VARAN: a web server for variability analysis of DNA microarray experiments

SUMMARY: Here, we describe a tool for VARiability Analysis of DNA microarrays experiments (VARAN), a freely available Web server that performs a signal intensity based analysis of the log2 expression ratio variability deduced from DNA microarray data (one or two channels). Two modules are proposed: VARAN generator to compute a sliding windows analysis of the experimental variability (mean and SD) and VARAN analyzer to compare experimental data with an asymptotic variability model previously built with the generator module from control experiments. Both modules provide normalized intensity signals with five possible methods, log ratio values and a list of genes showing significant variations between conditions. AVAILABILITY: http://www.bionet.espci.fr/varan/ SUPPLEMENTARY INFORMATION: http://www.bionet.espci.fr/varan/help.html     

Myosin II Activity Softens Cells in Suspension

The cellular cytoskeleton is crucial for many cellular functions such as cell motility and wound healing, as well as other processes that require shape change or force generation. Actin is one cytoskeleton component that regulates cell mechanics. Important properties driving this regulation include the amount of actin, its level of cross-linking, and its coordination with the activity of specific molecular motors like myosin. While studies investigating the contribution of myosin activity to cell mechanics have been performed on cells attached to a substrate, we investigated mechanical properties of cells in suspension. To do this, we used multiple probes for cell mechanics including a microfluidic optical stretcher, a microfluidic microcirculation mimetic, and real-time deformability cytometry. We found that nonadherent blood cells, cells arrested in mitosis, and naturally adherent cells brought into suspension, stiffen and become more solidlike upon myosin inhibition across multiple timescales (milliseconds to minutes). Our results hold across several pharmacological and genetic perturbations targeting myosin. Our findings suggest that myosin II activity contributes to increased whole-cell compliance and fluidity. This finding is contrary to what has been reported for cells attached to a substrate, which stiffen via active myosin driven prestress. Our results establish the importance of myosin II as an active component in modulating suspended cell mechanics, with a functional role distinctly different from that for substrate-adhered cells.     

Bioinformatics in glycobiology

In comparison with genes and proteins, attention paid to oligosaccharides that modify proteins is still marginal. Accordingly, bioinformatics is so far poorly involved in glycobiology. Some initiatives have been taken, however, to collect in databases all glycobiology-relevant information or to design specific data mining algorithms to infer predictions or identify oligosaccharide structures. In this review, we make a non-exhaustive survey of the available glycobiology-related bioinformatic resources, focussing mainly on those resources that are available through the World Wide Web. Some well-curated databases are identified, but the development of specialised algorithms appears to be limited.     

Microarray-based detection and typing of the Rhizobium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest

Environmental screening of bacteria for the presence of genes of interest is a challenging problem, due to the high variability of the nucleotide sequence of a given gene between species. Here, we tackle this general issue using a particularly well-suited model system that consists of the nodulation gene nodC, which is shared by phylogenetically distant rhizobia. 41mer and 50mer oligonucleotides featuring the nucleotide diversity of two highly conserved regions of the NodC protein were spotted on glass slides and cross hybridized with the radioactive-labeled target genomic DNA under low-stringency conditions. Statistical analysis of the hybridization patterns allowed the detection of known, as well as new, nodC sequences and classified the rhizobial strains accordingly. The microarray was successfully used to type the nodC gene directly from legume nodules, thus eliminating the need of cultivation of the endosymbiont. This approach could be extended to a panel of diagnostic genes and constitute a powerful tool for studying the distribution of genes of interest in the environment, as well as for bacteria identification.     

Pituicyte Stellation is Prevented by RhoA-or Cdc42-Dependent Actin Polymerization

Our aim was to shed light on different steps leading from metabotropic receptor activation to changes in cell shape, such as those that characterize the morphological plasticity of neurohypophysial astrocytes (pituicytes). Using explant cultures of adult rat pituicytes, we have previously established that adenosine A1 receptor activation induces stellation via inhibition of RhoA monomeric GTPase and subsequent disruption of actin stress fibers. Here, we rule out RhoA phosphorylation as a mechanism for that inhibition. Rather, our results are more consistent with involvement of a GTPase-activating protein (GAP). siRNA and pull-down experiments suggest that a step downstream of RhoA might involve Cdc42, another GTPase of the Rho family. However, RhoA activation, e.g., in the presence of serum, induces stress fibers, whereas direct Cdc42 activation appears to confine actin within a submembrane—i.e., cortical—network, which also prevents stellation. Therefore, we propose that RhoA may activate Cdc42 in parallel with an effector, such as p160Rho-kinase, that induces and maintains actin stress fibers in a dominant fashion. Rac1 is not involved in the stellation process per se but appears to induce a dendritogenic effect. Ultimately, it may be stated that pituicyte stellation is inducible upon mere actin depolymerization, and preventable upon actin organization, be it in the form of stress fibers or in a cortical configuration.