Assessment of the nursery species pool for restoring landscapes in southeastern Brazil

Brazil has committed to fulfilling international restoration goals and to enforcing environmental legislation that will require private landowners to undertake ecological restoration of 21 million hectares of degraded and deforested landscapes. To support a broad range of restoration practices, a well‐established supply chain capable of representing regional plant diversity is essential. This study investigated the restoration species pool in native plant nurseries in São Paulo state, located in southeastern Brazil, and evaluated their geographic distribution, similarity of their plant stocks, and the proportion of species represented from regional floras. Despite a lack of technical assistance and a significant presence of nonnative species (126 species, average 7.5 species/nursery), we found an impressive native species richness in plant nurseries (561 species, average 86.4 species/nursery) from both the Atlantic Forest and Cerrado domains, representing 38–44% of regional floras. There was a huge bias toward tree and shrub species (96.6%) and an absence or underrepresentation of other growth forms, as well as of savanna specialists, animal‐dispersed, and threatened species. The dissimilarity of species observed among the different nurseries surveyed highlights their role in representing regional diversity, which reflects their regional seed collection practices. Effective assistance and training are essential to address issues related to misidentification of species, underrepresentation of most functional plant groups, and the presence of nonnative species, as well as to support the supply chain, which is currently undergoing a market downturn.     

The Impact of Aminoglycosides on the Dynamics of Translation Elongation

1. Download : Download full-size image

Highlights? Combined single-molecule, structural, and biochemical studies on aminoglycoside action ? Aminoglycosides disrupt translation through inhibiting the dynamics of elongation ? Apramycin blocks translocation in translation elongation ? Paromomycin and gentamicin disrupt ribosomal rotation and translocation     

Overexpression of a bacterial chymotrypsin: application for L-amino acid ester hydrolysis

In this work, a reliable protocol was designed to rapidly express and purify a microbial chymotrypsin(ogen) as a useful alternative to using animal proteases. The cDNA encoding for chymotrypsinogen from the deuteromycete Metarhizium anisopliae (chy1) was overexpressed in an Origami2(DE3) E. coli strain deficient in thioredoxin reductase and glutathione reductase activities, thus possibly allowing disulfide exchange. By using a quick purification protocol, in which the hexahistidine tag was added at the C-terminal end of the protease, the recombinant CHY1 protein could be purified in a single step on an Ni-NTA column as a mixture of 19.5- and 15-kDa mature active forms and did not require further activation/maturation steps. This expression and purification procedure offers an easier and faster means of producing recombinant CHY1 chymotrypsin than that previously described for Pichia pastoris. The kinetic properties could be characterized and CHY1 chymotrypsin was demonstrated to efficiently catalyze N-acetylated L-phenylalanine and L-tyrosine methyl ester hydrolysis.     

Sphingosine-1-Phosphate and Calcium Signaling in Cerebellar Astrocytes and Differentiated Granule Cells

S1P is involved in the regulation of multiple biological processes (cell survival, growth, migration and differentiation) both in neurons and glial cells. The study was aimed at investigating the possible effects of S1P on calcium signaling in cerebellar astrocytes and differentiated granule cells. In cerebellar astrocytes S1P is able to mediate calcium signaling mainly through G_i protein coupled receptors, whereas in differentiated neurons it failed to evoke any calcium signaling, despite acting both extracellularly and intracellularly. The data indicate strict cell specificity in S1P-evoked calcium response, which could be relevant to communication between neurons and glial cells in the cerebellum.     

Iron limitation by transferrin promotes simultaneous cheating of pyoverdine and exoprotease in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a primary bacterial model to study cooperative behaviors because it yields exoproducts such as siderophores and exoproteases that act as public goods and can be exploited by selfish nonproducers behaving as social cheaters. Iron-limited growth medium, mainly casamino acids medium supplemented with transferrin, is typically used to isolate and study nonproducer mutants of the siderophore pyoverdine. However, using a protein as the iron chelator could inadvertently select mutants unable to produce exoproteases, since these enzymes can degrade the transferrin to facilitate iron release. Here we investigated the evolutionary dynamics of pyoverdine and exoprotease production in media in which iron was limited by using either transferrin or a cation chelating resin. We show that concomitant loss of pyoverdine and exoprotease production readily develops in media containing transferrin, whereas only pyoverdine loss emerges in medium treated with the resin. Characterization of exoprotease- and pyoverdine-less mutants revealed loss in motility, different mutations, and large genome deletions (13–33 kb) including Quorum Sensing (lasR, rsal, and lasI) and flagellar genes. Our work shows that using transferrin as an iron chelator imposes simultaneous selective pressure for the loss of pyoverdine and exoprotease production. The unintended effect of transferrin uncovered by our experiments can help to inform the design of similar studies.Subject terms: Bacteriology, Microbial ecology     

Distinct Actions of Rab3 and Rab27 GTPases on Late Stages of Exocytosis of Insulin

Rab GTPases associated with insulin‐containing secretory granules (SGs) are key in targeting, docking and assembly of molecular complexes governing pancreatic β‐cell exocytosis. Four Rab3 isoforms along with Rab27A are associated with insulin granules, yet elucidation of the distinct roles of these Rab families on exocytosis remains unclear. To define specific actions of these Rab families we employ Rab3GAP and/or EPI64A GTPase‐activating protein overexpression in β‐cells from wild‐type or Ashen mice to selectively transit the entire Rab3 family or Rab27A to a GDP‐bound state. Ashen mice carry a spontaneous mutation that eliminates Rab27A expression. Using membrane capacitance measurements we find that GTP/GDP nucleotide cycling of Rab27A is essential for generation of the functionally defined immediately releasable pool (IRP) and central to regulating the size of the readily releasable pool (RRP). By comparison, nucleotide cycling of Rab3 GTPases, but not of Rab27A, is essential for a kinetically rapid filling of the RRP with SGs. Aside from these distinct functions, Rab3 and Rab27A GTPases demonstrate considerable functional overlap in building the readily releasable granule pool. Hence, while Rab3 and Rab27A cooperate to generate release‐ready SGs in β‐cells, they also direct unique kinetic and functional properties of the exocytotic pathway.      

Core and accessory genome architecture in a group of Pseudomonas aeruginosa Mu-like phages

Background

Bacteriophages that infect the opportunistic pathogen Pseudomonas aeruginosa have been classified into several groups. One of them, which includes temperate phage particles with icosahedral heads and long flexible tails, bears genomes whose architecture and replication mechanism, but not their nucleotide sequences, are like those of coliphage Mu. By comparing the genomic sequences of this group of P. aeruginosa phages one could draw conclusions about their ontogeny and evolution.

Results

Two newly isolated Mu-like phages of P. aeruginosa are described and their genomes sequenced and compared with those available in the public data banks. The genome sequences of the two phages are similar to each other and to those of a group of P. aeruginosa transposable phages. Comparing twelve of these genomes revealed a common genomic architecture in the group. Each phage genome had numerous genes with homologues in all the other genomes and a set of variable genes specific for each genome. The first group, which comprised most of the genes with assigned functions, was named “core genome”, and the second group, containing mostly short ORFs without assigned functions was called “accessory genome”. Like in other phage groups, variable genes are confined to specific regions in the genome.

Conclusion

Based on the known and inferred functions for some of the variable genes of the phages analyzed here, they appear to confer selective advantages for the phage survival under particular host conditions. We speculate that phages have developed a mechanism for horizontally acquiring genes to incorporate them at specific loci in the genome that help phage adaptation to the selective pressures imposed by the host.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1146) contains supplementary material, which is available to authorized users.     

Signal detection in high-resolution mass spectrometry data

Mass spectrometry data from high-resolution time-of-flight instruments often contain a vast number of noninformative background-ion peaks whose signal is similar to that of peptide peaks. Consequently, seeking peptide signal in these spectra based on a signal-to-noise ratio will remove signal peaks as well as noise. This work characterizes the background as a precursor to seeking peptide-related features. Robust-regression methods are used to estimate distributions for null (background) peak intensities and locations. Defining signal peaks as outliers with respect to these distributions leads to more precision in detecting the isotopic envelope of peaks from low-abundance peptides in high-resolution spectra.     

Factors influencing the release of volatiles in Anastrepha obliqua males (Diptera: Tephritidae)

During sexual signaling, males of Anastrepha obliqua (Macquart) form leks and attract females by producing sounds and releasing volatile compounds. The objective of this study was to investigate the influence time of time of day, age, irradiation, mating status, and the presence of host fruit on the release of volatile components by laboratory-reared A. obliqua males. A. obliqua males released four compounds identified by gas chromatography coupled with mass spectrometry (GC-MS) as (E,E)-alpha-farnesene, (Z,E)-alpha-farnesene, (Z)-3-nonenol, and a farnesene isomer during calling behavior. Although males released volatiles during the entire day, the amount of volatiles was higher in the early morning and afternoon hours. Males began to emit volatiles when they were 6 d old, but only the amount of (Z)-3-nonenol was affected by age. Irradiation of flies with gamma rays from a (60)Co source at a dose rate of 0.8 Gy significantly reduced the amount of volatiles released during calling behavior. The amount of volatiles was lower in recently mated males than virgin males. However, there were no significant differences between virgin males and males 24 h after mating. The presence of host fruit did not affect the amount of volatiles compared with the control.