Tree community features of two stands of riverine forest under different flooding regimes in Southern Brazil

Two 1 ha plots of a Southern Brazilian subtropical riverine forest, subject to different frequency and duration of floods, were compared to detect the differences in physiognomic structure, tree community composition, richness and diversity. Each plot was made up of 100 contiguous 10×10 m subplots, where 3451 trees with pbh 15 cm were measured and identified. The survey observed 30 tree species, in the frequently flooded plot and 48 in the occasionally flooded plot. A detailed topographical and soil survey was carried out in both plots and indicated that the levels of organic matter and most mineral nutrients were higher in the frequently flooded stand. The forest understory was denser in the occasionally flooded stand which also showed taller emergent trees. Multivariate ordination and grouping techniques showed that the species’ abundance distribution was strongly related to the topographical variation. There was a clear pattern of species turnover according to topographic position, indicating that tree species developed different abilities to survive flooding events. As a result, the two plots also differed in their tree frequency per species regeneration, vertical distribution and dispersion groups. Both species richness and diversity decreased with increasing flood frequency, also showing a patchy distribution within both stands. At a local scale, flooding regime is regulating the spatial variation of α-diversity by forming different seral stages of predictable species composition. Compared to regularly flooded riverine and floodplain forests, riverine forests, with unpredictable flooding regimes, may show higher diversity at a local scale and more abundant opportunistic species of high environmental plasticity.     

Vertebrate dispersal syndromes along the Atlantic forest: broad-scale patterns and macroecological correlates

Aim To assess the geographical variation in the relative importance of vertebrates, and more specifically of birds and mammals, as seed dispersal agents in forest communities, and to evaluate the influence of geographical and climatic factors on the observed trends. Location One hundred and thirty‐five forest communities in the Brazilian Atlantic forest. Methods We collected data on dispersal modes for 2292 woody species. By combining species × site with species × trait matrices, we obtained the percentages of endozoochory, ornithochory, mastozoochory and the mean fruit diameter for the local forest communities. We used Spearman's correlation to assess bivariate relationships between variables. Subsequently, we performed paired t‐tests to verify if variations in frequency of dispersal modes and mean fruit diameter were influenced by altitude or temperature. Then, we applied multiple linear regressions to evaluate the effect of geographical and climatic variables on variation in the relative frequency of dispersal modes and mean fruit diameter across communities. Results We found no consistent latitudinal or longitudinal trend in the percentage of vertebrate‐dispersed species, neither bird‐ nor mammal‐dispersed species along the Atlantic forest. Endozoochory was affected chiefly by annual mean rainfall, increasing towards moister sites. Forest communities located at higher altitudes had a higher percentage of bird‐dispersed species. Even when sites with identical values of annual mean temperature were compared, altitude had a positive effect on ornithochory. Conversely, we found a higher percentage of mammal‐dispersed species in warmer forests, even when locations at the same altitudinal belts were contrasted. Fruit diameter was clearly related to altitude, decreasing towards higher elevations. Main conclusions This is the first analysis of a large data set on dispersal syndromes in tropical forest communities. Our findings support the hypotheses that: (1) geographical variation in the relative number of fleshy fruit species is mainly driven by moisture conditions and is relatively independent of geographical location, and (2) broad‐scale trends in fruit size correspond to geographical variation in the relative importance of mammals and birds as seed dispersal agents at the community level.     

<Emphasis Type="Italic">Pichia stipitis</Emphasis> xylose reductase helps detoxifying lignocellulosic hydrolysate by reducing 5-hydroxymethyl-furfural (HMF)

Background  

Pichia stipitis xylose reductase (Ps-XR) has been used to design Saccharomyces cerevisiae strains that are able to ferment xylose. One example is the industrial S. cerevisiae xylose-consuming strain TMB3400, which was constructed by expression of P. stipitis xylose reductase and xylitol dehydrogenase and overexpression of endogenous xylulose kinase in the industrial S. cerevisiae strain USM21.     

Effects of flooding regime and woody bamboos on tree community dynamics in a section of tropical semideciduous forest in South-Eastern Brazil

The influence of a population of the understorey woody bamboo Merostachys riedeliana and different flooding regimes on tree community dynamics in a section of tropical semideciduous forest in South-Eastern Brazil was examined. A forest section with an area of 1.6 ha composed of 71 adjacent plots was located on a slope ending at the river margin. The section was divided into five topographical sectors according to the mean duration of river floods. In 1991 and 1998 all trees with a diameter at the base of the trunk ≥ 5 cm were measured, identified and tagged, and all live bamboo culms were counted. Annualised estimates of the rates of tree mortality and recruitment, gain and loss of tree basal area, and change in bamboo density were calculated for each of the 71 plots and five topographical sectors as well as for diameter classes and tree species. To segregate patterns arising from spatially autocorrelated events, geostatistical analyses were used prior to statistical comparisons and correlations. In general, mortality rates were not compensated by recruitment rates but there was a net increase in basal area in all sectors, suggesting that the tree community as a whole was in a building phase. Tree community dynamics of the point bar forest (Depression and Levée sectors) differed from that of the upland forest (Ridgetop, Middle Slope and Lower Slope sectors) in the extremely high rates of gain in basal area. The predominant and specialised species, Inga vera and Salix humboldtiana, are probably favoured by relaxed competition in an environment stressed by long-lasting floods. In the upland forest, mortality rates were highest at the Middle Slope, particularly for smaller trees, while recruitment rates were lowest. As bamboo clumps were concentrated in this sector, the locally higher instability in the tree community probably resulted from the direct interference of bamboos. The density of bamboo culms in the upland forest was negatively correlated with the rates of tree recruitment and gain in basal area, and positively correlated with tree mortality rates. Bamboos therefore seemed to restrict the recruitment, growth and survival of trees. This revised version was published online in June 2006 with corrections to the Cover Date.     

Reduced natural selection associated with low recombination in Drosophila melanogaster

Synonymous codons are not used equally in many organisms, and the extent of codon bias varies among loci. Earlier studies have suggested that more highly expressed loci in Drosophila melanogaster are more biased, consistent with findings from several prokaryotes and unicellular eukaryotes that codon bias is partly due to natural selection for translational efficiency. We link this model of varying selection intensity to the population-genetics prediction that the effectiveness of natural selection is decreased under reduced recombination. In analyses of 385 D. melanogaster loci, we find that codon bias is reduced in regions of low recombination (i.e., near centromeres and telomeres and on the fourth chromosome). The effect does not appear to be a linear function of recombination rate; rather, it seems limited to regions with the very lowest levels of recombination. The large majority of the genome apparently experiences recombination at a sufficiently high rate for effective natural selection against suboptimal codons. These findings support models of the Hill-Robertson effect and genetic hitchhiking and are largely consistent with multiple reports of low levels of DNA sequence variation in regions of low recombination.      

Kappa-chain constant-region gene sequences in genus Rattus: coding regions are diverging more rapidly than noncoding regions

We have determined the nucleotide sequence of a 1,200-base pair (bp) genomic fragment that includes the kappa-chain constant-region gene (C kappa) from two species of native Australian rodents, Rattus leucopus cooktownensis and Rattus colletti. Comparison of these sequences with each other and with other rodent C kappa genes shows three surprising features. First, the coding regions are diverging at a rate severalfold higher than that of the nearby noncoding regions. Second, replacement changes within the coding region are accumulating at a rate at least as great as that of silent changes. Third, most of the amino acid replacements are localized in one region of the C kappa domain--namely, the carboxy-terminal "bends" in the alpha-carbon backbone. These three features have previously been described from comparisons of the two allelic forms of C kappa genes in R. norvegicus. These data imply the existence of considerable evolutionary constraints on the noncoding regions (based on as yet undetermined functions) or powerful positive selection to diversify a portion of the constant-region domain (whose physiological significance is not known). These surprising features of C kappa evolution appear to be characteristic only of closely related C kappa genes, since comparison of rodent with human sequences shows the expected greater conservation of coding regions, as well as a predominance of silent nucleotide substitutions within the coding regions.      

Quantification of the virus-host interaction in human T lymphotropic virus I infection

Background

Cellular infection with human immunodeficiency virus (HIV) both in vitro and in vivo requires a member of the chemokine receptor family to act as a co-receptor for viral entry. However, it is presently unclear to what extent the interaction of HIV proteins with chemokine receptors generates intracellular signals that are important for productive infection.

Results

In this study we have used a recently described family of chemokine inhibitors, termed BSCIs, which specifically block chemokine-induced chemotaxis without affecting chemokine ligands binding to their receptors. The BSCI termed Peptide 3 strongly inhibited CCR5 mediated HIV infection of THP-1 cells (83 ± 7% inhibition assayed by immunofluoresence staining), but had no effect on gp120 binding to CCR5. Peptide 3 did not affect CXCR4-dependent infection of Jurkat T cells.

Conclusion

These observations suggest that, in some cases, intracellular signals generated by the chemokine coreceptor may be required for a productive HIV infection.     

<Emphasis Type="Italic">xylA</Emphasis> and <Emphasis Type="Italic">xylB</Emphasis> overexpression as a successful strategy for improving xylose utilization and poly-3-hydroxybutyrate production in <Emphasis Type="Italic">Burkholderia sacchari</Emphasis>

Despite the versatility and many advantages of polyhydroxyalkanoates as petroleum-based plastic substitutes, their higher production cost compared to petroleum-based polymers has historically limited their large-scale production. One appealing approach to reducing production costs is to employ less expensive, renewable feedstocks. Xylose, for example is an abundant and inexpensive carbon source derived from hemicellulosic residues abundant in agro-industrial waste (sugarcane bagasse hemicellulosic hydrolysates). In this work, the production of poly-3-hydroxybutyrate P(3HB) from xylose was studied to develop technologies for conversion of agro-industrial waste into high-value chemicals and biopolymers. Specifically, this work elucidates the organization of the xylose assimilation operon of Burkholderia sacchari, a non-model bacterium with high capacity for P(3HB) accumulation. Overexpression of endogenous xylose isomerase and xylulokinase genes was successfully assessed, improving both specific growth rate and P(3HB) production. Compared to control strain (harboring pBBR1MCS-2), xylose utilization in the engineered strain was substantially improved with 25% increase in specific growth rate, 34% increase in P(3HB) production, and the highest P(3HB) yield from xylose reported to date for B. sacchari (Y_P3HB/Xil = 0.35 g/g). This study highlights that xylA and xylB overexpression is an effective strategy to improve xylose utilization and P(3HB) production in B. sacchari.     

Effects of past disturbance and edges on tree community structure and dynamics within a fragment of tropical semideciduous forest in south-eastern Brazil over a five-year period (1987–1992)

Tree community structure and dynamics of a 5.8 ha fragment of montane semideciduous forest in south-eastern Brazil are described based on two successive surveys of trees with dbh 5 cm carried out in 1987 and 1992 in 126 20 × 20 m quadrats. The main purpose was to assess whether the spatial variation of dynamic and structural variables were related to edge-effects and past disturbance regimes. The totals for the two surveys were, respectively, 6528 and 6770 trees, and 94.89 and 108.53 m² of basal area. The forest fragment was at an aggrading sylvigenetic phase, indicated by an overall net increase in density and basal area, and by a declining proportion of trees of smaller size. The overall annual mortality and recruitment rates were 2.6% and 3.0%, respectively. The dynamic process, however, was strongly affected by spatial heterogeneity. The more severely disturbed sectors had lower average canopy heights and basal areas per hectare, and higher tree densities, proportions of smaller trees, and relative area of canopy gaps. They also had higher mortality and recruitment rates, resulting in higher turnover rates compared to the sectors which suffered only moderate disturbance regimes. Edge sectors were also affected by different past disturbance regimes. However, they stood out by having a particularly high frequency of liana tangles and the highest rates of net increase both in density and basal area. A canonical correspondence analysis indicated that the effects of past disturbance regimes and edges were highly related to the species distribution in the area. Pioneer species were concentrated on the edges and more severely disturbed sectors, shade-tolerant species were particularly more abundant on the moderately disturbed sites, while light-demanding ones were more widely distributed. Tree community structure was also undergoing important changes, with less common species enjoying higher recruitment rates and density increase compared to the more common ones. Shade-tolerant species were increasing in relative abundance and had comparatively lower mortality rates and higher recruitment rates. On the other hand, pioneer species were under retreat, with a decreasing relative abundance, higher mortality rates and lower recruitment rates.Nomenclature: Oliveira-Filho et al. 1994a,d.     

Effect of flooding regime and understorey bamboos on the physiognomy and tree species composition of a tropical semideciduous forest in Southeastern Brazil

The interrelationship between river flooding regime, topography, soil properties and the distribution of tree and bamboo species was analysed in an area of tropical semideciduous forest on the margins of the Rio Grande, in Madre de Deus de Minas, Southeastern Brazil. A survey was carried out in a single forest plot (1.597 ha, 71 adjacent 225 m² quadrats) located in the inner side of a river bend and extending from the point bar to the top of the slope. All trees (5 cm diameter at the base of the trunk) and bamboo culms were registered. Soil samples were collected and analysed for their properties and the river level was monitored during a two year period. In the point bar the forest was dominated by only two tree species, Salix humboldtiana and Inga affinis, that tended to occur in distinct areas. Differences in soil properties between these areas suggest variation in sedimentation dynamics. In the sloping part of the plot, a canonical correspondence analysis (CCA) indicated that the floristic composition was significantly correlated with three topographic sectors and their corresponding flood regimes. The Lower Slope corresponds to the sharp transition to the point bar forest, endures partial and annual floods and shows a very distinct flora that includes many light-demanding species. The Middle Slope is only occasionally reached by exceptional river floods and is characterised by a high density of the bamboo Merostachys neesii. The comparatively low density and basal area of trees, particularly for the smaller ones, provide evidence that the bamboos are problably interfering with the trees by restricting their recruitment. The Ridgetop lies entirely above the highest flooding level registered. The density of bamboos is lower and the understorey trees abundant.