Biological sequences as pictures – a generic two dimensional solution for iterated maps

Background  

Representing symbolic sequences graphically using iterated maps has enjoyed an enduring popularity since it was first proposed in Jeffrey 1990 as chaos game representation (CGR). The usefulness of this representation goes beyond the convenience of a scale independent representation, it provides a variable memory length representation of transition. This includes the representation of succession with non-integer order, which comes with the promise of generalizing Markovian formalisms. The original proposal targeted genomic sequences only but since then several generalizations have been proposed, many specifically designed to handle protein data.     

The protective role of yeast Cathepsin D in acetic acid-induced apoptosis depends on ANT (Aac2p) but not on the voltage-dependent channel (Por1p)

We have previously shown that the yeast Cathepsin D (CatD) Pep4p translocates from the vacuole to the cytosol during acetic acid-induced apoptosis and is required for efficient mitochondrial degradation, though its specific role in this process is still elusive. Here, we show that the protective role of Pep4p in acetic acid-induced apoptosis depends on its catalytic activity and is independent of the yeast voltage-dependent anion channel Por1p (which has no role on mitochondrial degradation) but dependent on AAC proteins, the yeast adenine nucleotide translocator. Our results demonstrate a differential interplay between yeast vacuolar CatD and mitochondrial proteins involved in apoptosis regulation.     

Net Carbon Emissions from Deforestation in Bolivia during 1990-2000 and 2000-2010: Results from a Carbon Bookkeeping Model

Accurate estimates of global carbon emissions are critical for understanding global warming. This paper estimates net carbon emissions from land use change in Bolivia during the periods 1990–2000 and 2000–2010 using a model that takes into account deforestation, forest degradation, forest regrowth, gradual carbon decomposition and accumulation, as well as heterogeneity in both above ground and below ground carbon contents at the 10 by 10 km grid level. The approach permits detailed maps of net emissions by region and type of land cover. We estimate that net CO₂ emissions from land use change in Bolivia increased from about 65 million tons per year during 1990–2000 to about 93 million tons per year during 2000–2010, while CO₂ emissions per capita and per unit of GDP have remained fairly stable over the sample period. If we allow for estimated biomass increases in mature forests, net CO₂ emissions drop to close to zero. Finally, we find these results are robust to alternative methods of calculating emissions.     

Genomic and Proteomic Studies on Plesiomonas shigelloides Lipopolysaccharide Core Biosynthesis

We report here the identification of waa clusters with the genes required for the biosynthesis of the core lipopolysaccharides (LPS) of two Plesiomonas shigelloides strains. Both P. shigelloides waa clusters shared all of the genes besides the ones flanking waaL. In both strains, all of the genes were found in the waa gene cluster, although one common core biosynthetic gene (wapG) was found in a different chromosome location outside the cluster. Since P. shigelloides and Klebsiella pneumoniae share a core LPS carbohydrate backbone extending up at least to the second outer-core residue, the functions of the common P. shigelloides genes were elucidated by genetic complementation studies using well-defined K. pneumoniae mutants. The function of strain-specific inner- or outer-core genes was identified by using as a surrogate acceptor LPS from three well-defined K. pneumoniae core LPS mutants. Using this strategy, we were able to assign a proteomic function to all of the P. shigelloides waa genes identified in the two strains encoding six new glycosyltransferases (WapA, -B, -C, -D, -F, and -G). P. shigelloides demonstrated an important variety of core LPS structures, despite being a single species of the genus, as well as high homologous recombination in housekeeping genes.     

Plant species diversity in remnant grasslands on arable soils in the cropping Pampa

In order to provide a baseline for management decisions, we evaluated vegetation heterogeneity among 38 remnant grasslands located on high agronomic potential soils along a five degree-east–west transect in the cropping Pampa. This extensive region has been cultivated for well over a century, small-scale traditional forms of agriculture were progressively replaced with large-scale industrial forms and its cropped area has more than doubled in the last 25 years, threatening the maintenance of biodiversity associated to productive soils. We characterized the diversity of this grassland patches, identified its main environmental drivers and searched for factors that favor their invasion by exotic plant species. Vegetation samples were analysed through Canonical Correspondence Analysis, proportional distribution of functional groups was compared and regression models were estimated to identify variables associated with exotic species importance. Water availability, determined by climate and soil characteristics, was the main driving factor of floristic heterogeneity in these grasslands. Exotic richness, mostly of Eurasian species, increases toward the east, related to proximity to the entrance port. The functional group of C₄ native grasses seems to be responsible for biotic resistance to invasion. More than 80% of the species recorded during the first vegetation registers in 1930 are still present, while the number of exotics was seven-fold increased. Despite covering small areas as isolated stands, these are hot spots of native biodiversity and must be the object of increasing attention for conservation and restoration in order to protect the biodiversity of an extensive agricultural landscape.     

New Data on the Distribution of Kellicottia bostoniensis (Rousselet, 1908) (Rotifera: Monogononta: Brachionidae): Its Presence in Argentina

The discovery of this species in plankton samples taken at five stations in the Iguazú River and Uruguay River (in a reservoir and an affluent) is reported. Data on the morphology and measurements of individuals collected are shown. This species had previously been registered in Brazil, South America, where it has dispersed widely. The Iguazú River, tributary of the Paraná River, and the Uruguay River could constitute an important dispersal path from Brazilian territory to aquatic environments of Del Plata basin which contains 85% of the freshwater of Argentina.     

Isolation and Sequencing of a Temperate Transducing Phage for Pasteurella multocida

A temperate bacteriophage (F108) has been isolated through mitomycin C induction of a Pasteurella multocida serogroup A strain. F108 has a typical morphology of the family Myoviridae, presenting a hexagonal head and a long contractile tail. F108 is able to infect all P. multocida serogroup A strains tested but not those belonging to other serotypes. Bacteriophage F108, the first P. multocida phage sequenced so far, presents a 30,505-bp double-stranded DNA genome with cohesive ends (CTTCCTCCCC cos site). The F108 genome shows the highest homology with those of Haemophilus influenzae HP1 and HP2 phages. Furthermore, an F108 prophage attachment site in the P. multocida chromosome has been established to be inside a gene encoding tRNA^Leu. By using several chromosomal markers that are spread along the P. multocida chromosome, it has been demonstrated that F108 is able to perform generalized transduction. This fact, together with the absence of pathogenic genes in the F108 genome, makes this bacteriophage a valuable tool for P. multocida genetic manipulation.     

The Comparative Osmoregulatory Ability of Two Water Beetle Genera Whose Species Span the Fresh-Hypersaline Gradient in Inland Waters (Coleoptera: Dytiscidae,Hydrophilidae)

A better knowledge of the physiological basis of salinity tolerance is essential to understanding the ecology and evolutionary history of organisms that have colonized inland saline waters. Coleoptera are amongst the most diverse macroinvertebrates in inland waters, including saline habitats; however, the osmoregulatory strategies they employ to deal with osmotic stress remain unexplored. Survival and haemolymph osmotic concentration at different salinities were examined in adults of eight aquatic beetle species which inhabit different parts of the fresh—hypersaline gradient. Studied species belong to two unrelated genera which have invaded saline waters independently from freshwater ancestors; Nebrioporus (Dytiscidae) and Enochrus (Hydrophilidae). Their osmoregulatory strategy (osmoconformity or osmoregulation) was identified and osmotic capacity (the osmotic gradient between the animal’s haemolymph and the external medium) was compared between species pairs co-habiting similar salinities in nature. We show that osmoregulatory capacity, rather than osmoconformity, has evolved independently in these different lineages. All species hyperegulated their haemolymph osmotic concentration in diluted waters; those living in fresh or low-salinity waters were unable to hyporegulate and survive in hyperosmotic media (> 340 mosmol kg^-1). In contrast, the species which inhabit the hypo-hypersaline habitats were effective hyporegulators, maintaining their haemolymph osmolality within narrow limits (ca. 300 mosmol kg^-1) across a wide range of external concentrations. The hypersaline species N. ceresyi and E. jesusarribasi tolerated conductivities up to 140 and 180 mS cm^-1, respectively, and maintained osmotic gradients over 3500 mosmol kg^-1, comparable to those of the most effective insect osmoregulators known to date. Syntopic species of both genera showed similar osmotic capacities and in general, osmotic responses correlated well with upper salinity levels occupied by individual species in nature. Therefore, osmoregulatory capacity may mediate habitat segregation amongst congeners across the salinity gradient.