Estoque de carbono na necromassa depositada no chão nos remanescentes florestais em Santa Catarina.

Resumo

Telomere length homeostasis

The physical ends of chromosomes, known as telomeres, protect chromosome ends from nucleolytic degradation and DNA repair activities. Conventional DNA replication enzymes lack the ability to fully replicate telomere ends. In addition, nucleolytic activities contribute to telomere erosion. Short telomeres trigger DNA damage checkpoints, which mediate cellular senescence. Telomere length homeostasis requires telomerase, a cellular reverse transcriptase, which uses an internal RNA moiety as a template for the synthesis of telomere repeats. Telomerase elongates the 3' ends of chromosomes, whereas the complementary strand is filled in by conventional DNA polymerases. In humans, telomerase is ubiquitously expressed only during the first weeks of embryogenesis, and is subsequently downregulated in most cell types. Correct telomere length setting is crucial for long-term survival. The telomere length reserve must be sufficient to avoid premature cellular senescence and the acceleration of age-related disease. On the other side, telomere shortening suppresses tumor formation through limiting the replicative potential of cells. In recent years, novel insight into the regulation of telomerase at chromosome ends has increased our understanding on how telomere length homeostasis in telomerase-positive cells is achieved. Factors that recruit telomerase to telomeres in a cell cycle-dependent manner have been identified in Saccharomyces cerevisiae. In humans, telomerase assembles with telomeres during S phase of the cell cycle. Presumably through mediating formation of alternative telomere structures, telomere-binding proteins regulate telomerase activity in cis to favor preferential elongation of the shortest telomeres. Phosphoinositide 3-kinase related kinases are also required for telomerase activation at chromosome ends, at least in budding and fission yeast. In vivo analysis of telomere elongation kinetics shows that telomerase does not act on every telomere in each cell cycle but that it exhibits an increasing preference for telomeres as their lengths decline. This suggests a model in which telomeres switch between extendible and nonextendible states in a length-dependent manner. In this review we expand this model to incorporate the finding that telomerase levels also limit telomere length and we propose a second switch between a non-telomerase-associated "extendible" and a telomerase-associated "extending" state

The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code

Translational readthrough gives rise to C-terminally extended proteins, thereby providing the cell with new protein isoforms. These may have different properties from the parental proteins if the extensions contain functional domains. While for most genes amino acid incorporation at the stop codon is far lower than 0.1%, about 4% of malate dehydrogenase (MDH1) is physiologically extended by translational readthrough and the actual ratio of MDH1x (extended protein) to ‘normal' MDH1 is dependent on the cell type. In human cells, arginine and tryptophan are co-encoded by the MDH1x UGA stop codon. Readthrough is controlled by the 7-nucleotide high-readthrough stop codon context without contribution of the subsequent 50 nucleotides encoding the extension. All vertebrate MDH1x is directed to peroxisomes via a hidden peroxisomal targeting signal (PTS) in the readthrough extension, which is more highly conserved than the extension of lactate dehydrogenase B. The hidden PTS of non-mammalian MDH1x evolved to be more efficient than the PTS of mammalian MDH1x. These results provide insight into the genetic and functional co-evolution of these dually localized dehydrogenases

Protein-RNA and protein-protein interactions mediate association of human EST1A/SMG6 with telomerase

The human EST1A/SMG6 polypeptide physically interacts with the chromosome end replication enzyme telomerase. In an attempt to better understand hEST1A function, we have started to dissect the molecular interactions between hEST1A and telomerase. Here, we demonstrate that the interaction between hEST1A and telomerase is mediated by protein-RNA and protein-protein contacts. We identify a domain within hEST1A that binds the telomerase RNA moiety hTR while full-length hEST1A establishes in addition RNase-resistant and hTR-independent protein-protein contacts with the human telomerase reverse transcriptase polypeptide (TERT). Conversely, within hTERT, we identify a hEST1A interaction domain, which comprises hTR-binding activity and RNA-independent hEST1A-binding activity. Purified, recombinant hEST1A binds the telomerase RNA moiety (hTR) with high affinity (apparent overall K(d) = 25 nM) but low specificity. We propose that hEST1A assembles specifically with telomerase in the context of the hTR-hTERT ribonucleoprotein, through the high affinity of hEST1A for hTR and specific protein-protein contacts with hTERT

The Telomerase Database

Telomerase is a ribonucleoprotein enzyme that extends DNA at the chromosome ends in most eukaryotes. Since 1985, telomerase has been studied intensively and components of the telomerase complex have been identified from over 160 eukaryotic species. In the last two decades, there has been a growing interest in studying telomerase owing to its vital role in chromosome stability and cellular immortality. To keep up with the remarkable explosion of knowledge about telomerase, we compiled information related to telomerase in an exhaustive database called the Telomerase Database (http://telomerase.asu.edu/). The Telomerase Database provides comprehensive information about (i) sequences of the RNA and protein subunits of telomerase, (ii) sequence alignments based on the phylogenetic relationship and structure, (iii) secondary structures of the RNA component and tertiary structures of various subunits of telomerase, (iv) mutations of telomerase components found in human patients and (v) active researchers who contributed to the wealth of current knowledge on telomerase. The information is hierarchically organized by the components, i.e. the telomerase reverse transcriptase (TERT), telomerase RNA (TR) and other telomerase-associated proteins. The Telomerase Database is a useful resource especially for researchers who are interested in investigating the structure, function, evolution and medical relevance of the telomerase enzyme

Word correlation matrices for protein sequence analysis and remote homology detection

<p>Abstract</p> <p>Background</p> <p>Classification of protein sequences is a central problem in computational biology. Currently, among computational methods discriminative kernel-based approaches provide the most accurate results. However, kernel-based methods often lack an interpretable model for analysis of discriminative sequence features, and predictions on new sequences usually are computationally expensive.</p> <p>Results</p> <p>In this work we present a novel kernel for protein sequences based on average word similarity between two sequences. We show that this kernel gives rise to a feature space that allows analysis of discriminative features and fast classification of new sequences. We demonstrate the performance of our approach on a widely-used benchmark setup for protein remote homology detection.</p> <p>Conclusion</p> <p>Our word correlation approach provides highly competitive performance as compared with state-of-the-art methods for protein remote homology detection. The learned model is interpretable in terms of biologically meaningful features. In particular, analysis of discriminative words allows the identification of characteristic regions in biological sequences. Because of its high computational efficiency, our method can be applied to ranking of potential homologs in large databases.</p

Inventário Florístico Florestal de Santa Catarina: espécies da Floresta Estacional Decidual.

O presente trabalho visou apresentar e analisar a flora da Floresta Estacional Decidual em Santa Catarina, Brasil, tendo como fonte de dados os levantamentos realizados durante o Inventário Florístico Florestal de Santa Catarina. Foram avaliadas as espécies de indivíduos lenhosos de 79 unidades amostrais de 4.000 m². Foram feitas coletas extras de indivíduos férteis, no entorno e nas unidades amostrais, das demais formas de vida. Este esforço amostral registrou 420 espécies, abrangendo 90 famílias e 275 gêneros. Nas unidades amostrais, registrou-se 233 espécies, sendo 204 com diâmetro na altura do peito (DAP) ? 10 cm e 162 com diâmetro na altura do peito DAP ? 10 cm e altura ? 1,50 m, portanto com espécies em comuns. A coleta de material extra registrou 332 angiospermas e uma gimnosperma (Araucaria angustifolia), demonstrando a importância de coletas externas às áreas previamente delimitadas. Entre as ameaçadas de extinção foram registradas Ocotea odorifera e Araucaria angustifolia

Floristic change in Brazil’s southern Atlantic Forest biodiversity hotspot: from the Last Glacial Maximum to the late 21st Century

Brazil’s Atlantic Forest biome is one of the world’s biodiversity hotspots, whose heterogeneous ecosystems are threatened by habitat loss and climate change. Palaeoecological research can provide essential context for the impacts of anthropogenic climate change in the 21st Century and beyond, but existing studies have notable limitations in the insights they can provide: vegetation proxy data are spatially and temporally skewed with inconsistent taxonomic resolution; existing modelling studies typically overlook individualistic species-level responses, are limited in temporal coverage, and lack close integration with empirical palaeoecological data. Here, we investigate the impact of major climate changes upon the species-level floristic composition of southern Brazil’s Atlantic Forest, from the Last Glacial Maximum (LGM) to the late 21st century, by modelling the distributions of 30 key species at seven time slices since the LGM and comparing the assemblages they form with an unprecedented dataset of palaeoecological proxy data. We find notable compositional changes through time across our study area, especially during the early Holocene, which was characterised by extensive no-analogue plant communities. Aspects of these modelled floristic changes are captured in proxy records but many occur in data-sparse regions, highlighting geographic foci for future palaeoecological investigation to test these model predictions. Our findings highlight the individualistic responses of Atlantic Forest plant species to climate change and help resolve long-standing palaeoecological questions – explaining the dominance of highland grasslands at the Last Glacial Maximum (likely due to low atmospheric CO2 concentrations), clarifying the LGM extent of coastal tropical forest (probably in a grassland matrix on exposed continental shelf), and explaining the origins of Araucaria angustifolia’s western populations (from climatic (micro-)refugia rather than human-mediated dispersal). Our results also set the 21st Century’s impending climate and vegetation changes in a 21,000-year temporal context, revealing that, under a high emissions scenario, more than 100,000 km2 of the southern Atlantic Forest will experience more climate-driven floristic change in the coming decades than it has in the last 21 millennia