Monalysin,a Novel ?-Pore-Forming Toxin from the Drosophila Pathogen Pseudomonas entomophila,Contributes to Host Intestinal Damage and Lethality

Pseudomonas entomophila is an entomopathogenic bacterium that infects and kills Drosophila. P. entomophila pathogenicity is linked to its ability to cause irreversible damages to the Drosophila gut, preventing epithelium renewal and repair. Here we report the identification of a novel pore-forming toxin (PFT), Monalysin, which contributes to the virulence of P. entomophila against Drosophila. Our data show that Monalysin requires N-terminal cleavage to become fully active, forms oligomers in vitro, and induces pore-formation in artificial lipid membranes. The prediction of the secondary structure of the membrane-spanning domain indicates that Monalysin is a PFT of the ß-type. The expression of Monalysin is regulated by both the GacS/GacA two-component system and the Pvf regulator, two signaling systems that control P. entomophila pathogenicity. In addition, AprA, a metallo-protease secreted by P. entomophila, can induce the rapid cleavage of pro-Monalysin into its active form. Reduced cell death is observed upon infection with a mutant deficient in Monalysin production showing that Monalysin plays a role in P. entomophila ability to induce intestinal cell damages, which is consistent with its activity as a PFT. Our study together with the well-established action of Bacillus thuringiensis Cry toxins suggests that production of PFTs is a common strategy of entomopathogens to disrupt insect gut homeostasis.     

Rapid acquisition of Raman spectral maps through minimal sampling: applications in tissue imaging

A method is presented for acquiring high‐spatial‐resolution spectral maps, in particular for Raman micro‐spectroscopy (RMS), by selectively sampling the spatial features of interest and interpolating the results. This method achieves up to 30 times reduction in the sampling time compared to raster‐scanning, the resulting images have excellent correlation with conventional histopathological staining, and are achieved with sufficient spectral signal‐to‐noise ratio to identify individual tissue structures. The benefits of this selective sampling method are not limited to tissue imaging however; it is expected that the method may be applied to other techniques which employ point‐by‐point mapping of large substrates. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions

The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes Arabidopsis thaliana an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the most commonly used mapping combination, Columbia×Landsberg erecta (Col-0×Ler-0), the Cereon polymorphism database is a valuable resource for the generation of polymorphic markers. However, because the number of markers available in public databases for accessions other than Col-0 and Ler-0 is extremely low, mapping using other accessions is far from straightforward. This issue arose while cloning mutations in the Wassilewskija (Ws-4) background. In this work, approaches are described for marker generation in Ws-4 x Col-0. Complementary strategies were employed to generate 229 INDEL markers. Firstly, existing Col-0/Ler-0 Cereon predicted polymorphisms were mined for transferability to Ws-4. Secondly, Ws-0 ecotype Illumina sequence data were analyzed to identify INDELs that could be used for the development of PCR-based markers for Col-0 and Ws-4. Finally, shotgun sequencing allowed the identification of INDELs directly between Col-0 and Ws-4. The polymorphism of the 229 markers was assessed in seven widely used Arabidopsis accessions, and PCR markers that allow a clear distinction between the diverged Ws-0 and Ws-4 accessions are detailed. The utility of the markers was demonstrated by mapping more than 35 mutations in a Col-0×Ws-4 combination, an example of which is presented here. The potential contribution of next generation sequencing technologies to more traditional map-based cloning is discussed.     

Investigations of the supramolecular structure of individual diphenylalanine nano- and microtubes by polarized Raman microspectroscopy

Polarized Raman microspectroscopy and atomic force microscopy were used to obtain quantitative information regarding the molecular structure of individual diphenylalanine (FF) nano- and microtubes. The frequencies of the Raman spectral bands corresponding to the amide I (1690 cm(-1)) and amide III (1249 cm(-1)) indicated that the FF-molecules interact by hydrogen bonding at the N-H and not at the C═O sites. The calculated mean orientation angles of the principal axes of the Raman tensors (PARTs) obtained from the polarized Raman spectral measurements were 41 ± 4° for the amide I and 59 ± 5° for amide III. On the basis of the orientation of the PART for the amide I mode, it was found that the C═O bond is oriented at an angle of 8 ± 4° to the tube axis. These values did not vary significantly with the diameter of the tubes (range 400-1700 nm) and were in agreement with the molecular structure proposed previously for larger crystalline specimens.     

Free Convection in a Parallelogrammic Porous Cavity Filled with a Nanofluid Using Tiwari and Das’ Nanofluid Model

The free convection heat transfer of Cu-water nanofluids in a parallelogrammic enclosure filled with porous media is numerically analyzed. The bottom and top of the enclosure are insulated while the sidewalls are subject to limited temperature difference. The Darcy flow and the Tiwari and Das’ nanofluid models are considered. The governing dimensionless partial differential equations are numerically solved using a finite difference code. The results are reported for isotherms and streamlines as well as Nusselt number as a function of the volume fraction of nanoparticles, porosity, types of the porous matrix, inclination angle, aspect ratio and different Rayleigh numbers. It is found that the presence of the nanoparticles inside the enclosure deteriorates the heat transfer rate, which is caused due to the increase of dynamic viscosity by the presence of nanoparticles. Therefore, in applications in which the nanofluids are used for their advantages, such as enhanced dielectric properties or antibacterial properties, more caution for the heat transfer design of the enclosure is necessary.     

Induction and measurement of the early stage of a host‐parasite interaction using a combined optical trapping and Raman microspectroscopy system

Understanding and quantifying the temporal acquisition of host cell molecules by intracellular pathogens is fundamentally important in biology. In this study, a recently developed holographic optical trapping (HOT)‐based Raman microspectroscopy (RMS) instrument is applied to detect, characterize and monitor in real time the molecular trafficking of a specific molecular species (isotope‐labeled phenylalanine (L‐Phe(D8)) at the single cell level. This approach enables simultaneous measurement of the chemical composition of human cerebrovascular endothelial cells and the protozoan parasite Toxoplasma gondii in isolation at the very start of the infection process. Using a model to decouple measurement contributions from host and pathogen sampling in the excitation volume, the data indicate that manipulating parasites with HOT coupled with RMS chemical readout was an effective method for measurement of L‐Phe(D8) transfer from host cells to parasites in real‐time, from the moment the parasite enters the host cell.     

Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis

The HIV-1 transactivation response element (TAR) RNA binds a variety of proteins and is a target for developing anti-HIV therapies. TAR has two primary binding sites: a UCU bulge and a CUGGGA apical loop. We used NMR residual dipolar couplings, carbon spin relaxation (R₁ and R₂), and relaxation dispersion (R_1ρ) in conjunction with molecular dynamics and mutagenesis to characterize the dynamics of the TAR apical loop and investigate previously proposed long-range interactions with the distant bulge. Replacement of the wild-type apical loop with a UUCG loop did not significantly affect the structural dynamics at the bulge, indicating that the apical loop and the bulge act largely as independent dynamical recognition centers. The apical loop undergoes complex dynamics at multiple timescales that are likely important for adaptive recognition: U31 and G33 undergo limited motions, G32 is highly flexible at picosecond-nanosecond timescales, and G34 and C30 form a dynamic Watson-Crick basepair in which G34 and A35 undergo a slow (∼30 μs) likely concerted looping in and out motion, with A35 also undergoing large amplitude motions at picosecond-nanosecond timescales. Our study highlights the power of combining NMR, molecular dynamics, and mutagenesis in characterizing RNA dynamics.