 1957 accident (the so called "Kyshtym accident"). However, for individual settlements this dependence may be weakened as a result of the influence of different biological and social factors. No influence of gender on 90Sr accumulation in the skeleton was found in the study. The analysis of age characteristics of 90Sr accumulation in bone, as influenced by skeleton growth and maturation, showed maximal levels of 90Sr from global fallout to be accumulated in bones of the persons born in 1949-1955.     

Reconstruction of the contamination of the Techa River in 1949–1951 as a result of releases from the “MAYAK” Production Association

More accurate reconstruction of the radioactive contamination of the Techa River system in 1949–1951 has been made on the basis of refined data on the amounts and the rate of discharge of radionuclides into the Techa River from the Mayak Production Association; this has led to the development of a modified Techa River model that describes the transport of radionuclides through the up-river ponds and along the Techa River and deposition of radionuclides in the river-bottom sediments and flooded areas. The refined Techa River source-term data define more precisely the time-dependent rates of release and radionuclide composition of the releases that occurred during 1949–1951. The Techa River model takes into account the time-dependent characteristics of the releases and considers (a) the transport of radionuclides adsorbed on solid particles originally contained in the discharges or originating in the up-river ponds as a result of stirring up of contaminated bottom sediments and (b) the transport of radionuclides in soluble form. The output of the Techa River model provides concentrations of all source-term radionuclides in the river water, bottom sediments, and floodplain soils at different distances from the site of radioactive releases for the period of major contamination in 1950–1951. The outputs of the model show good agreement with historical measurements of water and sediment contamination. In addition, the river-model output for ⁹⁰Sr concentration in the river water is harmonized with retrospective estimates derived from the measurements of ⁹⁰Sr in the residents of the Techa Riverside villages. Modeled contamination of the floodplain soils by ¹³⁷Cs is shown to be in agreement with the values reconstructed from late measurements of this radionuclide. Reconstructed estimates of the Techa River contamination are being used for the quantification of internal and external doses received by residents of the Techa Riverside communities.     

A radioimmunoprecipitation method in the serodiagnosis of HIV infection: the development of the optimal conditions for its performance and the evaluation of the possibilities for its use

The optimum conditions for using the method of radioimmunoprecipitation (RIP) for the detection of human immunodeficiency virus (HIV) in serum samples have been established. Out of several available cell lines persistently infected with HIV, specially selected line 17 has been chosen. The characteristic feature of this is the high and stable (under the conditions of prolonged cultivation) accumulation of virus-specific proteins in infected cells. The optimum conditions for making the test and its evaluation have also been established. The data of literature on the advantages of the method of RIP over such traditional methods as the enzyme immunoassay and immunoblotting have been confirmed. Thus, the presence of specific antibodies in several serum samples registered as false negative has been established. The intertypical reactivity of two serotypes of the virus, HIV-1 and HIV-2, has been studied. Cross reactivity of antibodies with respect to the HIV gene gag, but not with respect to viral glycoproteids, has been established. Ideas on the expediency and prospects of using RIP for the serological control of HIV infection are presented.     

Recruitment of TBK1 to cytosol‐invading Salmonella induces WIPI2‐dependent antibacterial autophagy

Mammalian cells deploy autophagy to defend their cytosol against bacterial invaders. Anti‐bacterial autophagy relies on the core autophagy machinery, cargo receptors, and “eat‐me” signals such as galectin‐8 and ubiquitin that label bacteria as autophagy cargo. Anti‐bacterial autophagy also requires the kinase TBK1, whose role in autophagy has remained enigmatic. Here we show that recruitment of WIPI2, itself essential for anti‐bacterial autophagy, is dependent on the localization of catalytically active TBK1 to the vicinity of cytosolic bacteria. Experimental manipulation of TBK1 recruitment revealed that engagement of TBK1 with any of a variety of Salmonella‐associated “eat‐me” signals, including host‐derived glycans and K48‐ and K63‐linked ubiquitin chains, suffices to restrict bacterial proliferation. Promiscuity in recruiting TBK1 via independent signals may buffer TBK1 functionality from potential bacterial antagonism and thus be of evolutionary advantage to the host.     

Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

Background  

The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20^th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease.     

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.