Comparison of the Bruker MALDI-TOF Mass Spectrometry System and Conventional Phenotypic Methods for Identification of Gram-Positive Rods

In recent years, MALDI-TOF Mass Spectrometry (MS) method has emerged as a promising and a reliable tool for bacteria identification. In this study we compared Bruker MALDI-TOF MS and conventional phenotypic methods to identify a collection of 333 Gram-positive clinical isolates comprising 22 genera and 60 species. 16S rRNA sequencing was the reference molecular technique, and rpoB gene sequecing was used as a secondary gene target when 16Sr RNA did not allow species identification of Corynebacterium spp. We also investigate if score cut-offs values of ≥1,5 and ≥1,7 were accurate for genus and species-level identification using the Bruker system. Identification at species level was obtained for 92,49% of Gram-positive rods by MALDI-TOF MS compared to 85,89% by phenotypic method. Our data validates the score ≥1,5 for genus level and ≥1,7 for species-level identification in a large and diverse collection of Gram-positive rods. The present study has proved the accuracy of MALDI-TOF MS as an identification method in Gram-positive rods compared to currently used methods in routine laboratories.     

Morphological variation of Aechmea distichantha (Bromeliaceae) in a Chaco forest: habitat and size-related effects

Plants show different morphologies when growing in different habitats, but they also vary in their morphology with plant size. We examined differences in sun- and shade-grown plants of the bromeliad Aechmea distichantha with respect to relationships between plant size and variables related to plant architecture, biomass allocation and tank water dynamics. We selected vegetative plants from the understorey and from forest edges of a Chaco forest, encompassing the whole size range of this bromeliad. Plant biomass was positively correlated with most architectural variables and negatively correlated with most biomass allocation variables. Understorey plants were taller and had larger diameters, whereas sun plants had more leaves, larger sheath area, sheath biomass and sheath mass fraction. All tank water-related variables were positively correlated with plant biomass. Understorey plants had a greater projected leaf area, whereas sun plants had higher water content and evaporative area. Plasticity indices were higher for water-related than for allocation variables. In conclusion, there were architectural and biomass allocation differences between sun- and shade-grown plants along a size gradient, which, in turn, affected tank water-related variables.     

Influence of global warming on forest coleopteran communities with special reference to ambrosia and bark beetles

Forest insect pests are one of the major disturbance factors in forest ecosystems and their outbreaks are expected to be more severe under the influence of global warming. Coleopterans are dominant among forest insects and their ecological functions include general detritivores, dead wood feeders, fungivores, herbivores, live wood feeders and predators. Ambrosia and bark beetles contribute to ecological succession of forests and, therefore, ecological functions of forests can be changed in response to their outbreaks. Mountain pine beetle (MPB) outbreaks are the most dramatic example of changes in the ecological functions of forest due to the outbreak of a forest insect pest altered by global warming. Composition of coleopteran species varies with latitude. However, composition of functional groups is consistent with latitude which indicates that resources available to beetles are consistent. In coleopteran communities, ambrosia and bark beetles can become dominant due to increases of dead or stressed trees due to the warming climate. This can also induce changes in the ecological functions of coleopterans, i.e. selective force to displace trees that have lower ecological fitness due to temperature increase. Therefore, recent increases in the density ambrosia and bark beetles offer a chance to study ecological processes in forests under the influence of global warming.     

Antifungal activity of two Lactobacillus strains with potential probiotic properties

Aflatoxin (highly toxic and carcinogenic secondary metabolites produced by fungi) contamination is a serious problem worldwide. Modern agriculture and animal production systems need to use high-quality and mycotoxin-free feedstuffs. The use of microorganisms to preserve food has gained importance in recent years due to the demand for reduced use of chemical preservatives by consumers. Lactic acid bacteria are known to produce various antimicrobial compounds that are considered to be important in the biopreservation of food and feed. Lactobacillus rhamnosus L60 and Lactobacillus fermentum L23 are producers of secondary metabolites, such as organic acids, bacteriocins and, in the case of L60, hydrogen peroxide. The antifungal activity of lactobacilli strains was determined by coculture with Aspergillus section Flavi strains by two qualitative and one quantitative methods. Both L23 and L60 completely inhibited the fungal growth of all aflatoxicogenic strains assayed. Aflatoxin B (1) production was reduced 95.7-99.8% with L60 and 27.5-100% with L23. Statistical analysis of the data revealed the influence of L60 and L23 on growth parameters and aflatoxin B (1) production. These results are important given that these aflatoxicogenic fungi are natural contaminants of feed used for animal production, and could be effectively controlled by Lactobacillus L60 and L23 strains with probiotic properties.     

Proteomic analysis of apoptosis related proteins regulated by proto‐oncogene protein DEK

A nuclear phosphoprotein, DEK, is implicated in certain human diseases, such as leukemia and antoimmune disorders, and a major component of metazoan chromatin. Basically as a modulator of chromatin structure, it can involve in various DNA and RNA‐dependent processes and function as either an activator or repressor. Despite of numerous efforts to suggest the biological role of DEK, direct target proteins of DEK in different physiological status remains elusive. To investigate if DEK protein triggers the changes in certain protein networks, DEK was knocked down at both types of cell clones using siRNA expression. Here we provide a catalogue of proteome profiles in total cell lysates derived from normal HeLa and DEK knock‐down HeLa cells and a good in vitro model system for dissecting the protein networks due to this proto‐oncogenic DEK protein. In this biological context, we compared total proteome changes by the combined methods of two‐dimensional gel electrophoresis, quantitative image analysis and MALDI‐TOF MS analysis. There were a large number of targets for DEK, which were differentially expressed in DEK knock‐down cells and consisted of 58 proteins (41 up‐regulated and 17 down‐regulated) differentially regulated expression was further confirmed for some subsets of candidates by Western blot analysis using specific antibodies. In the identified 58 spots, 16% of proteins are known to be associated with apoptosis. Among others, we identified apoptosis related proteins such as Annexins, Enolase1, Lamin A, and Glutathione‐S‐transferase omega 1. These results are consistent with recent studies indicating the crucial role of DEK in apoptosis pathway. We further demonstrated by ChIP analysis that knock‐down of DEK caused hyperacetylation of histones around Prx VI promoter which is upregulated in our profile. Using immunoblotting analysis, we have demonstrated the modulation of other caspase‐dependent apoptosis related proteins by DEK knock‐down and further implicate its role in apoptosis pathway. J. Cell. Biochem. 106: 1048–1059, 2009. © 2009 Wiley‐Liss, Inc.     

Woody vegetation structure and composition of the last relicts of Espinal vegetation in subtropical Argentina

Until the beginning of the twentieth century there were extensive subtropical seasonal thorny forests surrounding the Pampas grasslands of Argentina, known as the ‘Espinal’. In central Argentina there still exist relicts of the Espinal, belonging to the ‘Entrerrianense District’. These forests were never described or analyzed in detail. In 2004 we studied 10 randomly located plots of 50 × 2 m. All individuals and stems of woody species were counted and their diameters at breast height (DBH) were measured; individuals with <1 cm DBH were considered juveniles. We recorded 2,300 woody individuals/ha corresponding to 12 species. The more constant species are the palm Trithrinax campestris (100%), Celtis tala (90%), Prosopis alba and Celtis pallida (both 50%). The plots are relatively homogeneous, but once classified with cluster analysis two groups are formed according to the relative abundance of C. tala and T. campestris; the latter species is more frequent in more open or fire-disturbed habitats. The results of Canonical Analysis of Principal coordinates are in agreement with the classification. We postulate that the differences between both groups are caused by a differential degree of disturbance (probably caused by fires). Both dominant species show abundant juveniles, and the invasion by exotic woody species is limited. These forest relicts are among the last remnants of the massive expansions of forests in central Argentina. Besides their historical value, an urgent call is made for their preservation, sustainable use and defence from biological invasions.     

Inventory and functional analysis of the large Hrp regulon in Ralstonia solanacearum: identification of novel effector proteins translocated to plant host cells through the type III secretion system

The ability of Ralstonia solanacearum strain GMI1000 to cause disease on a wide range of host plants (including most Solanaceae and Arabidopsis thaliana) depends on genes activated by the regulatory gene hrpB. HrpB controls the expression of the type III secretion system (TTSS) and pathogenicity effectors transiting through this pathway. In order to establish the complete repertoire of TTSS-dependent effectors belonging to the Hrp regulon and to start their functional analysis, we developed a rapid method for insertional mutagenesis, which was used to monitor the expression of 71 candidate genes and disrupt 56 of them. This analysis yielded a total of 48 novel hrpB-regulated genes. Using the Bordetella pertussis calmodulin-dependent adenylate cyclase reporter fusion system, we provide direct biochemical evidence that five R. solanacearum effector proteins are translocated into plant host cells through the TTSS. Among these novel TTSS effectors, RipA and RipG both belong to multigenic families, RipG defining a novel class of leucine-rich-repeats harbouring proteins. The members of these multigenic families are differentially regulated, being composed of genes expressed in either an hrpB-dependent or an hrpB-independent manner. Pathogenicity assays of the 56 mutant strains on two host plants indicate that, with two exceptions, mutations in individual effectors have no effect on virulence, a probable consequence of genetic and functional redundancy. This large repertoire of HrpB-regulated genes, which comprises > 20 probable TTSS effector genes with no counterparts in other bacterial species, represents an important step towards a full-genome understanding of R. solanacearum virulence.