nucleR: a package for non-parametric nucleosome positioning

SUMMARY: nucleR is an R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats. AVAILABILITY: Additional information and methodological details can be found at http://mmb.pcb.ub.es/nucleR     

Identification of molecular-mimicry-based ligands for cholera diagnostics using magnetic relaxation

When covalently bound to an appropriate ligand, iron oxide nanoparticles can bind to a specific target of interest. This interaction can be detected through changes in the solution's spin-spin relaxation times (T2) via magnetic relaxation measurements. In this report, a strategy of molecular mimicry was used in order to identify targeting ligands that bind to the cholera toxin B subunit (CTB). The cellular CTB-receptor, ganglioside GM1, contains a pentasaccharide moiety consisting in part of galactose and glucose units. We therefore predicted that CTB would recognize carbohydrate-conjugated iron oxide nanoparticles as GM1 mimics, thus producing a detectable change in the T2 relaxation times. Magnetic relaxation experiments demonstrated that CTB interacted with the galactose-conjugated nanoparticles. This interaction was confirmed via surface plasmon resonance studies using either the free or nanoparticle-conjugated galactose molecule. The galactose-conjugated nanoparticles were then used as CTB sensors achieving a detection limit of 40 pM. Via magnetic relaxation studies, we found that CTB also interacted with dextran-coated nanoparticles, and surface plasmon resonance studies also confirmed this interaction. Additional experiments demonstrated that the dextran-coated nanoparticle can also be used as CTB sensors and that dextran can prevent the internalization of CTB into GM1-expressing cells. Our work indicates that magnetic nanoparticle conjugates and magnetic relaxation detection can be used as a simple and fast method to identify targeting ligands via molecular mimicry. Furthermore, our results show that the dextran-coated nanoparticles represent a low-cost approach for CTB detection.     

Forests are not immune to plant invasions: phenotypic plasticity and local adaptation allow <Emphasis Type="Italic">Prunella vulgaris</Emphasis> to colonize a temperate evergreen rainforest

In the South American temperate evergreen rainforest (Valdivian forest), invasive plants are mainly restricted to open sites, being rare in the shaded understory. This is consistent with the notion of closed-canopy forests as communities relatively resistant to plant invasions. However, alien plants able to develop shade tolerance could be a threat to this unique forest. Phenotypic plasticity and local adaptation are two mechanisms enhancing invasiveness. Phenotypic plasticity can promote local adaptation by facilitating the establishment and persistence of invasive species in novel environments. We investigated the role of these processes in the recent colonization of Valdivian forest understory by the perennial alien herb Prunella vulgaris from nearby populations in open sites. Using reciprocal transplants, we found local adaptation between populations. Field data showed that the shade environment selected for taller plants and greater specific leaf areas. We found population differentiation and within-population genetic variation in both mean values and reaction norms to light variation of several ecophysiological traits in common gardens from seeds collected in sun and shade populations. The colonization of the forest resulted in a reduction of plastic responses to light variation, which is consistent with the occurrence of genetic assimilation and suggests that P. vulgaris individuals adapted to the shade have reduced probabilities to return to open sites. All results taken together confirm the potential for rapid evolution of shade tolerance in P. vulgaris and suggest that this alien species may pose a threat to the native understory flora of Valdivian forest.     

Efficacy of <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> (Berliner) in controlling the tomato borer, <Emphasis Type="Italic">Tuta absoluta</Emphasis> (Meyrick) (Lepidoptera: Gelechiidae)

The tomato borer, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), is considered to be one of the most devastating pests affecting tomato crops in South America, where crop losses range from 60 to 100%. After its detection in the Spanish tomato-growing area at the end of 2006, it spread quickly to other European and northern African countries. Currently, T. absoluta management in these countries is mainly based on chemical treatments. Nonetheless, special emphasis is being placed on implementing environmentally safe strategies. Commercial formulates based on Bacillus thuringiensis may be a good alternative, as they have been used to control other insect pests successfully. The laboratory, greenhouse, and open-field experiments presented in this work are evidence that B. thuringiensis is highly efficient in controlling T. absoluta. First instar larvae were the most susceptible, while susceptibility was lower in second and third instar larvae. Our results have shown that the impact of T. absoluta can be greatly reduced by spraying only B. thuringiensis-based formulates, with no need for chemical insecticides. Furthermore, the integration of this technology with other biological control methods focused on T. absoluta eggs, such as the use of mirid predators or parasitoids, could reduce the number of B. thuringiensis treatments and the use of chemicals, with the consequent reduction of residues on fruits.     

Might makes right: Using force to align the mitotic spindle

Both symmetric and asymmetric divisions rely on alignment of the mitotic spindle with cues from the environment. A study now shows that mitotic spindles find their position by reading the map of forces that load-bearing retraction fibres exert on the cell body.     

Lac operator repeats generate a traceable fragile site in mammalian cells

One limitation for the study of chromosomal fragile sites is that they must be studied on metaphase spreads, after the breakage. We show here that bacterial lac operator (lacO) repeats are prone to spontaneous breakage, which when combined with a fluorescent lac repressor (lacR) has allowed us to track a fragile site through the cell cycle. By using this system, we show that Plk1-interacting checkpoint helicase (PICH) is already present at fragile sites during interphase, suggesting roles for this helicase beyond mitosis. In addition, we report that the oncogene Myc promotes the formation of anaphase bridges and micronuclei containing fragile-site sequences.