Complete nucleotide sequence and structural organization of pPB1, a small Lactobacillus plantarum cryptic plasmid that originated by modular exchange

A small cryptic plasmid designated pPB1 was isolated from Lactobacillus plantarum BIFI-38 and its complete 2899 bp nucleotide sequence was determined. Sequence analysis revealed four putative open reading frames. Based on sequence analysis two modules could be identified. First, the replication module consisted of a sequence coding for a replication protein (RepB) and its corresponding target site, and two putative repressor proteins (RepA and RepC). Sequence analysis indicated the possible synthesis of an antisense RNA that might regulate RepB production. A putative laggingstrand initiation site was also found, suggesting that pPB1 replicates via a rolling circle mechanism. The second module of pPB1 consisted of a sequence coding for a putative mobilization protein and its corresponding oriT site. Since the nucleotide sequence of the replication module showed 94.5% identity to the similar region on the Leuconostoc lactis plasmid pCI411, and the nucleotide sequence of the mobilization module had 97.5% identity to L. plantarum plasmid pLB4, it is concluded that pPB1 originated by modular exchange between two such plasmids by homologous recombination. Putative recombination sites where crossover might have taken place were also identifiedThis work was supported by Grant 07G/0035/2003 from the Comunidad de Madrid and RM03-002 from the Instituto Nacional de Investigación y Tecnologı´a Agraria y Alimentaria (INIA). We thank R. Gonza´lez and A.V. Carrascosa for their advice and critical reading of the manuscript. B. de las Rivas was a recipient of a postdoctoral fellowship and A. Marcobal of a predoctoral fellowship both from the Comunidad de Madrid.Peer reviewe

Highlights from the Student Council Symposium 2011 at the International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology

The Student Council (SC) of the International Society for Computational Biology (ISCB) organized their annual symposium in conjunction with the Intelligent Systems for Molecular Biology (ISMB) conference

Persistence of dissolved organic matter explained by molecular changes during its passage through soil

Dissolved organic matter affects fundamental biogeochemical processes in the soil such as nutrient cycling and organic matter storage. The current paradigm is that processing of dissolved organic matter converges to recalcitrant molecules (those that resist degradation) of low molecular mass and high molecular diversity through biotic and abiotic processes. Here we demonstrate that the molecular composition and properties of dissolved organic matter continuously change during soil passage and propose that this reflects a continual shifting of its sources. Using ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, we studied the molecular changes of dissolved organic matter from the soil surface to 60 cm depth in 20 temperate grassland communities in soil type Eutric Fluvisol. Applying a semi-quantitative approach, we observed that plant-derived molecules were first broken down into molecules containing a large proportion of low-molecular-mass compounds. These low-molecular-mass compounds became less abundant during soil passage, whereas larger molecules, depleted in plant-related ligno-cellulosic structures, became more abundant. These findings indicate that the small plant-derived molecules were preferentially consumed by microorganisms and transformed into larger microbial-derived molecules. This suggests that dissolved organic matter is not intrinsically recalcitrant but instead persists in soil as a result of simultaneous consumption, transformation and formation

No depth-dependence of fine root litter decomposition in temperate beech forest soils

Aims Subsoil organic carbon (OC) tends to be older and is presumed to be more stable than topsoil OC, but the reasons for this are not yet resolved. One hypothesis is that decomposition rates decrease with increasing soil depth. We tested whether decomposition rates of beech fine root litter varied with depth for a range of soils using a litterbag experiment in German beech forest plots. Methods In three study regions (Schorfheide-Chorin, Hainich-Dün and Schwäbische-Alb), we buried 432 litterbags containing 0.5 g of standardized beech root material (fine roots with a similar chemical composition collected from 2 year old Fagus sylvatica L. saplings, root diameter<2mm) at three different soil depths (5, 20 and 35 cm). The decomposition rates as well as the changes in the carbon (C) and nitrogen (N) concentrations of the decomposing fine root litter were determined at a 6 months interval during a 2 years field experiment. Results The amount of root litter remaining after 2 years of field incubation differed between the study regions (76 ± 2 % in Schorfheide-Chorin, 85 ± 2 % in Schwäbische-Alb, and 88±2 % in Hainich-Dün) but did not vary with soil depth. Conclusions Our results indicate that the initial fine root decomposition rates are more influenced by regional scale differences in environmental conditions including climate and soil parent material, than by changes in microbial activities with soil depth. Moreover, they suggest that a similar potential to decompose new resources in the form of root litter exists in both surface and deep soils

Structure and chemical composition of BN thin films grown by pulsed-laser deposition

BN thin films are grown on Si(100) substrates in a pulsed-laser-deposition (PLD) process using a pulsed CO2 laser, a hexagonal-phase BN (h-BN) target, and N2 as processing gas. The effect of RF power coupled to the substrate during PLD is invesigated. Films are analysed using optical microscopy and micro-Raman and X-ray photomission spectroscopies. They are generally composed of a fine-grained matrix in which particles 10-100 micron meter in size are embedded, with the morphology and chemical composition dependent on the lateral position on the film surface relative to the laser-induced plasma plume from the target. The roughness and contaminant concentration (B2O3, elemental B, and boron-oxynitride) are largest nearest the plasma-affected region. The matrix material over the entire film surface exhibits weak, broad spectral structures, indicating an amorphous structure. Certain regions have in in addition h-BN Raman peaks that are shifted by up to 15 cm-1 to lower wave numbers relativ e to crystaline h-BN due to strain built in during deposition. No peaks characteristic of cubic BN or B2O3 are found. Positions further from the plasma-affected region show stronger peaks, implying more crystalline order. The highest degree of crystallinity is reached for deposition with RF power applied to the substrate mainly during the laser pulses, as opposed to deposition with power applied between pulses or to deposition without RF power. In general, embedded particles have more intense Raman peaks than the surrounding matrix, comparable in strength to those of the target, suggesting that they arise from material ejection

Functional and structural properties of thin electroceramic films by laser radiation

The deposition of single layer electroceramic thin films by pulsed excimer laser radiation (248 nm) on Ti/Pt/Si (111) substrates is investigated as a function af laser parameters (fluence, repetition rate, beam geometry) and processing variables (pressure and composition of processing gas, target-substrate arrangement) under conditions of various temporal and spatial properties of the involves vapor and/or plasma states represented in the type, number, ionization degree, momentum, and energy of the ensemble of species generated. The film characteristics were measured using scanning electron microscopy, X-ray diffraction, Raman spectroscopy, ellipsometry and impendance measurements. The experimental results are related to theoretical results of film growth calculating the densification of the films via momentum trasfer and the temperature of the films via energy storage. The film properties are dicussed in view of suitable permittivities and coupling coefficients for electrical, sensoric and actuatoric applications