Does landscape composition alter the spatiotemporal distribution of the pine processionary moth in a pine plantation forest?

Landscape composition and physiognomy affect community structure and species distribution across space and time. The pine processionary moth (PPM) (Thaumetopoea pityocampa Den. & Schiff., Lepidoptera, Notodontidae) is a common pine defoliator throughout southern Europe and Mediterranean countries. We surveyed the spatiotemporal distribution of the PPM in a pine plantation forest in southwestern France and used the density of the winter nests as a proxy for population density. The study spanned 4 years (2005–2008) and showed a high temporal variability in nest density. We found a strong edge effect with nest densities at stand edges more than twice as large as within-stand densities. At the landscape scale, the spatial distribution of the moth exhibited a significant spatial autocorrelation in 3 out of 4 years of our study. The spatial scales of the autocorrelation ranged from ca. 2 km to more than 22 km. We found a positive correlation between spatial distributions corresponding to certain sampling years, but the relationship was not systematic. Landscape configuration appeared to be an important driver of the PPM spatial pattern. Bivariate Moran’s I correlograms showed that patch richness density as well as the percentage of local landscape covered by various land uses were correlated with population density. The study showed that accounting for landscape characteristics may be important in order to understand forest insect pest distribution, even in cases where the host species is abundant and homogeneously distributed throughout the study area, e.g., pure plantation forests.     

Ex vivo time-lapse confocal imaging of the mouse embryo aorta

Time-lapse confocal microscopy of mouse embryo slices was developed to access and image the living aorta. In this paper, we explain how to label all hematopoietic and endothelial cells inside the intact mouse aorta with fluorescent directly labeled antibodies. Then we describe the technique to cut nonfixed labeled embryos into thick slices that are further imaged by time-lapse confocal imaging. This approach allows direct observation of the dynamic cell behavior in the living aorta, which was previously inaccessible because of its location deep inside the opaque mouse embryo. In particular, this approach is sensitive enough to allow the experimenter to witness the transition from endothelial cells into hematopoietic stem/progenitor cells in the aorta, the first site of hematopoietic stem cell generation during development. The protocol can be applied to observe other embryonic sites throughout mouse development. A complete experiment requires ～2 d of practical work.     

Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles

The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical evolution than to the acquisition of DNA by horizontal transfer.     

Kinetoplast DNA from plant trypanosomatids responsible for the Hartrot disease in coconut trees

Summary— Phytomonas parasites were isolated from crude sap of coconut trees affected with Hartrot disease in French Guyana (Hart 1 and Hart 2) and Brazil (Hart 3) and cultured in vitro. Two Phytomonas isolates obtained from weeds belonging to the Euphorbiaceae family and growing in an infected coconut tree plantation were also cultured (E hys and E hir). The kinetoplast DNA (kDNA) was purified and incubated with topoisomerase II which decatenates the huge network into free minicircles of 1.6 kilobase (kb) pair for Hart 1, Hart 2 and Hart 3 and 1.3 kb for E hys and E hir. Restriction endonuclease analysis showed that more than 90% of Hart 1 and Hart 2 minicircle content was homogeneous in base sequence while minicircles from Hart 3, E hys and E hir were heterogeneous. Minicircles exhibited restriction cleavage patterns characteristic of each Phytomonas isolate allowing their identification, except for the major class of Hart I and Hart 2 minicircles whose restriction maps were identical. Cross-hybridization experiments were performed by Southern blot. A high sequence homology was found between minicircies from Hart 1, Hart 2 and Hart 3 on one hand and those from E hys and E hir on the other. In contrast, minicircles from the Hartrot Phytomonas and those from the two Euphorbiaceae Phytomonas present little sequence homology. These data showed that minicircles from Phytomonas infecting coconut trees displayed biochemical properties different from those of other Phytomonas. This could lead to the elaboration of new molecular tools aimed to help to epidemiological studies, to an early diagnosis and to a better control of the disease.     

Insulin-mediated down-regulation of apolipoprotein A5 gene expression through the phosphatidylinositol 3-kinase pathway: role of upstream stimulatory factor

The apolipoprotein A5 gene (APOA5) has been repeatedly implicated in lowering plasma triglyceride levels. Since several studies have demonstrated that hyperinsulinemia is associated with hypertriglyceridemia, we sought to determine whether APOA5 is regulated by insulin. Here, we show that cell lines and mice treated with insulin down-regulate APOA5 expression in a dose-dependent manner. Furthermore, we found that insulin decreases human APOA5 promoter activity, and subsequent deletion and mutation analyses uncovered a functional E box in the promoter. Electrophoretic mobility shift and chromatin immunoprecipitation assays demonstrated that this APOA5 E box binds upstream stimulatory factors (USFs). Moreover, in transfection studies, USF1 stimulates APOA5 promoter activity, and the treatment with insulin reduced the binding of USF1/USF2 to the APOA5 promoter. The inhibition of the phosphatidylinositol 3-kinase (PI3K) pathway abolished insulin's effect on APOA5 gene expression, while the inhibition of the P70 S6 kinase pathway with rapamycin reversed its effect and increased APOA5 gene expression. Using an oligonucleotide precipitation assay for USF from nuclear extracts, we demonstrate that phosphorylated USF1 fails to bind to the APOA5 promoter. Taken together, these data indicate that insulin-mediated APOA5 gene transrepression could involve a phosphorylation of USFs through the PI3K and P70 S6 kinase pathways that modulate their binding to the APOA5 E box and results in APOA5 down-regulation. The effect of exogenous hyperinsulinemia in men showed a decrease in the plasma ApoAV level. These results suggest a potential contribution of the APOA5 gene in hypertriglyceridemia associated with hyperinsulinemia.     

MSight: an image analysis software for liquid chromatography-mass spectrometry

Images obtained from high-throughput mass spectrometry (MS) contain information that remains hidden when looking at a single spectrum at a time. Image processing of liquid chromatography-MS datasets can be extremely useful for quality control, experimental monitoring and knowledge extraction. The importance of imaging in differential analysis of proteomic experiments has already been established through two-dimensional gels and can now be foreseen with MS images. We present MSight, a new software designed to construct and manipulate MS images, as well as to facilitate their analysis and comparison.     

SPS' Digest: the Swiss Proteomics Society selection of proteomics articles

Despite the consolidation of the specialized proteomics literature around a few established journals, such as Proteomics, Molecular and Cellular Proteomics, and the Journal of Proteome Research, a lot of information is still spread in many different publications from different fields, such as analytical sciences, MS, bioinformatics, etc. The purpose of SPS' Digest is to gather a selection of proteomics articles, to categorize them, and to make the list available on a periodic basis through a web page and email alerts.     

A novel strategy using MASCOT Distiller for analysis of cleavable isotope-coded affinity tag data to quantify protein changes in plasma

A novel strategy consisting of cleavable Isotope-Coded Affinity Tag (cICAT) combined with MASCOT Distiller was evaluated as a tool for the quantification of proteins in "abnormal" patient plasma, prepared by pooling samples from patients with acute stroke. Quantification of all light and heavy cICAT-labelled peptide ion pairs was obtained using MASCOT Distiller combined with a proprietary software. Peptides displaying differences were selected for identification by MS. These preliminary results show the promise of our approach to identify potential biomarkers.