Diversity of carbofuran-degrading soil bacteria and detection of plasmid-encoded sequences homologous to the mcd gene

Abstract: Fifty-five bacterial isolates, from English and French soils with different histories of carbofuran field treatment, which hydrolysed the N -methylcarbamate insecticide carbofuran to carbofuran 7-phenol were characterised phenotypically and genetically. The isolates were compared by using 125 physiological tests and morphological features, plasmid profiles and restriction fragment length polymorphism (RFLP) patterns of total DNA using the rRNA operon of Escherichia coli as a DNA probe. Cluster analysis of both phenotypic characters and RFLP patterns showed a high degree of diversity amongst the bacteria. Ten distinct plasmid profiles with 2–4 plasmids ranging in size from 84 to about 438 kb were visualised in 50 isolates. The majority of isolates had one of two types of plasmid profiles. Plasmid profiles and Eco RI restricted total DNA patterns were hybridised with an internal fragment of the carbofuran hydrolase ( mcd ) gene and 22 diverse soil isolates exhibited sequence homology with this gene probe. Our results indicate that sequences homologous to the mcd gene are located on a conserved Eco RI fragment (12 or 14 kb) of a plasmid (100, 105, 115 or 124 kb) found in diverse soil isolates from geographically distant areas. Thirty-three isolates did not exhibit detectable homology to the mcd gene probe and the hydrolase enzymes and genes in these isolates need further investigation.     

Presence of functional TLR2 and TLR4 on human adipocytes

In addition to the well-known role of adipose tissue in energy metabolism, it has recently been demonstrated that this tissue can secrete a large array of molecules, including inflammatory cytokines. Furthermore, recent studies suggest that adipose cells can behave as immune cells. Therefore, the aim of this study was to determine the presence of the two most prominent ‘pattern recognition receptors’ for bacterial and fungal cell wall components, TLR2 and TLR4 on human adipose cells, as well as to assess their functionality. We demonstrated that TLR2 and TLR4 were expressed at relatively high levels (compared to a monocyte cell line) on the surface of human adipose cells. Stimulation of human adipocytes with lipopolysaccharide (LPS), or with lipoteichoic acid (LTA), two specific ligands of TLR4 and TLR2, respectively, induced a strong increase in TNFα production. The specificity of the response was demonstrated by the use of anti-TLR4 and anti-TLR2 blocking antibodies, which were able to decrease LPS- or LTA-induced TNFα secretion. Thus, it is clear that these receptors are functional in human adipocytes. This study adds weight to the argument that human fat tissue plays a potential role in innate immunity. Sandrine Bés-Houtmann, Régis Roche, Christian Lefebvre d’Hellencourt and Maya Cesari have contributed equally to this work.     

Role of oxidative stress in lysosomal membrane permeabilization and apoptosis induced by gentamicin, an aminoglycoside antibiotic

Gentamicin, an aminoglycoside antibiotic used to treat severe bacterial infections, may cause acute renal failure. At therapeutic concentrations, gentamicin accumulates in lysosomes and induces apoptosis in kidney proximal tubular cells. In gentamicin-treated renal LLC-PK1 cells, acridine orange release from lysosomes, previously interpreted as lysosomal membrane permeabilization, precedes the apoptotic cascade that develops during incubation with gentamicin. However, the link between gentamicin lysosomal accumulation and apoptosis remains unclear. We here examined if reactive oxygen species (ROS) production could account for gentamicin-induced acridine orange release and apoptosis, and the implication of iron in these events. We found that gentamicin induced ROS production prior to, and at lower drug concentrations than required for, acridine orange release and apoptosis. ROS antioxidant or scavenger, catalase, and N-acetylcysteine largely prevented these events. Vital confocal imaging revealed that gentamicin-induced ROS production occurs in lysosomes. Deferoxamine, an iron chelator, which is endocytosed and accumulates in lysosomes, largely prevented gentamicin-induced ROS production as well as apoptosis. Direct evidence for gentamicin-induced permeabilization of lysosomal membrane was provided by showing the release into the cytosol of Lucifer yellow, a membrane-impermeant endocytic tracer with a comparable molecular weight as gentamicin. Altogether, our data demonstrate a key role of lysosomal iron and early ROS production in gentamicin-induced lysosomal membrane permeabilization and apoptosis.     

Structure of Transmembrane Domain of Lysosome-associated Membrane Protein Type 2a (LAMP-2A) Reveals Key Features for Substrate Specificity in Chaperone-mediated Autophagy

Chaperone-mediated autophagy (CMA) is a highly regulated cellular process that mediates the degradation of a selective subset of cytosolic proteins in lysosomes. Increasing CMA activity is one way for a cell to respond to stress, and it leads to enhanced turnover of non-critical cytosolic proteins into sources of energy or clearance of unwanted or damaged proteins from the cytosol. The lysosome-associated membrane protein type 2a (LAMP-2A) together with a complex of chaperones and co-chaperones are key regulators of CMA. LAMP-2A is a transmembrane protein component for protein translocation to the lysosome. Here we present a study of the structure and dynamics of the transmembrane domain of human LAMP-2A in n-dodecylphosphocholine micelles by nuclear magnetic resonance (NMR). We showed that LAMP-2A exists as a homotrimer in which the membrane-spanning helices wrap around each other to form a parallel coiled coil conformation, whereas its cytosolic tail is flexible and exposed to the cytosol. This cytosolic tail of LAMP-2A interacts with chaperone Hsc70 and a CMA substrate RNase A with comparable affinity but not with Hsp40 and RNase S peptide. Because the substrates and the chaperone complex can bind at the same time, thus creating a bimodal interaction, we propose that substrate recognition by chaperones and targeting to the lysosomal membrane by LAMP-2A are coupled. This can increase substrate affinity and specificity as well as prevent substrate aggregation, assist in the unfolding of the substrate, and promote the formation of the higher order complex of LAMP-2A required for translocation.     

Phylogeographical analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deeply divergent mitochondrial lineages

Isopods of the species Ligia oceanica are typical inhabitants of the rocky intertidal of the northern European coastline. The aim of this study was to assess the genetic structure of this species using mitochondrial and nuclear sequence data. We analysed partial mitochondrial cytochrome c oxidase subunit I (CO1) and 16S rRNA gene sequence data of 161 specimens collected from ten sites ranging from Spain to Norway. For selected specimens, we also sequenced the hypervariable V7 expansion segment of the nuclear 18S rRNA gene as a supplementary marker. Furthermore, we studied the infection rate of all analysed specimens by the alphaproteobacterium Wolbachia. Our analyses revealed two deeply divergent mitochondrial lineages for Ligia oceanica that probably diverged in the late Pliocene to mid Pleistocene. One lineage comprised specimens from northern populations (‘lineage N’) and one primarily those from France and Spain (‘lineage S’). Distribution patterns of the haplotypes and the genetic distances between both lineages revealed two populations that diverged before the Last Glacial Maximum. Given that we found no homogenization of mitochondrial haplotypes, our present results also reject any influence of Wolbachia on the observed mtDNA variability. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 16–30.     

An Engineered Palette of Metal Ion Quenchable Fluorescent Proteins

Many fluorescent proteins have been created to act as genetically encoded biosensors. With these sensors, changes in fluorescence report on chemical states in living cells. Transition metal ions such as copper, nickel, and zinc are crucial in many physiological and pathophysiological pathways. Here, we engineered a spectral series of optimized transition metal ion-binding fluorescent proteins that respond to metals with large changes in fluorescence intensity. These proteins can act as metal biosensors or imaging probes whose fluorescence can be tuned by metals. Each protein is uniquely modulated by four different metals (Cu²⁺, Ni²⁺, Co²⁺, and Zn²⁺). Crystallography revealed the geometry and location of metal binding to the engineered sites. When attached to the extracellular terminal of a membrane protein VAMP2, dimeric pairs of the sensors could be used in cells as ratiometric probes for transition metal ions. Thus, these engineered fluorescent proteins act as sensitive transition metal ion-responsive genetically encoded probes that span the visible spectrum.     

Light Restriction Delays Leaf Senescence in Winter Oilseed Rape (Brassica napus L.)

Oilseed rape (Brassica napus L.) is a crop with a complex aerial architecture that can cause self-shading leading to a vertical light gradient over the foliage. Mutual shading between neighboring plants at a high sowing density also results in an alteration of photosynthetically active radiation (PAR) absorption by lower leaves. The aim of this study was to analyze the impact that light restriction on lower leaves has on shoot architecture, biomass production and allocation, nitrogen (N) fluxes, and progression of sequential senescence. Field-grown plants were collected at the end of the vegetative rest period and grown in hydroponic conditions until pod maturity. A shading treatment corresponding to a 43.4 % reduction of PAR was applied at the early flowering stage. N uptake and fluxes of N allocation and remobilization were determined by supplying K¹⁵NO₃ in the nutrient solution. Photosynthesis and expression of SAG12 and Cab genes (indicators of leaf senescence progression) were also analyzed on different leaf ranks. The results showed that shading enhanced leaf development on the main stem and ramifications to optimize light capture. The expression pattern of the SAG12/Cab molecular indicator suggested a delay in leaf senescence that allowed leaf life span to be extended resulting in a more efficient leaf compound remobilization, with lower N residual contents in fallen leaves under shading. N uptake increased and N remobilization fluxes were enhanced from source organs (leaves and stem) toward sink organs (flowers). Profuse branching and late senescing varieties would be of interest for further selection programs under high sowing densities.     

A phylogenetic supertree of the fowls (Galloanserae, Aves)

The fowls (Anseriformes and Galliformes) comprise one of the major lineages of birds and occupy almost all biogeographical regions of the world. The group contains the most economically important of all bird species, each with a long history of domestication, and is an ideal model for studying ecological and evolutionary patterns. Yet, despite the relatively large amount of systematic attention fowls have attracted because of their socio‐economic and biological importance, the species‐level relationships within this clade remain controversial. Here we used the supertree method matrix representation with parsimony to generate a robust estimate of species‐level relationships of fowls. The supertree represents one of the most comprehensive estimates for the group to date, including 376 species (83.2% of all species; all 162 Anseriformes and 214 Galliformes) and all but one genera. The supertree was well‐resolved (81.1%) and supported the monophyly of both Anseriformes and Galliformes. The supertree supported the partitioning of Anseriformes into the three traditional families Anhimidae, Anseranatidae, and Anatidae, although it provided relatively poor resolution within Anatidae. For Galliformes, the majority‐rule supertree was largely consistent with the hypothesis of sequential sister‐group relationships between Megapodiidae, Cracidae, and the remaining Galliformes. However, our species‐level supertree indicated that more than 30% of the polytypic genera examined were not monophyletic, suggesting that results from genus‐level comparative studies using the average of the constituent species’ traits should be interpreted with caution until analogous species‐level comparative studies are available. Poorly resolved areas of the supertree reflect gaps or outstanding conflict within the existing phylogenetic database, highlighting areas in need of more study in addition to those species not present on the tree at all due to insufficient information. Even so, our supertree will provide a valuable foundation for understanding the diverse biology of fowls in a robust phylogenetic framework.