Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome

Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when experimental, restricted to small datasets; particularly poor attention has been given to genes with low CUB. In this work, correspondence analysis on codon usage is used to classify E.coli genes into three groups, and the relationship between them and expression levels from microarray experiments is studied. These groups are: group 1, highly biased genes; group 2, moderately biased genes; and group 3, AT-rich genes with low CUB. It is shown that, surprisingly, there is a negative correlation between codon bias and expression levels for group 3 genes, i.e. genes with extremely low codon adaptation index (CAI) values are highly expressed, while group 2 show the lowest average expression levels and group 1 show the usual expected positive correlation between CAI and expression. This trend is maintained over all functional gene groups, seeming to contradict the E.coli–yeast paradigm on CUB. It is argued that these findings are still compatible with the mutation–selection balance hypothesis of codon usage and that E.coli genes form a dynamic system shaped by these factors

The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

MdR was supported by Biotechnology and Biological Sciences Research Council (UK) grant BB/J009709/1 awarded to ZY

Uso de imunocaptura para o isolamento de bactérias do ambiente.

Obtenção do soro. Imunocaptura. Procedimentos para imunocaptura. Preparo das amostras. Amostras de plantas.bitstream/CNPAB-2010/32965/1/doc198.pd

Gauge invariance of the background average effective action

Using the background field method for the functional renormalization group approach in the case of a generic gauge theory, we study the background field symmetry and gauge dependence of the background average effective action, when the regulator action depends on external fields. The final result is that the symmetry of the average effective action can be maintained for a wide class of regulator functions, but in all cases the dependence of the gauge fixing remains on-shell. The Yang-Mills theory is considered as the main particular example.Comment: Fits the version accepted in EPJ

Organização da coleção entomológica da Embrapa Florestas.

Resumo

Ising-type Magnetic Anisotropy in CePd2_2As2_2

We investigated the anisotropic magnetic properties of CePd$_2$As$_2$ by magnetic, thermal and electrical transport studies. X-ray diffraction confirmed the tetragonal ThCr$_2$Si$_2$-type structure and the high-quality of the single crystals. Magnetisation and magnetic susceptibility data taken along the different crystallographic directions evidence a huge crystalline electric field (CEF) induced Ising-type magneto-crystalline anisotropy with a large $c$-axis moment and a small in-plane moment at low temperature. A detailed CEF analysis based on the magnetic susceptibility data indicates an almost pure $\langle\pm5/2 \rvert$ CEF ground-state doublet with the dominantly $\langle\pm3/2 \rvert$ and the $\langle\pm1/2 \rvert$ doublets at 290 K and 330 K, respectively. At low temperature, we observe a uniaxial antiferromagnetic (AFM) transition at $T_N=14.7$ K with the crystallographic $c$-direction being the magnetic easy-axis. The magnetic entropy gain up to $T_N$ reaches almost $R\ln2$ indicating localised $4f$-electron magnetism without significant Kondo-type interactions. Below $T_N$, the application of a magnetic field along the $c$-axis induces a metamagnetic transition from the AFM to a field-polarised phase at $\mu_0H_{c0}=0.95$ T, exhibiting a text-book example of a spin-flip transition as anticipated for an Ising-type AFM.Comment: 9 Pages, 8 figure

Thermopower and thermal conductivity in the Weyl semimetal NbP

The Weyl semimetal NbP exhibits an extremely large magnetoresistance (MR) and an ultra-high mobility. The large MR originates from a combination of the nearly perfect compensation between electron- and hole-type charge carriers and the high mobility, which is relevant to the topological band structure. In this work we report on temperature- and field-dependent thermopower and thermal conductivity experiments on NbP. Additionally, we carried out complementary heat capacity, magnetization, and electrical resistivity measurements. We found a giant adiabatic magnetothermopower with a maximum of 800 $\mu$V/K at 50 K in a field of 9 T. Such large effects have been observed rarely in bulk materials. We suggest that the origin of this effect might be related to the high charge-carrier mobility. We further observe pronounced quantum oscillations in both thermal conductivity and thermopower. The obtained frequencies compare well with our heat capacity and magnetization data.Comment: 6 pages, 3 figure