New methods for chicken embryo manipulations

The capacity to image a growing embryo while simultaneously studying the developmental function of specific molecules provides invaluable information on embryogenesis. However, until recently, this approach was accomplished with difficulty both because of the advanced technology needed and because an easy method of minimizing damage to the embryo was unavailable. Here, we present a novel way of adapting the well-known EC culture of whole chick embryos to time-lapse imaging and to functional molecular studies using blocking agents. The novelty of our method stems from the ability to apply blocking agents ex ovo as well as in ovo. We were able to study the function of a set of molecules by culturing developing embryos ex ovo in tissue culture media containing these molecules or by injecting them underneath the live embryo in ovo. The in ovo preparation is particularly valuable, because it extends the period of time during which the developmental function of the molecule can be studied and it provides an easy, reproducible method for screening a batch of molecules. These new techniques will prove very helpful in visualizing and understanding the role of specific molecules during embryonic morphogenesis, including blood vessel formation

Post-pulse addition of trans-cyclohexane-1,2-diol improves electrotransfer mediated gene expression in mammalian cells

AbstractElectric field mediated gene transfer is facing a problem in expression yield due to the poor transfer across the nuclear envelope. Trans-cyclohexane-1,2-diol (TCHD) was shown to significantly increase chemically mediated transfection by collapsing the permeability barrier of the nuclear pore complex. We indeed observed a significant increase in expression by electrotransfer when cells are treated post pulse by a low non toxic concentration of TCHD. This was obtained for different pulsing conditions, cell strains and plasmid constructs. An interesting improvement in cell viability can be obtained. This can significantly enhance the non-viral gene electrical delivery

An integrated concurrency and core-ISA architectural envelope definition, and test oracle, for IBM POWER multiprocessors

Funding: Scottish Funding Council (SICSA Early Career Industry Fellowship)Weakly consistent multiprocessors such as ARM and IBM POWER have been with us for decades, but their subtle programmer-visible concurrency behaviour remains challenging, both to implement and to use; the traditional architecture documentation, with its mix of prose and pseudocode, leaves much unclear. In this paper we show how a precise architectural envelope model for such architectures can be defined, taking IBM POWER as our example. Our model specifies, for an arbitrary test program, the set of all its allowable executions, not just those of some particular implementation. The model integrates an operational concurrency model with an ISA model for the fixedpoint non-vector user-mode instruction set (largely automatically derived from the vendor pseudocode, and expressed in a new ISA description language). The key question is the interface between these two: allowing all the required concurrency behaviour, without overcommitting to some particular microarchitectural implementation, requires a novel abstract structure. Our model is expressed in a mathematically rigorous language that can be automatically translated to an executable test-oracle tool; this lets one either interactively explore or exhaustively compute the set of all allowed behaviours of intricate test cases, to provide a reference for hardware and software development.Postprin

Patterns and drivers of climatic niche dynamics during biological invasions of island-endemic amphibians, reptiles, and birds

Shifts between native and alien climatic niches pose a major challenge for predicting biological invasions. This is particularly true for insular species because geophysical barriers could constrain the realization of their fundamental niches, which may lead to underestimates of their invasion potential. To investigate this idea, we estimated the frequency of shifts between native and alien climatic niches and the magnitude of climatic mismatches using 80,148 alien occurrences of 46 endemic insular amphibian, reptile, and bird species. Then, we assessed the influence of nine potential predictors on climatic mismatches across taxa, based on species' characteristics, native range physical characteristics, and alien range properties. We found that climatic mismatch is common during invasions of endemic insular birds and reptiles: 78.3% and 55.1% of their respective alien records occurred outside of the environmental space of species' native climatic niche. In comparison, climatic mismatch was evident for only 16.2% of the amphibian invasions analyzed. Several predictors significantly explained climatic mismatch, and these varied among taxonomic groups. For amphibians, only native range size was associated with climatic mismatch. For reptiles, the magnitude of climatic mismatch was higher for species with narrow native altitudinal ranges, occurring in topographically complex or less remote islands, as well as for species with larger distances between their native and alien ranges. For birds, climatic mismatch was significantly larger for invasions on continents with higher phylogenetic diversity of the recipient community, and when the invader was more evolutionarily distinct. Our findings highlight that apparently common niche shifts of insular species may jeopardize our ability to forecast their potential invasions using correlative methods based on climatic variables. Also, we show which factors provide additional insights on the actual invasion potential of insular endemic amphibians, reptiles, and birds

Structural insights into ring-building motif domains involved in bacterial sporulation.

Components of specialized secretion systems, which span the inner and outer membranes in Gram-negative bacteria, include ring-forming proteins whose oligomerization was proposed to be promoted by domains called RBM for "Ring-Building Motifs". During spore formation in Gram-positive bacteria, a transport system called the SpoIIIA-SpoIIQ complex also assembles in the double membrane that surrounds the forespore following its endocytosis by the mother cell. The presence of RBM domains in some of the SpoIIIA proteins led to the hypothesis that they would assemble into rings connecting the two membranes and form a conduit between the mother cell and forespore. Among them, SpoIIIAG forms homo-oligomeric rings in vitro but the oligomerization of other RBM-containing SpoIIIA proteins, including SpoIIIAH, remains to be demonstrated. In this work, we identified RBM domains in the YhcN/YlaJ family of proteins that are not related to the SpoIIIA-SpoIIQ complex. We solved the crystal structure of YhcN from Bacillus subtilis, which confirmed the presence of a RBM fold, flanked by additional secondary structures. As the protein did not show any oligomerization ability in vitro, we investigated the structural determinants of ring formation in SpoIIIAG, SpoIIIAH and YhcN. We showed that in vitro, the conserved core of RBM domains alone is not sufficient for oligomerization while the β-barrel forming region in SpoIIIAG forms rings on its own. This work suggests that some RBMs might indeed participate in the assembly of homomeric rings but others might have evolved toward other functions

How biological invasions affect animal behaviour: A global, cross-taxonomic analysis

In the Anthropocene, species are faced with drastic challenges due to rapid, human-induced changes, such as habitat destruction, pollution and biological invasions. In the case of invasions, native species may change their behaviour to minimize the impacts they sustain from invasive species, and invaders may also adapt to the conditions in their new environment in order to survive and establish self-sustaining populations. We aimed at giving an overview of which changes in behaviour are studied in invasions, and what is known about the types of behaviour that change, the underlying mechanisms and the speed of behavioural changes. Based on a review of the literature, we identified 191 studies and 360 records (some studies reported multiple records) documenting behavioural changes caused by biological invasions in native (236 records from 148 species) or invasive (124 records from 50 species) animal species. This global dataset, which we make openly available, is not restricted to particular taxonomic groups. We found a mild taxonomic bias in the literature towards mammals, birds and insects. In line with the enemy release hypothesis, native species changed their anti-predator behaviour more frequently than invasive species. Rates of behavioural change were evenly distributed across taxa, but not across the types of behaviour. Our findings may help to better understand the role of behaviour in biological invasions as well as temporal changes in both population densities and traits of invasive species, and of native species affected by them

BotSwindler: Tamper Resistant Injection of Believable Decoys in VM-Based Hosts for Crimeware Detection

We introduce BotSwindler, a bait injection system designed to delude and detect crimeware by forcing it to reveal during the exploitation of monitored information. The implementation of BotSwindler relies upon an out-of-host software agent that drives user-like interactions in a virtual machine, seeking to convince malware residing within the guest OS that it has captured legitimate credentials. To aid in the accuracy and realism of the simulations, we propose a low overhead approach, called virtual machine verification, for verifying whether the guest OS is in one of a predefined set of states. We present results from experiments with real credential-collecting malware that demonstrate the injection of monitored financial bait for detecting compromises. Additionally, using a computational analysis and a user study, we illustrate the believability of the simulations and we demonstrate that they are sufficiently human-like. Finally, we provide results from performance measurements to show our approach does not impose a performance burden

Invasion Biology: Specific Problems and Possible Solutions

International audienceBiological invasions have been unambiguously shown to be one of the major global causes of biodiversity loss. Despite the magnitude of this threat and recent scientific advances, this field remains a regular target of criticism – from outright deniers of the threat to scientists questioning the utility of the discipline. This unique situation, combining internal strife and an unaware society, greatly hinders the progress of invasion biology. It is crucial to identify the specificities of this discipline that lead to such difficulties. We outline here 24 specificities and problems of this discipline and categorize them into four groups: understanding, alerting, supporting, and implementing the issues associated with invasive alien species, and we offer solutions to tackle these problems and push the field forward