X-ray microanalysis of toluidine blue stained chromosomes: a quantitative study of the metachromatic reaction of chromatin

The stoichiometry of metachromatic staining of chromatin by toluidine blue was investigated in isolated metaphase chromosomes from L929 cells using X-ray microanalysis. Microspectrophotometric measurements revealed that a hypsochromic shift (from 595 to 570 nm) occurs in toluidine blue stained chromosomes in relation to the staining solution. Under the electron microscope, stained chromosomes. After toluidine blue staining, X-ray microanalysis of chromosomes revealed a large increase for sulphur counts and a considerable increase for Fe and Cu counts, while the signal of Mg, Ca, Cl, K and Zn was reduced. After subtraction of the intrinsic sulphur signal, S/P ratios of 0.82--for euchromatic arms--and 0.85--for centromeric heterochromatin--were obtained. They are considered representative of dye/DNA phosphate ratios. These results indicate the occurrence of a nearly stoichiometric binding of toluidine blue to chromatin DNA and suggest that an external dye stacking is responsible for the metachromatic staining of metaphase chromosomes.     

A preliminary report on the distribution of lizards in Qatar

We have updated the list of the lizard species present in Qatar and produced the first distribution maps based on two field surveys in 2012 and 2013. We used the QND95/Qatar National Grid with a grid of 10 × 10 km squares for mapping. Our results show the occurrence of 21 lizard species in Qatar, from the 15 species indicated in the last biodiversity report conducted in 2004. The most abundant family found in Qatar is Gekkonidae with nine species (Bunopus tuberculatus, Cyrtopodion scabrum, Hemidactylus robustus, H. flaviviridis, H. persicus, Stenodactylus arabicus, S. slevini, S. doriae, Pseudoceramodactylus khobarensis), followed by Lacertidae with four species (Acanthodactylus schmidti, A. opheodurus, Mesalina brevirostris, M. adramitana), Agamidae with three species (Trapelus flavimaculatus, Uromastyx aegyptia, Phrynocephalus arabicus), Scincidae with two species (Scincus mitranus, Trachylepis septemtaeniata), and Varanidae (Varanus griseus), Sphaerodactylidae (Pristurus rupestris) and Trogonophiidae (Diplometopon zarudnyi) with one species each. The species richness fluctuated largely across Qatar between one and eleven species per grid square. We believe that the lizard fauna records in Qatar are still incomplete and that additional studies are required. However, our study here fills a gap concerning lizard biodiversity knowledge in the Gulf Region.     

esyN: Network Building,Sharing and Publishing

The construction and analysis of networks is increasingly widespread in biological research. We have developed esyN (“easy networks”) as a free and open source tool to facilitate the exchange of biological network models between researchers. esyN acts as a searchable database of user-created networks from any field. We have developed a simple companion web tool that enables users to view and edit networks using data from publicly available databases. Both normal interaction networks (graphs) and Petri nets can be created. In addition to its basic tools, esyN contains a number of logical templates that can be used to create models more easily. The ability to use previously published models as building blocks makes esyN a powerful tool for the construction of models and network graphs. Users are able to save their own projects online and share them either publicly or with a list of collaborators. The latter can be given the ability to edit the network themselves, allowing online collaboration on network construction. esyN is designed to facilitate unrestricted exchange of this increasingly important type of biological information. Ultimately, the aim of esyN is to bring the advantages of Open Source software development to the construction of biological networks.     

Dynamic assessment of human sperm DNA damage III: the effect of sperm freezing techniques

Cell and Tissue Banking - Among the currently available strategies for sperm freezing, vitrification may be considered as the leading alternative to conventional cryopreservation. Nevertheless, a...     

Bayesian modelling of shared gene function

MOTIVATION: Biological assays are often carried out on tissues that contain many cell lineages and active pathways. Microarray data produced using such material therefore reflect superimpositions of biological processes. Analysing such data for shared gene function by means of well-matched assays may help to provide a better focus on specific cell types and processes. The identification of genes that behave similarly in different biological systems also has the potential to reveal new insights into preserved biological mechanisms. RESULTS: In this article, we propose a hierarchical Bayesian model allowing integrated analysis of several microarray data sets for shared gene function. Each gene is associated with an indicator variable that selects whether binary class labels are predicted from expression values or by a classifier which is common to all genes. Each indicator selects the component models for all involved data sets simultaneously. A quantitative measure of shared gene function is obtained by inferring a probability measure over these indicators. Through experiments on synthetic data, we illustrate potential advantages of this Bayesian approach over a standard method. A shared analysis of matched microarray experiments covering (a) a cycle of mouse mammary gland development and (b) the process of in vitro endothelial cell apoptosis is proposed as a biological gold standard. Several useful sanity checks are introduced during data analysis, and we confirm the prior biological belief that shared apoptosis events occur in both systems. We conclude that a Bayesian analysis for shared gene function has the potential to reveal new biological insights, unobtainable by other means. AVAILABILITY: An online supplement and MatLab code are available at http://www.sykacek.net/research.html#mcabf     

FlyMine: an integrated database for Drosophila and Anopheles genomics

FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists.     

Shaping carnivore communities by predator control: competitor release revisited

The traditional way to deal with hunting interests is often focused on predator control. This approach requires a detailed understanding of predator responses to game management. Control methods can be non-selective and, consequently, can potentially have a negative impact on non-target predator species, affecting carnivore guild. In order to assess the potential risks associated with non-selective predator control in the presence of intraguild competition, the classical Lotka?CVolterra competition model was used, but with two additional factors: a linear factor for capture mortality (mortality caused by predator control) and a factor for vacated niche occupancy associated with immigration. Simulation in a scenario with three species revealed that one of them, the red fox Vulpes vulpes, which presented the highest intrinsic growth rate, can show population increases even under moderate control, whereas the population of European badger Meles meles, with a lower intrinsic growth rate, was reduced and, in some cases, may even become extinct. Lastly, the stone marten Martes foina presented a differential response, depending on the removal intensity and strategy employed. This behaviour is compatible with the results observed in a Mediterranean environment subjected to two types of game management: non-selective predator control (culling) and no control. In areas with non-selective control and moderate predator removal, the red fox population remained stable, while the stone marten and the European badger populations reduced markedly or disappeared.     

Mural Cell Associated VEGF Is Required for Organotypic Vessel Formation

Background

Blood vessels comprise endothelial cells, mural cells (pericytes/vascular smooth muscle cells) and basement membrane. During angiogenesis, mural cells are recruited to sprouting endothelial cells and define a stabilizing context, comprising cell-cell contacts, secreted growth factors and extracellular matrix components, that drives vessel maturation and resistance to anti-angiogenic therapeutics.

Methods and Findings

To better understand the basis for mural cell regulation of angiogenesis, we conducted high content imaging analysis on a microtiter plate format in vitro organotypic blood vessel system comprising primary human endothelial cells co-cultured with primary human mural cells. We show that endothelial cells co-cultured with mural cells undergo an extensive series of phenotypic changes reflective of several facets of blood vessel formation and maturation: Loss of cell proliferation, pathfinding-like cell migration, branching morphogenesis, basement membrane extracellular matrix protein deposition, lumen formation, anastamosis and development of a stabilized capillary-like network. This phenotypic sequence required endothelial-mural cell-cell contact, mural cell-derived VEGF and endothelial VEGFR2 signaling. Inhibiting formation of adherens junctions or basement membrane structures abrogated network formation. Notably, inhibition of mural cell VEGF expression could not be rescued by exogenous VEGF.

Conclusions

These results suggest a unique role for mural cell-associated VEGF in driving vessel formation and maturation.     

High frequency of constitutive alkali-labile sites in mouse major satellite DNA, detected by DNA breakage detection-fluorescence in situ hybridization

Electromagnetic fields (EMFs) have been associated with increased incidence of cancer suggested by epidemiological studies. To test the carcinogenic potency of EMF, the in vitro micronucleus assay with SHE cells has been used as a screening method for genotoxicity. A 50Hz magnetic field (MF) of 1mT field strength was applied either alone or with the tumour initiator benzo(a)pyrene (BP) or the tumour promoter 12-O-tetradecanoylphorbol-13-acetate (TPA). All three treatments were applied in single, double or triple treatment regimes. MF or TPA (1nM) alone did not affect the number of micronuclei (MN) in initiated and non-initiated SHE cells. Changing the schedule of the typical initiation protocol, namely applying the initiator (BP) during exposure to MF, results in an 1.8-fold increased MN formation compared to BP treatment alone. Combined experiment with BP, TPA and MF did not cause further MN formation. Since initiation during MF exposure caused a significant increased MN formation, our findings suggest that MFs enhance the initiation process of BP. We think that this MF-enhanced co-carcinogenic effect is caused by an indirect "cell activation" process. The resulting genomic instability is proposed to be due to free radicals and/or to the unscheduled "switching-on" of signal transduction pathways.