Mitochondrial

The performance of DNA barcoding as a tool for fast taxonomic verification in ecological assessment projects of small mammals was evaluated during a collecting trip to a lowland tropical rainforest site in Suriname. We also compared the performance of tissue sampling onto FTA CloneSaver cards vs. liquid nitrogen preservation. DNA barcodes from CloneSaver cards were recovered from 85% of specimens, but DNA degradation was apparent, because only 36% of sequence reads were long (over 600 bp). In contrast, cryopreserved tissue delivered 99% barcode recovery (97% > 600 bp). High humidity, oversampling or tissue type may explain the poor performance of CloneSaver cards. Comparison of taxonomic assignments made in the field and from barcode results revealed inconsistencies in just 3.4% of cases and most of the discrepancies were due to field misidentifications (3%) rather than sampling/analytical error (0.5%). This result reinforces the utility of DNA barcoding as a tool for verification of taxonomic identifications in ecological surveys, which is especially important when the collection of voucher specimens is not possible.

ABSTRACT We assess whether correlative paleoclimatic models of species ranges accurately predict genetic diversity patterns in species of distinct life histories traits in the Atlantic Forest (AF) of Brazil. To this end, we use sequences of the mitochondrial gene ND2 from Dendropsophus elegans and Chiasmocleis carvalhoi – summarized in the shape of phylogenies and population genetic statistics – and maximum entropy models of species distributions under current, 21 kya BP and 120 kya BP climatic reconstructions. The two target species have distinct ranges, habitat tolerances, rates of reproduction and dispersal abilities, yet are endemic to the AF. Although the more restricted and semi-fossorial C. carvalhoi is associated with forested habitats and thought to be a poor disperser, the widely ranged arboreal D. elegans inhabits open areas such as pastures and human-impacted regions of the AF, and is easily found perched on herbaceous vegetation in inundated areas. We had anticipated that correlative distribution models of the broadly distributed D. elegans would perform better then models of the narrowly ranged C. carvalhoi, thus better predicting current patterns of genetic diversity. The results demonstrate poor predictive ability of climate-based models of C. carvalhoi under current climatic conditions, suggesting that factors such as biotic interactions or dispersal ability may be playing a central role in defining this species distribution – both now and in the recent past. Models under current climate are nonetheless accurate in the broadly ranged D. elegans. As a corollary, paleoclimatic models accurately predicted patterns of diversity of the ND2 mitochondrial gene in D. elegans, but not in C. carvalhoi. We attribute these distinct responses to the poor explanatory power of paleodistributions models when applied to species that violate the basic assumption of the environment as main driver of distribution patterns. This calls for a careful use of distribution models for the purpose of evolutionary biogeographical inference. Like C. carvalhoi, other species whose ranges are not yet at equilibrium, or which are impacted by competitor, parasite or pathogen presence, may not be suitable to the combined use of paleoclimatic-model based phylogeographic inference, as here implemented – despite relatively high area under the curve values.

The entire operon encoding the sodium pumping cytochrome bo from the bacterium Vitreoscilla was isolated and sequenced, and this sequence was analyzed by blast and hydropathy plots. There are fairly similar phylogenetic relationships which apply to all five proteins, but overall greater similarity to members of the gamma subdivision than the beta subdivision of the Proteobacteria. Hydropathy plots of all five Cyo proteins show near identity with those of the corresponding E. coli subunits, indicating that the similarity extends from sequence to structure. The operon appears to have a typical Shine-Dalgarno sequence, an E. coli-like promoter, and several possible binding sites for regulatory proteins. The Vitreoscilla Cyo B subunit (the probable Na+ pump) is almost identical to E. coli Cyo B at 18 key amino acids; thus, there are no obvious changes in Vitreoscilla Cyo B that hint at the details of its Na+ pumping ability.

Resumen: La identificación de la especie en productos de origen animal (carne, leche o sus derivados) se hace necesaria y de exigencia por los consumidores modernos, entre otras razones: i) para evitar fraude económico, ya sea por sustitución o adulteración del mismo, ...

c-jun, which is overexpressed in a number of human cancers encodes a critical component of the AP-1 complex. c-jun has been shown to either induce or inhibit cellular apoptosis. Germ line deletion of both c-jun alleles is embryonically lethal. To determine the role of the endogenous c-jun gene in apoptosis, we performed mammary epithelial cell–targeted somatic deletion using floxed c-jun (c-junf/f) conditional knockout mice. Laser capture microdissection demonstrated endogenous c-jun inhibits expression of apoptosis inducing genes and reactive oxygen species (ROS)-reducing genes (MnSOD, catalase). ROS have been implicated in apoptosis and undergo enzymatic elimination via MnSOD and CuZnSOD with further detoxification via catalase. c-jun–mediated survival was in part dependent on ROS production. c-jun–mediated repression of MnSOD and catalase occurred via mitochondrial complex I and NOX I. Collectively, these studies define a pivotal role of endogenous c-jun in promoting cell surviva...

The Afro-Asiatic and Nilo-Saharan language families come into contact in Western Ethiopia. Ethnic diversity is particularly high in the South, where the Nilo-Saharan Nyangatom and the Afro-Asiatic Daasanach dwell. Despite their linguistic differentiation, both populations rely on a similar agripastoralist mode of subsistence. Analysis of mitochondrial DNA extracted from Nyangatom and Daasanach archival sera revealed high levels of diversity, with most sequences belonging to the L haplogroups, the basal branches of the mitochondrial phylogeny. However, in sharp contrast with other Ethiopian populations, only 5% of the Nyangatom and Daasanach sequences belong to haplogroups M and N. The Nyangatom and Daasanach were found to be significantly differentiated, while each of them displays close affinities with some Tanzanian populations. The strong genetic structure found over East Africa was neither associated with geography nor with language, a result confirmed by the analysis of 6711 HVS-I sequences of 136 populations mainly from Africa. Processes of migration, language shift and group absorption are documented by linguists and ethnographers for the Nyangatom and Daasanach, thus pointing to the probably transient and plastic nature of these ethnic groups. These processes, associated with periods of isolation, could explain the high diversity and strong genetic structure found in East Africa.

The role of Pleistocene forest refugia and rivers in the evolutionary diversification of tropical biota has been the subject of considerable debate. A range-wide analysis of gorilla mitochondrial and nuclear variation was used to test the potential role of both refugia and rivers in shaping genetic diversity in current populations. Results reveal strong patterns of regional differentiation that are consistent with refugial hypotheses for central Africa. Four major mitochondrial haplogroups are evident with the greatest divergence between ...