Acoustic transport of charge and spins in GaAs-based heterostructures

Report for the scientific sojourn carried out at the Paul Drude Institut für Festkörperelektronik of the Stanford University, USA, from 2010 to 2012. The objective of this project is the transport and control of electronic charge and spin along GaAs-based semiconductor heterostructures. The electronic transport has been achieved by taking advantage of the piezolectric field induced by surface acoustic waves in non-centrosymmetric materials like GaAs. This piezolectric field separates photogenerated electrons and holes at different positions along the acoustic wave, where they acummulate and are transported at the same velocity as the wave. Two different kinds of structures have been studied: quantum wells grown along the (110) direction, both intrinsic and n-doped, as well as GaAs nanowires. The analysis of the charge acoustic transport was performed by micro-photoluminescence, whereas the detection of the spin transport was done either by analyzing the polarization state of the emitted photoluminescence or by Kerr reflectometry. Our results in GaAs quantum wells show that charge and spin transport is clearly observed at the non-doped structures,obtaining spin lifetimes of the order of several nanoseconds, whereas no acoutically induced spin transport was detected for the n-doped quantum wells. In the GaAs nanowires, we were able of transporting successfully both electrons and holes along the nanowire axis, but no conservation of the spin polarization has been observed until now. The photoluminescence emitted by these structures after acoustic transport, however, shows anti-bunching characteristics, making this system a very good candidate for its use as single photon emitters.

NCoR1 is a conserved physiological modulator of muscle mass and oxidative function.

Transcriptional coregulators control the activity of many transcription factors and are thought to have wide-ranging effects on gene expression patterns. We show here that muscle-specific loss of nuclear receptor corepressor 1 (NCoR1) in mice leads to enhanced exercise endurance due to an increase of both muscle mass and of mitochondrial number and activity. The activation of selected transcription factors that control muscle function, such as MEF2, PPARβ/δ, and ERRs, underpins these phenotypic alterations. NCoR1 levels are decreased in conditions that require fat oxidation, resetting transcriptional programs to boost oxidative metabolism. Knockdown of gei-8, the sole C. elegans NCoR homolog, also robustly increased muscle mitochondria and respiration, suggesting conservation of NCoR1 function. Collectively, our data suggest that NCoR1 plays an adaptive role in muscle physiology and that interference with NCoR1 action could be used to improve muscle function.

Structured RNAs in the ENCODE selected regions of the human genome

Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic–stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to ∼2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3′-UTRs. While we estimate a significant false discovery rate of ∼50%–70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).

Peak and persistent excess of genetic diversity following an abrupt migration increase.

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species' lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population's demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.

A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants.

BACKGROUND: Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species. RESULTS: Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic self-incompatibility. CONCLUSIONS: We present a new systematic strategy of gene discovery based on conservation of the protein-coding sequence that complements classical forward and reverse genetics. This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest.

Quotient spaces of boundedly rational types

By identifying types whose low-order beliefs up to level li about the state of nature coincide, weobtain quotient type spaces that are typically smaller than the original ones, preserve basic topologicalproperties, and allow standard equilibrium analysis even under bounded reasoning. Our Bayesian Nash(li; l-i)-equilibria capture players inability to distinguish types belonging to the same equivalence class.The case with uncertainty about the vector of levels (li; l-i) is also analyzed. Two examples illustratethe constructions.

Concepção de uma Estratégia de Geoconservação para Cabo Verde e sua Aplicação à Ilha de Santiago

A singularidade de certos registos geológicos impressos em rochas, as peculiaridades estruturais e dinâmicas dos diversos elementos dos geossistemas, a análise dos seus valores intrínsecos, bem como da sua vulnerabilidade e dos perigos de degradação que os podem afectar, entre outros parâmetros, são factores que concorrem para a necessidade de assegurar a conservação do património geológico. É neste contexto que surge a geoconservação que preconiza a gestão do património geológico com base num conjunto de medidas e acções para a identificação, manutenção ou recuperação do valor natural dos elementos da geodiversidade numa perspectiva de sustentabilidade dos recursos geológicos que integram a componente abiótica do sistema natural. A geoconservação, à escala internacional, tem um desenvolvimento irregular. Enquanto algumas regiões estão bastante avançadas, como na Europa, outras revelam ainda alguma inércia relativamente à implementação de iniciativas que se devem enquadrar no âmbito da conservação da Natureza e do ordenamento do território. Em África, são ainda pontuais os exemplos de geoconservação pelo que, este trabalho, pretende ser promotor de uma política de geoconservação neste continente. No presente trabalho, concebemos uma estratégia de geoconservação para Cabo Verde e aplicamo-la, a título de exemplo, à ilha de Santiago. A metodologia utilizada, baseada em critérios internacionalmente reconhecidos e aceites para o inventário do património geológico de valor científico, consiste no estabelecimento de “categorias temáticas” que representam as características e evolução geológica do arquipélago. Foram propostas nove categorias para Cabo Verde e, para cada uma delas, foram inventariados diversos locais de interesse, dos quais 40 foram propostos como geossítios na ilha de Santiago. Com base nestes geossítios, propuseram-se linhas metodológicas para as etapas subsequentes que integram uma estratégia de geoconservação, nomeadamente, a quantificação, classificação, conservação, valorização, divulgação e monitorização de geossítios. Embora a conservação da geodiversidade esteja prevista, embora de forma pouco clara, na actual legislação ambiental cabo-verdiana, a execução desta estratégia de geoconservação poderá representar um dos primeiros passos para a definição, caracterização e valorização, sistemáticas, do património geológico nacional e contribuir para a implementação de uma política de sustentabilidade ambiental para o país.

Governança das áreas marinhas protegidas da província biogeográfica da Macaronésia

As áreas marinhas protegidas (AMPs), enquanto instrumentos de conservação da natureza, contribuem para a conservação, preservação e gestão dos ecossistemas costeiros e marinhos a nível mundial. Na Província Biogeográfica da Macaronésia, as AMPs existentes desempenham este papel de forma preponderante, principalmente no que diz respeito às espécies com impacte económico local. A governança consiste nas interacções entre estruturas, processos e tradições, as quais determinam como são exercidas as responsabilidades, como as decisões são tomadas e como é que a opinião dos cidadãos e grupos de interesse (stakeholders) é integrada no processo de decisão. Assim, a governança das AMPs é um factor determinante para o seu sucesso. Foi estudada a governança das AMPs na Província Biogeográfica da Macaronésia (arquipélagos dos Açores, Madeira, Canárias e Cabo Verde), com a finalidade de verificar se o actual estado de estabelecimento e gestão de AMPs nos quatro arquipélagos é ou não favorável a uma governança conjunta do meio marinho nesta província biogeográfica, tendo em vista os objectivos de conservação da natureza à escala global. Foi desenvolvida uma metodologia própria baseada na análise do quadro legal nacional e internacional e das estruturas governativas das AMPs, e ainda em entrevistas no arquipélago com menor disponibilidade de informação (Cabo Verde). Conclui-se que os três países que fazem parte da área de estudo detêm os quadros legais (internacional, regional e nacional) e institucional considerados suficientes para a conservação dos ecossistemas costeiros e marinhos. Esta análise permitiu a definição de acções que poderão ser desenvolvidas pelos quatro arquipélagos, visando uma gestão conjunta integrada das AMPs na área de estudo. Apesar de existirem vários diplomas e regulamentos jurídicos a nível nacional/regional sobre a conservação marinha, há ainda um longo caminho a percorrer no que diz respeito aos planos de gestão destinados a promover uma abordagem integrada da conservação à escala biogeográfica

Public perceptions of animal experimentation across Europe

The goal of this article is to map out public perceptions of animal experimentation in 28 European countries. Postulating cross-cultural differences, this study mixes country-level variables (from the Eurostat database) and individual-level variables (from Eurobarometer Science and Technology 2010). It is shown that experimentation on animals such as mice is generally accepted in European countries, but perceptions are divided on dogs and monkeys. Between 2005 and 2010, we observe globally a change of approval on dogs and monkeys, with a significant decrease in nine countries. Multilevel analysis results show differences at country level (related to a post-industrialism model) and at individual level (related to gender, age, education, proximity and perceptions of science and the environment). These results may have consequences for public perceptions of science and we call for more cross-cultural research on press coverage of animal research and on the level of public engagement of scientists doing animal research

Stereological analysis of the rat and monkey amygdala

The amygdala is part of a neural network that contributes to the regulation of emotional behaviors. Rodents, especially rats, are used extensively as model organisms to decipher the functions of specific amygdala nuclei, in particular in relation to fear and emotional learning. Analysis of the role of the nonhuman primate amygdala in these functions has lagged work in the rodent but provides evidence for conservation of basic functions across species. Here we provide quantitative information regarding the morphological characteristics of the main amygdala nuclei in rats and monkeys, including neuron and glial cell numbers, neuronal soma size, and individual nuclei volumes. The volumes of the lateral, basal, and accessory basal nuclei were, respectively, 32, 39, and 39 times larger in monkeys than in rats. In contrast, the central and medial nuclei were only 8 and 4 times larger in monkeys than in rats. The numbers of neurons in the lateral, basal, and accessory basal nuclei were 14, 11, and 16 times greater in monkeys than in rats, whereas the numbers of neurons in the central and medial nuclei were only 2.3 and 1.5 times greater in monkeys than in rats. Neuron density was between 2.4 and 3.7 times lower in monkeys than in rats, whereas glial density was only between 1.1 and 1.7 times lower in monkeys than in rats. We compare our data in rats and monkeys with those previously published in humans and discuss the theoretical and functional implications that derive from our quantitative structural findings.

Mites associated to Xylopia aromatica (Lam.) Mart. (Annonaceae) in urban and rural fragments of semidecidual forest

Mites associated to Xylopia aromatica (Lam.) Mart. (Annonaceae) in urban and rural fragments of semidecidual forest. Native plants can shelter a great diversity of mites. Notwithstanding, the conservation of the forest fragments where the plants are located can influence the structure of the mites community. Generally, in homogenous environments the diversity is lower due to the dominance of one or a few species. In this work, we studied the mite community on Xylopia aromatica (Lam.) Mart. (Annonaceae) in two fragments of semidecidual forest: one on rural and other on urban area. Seven individuals of X. aromatica were monthly sampled from April 2007 to March 2008, in each of these fragments. Descriptive indexes of diversity, dominance and evenness were applied to verify the ecological patterns of the mite community, besides the Student's t-test to compare the abundance between the fragments. We collected 27,365 mites of 37 species belonging to 11 families. Calacarus sp. (Eriophyidae) was the most abundant species, representing 73% of the total sampled. The abundance was greater in the urban fragment (67.7%), with the diversity index reaching only 25% of the theoretical maximum expected. Probably, these values might have been influenced by the location of this fragment in the urban area, being more homogeneous and submitted directly to the presence of atmospheric pollution. In this manner, X. aromatica is able to shelter a higher diversity of mites when inserted in preserved ecosystems, since the highest diversity of available resources allows the establishment of richer and most diverse mite community.

Euglossine bee communities in small forest fragments of the Atlantic Forest, Rio de Janeiro state, southeastern Brazil (Hymenoptera, Apidae)

Euglossine bee communities in small forest fragments of the Atlantic Forest, Rio de Janeiro state, southeastern Brazil (Hymenoptera, Apidae). Euglossine bees are important pollinators in forests and agricultural areas. Although the structure of their communities is critically affected by anthropogenic disturbances, little is known about these bees in small forest fragments. The objectives of this study were to analyze the composition, abundance, and diversity of euglossine bee species in nine small fragments of different phytophysiognomies of the Atlantic Forest in southeastern Brazil, and to identify the environmental variables that may be related to the species composition of these communities. Males were sampled quarterly from May 2007 to May 2009 with aromatic traps containing methyl cinnamate, vanillin, eucalyptol, benzyl acetate, and methyl salicylate. A total of 1558 males, belonging to 10 species and three genera of Euglossina were collected. The richness ranged from five to seven species per fragment. Euglossa cordata, E. securigera, Eulaema nigrita e E. cingulata were common to all fragments studied. The diversity differed significantly among areas, ranging from H' = 1.04 to H' = 1.65. The precipitation, phytophysiognomy, and altitude had the highest relative importance over the species composition variation. The results presented in this study demonstrate that small forest fragments are able to support populations of euglossine bee species, most of which are widely distributed and reportedly tolerant to open and/or disturbed areas and suggest that the conservation of such areas is important, particularly in areas that are regenerating and in regions with agricultural matrices where these bees can act as important pollinators

An estimate of the potential number of mayfly species (Ephemeroptera, Insecta) still to be described in Brazil

ABSTRACTThis study reviewed the data on the Brazilian Ephemeroptera, based on the studies published before July, 2013, estimated the number of species still to be described, and identified which regions of the country have been the subject of least research. More than half the species are known from the description of only one developmental stage, with imagoes being described more frequently than nymphs. The Brazilian Northeast is the region with the weakest database. Body size affected description rates, with a strong tendency for the larger species to be described first. The estimated number of unknown Brazilian species was accentuated by the fact that so few species have been described so far. The steep slope of the asymptote and the considerable confidence interval of the estimate reinforce the conclusion that a large number of species are still to be described. This emphasizes the need for investments in the training of specialists in systematics and ecology for all regions of Brazil to correct these deficiencies, given the role of published papers as a primary source of information, and the fundamental importance of taxonomic knowledge for the development of effective measures for the conservation of ephemeropteran and the aquatic ecosystems they depend on.

Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses.

Nucleotide composition analyses of bacterial genomes such as cumulative GC skew highlight the atypical, strongly asymmetric architecture of the recently published chromosome of Idiomarina loihiensis L2TR, suggesting that an inversion of a 600-kb chromosomal segment occurred. The presence of 3.4-kb inverted repeated sequences at the borders of the putative rearrangement supports this hypothesis. Reverting in silico this segment restores (1) a symmetric chromosome architecture; (2) the co-orientation of transcription of all rRNA operons with DNA replication; and (3) a better conservation of gene order between this chromosome and other gamma-proteobacterial ones. Finally, long-range PCRs encompassing the ends of the 600-kb segment reveal the existence of the reverted configuration but not of the published one. This demonstrates how cumulative nucleotide-skew analyses can validate genome assemblies.

Characterization of a surface metalloprotease from Herpetomonas samuelpessoai and comparison with Leishmania major promastigote surface protease.

The monogenetic kinetoplastid protozoan parasite Herpetomonas samuelpessoai expresses a surface-exposed metalloprotease. Comparable to the Leishmania promastigote surface protease, or PSP, the protease of Herpetomonas is active at the surface of fixed and live organisms, and both enzymes display an identical cleavage specificity toward a nonapeptide substrate. The protease was enriched 440 times by partition into Triton X-114 followed by 2 steps of anion exchange chromatography. The 56-kDa enzyme is inhibited by the metal chelator 1,10-phenanthroline and is susceptible to cleavage by glycosyl-phosphatidylinositol phospholipase C (GPI-PLC). The conservation of an identical surface protease activity in these monogenetic and digenetic trypanosomatids suggests that the enzyme has a physiological function in the promastigote (insect) stage of these parasites.