p21-Activated Kinase 2 Regulates Endothelial Development and Function through the Bmk1/Erk5 Pathway

p21-activated kinases (Paks) have been shown to regulate cytoskeleton rearrangements, cell proliferation, attachment, and migration in a variety of cellular contexts, including endothelial cells. However, the role of endothelial Pak in embryo development has not been reported, and currently, there is no consensus on the endothelial function of individual Pak isoforms, in particular p21-activated kinase 2 (Pak2), the main Pak isoform expressed in endothelial cells. In this work, we employ genetic and molecular studies that show that Pak2, but not Pak1, is a critical mediator of development and maintenance of endothelial cell function. Endothelial depletion of Pak2 leads to early embryo lethality due to flawed blood vessel formation in the embryo body and yolk sac. In adult endothelial cells, Pak2 depletion leads to severe apoptosis and acute angiogenesis defects, and in adult mice, endothelial Pak2 deletion leads to increased vascular permeability. Furthermore, ubiquitous Pak2 deletion is lethal in adult mice. We show that many of these defects are mediated through a newly unveiled Pak2/Bmk1 pathway. Our results demonstrate that endothelial Pak2 is essential during embryogenesis and also for adult blood vessel maintenance, and they also pinpoint the Bmk1/Erk5 pathway as a critical mediator of endothelial Pak2 signaling.     

Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0729-7) contains supplementary material, which is available to authorized users.     

Synthesis and evaluation of 1-(1H-indol-3-yl)ethanamine derivatives as new antibacterial agents

A collection of 3-substituted indole derivatives was prepared using nucleophilic addition of indoles to nitrones. The compounds were then tested for their antibacterial activity against almost thirty bacterial strains representative of common human pathogens. Two types of indolic molecules inhibit the growth of Staphylococcus aureus, including MRSA and VISA strains, with MIC values ranging from 8 to 16 mg/L.     

Thermal diffusion of a stiff rod-like mutant Y21M fd-virus

We investigated the thermal diffusion phenomena of a rodlike mutant filamentous fd-Y21M virus in the isotropic phase by means of an improved infrared thermal-diffusion-forced Rayleigh scattering (IR-TDFRS) setup optimized for measurements of slowly diffusing systems. Because this is the first thermal diffusion study of a stiff anisotropic solute, we investigate the influence of the shape anisotropy on the thermal diffusion behavior. The influence of temperature, fd-Y21M concentration, and ionic strength in relation with the thermodiffusion properties is discussed. We characterize and eliminate the effect of these parameters on the absolute diffusion of the rods and show that diffusion determines the behavior of the Soret coefficient because the thermal diffusion coefficient is constant in the investigated regime. Our results indicate that for the thermal diffusion behavior structural changes of the surrounding water are more important than structural changes between the charged macroions. In the investigated temperature and concentration range, the fd-Y21M virus is thermophobic for the low salt content, whereas the solutions with the high salt content change from thermophobic to thermophilic behavior with decreasing temperature. A comparison with recent measurements of other charged soft and biological matter systems shows that the shape anisotropy of the fd-virus becomes not visible in the results.     

Diversification in the Andes: age and origins of South American Heliotropium lineages (Heliotropiaceae, Boraginales)

The uplift of the Andes was a major factor for plant diversification in South America and had significant effects on the climatic patterns at the continental scale. It was crucial for the formation of the arid environments in south-eastern and western South America. However, both the timing of the major stages of the Andean uplift and the onset of aridity in western South America remain controversial. In this paper we examine the hypothesis that the Andean South American groups of Heliotropium originated and diversified in response to Andean orogeny during the late Miocene and a the subsequent development of aridity. To this end, we estimate divergence times and likely biogeographical origins of the major clades in the phylogeny of Heliotropium, using both Bayesian and likelihood methods. Divergence times of all Andean clades in Heliotropium are estimated to be of late Miocene or Pliocene ages. At least three independent Andean diversification events can be recognized within Heliotropium. Timing of the diversification in the Andean lineages Heliotropium sects.Heliothamnus, Cochranea, Heliotrophytum, Hypsogenia, Plagiomeris, Platygyne clearly correspond to a rapid, late Miocene uplift of the Andes and a Pliocene development of arid environments in South America.