Focal adhesion kinase is not required for Src-induced formation of invadopodia in KM12C colon cancer cells and can interfere with their assembly

Overexpression of active Src induces invadopodia formation and associated matrix degradation in KM12C colon cancer cells. FAK is present with active Src at sites of matrix-degrading activity (invadopodia), specifically residing in rings surrounding the cortactin-containing invadopodia cores. Since FAK is a key effector protein in many aspects of Src function, we addressed whether FAK is necessary for Src-induced invadopodia formation and matrix degradation in KM12C colon cancer cells. We found that efficient knockdown of FAK expression by siRNA had no effect on invadopodia formation or matrix degradation. However, overexpression of FAK could actually suppress invadopodia formation and matrix degradation. FAK phosphorylation on the putative auto-phosphorylation tyrosine 397 and the Src-specific sites are all required for overexpressed FAK to inhibit invadopodia formation, while the kinase activity of exogenous FAK is apparently not required. These data imply that kinase activities other than FAK auto-phosphorylation may contribute to the phosphorylation of FAK tyrosine 397 in some contexts to promote an activity of FAK that can counteract invadopodia formation. Further work is required to determine how the strength of signalling through FAK suppresses invadopodia, but we propose that FAK controls the balance of adhesion types in cells, and that this is one of the determinants of whether a cancer cell can make stable matrix-degrading invadopodia.     

Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times

The genetic diversity of present-day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35,000 years. However, the post-last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.     

Molecular modelling of phthalates - PPARs interactions

Di(2-ethylhexyl) phthalate (DEHP) is the most widely plasticizer for polyvinyl chloride (PVC) that is used in plastic tubes, in medical and paramedical devices as well as in food storage packaging. The toxicological profile of DEHP has been evaluated in a number of experimental animal models and has been extensively documented. Its toxicity is in part linked to the activation of the peroxisome proliferator-activated receptor alpha (PPAR(alpha)). As a response, an intensive research for a new, biologically inert plasticizer has been initiated. Among the alternative studied, tri(2-ethylhexyl) trimellitate (TEHTM) or trioctyl trimellitate (TOTM) has attracted increasing interest. However, very little information is available on their biological effects. We proceeded to dock TOTM, DEHP and its metabolites in order to identify compounds that are likely to interact with PPAR(alpha) and PPAR(gamma) binding sites. The results obtained hint that TOTM is not able to bind to PPARs and should therefore be safer than DEHP.     

In vivo optical imaging of neurogenesis: watching new neurons in the intact brain

Adult neurogenesis is a highly dynamic process modulated by several pathologic and environmental factors, as well as by various compounds. So far, available techniques to study neurogenesis are lengthy and personnel and cost intensive. We developed a new tool based on the doublecortin promoter driving the expression of the luciferase reporter gene (DCX-promo-luciferase) in transgenic mice to perform in vivo imaging of neurogenesis. Indeed, the DCX-promo-luciferase mice allowed optical in vivo imaging of the onset of and increase in neurogenesis in developing fetal brains, as well as imaging of neurogenesis in the intact adult mouse central nervous system. Moreover, the capacity to specifically detect a small number of migrating neuronal precursors in vivo after transplantation is for the first time feasible using this DCX-promo-luciferase transgenic tool. The present imaging approach offers several crucial advantages over methods currently available, such as bromodeoxyuridine incorporation or labeling using iron oxide nanoparticles. Hence, it allows longitudinal study of neurogenesis in intact animals without the requirement of cellular prelabeling. Moreover, it guarantees that detection is specific for neuronal precursors and restricted to viable cells. Hence, our DCX-promo-luciferase transgenic model constitutes an effective tool that answers the pressing need for rapid investigation of the impact on neurogenesis of a large number of candidate compounds waiting to be tested.     

Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation

Whether functional magnetic resonance imaging (fMRI) allows the identification of neural drivers remains an open question of particular importance to refine physiological and neuropsychological models of the brain, and/or to understand neurophysiopathology. Here, in a rat model of absence epilepsy showing spontaneous spike-and-wave discharges originating from the first somatosensory cortex (S1BF), we performed simultaneous electroencephalographic (EEG) and fMRI measurements, and subsequent intracerebral EEG (iEEG) recordings in regions strongly activated in fMRI (S1BF, thalamus, and striatum). fMRI connectivity was determined from fMRI time series directly and from hidden state variables using a measure of Granger causality and Dynamic Causal Modelling that relates synaptic activity to fMRI. fMRI connectivity was compared to directed functional coupling estimated from iEEG using asymmetry in generalised synchronisation metrics. The neural driver of spike-and-wave discharges was estimated in S1BF from iEEG, and from fMRI only when hemodynamic effects were explicitly removed. Functional connectivity analysis applied directly on fMRI signals failed because hemodynamics varied between regions, rendering temporal precedence irrelevant. This paper provides the first experimental substantiation of the theoretical possibility to improve interregional coupling estimation from hidden neural states of fMRI. As such, it has important implications for future studies on brain connectivity using functional neuroimaging.     

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus

We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories".     

The separation of timescales in Bayesian survival modeling of the time-varying effect of a time-dependent exposure

In this paper, we apply flexible Bayesian survival analysis methods to investigate the risk of lymphoma associated with kidney transplantation among patients with end-stage renal disease. Of key interest is the potentially time-varying effect of a time-dependent exposure: transplant status. Bayesian modeling of the baseline hazard and the effect of transplant requires consideration of 2 timescales: time since study start and time since transplantation, respectively. Previous related work has not dealt with the separation of multiple timescales. Using a hierarchical model for the hazard function, both timescales are incorporated via conditionally independent stochastic processes; smoothing of each process is specified via intrinsic conditional Gaussian autoregressions. Features of the corresponding posterior distribution are evaluated from draws obtained via a Metropolis-Hastings-Green algorithm.     

Genomic imprinting mechanisms in mammals

Genomic imprinting is a form of epigenetic gene regulation that results in expression from a single allele in a parent-of-origin-dependent manner. This form of monoallelic expression affects a small but growing number of genes and is essential to normal mammalian development. Despite extensive studies and some major breakthroughs regarding this intriguing phenomenon, we have not yet fully characterized the underlying molecular mechanisms of genomic imprinting. This is in part due to the complexity of the system in that the epigenetic markings required for proper imprinting must be established in the germline, maintained throughout development, and then erased before being re-established in the next generation's germline. Furthermore, imprinted gene expression is often tissue or stage-specific. It has also become clear that while imprinted loci across the genome seem to rely consistently on epigenetic markings of DNA methylation and/or histone modifications to discern parental alleles, the regulatory activities underlying these markings vary among loci. Here, we discuss different modes of imprinting regulation in mammals and how perturbations of these systems result in human disease. We focus on the mechanism of genomic imprinting mediated by insulators as is present at the H19/Igf2 locus, and by non-coding RNA present at the Igf2r and Kcnq1 loci. In addition to imprinting mechanisms at autosomal loci, what is known about imprinted X-chromosome inactivation and how it compares to autosomal imprinting is also discussed. Overall, this review summarizes many years of imprinting research, while pointing out exciting new discoveries that further elucidate the mechanism of genomic imprinting, and speculating on areas that require further investigation.