Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations

Codon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution.Here we study codon-context biases using a set of 72 orthologous highly conserved genes from bacteria, archaea, fungi and high eukaryotes to identify 7 distinct groups of codon context rules. We show that synonymous mutations, i.e., neutral mutations that occur in synonymous codons of codon-pairs, are selected to maintain context biases and that non-synonymous mutations, i.e., non-neutral mutations that alter protein amino acid sequences, are also under selective pressure to preserve codon-context biases.Since in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli and for decoding efficiency in mammalian cells, our data support the hypothesis that, like codon usage, codon context modulates the evolution of gene primary structure and fine tunes the structure of open reading frames for high genome translational fidelity and efficiency in the 3 domains of life

Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast

Organisms use highly accurate molecular processes to transcribe their genes and a variety of mRNA quality control and ribosome proofreading mechanisms to maintain intact the fidelity of genetic information flow. Despite this, low level gene translational errors induced by mutations and environmental factors cause neurodegeneration and premature death in mice and mitochondrial disorders in humans. Paradoxically, such errors can generate advantageous phenotypic diversity in fungi and bacteria through poorly understood molecular processes.publishe

Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover

Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome–mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that translational fidelity and the ubiquitin-proteasome system are functionally linked to each other and may, therefore, co-evolve in nature. © 2015 Kalapis et al

Objective assessment of the cryoprotective effects of dimethylformamide for freezing goat semen

AbstractThe aim of this work was to assess the cryoprotective effects of dimethylformamide (DMF) for freezing goat semen, using an objective analysis by computer-assisted sperm analysis (CASA). Twenty-one ejaculates (seven per animal) were collected from three stud bucks with the aid of an artificial vagina and immediately evaluated for gross and microscopic characteristics. The semen was diluted in two steps with a Tris–egg yolk extender containing 6% glycerol or 6% DMF, frozen in 0.50-mL straws, and stored in liquid nitrogen. Samples were accessed for sperm morphology, sperm membrane structural and functional integrity, and by CASA, immediately after thawing. There were differences (P<0.05) between glycerol and DMF with regard to subjective progressive motility (23.9±2.2% vs. 16.6±2.0%), objective progressive motility (3.5±0.4% vs. 1.8±0.3%), linearity (53.9±1.6% vs. 48.1±1.4%) and amplitude of lateral head (2.3±0.1 vs. 2.9±0.1mm), which confirmed the efficiency of glycerol. In conclusion, dimethylformamide could be used as an alternative cryoprotectant for goat semen freezing. However it was showed that no benefits were derived by using dimethylformamide to replace glycerol at an equal 6% concentration

Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover

Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome-mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that translational fidelity and the ubiquitin-proteasome system are functionally linked to each other and may, therefore, co-evolve in nature

Uso de softwares educativos como ferramenta na construção do conhecimento de educação ambiental

Atualmente, a informação assume um papel cada vez mais importante, com grande crescimento da Internet, multimídia, do ciberespaço, a educação para a cidadania representa a possibilidade de motivar e sensibilizar as pessoas em transformar as diversas formas de participação na defesa da qualidade de vida. Assim, a educação ambiental assume cada vez mais uma função transformadora, na qual a educação e responsabilização dos indivíduos tornam-se um objetivo essencial para promover o desenvolvimento sustentável.Dessa forma, o presente projeto teve por objetivo desenvolver um software educacional chamado “EcoMemória”, com o mesmo princípio de funcionamento do “Jogo Memória” tradicional, para facilitar o aprendizado das noções básicas de Educação Ambiental, visto que há certa dificuldade na abordagem desses conteúdos pelo corpo docente. Como motivos para esta dificuldade podemos citar: a pequena disponibilidade de material didático adequado para ser utilizado em sala de aula e os jogos didáticos desenvolvidos até o momento, não provocarem o devido estímulo a construção da cidadania e desses conhecimentos. Aos estudantes foram aplicados dois questionários previamente elaborados pela equipe. Quando questionados sobre como consideram seu nível de conhecimento em educação ambiental, 80% responderam bom, 10% muito bom, 5% regular, excelente 3% e insuficiente 2%. Entretanto, 75% dos alunos avaliados não têm informações sólidas a respeito de questões ambientais. A aplicação do Jogo EcoMemória foi realizada após uma palestra explicativa sobre Educação Ambiental e alguns aspectos relevantes (tipos de lixo, como economizar água e importância de se reciclar os resíduos, entre outros), posteriormente o jogo foi utilizado como exercício de fixação do conteúdo exposto em sala de aula. Durante a aplicação do Software em sala de aula, houve grande participação dos alunos, assim como foi possível observá-los compartilhando idéias e explorando melhor o conteúdo abordado, sendo assim o jogo EcoMemória obteve aceitação de 75% dos alunos

ABORDAGEM LÚDICA NO ENSINO DE INFORMÁTICA NA MELHOR IDADE A UTILIZAÇÃO DE JOGOS DE CARTAS

Este projeto tem como objetivo proporcionar atividades que envolvam informática de forma lúdica a residentes de dois asilos localizados nos municípios catarinenses de Rio do Sul e Ituporanga. As atividades desenvolvidas levam em conta seus conhecimentos, histórico e memórias, e entre outras atividades, são utilizados jogos de cartas, especificamente o jogo paciência spider, pois é a abordagem que tem maior aceitabilidade por parte dos residentes. O conhecimento prévio do residente, as regras do jogo e as próprias cartas facilitam a aproximação do equipamento, e assim,&nbsp; pode-se perceber, ao longo do tempo, a melhora na agilidade no reconhecimento de padrões, no raciocínio lógico e no manejo, assim como na sociabilidade dos estudantes

Conservation units in the core area of the Cerrado domain: an overview on the small nonvolant mammals (Rodentia and Didelphimorphia)

A review of small non-volant mammal species of the APA Gama e Cabeça de Veado was carried out, including new surveys in the "Estação Ecológica do Jardim Botânico" (EEJBB) and "Reserva Ecológica do Instituto Brasileiro de Geografia e Estatí­stica" (REIBGE). Thirty-one small mammal's species are registered for the APA Gama and Cabeça de Veado, including one exotic species. Didelphis albiventris, Hylaeamys megacephalus, and Oxymycterus delator were collected for the first time in EEJBB. The APA Gama-Cabeça de Veado has a central position in the Cerrado domain sharing six species with the Amazon domain, five with Atlantic Forest, and 13 with Caatinga. The APA Gama-Cabeça de Veado encompasses the home range of at least six non-volant small mammal species endemic of Cerrado domain, and it has an important role in the protection of these endemic species and species that occurs in those four South America morphoclimatic domains

The Prevalence and Correlation of Non-motor Symptoms in Adult Patients with Idiopathic Focal or Segmental Dystonia

Background: Idiopathic focal dystonia is a motor syndrome associated with dysfunction of basal ganglia circuits. Observations have suggested that many other non-motor symptoms may also be part of the clinical picture. The aim was to assess the prevalence and correlation of non-motor symptoms in patients with common idiopathic focal or segmental dystonia. Methods: In a single-center cross-sectional case–control study, we evaluated the presence of pain, neuropsychiatric symptoms, and sleep alterations in 28 patients with blepharospasm, 28 patients with cervical dystonia, 24 patients with writer’s cramp, and 80 control subjects matched for sex, age, and schooling. We obtained clinical and demographic data, and evaluated patients using the Fahn–Marsden Dystonia Rating Scale and other specific scales for dystonia. All subjects completed the following questionnaires: Beck Depression Inventory, Beck Anxiety Inventory, Social Phobia Inventory, Apathy Scale, Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index, Brief Pain Scale, and the World Health Organization Quality of Life brief scale. Results: The patients presented more symptoms of depression, anxiety, and apathy than the control subjects. They also reported worse quality of sleep and more pain complaints. Patients with blepharospasm were the most symptomatic subgroup. The patients had worse quality of life, and the presence of pain and symptoms of apathy and depression were the main influences for these findings, but not the severity of motor symptoms. Discussion: Patients with dystonia, especially those with blepharospasm, showed higher prevalence of symptoms of depression, anxiety, apathy, worse quality of sleep, and pain. These symptoms had a negative impact on their quality of life

Aceptación final 21 septiembre

ABSTRACT: The maned wolf feeds mainly on fruits and small vertebrates. The diet of maned wolf was studied at Águas Emendadas Ecological Station (AEES) through 328 faecal samples collected from November 1996 to August 1999. To evaluate the seasonal variation in food availability, the fruit phenology of the wolf&apos;s fruit, the main food item in maned wolf&apos;s diet, was monitored counting the fruits produced in 20 marked plants. Fructification phenology of fleshy fruit plants in the cerrado habitat of AEES was recorded monitoring five plots of 100 x 20 m, where the number of fruit producing species and individuals were recorded. The diet composition was 60% vegetal items and 40% animal ones. The wolf&apos;s fruit, other fruits and small mammals were the most frequent consumed categories, but armadillos, wolf&apos;s fruit, medium size mammals, and small mammals were the most important categories considering biomass. Maned wolves are generalist, with a broad diet, and consume most of the food items according to their availability. However, wolves are selective with regard to some food items, particularly the wolf&apos;s fruit during the dry season. RESUMEN: Hábitos alimentarios del aguará guazú (Chrysocyon brachyurus) en el dominio del Cerrado, Brasil. El aguará guazú se alimenta principalmente de frutos y vertebrados pequeños. Si bien se ha obtenido mucha información acerca de la dieta del aguará guazú, datos sobre la ecología trófica de esta especie en reservas pequeñas del Cerrado son importantes para establecer estrategias de conservación. Se estudió la dieta del aguará guazú en la Estación Ecológica de Águas Emendadas (EEAE) a través de 328 muestras de heces colectadas entre noviembre de 1996 y agosto de 1999. Para evaluar la variación estacional en la disponibilidad de alimentos se analizó la fenología frutal de Solanum lycocarpum, el principal componente de la dieta de este cánido, contando los frutos producidos en 20 plantas marcadas. Se estudió la fenología de fructificación de plantas con frutos carnosos en el ambiente de Cerrado de la EEAE en cinco parcelas de 100 x 20 m, registrándose el número de especies productoras de frutos y sus individuos. La composición de la dieta fue de 60% de ítems vegetales y de 40% de ítems animales. Solanum lycocarpum, otros frutos y los micromamíferos fueron las categorías consumidas con mayor frecuencia, pero considerando la biomasa las categorías más importantes fueron los armadillos, el Solanum lycocarpum y los mamíferos medianos y pequeños. El aguará guazú es generalista, con una dieta amplia, consumiendo la mayor parte del ali-38 FHG Rodrigues et al