A Warm Tea: The Role of Temperature and Hydroperiod on Litter Decomposition in Temporary Wetlands

Ecosystems - Increasing global temperature and changes in the precipitation regime affect the global carbon cycle by altering the process of organic matter decomposition. Temporary aquatic systems...     

A novel role for RecA under non-stress: promotion of swarming motility in Escherichia coli K-12

Background  

Bacterial motility is a crucial factor in the colonization of natural environments. Escherichia coli has two flagella-driven motility types: swimming and swarming. Swimming motility consists of individual cell movement in liquid medium or soft semisolid agar, whereas swarming is a coordinated cellular behaviour leading to a collective movement on semisolid surfaces. It is known that swimming motility can be influenced by several types of environmental stress. In nature, environmentally induced DNA damage (e.g. UV irradiation) is one of the most common types of stress. One of the key proteins involved in the response to DNA damage is RecA, a multifunctional protein required for maintaining genome integrity and the generation of genetic variation.     

Genome sequence of the biocontrol strain Pseudomonas fluorescens F113

Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) that has biocontrol activity against fungal plant pathogens and is a model for rhizosphere colonization. Here, we present its complete genome sequence, which shows that besides a core genome very similar to those of other strains sequenced within this species, F113 possesses a wide array of genes encoding specialized functions for thriving in the rhizosphere and interacting with eukaryotic organisms.     

Tumor necrosis factor alpha modulates the dynamics of the plasminogen-mediated early interaction between Bifidobacterium animalis subsp. lactis and human enterocytes

The capacity to intervene with the host plasminogen system has recently been considered an important component in the interaction process between Bifidobacterium animalis subsp. lactis and the human host. However, its significance in the bifidobacterial microecology within the human gastrointestinal tract is still an open question. Here we demonstrate that human plasminogen favors the B. animalis subsp. lactis BI07 adhesion to HT29 cells. Prompting the HT29 cell capacity to activate plasminogen, tumor necrosis factor alpha (TNF-α) modulated the plasminogen-mediated bacterium-enterocyte interaction, reducing the bacterial adhesion to the enterocytes and enhancing migration to the luminal compartment.     

Poly-gamma-glutamate in bacteria

Poly-gamma-glutamate (PGA), a natural polymer, is synthesized by several bacteria (all Gram-positive), one archaea and one eukaryote. PGA has diverse biochemical properties, enabling it to play different roles, depending on the organism and its environment. Indeed, PGA allows bacteria to survive at high salt concentrations and may also be involved in virulence. The minimal gene sets required for PGA synthesis were recently defined. There are currently two nomenclatures depending on the PGA final status: cap, for 'capsule', when PGA is surface associated or pgs, for 'polyglutamate synthase', when PGA is released. The minimal gene sets contain four genes termed cap or pgs B, C, A and E. The PGA synthesis complex is membrane-anchored and uses glutamate and ATP as substrates. Schematically, the reaction may be divided into two steps, PGA synthesis and PGA transport through the membrane. PGA synthesis depends primarily on CapB-CapC (or PgsB-PgsC), whereas PGA transport requires the presence, or the addition, of CapA-CapE (or PgsAA-PgsE). The synthesis complex is probably responsible for the stereochemical specificity of PGA composition. Finally, PGA may be anchored to the bacterial surface or released. An additional enzyme is involved in this reaction: either CapD, a gamma-glutamyl-transpeptidase that catalyses anchorage of the PGA, or PgsS, a hydrolase that facilitates release. The anchoring of PGA to the bacterial surface is important for virulence. All cap genes are therefore potential targets for inhibitors specifically blocking PGA synthesis or anchorage.     

Genome size variation and morphological differentiation within Ranunculus parnassifolius group (Ranunculaceae) from calcareous screes in the Northwest of Spain

Ranunculus parnassifolius is an orophilous plant distributed throughout Central and Southwestern Europe (Alps, Pyrenees and Cantabrian Mountains). Its evolutionary history and taxonomy are often complicated, having been little studied before now. The purpose of this article is to present flow cytometry measurements and multivariate morphometric analyses to ascertain cytotype distribution patterns and the morphological differentiation of R. parnassifolius s.l. from calcareous screes in the Northwest of Spain. DNA ploidy level and morphometric analysis were determined for plants of R. parnassifolius s.l. using flow cytometry (112 individuals) and multivariate analysis (152 individuals). Specimens were collected in eight localities in the Northwest of the Iberian Peninsula. Different sample preservation methods (fresh, frozen, and herbarium specimens) were employed as well as the use of various buffers and internal standards, in order to test the reproducibility of DNA flow cytometry. Three ploidy levels were detected in the study area (diploid, tetraploid, and pentaploid), and mixed-cytotype populations were also found. The mean nuclear DNA content of the R. parnassifolius group ranged from 7.43 ± 0.185 to 7.63 ± 0.339 pg/2C in diploids and from 15.09 ± 0.161 to 15.85 ± 0.587 pg/2C in tetraploids. The analysis of the monoploid genome sizes (1Cx) did not reveal a clear difference among cytotypes. These results suggest low intraspecific variation, at least among the populations studied. In addition, a comparison of different DNA reference standards was conducted. A new value for the chicken genome size was used as internal reference standard (2C = 3.14 ± 0.155 pg), with similar results found using both animal and plant standards (Pisum sativum and Solanum lycopersicum). Finally, herbarium vouchers and frozen tissue were proved to be suitable for DNA ploidy level measurements. This study provided a first assessment of C values in the R. parnassifolius group using flow cytometry. The weak morphological distinction of the cytotypes and the existence of mixed-cytotype populations in the Northwest of Spain are reported here for the first time. The different distribution pattern of the two cytotypes is discussed.     

The RON1/FRY1/SAL1 Gene Is Required for Leaf Morphogenesis and Venation Patterning in Arabidopsis

To identify genes involved in vascular patterning in Arabidopsis (Arabidopsis thaliana), we screened for abnormal venation patterns in a large collection of leaf shape mutants isolated in our laboratory. The rotunda1-1 (ron1-1) mutant, initially isolated because of its rounded leaves, exhibited an open venation pattern, which resulted from an increased number of free-ending veins. We positionally cloned the RON1 gene and found it to be identical to FRY1/SAL1, which encodes an enzyme with inositol polyphosphate 1-phosphatase and 3′ (2′),5′-bisphosphate nucleotidase activities and has not, to our knowledge, previously been related to venation patterning. The ron1-1 mutant and mutants affected in auxin homeostasis share perturbations in venation patterning, lateral root formation, root hair length, shoot branching, and apical dominance. These similarities prompted us to monitor the auxin response using a DR5-GUS auxin-responsive reporter transgene, the expression levels of which were increased in roots and reduced in leaves in the ron1-1 background. To gain insight into the function of RON1/FRY1/SAL1 during vascular development, we generated double mutants for genes involved in vein patterning and found that ron1 synergistically interacts with auxin resistant1 and hemivenata-1 but not with cotyledon vascular pattern1 (cvp1) and cvp2. These results suggest a role for inositol metabolism in the regulation of auxin responses. Microarray analysis of gene expression revealed that several hundred genes are misexpressed in ron1-1, which may explain the pleiotropic phenotype of this mutant. Metabolomic profiling of the ron1-1 mutant revealed changes in the levels of 38 metabolites, including myoinositol and indole-3-acetonitrile, a precursor of auxin.During the vegetative development of Arabidopsis (Arabidopsis thaliana), leaves are produced from the shoot apical meristem in an orchestrated program that involves patterning and cell division, expansion, and differentiation. The mature vegetative leaves of Arabidopsis are histologically simple and consist of the outer epidermis and internal mesophyll and vasculature (Tsukaya, 2005). Veins are crucial for normal leaf function, transporting water, minerals, and photosynthate and providing mechanical support to the lamina (Evert and Eichhorn, 2006). The leaves of many vascular plants, such as the angiosperms, exhibit a closed reticulate venation pattern (Roth-Nebelsick et al., 2001). In Arabidopsis, the leaf venation pattern is brochidodromous, with a single primary vein (midvein) and a series of loops formed by secondary veins that connect other secondary and higher order veins (Hickey, 1973; Candela et al., 1999).Vein differentiation must be spatially and temporally regulated throughout leaf development. Many aspects of venation patterning in plant leaves can be explained by the auxin canalization model (Sachs, 1991; Rolland-Lagan and Prusinkiewicz, 2005), which is supported by considerable experimental evidence. The role of auxin in venation pattern formation is supported by the phenotypes of mutants possessing altered auxin biosynthesis or perception (Alonso-Peral et al., 2006; Cheng et al., 2006), experimental perturbation of auxin transport (Mattsson et al., 1999; Sieburth, 1999), and the expression pattern of auxin-responsive reporter transgenes (Mattsson et al., 2003; Scarpella et al., 2006). The phenotypes of mutants impaired in auxin transport, such as scarface (sfc; Deyholos et al., 2000; Sieburth et al., 2006) and pin-formed1 (pin1; Okada et al., 1991; Gälweiler et al., 1998), and perception, such as monopteros (mp; Hardtke and Berleth,1998), are pleiotropic and include defects in vein patterning or differentiation. The sfc mutant exhibits a disconnected venation pattern (Deyholos et al., 2000), and the lateral organs of strong mp mutants display a reduced venation pattern with no peripheral veins (Przemeck et al., 1996). In contrast, the leaf venation pattern of pin1 mutants resembles that of wild-type plants treated with auxin transport inhibitors, exhibiting extra primary and secondary veins and an accumulation of vascular elements along the leaf margin (Mattsson et al., 1999).Unlike sfc, pin1, or mp, other leaf venation mutants are not primarily affected in auxin production, perception, or transport (Carland et al., 1999). Examples include cotyledon vascular pattern1 (cvp1), the cotyledons of which exhibit isolated patches of vascular tissue (Carland et al., 1999, 2002), and cvp2, which exhibits increased numbers of free-ending veins in the cotyledons and leaves (Carland et al., 1999; Carland and Nelson, 2004). CVP1 encodes the STEROL METHYLTRANSFERASE2 (SMT2) protein, an enzyme that functions in the sterol biosynthetic pathway (Carland et al., 2002). CVP2 encodes an inositol polyphosphate 5′-phosphatase (5PTase; Carland and Nelson, 2004), which mediates the hydrolysis of inositol 1,4,5-trisphosphate (IP₃), a eukaryotic second messenger with a pivotal role in calcium signaling (Berridge, 2009). IP₃ controls cytosolic calcium levels by regulating calcium release from the vacuole and endoplasmic reticulum (Krinke et al., 2007). The disconnected, open venation pattern of cvp2 cotyledons and leaves suggested a role for intracellular IP₃ levels in vascular development (Carland and Nelson, 2004). Recently, CVP2 and another 5PTase, CVP2-LIKE1 (CVL1), have been shown to regulate vein patterning through the production of a specific phosphoinositide (PI) that acts as a ligand for SFC/VASCULAR NETWORK3 (VAN3), which in turn controls the traffic of vesicles that accounts for the polar subcellular localization of PIN1 proteins (Carland and Nelson, 2009; Naramoto et al., 2009). Another inositol 5PTase, At5PTase13, has been shown to play a role in auxin-mediated vein development in cotyledons (Lin et al., 2005). Furthermore, the open vein networks present in the leaves of forked and tornado mutants (Steynen and Schultz, 2003; Cnops et al., 2006) may be due to altered auxin perception or distribution.To identify genes required for venation patterning, we screened for naturally occurring variations in the venation pattern of Arabidopsis vegetative leaves (Candela et al., 1999). In this way, we discovered the spontaneously occurring hemivenata-1 (hve-1) mutation, which causes a venation pattern that is significantly simpler than those of other wild types, such as Landsberg erecta (Ler) and Columbia-0 (Col-0). We positionally cloned the HVE gene, which encodes a CAND1 protein involved in ubiquitin-mediated auxin signaling (Alonso-Peral et al., 2006). To identify additional loci necessary for vascular patterning, we screened for venation pattern defects in a collection of leaf shape mutants isolated in our laboratory after ethyl methanesulfonate (EMS) mutagenesis (Berná et al., 1999) and found that the rotunda1-1 (ron1-1) mutant, named after the round laminae of its vegetative leaves, displays disconnected leaf veins. Here, we describe the phenotypic characterization of the ron1-1 mutant and the map-based cloning of RON1, which encodes an inositol polyphosphate 1-phosphatase that plays a role in venation patterning, as determined by morphological, reporter gene, and double mutant analyses. Our results suggest an interplay between inositol and auxin signaling in a number of developmental pathways, including those responsible for leaf venation pattern formation.     

Development of a high-performance affinity chromatography-based method to study the biological interaction between whole micro-organisms and target proteins

Aims: The bacteria–host molecular cross‐talk is the matter of primary importance both in pathogenesis and in commensalism. Principally based on immunological methods, the methodologies commonly utilized for these studies are laborious and require specific antibodies. Here, we developed a new high‐performance affinity chromatography (HPAC)‐based approach that allows a direct measure of the interaction between whole bacterial cells and host molecules. Methods and Results: Bifidobacterium lactis BI07 cells immobilized on amino‐derivatized silica beads were utilized as stationary phase in a high‐performance affinity chromatography approach. The analytes plasminogen, collagen I and collagen IV were injected, and interactions were evaluated by the insertion in an HPLC system with UV detection. According to our data, Bif. lactis BI07 is capable of interacting with plasminogen, while it does not exhibit any binding activity to collagen I and IV. Conclusions: In this study, we implemented a high‐performance affinity chromatography‐based method to characterize the biological interaction between whole micro‐organisms and target proteins. Significance and Impact of the Study: With respect to the approaches commonly utilized to study the interaction between bacteria and host proteins, this HPAC‐based approach is fast and cheaper than other methods and allows a direct measure of the interaction between bacterial cells and target molecules.     

High taxonomic level fingerprint of the human intestinal microbiota by Ligase Detection Reaction - Universal Array approach

Background  

Affecting the core functional microbiome, peculiar high level taxonomic unbalances of the human intestinal microbiota have been recently associated with specific diseases, such as obesity, inflammatory bowel diseases, and intestinal inflammation.     

Simultaneous HPLC–UV analysis of rufinamide,zonisamide, lamotrigine,oxcarbazepine monohydroxy derivative and felbamate in deproteinized plasma of patients with epilepsy

We present an implementation of a method we previously reported allowing the newer antiepileptic drugs (AEDs) rufinamide (RFN) and zonisamide (ZNS) to be simultaneously determined with lamotrigine (LTG), oxcarbazepine's (OXC) main active metabolite monohydroxycarbamazepine (MHD) and felbamate (FBM) in plasma of patients with epilepsy using high performance liquid chromatography (HPLC) with UV detection. Plasma samples (250 μL) were deproteinized by 1 mL acetonitrile spiked with citalopram as internal standard (I.S.). HPLC analysis was carried out on a Synergi 4 μm Hydro-RP, 250 mm × 4.6 mm I.D. column. The mobile phase was a mixture of potassium dihydrogen phosphate buffer (50 mM, pH 4.5), acetonitrile and methanol (65:26.2:8.8, v/v/v) at an isocratic flow rate of 0.8 mL/min. The UV detector was set at 210 nm. The chromatographic run lasted 19 min. Commonly coprescribed AEDs did not interfere with the assay. Calibration curves were linear for both AEDs over a range of 2–40 μg/mL for RFN and 2–80 μg/mL for ZNS. The limit of quantitation was 2 μg/mL for both analytes and the absolute recovery ranged from 97% to 103% for RFN, ZNS and the I.S. Intra- and interassay precision and accuracy were lower than 10% at all tested concentrations. The present study describes the first simple and validated method for RFN determination in plasma of patients with epilepsy. By grouping different new AEDs in the same assay the method can be advantageous for therapeutic drug monitoring (TDM).