Control of pyrene fluorescence intensity by in situ addition of CO(2) to an amidine/amine mixture or CO(2) removal from an amidinium carbamate ionic liquid

Addition of CO(2) to an equimolar amidine/amine mixture leads to formation of a switchable ionic liquid, an amidinium carbamate, and appearance of strong fluorescence by a solute, pyrene. Passing a 'displacement gas', N(2), through the ionic liquid or heating it regenerates the amidine/amine mixture and quenches the fluorescence almost totally. No switching or appreciable fluorescence is found when an amidinium dithiocarbamate is the medium.     

The relationship between fire history and an exotic fungal disease in a deciduous forest

Exotic diseases have fundamentally altered the structure and function of forest ecosystems. Controlling exotic diseases across large expanses of forest has proven difficult, but fire may reduce the levels of diseases that are sensitive to environmental conditions. We examined Cornus florida populations in burned and unburned Quercus–Carya stands to determine if burning prior to anthracnose infection has reduced the impacts of an exotic fungal disease, dogwood anthracnose, caused by Discula destructiva. We hypothesized that fire has altered stand structure and created open conditions less conducive to dogwood anthracnose. We compared C. florida density, C. florida health, and species composition and density among four sampling categories: unburned stands, and stands that had burned once, twice, and 3 times over a 20-year period (late 1960s to late 1980s). Double burn stands contained the greatest density of C. florida stems (770 stems ha⁻¹) followed by triple burn stands (233 stems ha⁻¹), single burn stands (225 stems ha⁻¹) and unburned stands (70 stems ha⁻¹; P < 0.01). We observed less crown dieback in small C. florida trees (<5 cm diameter at breast height) in burned stands than in unburned stands (P < 0.05). Indicator species analysis showed that burning favored species historically associated with Quercus–Carya forests and excluded species associated with secondary succession following nearly a century of fire suppression. Our results suggest that fire may mitigate the decline of C. florida populations under attack by an exotic pathogen by altering forest structure and composition. Further, our results suggest that the burns we sampled have had an overall restorative effect on forest communities and were within the fire return interval of the historic fire regime. Consequently, prescribed fire may offer a management tool to reduce the impacts of fungal disease in forest ecosystems that developed under historic burning regimes.     

The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples

Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment.     

Potential risk of biologic pollution associated to the introduction of <i>Pinus radiata</i> in grassland areas

Afforestation is a recommended practice to mitigate global warming. However, their implementation may generate undesirable impacts, mostly if exotic species are used. Plantations of Pinus radiata D Don in Ventania (Bs. As., Argentina) soils showed notorious increments of extractable P (Pe), which could affect the dynamic of this element as well as the degree of phosphorus saturation (GSP_Bray). The objectives of this study were: i) to quantify the GSP_Bray in Mollisols afforested with P. radiata comparing the results with those coming from adjacent, natural grassland areas (base line); ii) to evaluate the potential environmental risk induced by afforestation through the identification of a change point (PC) in the GSP_Bray indicative of a phosphate leaching increment. Treatments included mature stands of P. radiata (TB) and adjacent areas with natural grassland vegetation (TP). Samples were taken at 0-15; 15-30 and 30-45 cm soil depth, and texture, pH, total organic carbon (COT), Pe, soluble reactive phosphorus (PSR), phosphorus sorption index (ISP) and GSP_Bray were determined. The results showed a significant acidification in TB and an increase in the COT stock, indicating an additional atmospheric CO₂ sequestration by the trees. The Pe and PSR values were notoriously higher in TB, and they were reflected in a significant increment in the GSP_Bray with respect to TP. The detection of a significant PC in the GSP_Bray-PSR regression indicates higher chances of phosphate leaching in the forest stands, which could reach water courses, lakes and artificial reservoirs promoting their eutrophication. Because of the potential environmental pollution risk of biologic origin derived from the afforestation with P. radiata in Mollisols areas, their inclusion in clean development practices must be reconsidered.     

Compensatory mechanisms of central U.S. hardwood forest communities in a changing environment

Although it is known that forest productivity is highly correlated with canopy leaf area, the influence of environmental gradients within a forest on leaf area-productivity relationships has not been well-documented, particularly for mixed-species forests. The present study was conducted to define the mechanisms by which Central Hardwood forest communities respond to changes in environment. Ecological Land Type Phases (ELTPs) of the Central Hardwood region, delineated by soils, topography, and indicator vegetation, provided a framework to examine the impacts of environmental gradients on leaf area-productivity relationships at a landscape level. Three ELTPs- (1) Quercus prinus / Carex picta-Vaccinium, Dry slope, (2) Quercus alba-Acer saccharum / Parthenocissus, Dry-Mesic Slope, and (3) Fagus-Acer saccharum / Arisaema, Mesic Slope- were selected and stratified into three slope positions viz. the upper edge of the community, the middle or center of the community on the slope, and the lower edge of the community. Circular plots of 0.02 ha in size were established for sampling. Standing stock (basal area, volume, and biomass), annual production, leaf area index, and growth efficiency were determined for each slope position and examined to determine the mechanisms and trends for community change across slope positions. Among the three communities studied, dry slopes compensated for drier conditions through both a shift in species composition and reduced annual production. Dry-mesic slopes exhibited adaptation only through changing species composition whereas mesic slopes compensated for drier conditions primarily through reduction in annual production. These results indicate that mixed-species forest communities adjust to environmental gradients through several mechanisms and that the relative importance of these mechanisms changes with community type.     

Populations Microbiennes Des Bois

Resumé Les auteurs ont étudié la composition chimique (N, substances humiques, lignine) de copeaux de bois blanc exposés à l'air libre depuis 2 à 10 ans, ainsi que leur type de peuplement fongique. En l'absence de lignivore, le pH, les taux de lignine et d'N s'élèvent et il se forme des quantités modérées d'humus à forte capacité d'échange. Dans le cas contraire, on voit apparaître, en abondance, des substances humiques peu condensées et la matière organique subit une évolution rappelant celle du mor.Avec la collaboration technique de Melle. M. Clet.Kononova, dans sa monographie⁵, signale de Troussov (1916) une étude que nous n'avons pas eu en mains.     

Studies of esterase 6 in Drosophila melanogaster. XVIII. Biochemical differences between the slow and fast allozymes

Most natural populations of Drosophila melanogaster are polymorphic for two major electrophoretic variants at the esterase-6 locus. The frequency of the EST 6F allozyme is greatest in populations in warmer latitudes, whereas the EST 6S allozyme is predominant in colder latitudes. Latitudinal clines in electromorph frequencies are found on three continents. Purified preparations of the allozymes have been characterized for their pH optimum, substrate specificity, organophosphate inhibition, alcohol activation, thermal stability, and kinetic parameters. These and previous analyses of the EST 6 allozymes reveal that the two variants have differences in their physical and kinetic properties that may provide a basis for the selective maintenance of the polymorphisms and an explanation of the clinal variation observed in natural populations.      

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly

Background

Metagenomics is a cultivation-independent approach that enables the study of the genomic composition of microbes present in an environment. Metagenomic samples are routinely sequenced using next-generation sequencing technologies that generate short nucleotide reads. Proteins identified from these reads are mostly of partial length. On the other hand, de novo assembly of a large metagenomic dataset is computationally demanding and the assembled contigs are often fragmented, resulting in the identification of protein sequences that are also of partial length and incomplete. Annotation of an incomplete protein sequence often proceeds by identifying its homologs in a database of reference sequences. Identifying the homologs of incomplete sequences is a challenge and can result in substandard annotation of proteins from metagenomic datasets. To address this problem, we recently developed a homology detection algorithm named GRASP (Guided Reference-based Assembly of Short Peptides) that identifies the homologs of a given reference protein sequence in a database of short peptide metagenomic sequences. GRASP was developed to implement a simultaneous alignment and assembly algorithm for annotation of short peptides identified on metagenomic reads. The program achieves significantly improved recall rate at the cost of computational efficiency. In this article, we adopted three techniques to speed up the original version of GRASP, including the pre-construction of extension links, local assembly of individual seeds, and the implementation of query-level parallelism.

Results

The resulting new program, GRASPx, achieves >30X speedup compared to its predecessor GRASP. At the same time, we show that the performance of GRASPx is consistent with that of GRASP, and that both of them significantly outperform other popular homology-search tools including the BLAST and FASTA suites. GRASPx was also applied to a human saliva metagenome dataset and shows superior performance for both recall and precision rates.

Conclusions

In this article we present GRASPx, a fast and accurate homology-search program implementing a simultaneous alignment and assembly framework. GRASPx can be used for more comprehensive and accurate annotation of short peptides. GRASPx is freely available at http://graspx.sourceforge.net/.