Defining Life: The Virus Viewpoint

Are viruses alive? Until very recently, answering this question was often negative and viruses were not considered in discussions on the origin and definition of life. This situation is rapidly changing, following several discoveries that have modified our vision of viruses. It has been recognized that viruses have played (and still play) a major innovative role in the evolution of cellular organisms. New definitions of viruses have been proposed and their position in the universal tree of life is actively discussed. Viruses are no more confused with their virions, but can be viewed as complex living entities that transform the infected cell into a novel organism—the virus—producing virions. I suggest here to define life (an historical process) as the mode of existence of ribosome encoding organisms (cells) and capsid encoding organisms (viruses) and their ancestors. I propose to define an organism as an ensemble of integrated organs (molecular or cellular) producing individuals evolving through natural selection. The origin of life on our planet would correspond to the establishment of the first organism corresponding to this definition

An improved method for large-scale preparation of negatively and positively supercoiled plasmid DNA

A rigorous understanding of the biological function of superhelical tension in cellular DNA requires the development of new tools and model systems for study. To this end, an ethidium bromide–free method has been developed to prepare large quantities of either negatively or positively super-coiled plasmid DNA. The method is based upon the known effects of ionic strength on the direction of binding of DNA to an archaeal histone, rHMfB, with low and high salt concentrations leading to positive and negative DNA supercoiling, respectively. In addition to fully optimized conditions for large-scale (>500 µg) supercoiling reactions, the method is advantageous in that it avoids the use of mutagenic ethidium bromide, is applicable to chemically modified plasmid DNA substrates, and produces both positively and negatively supercoiled DNA using a single set of reagents.National Cancer Institute (U.S.) (NCI; grant no. CA072936)National Cancer Institute (U.S.) (NCI; grant no. CA110261)National Cancer Institute (U.S.) (NCI; grant no. CA103146)National Institute of Environmental Health Sciences (ES002109)National Defense Science and Engineering Graduate Fellowshi

A constitutive law for dense granular flows

A continuum description of granular flows would be of considerable help in predicting natural geophysical hazards or in designing industrial processes. However, the constitutive equations for dry granular flows, which govern how the material moves under shear, are still a matter of debate. One difficulty is that grains can behave like a solid (in a sand pile), a liquid (when poured from a silo) or a gas (when strongly agitated). For the two extreme regimes, constitutive equations have been proposed based on kinetic theory for collisional rapid flows, and soil mechanics for slow plastic flows. However, the intermediate dense regime, where the granular material flows like a liquid, still lacks a unified view and has motivated many studies over the past decade. The main characteristics of granular liquids are: a yield criterion (a critical shear stress below which flow is not possible) and a complex dependence on shear rate when flowing. In this sense, granular matter shares similarities with classical visco-plastic fluids such as Bingham fluids. Here we propose a new constitutive relation for dense granular flows, inspired by this analogy and recent numerical and experimental work. We then test our three-dimensional (3D) model through experiments on granular flows on a pile between rough sidewalls, in which a complex 3D flow pattern develops. We show that, without any fitting parameter, the model gives quantitative predictions for the flow shape and velocity profiles. Our results support the idea that a simple visco-plastic approach can quantitatively capture granular flow properties, and could serve as a basic tool for modelling more complex flows in geophysical or industrial applications.Comment: http://www.nature.com/nature/journal/v441/n7094/abs/nature04801.htm

Granular Flows in Split-Bottom Geometries

There is a simple and general experimental protocol to generate slow granular flows that exhibit wide shear zones, qualitatively different from the narrow shear bands that are usually observed in granular materials . The essence is to drive the granular medium not from the sidewalls, but to split the bottom of the container that supports the grains in two parts and slide these parts past each other. Here we review the main features of granular flows in such split-bottom geometries.Comment: 8 pages, 10 figures, accepted for Soft Matte

Manufacturing-focused emissions reductions in footwear production

What is the burden upon your feet? With sales of running and jogging shoes in the world averaging a nontrivial 25 billion shoes per year, or 34 million per day, the impact of the footwear industry represents a significant portion of the apparel sector's environmental burden. A single shoe can contain 65 discrete parts that require 360 processing steps for assembly. While brand name companies dictate product design and material specifications, the actual manufacturing of footwear is typically contracted to manufacturers based in emerging economies. Using life cycle assessment methodology in accordance with the ISO 14040/14044 standards, this effort quantifies the life cycle greenhouse gas emissions, often referred to as a carbon footprint, of a pair of running shoes. Furthermore, mitigation strategies are proposed focusing on high leverage aspects of the life cycle. Using this approach, it is estimated that the carbon footprint of a typical pair of running shoes made of synthetic materials is 14 ± 2.7 kg CO[subscript 2]-equivalent. The vast majority of this impact is incurred during the materials processing and manufacturing stages, which make up around 29% and 68% of the total impact, respectively. Other similar studies in the apparel industry have reported carbon footprints of running shoes ranging between 18 and 41 kg CO[subscript 2]-equivalent/pair (PUMA, 2008; Timberland, 2009). For consumer products not requiring electricity during use, the intensity of emissions in the manufacturing phase is atypical; most commonly, materials make up the biggest percentage of impact. This distinction highlights the importance of identifying mitigation strategies within the manufacturing process, and the need to evaluate the emissions reduction efficacy of each potential strategy. By suggesting a few of the causes of manufacturing dominance in the global warming potential assessment of this product, this study hypothesizes the characteristics of a product that could lead to high manufacturing impact. Some of these characteristics include the source of energy in manufacturing and the form of manufacturing, in other words the complexity of processes used and the area over which these process are performed (particularly when a product involves numerous parts and light materials). Thereby, the work provides an example when relying solely on the bill of materials information for product greenhouse gas emissions assessment may underestimate life cycle burden and ignore potentially high impact mitigation strategies

Experimental fossilisation of viruses from extremophilic Archaea

The role of viruses at different stages of the origin of life has recently been reconsidered. It appears that viruses may have accompanied the earliest forms of life, allowing the transition from an RNA to a DNA world and possibly being involved in the shaping of tree of life in the three domains that we know presently. In addition, a large variety of viruses has been recently identified in extreme environments, hosted by extremophilic microorganisms, in ecosystems considered as analogues to those of the early Earth. Traces of life on the early Earth were preserved by the precipitation of silica on the organic structures. We present the results of the first experimental fossilisation by silica of viruses from extremophilic Archaea (SIRV2 – <i>Sulfolobus islandicus</i> rod-shaped virus 2, TPV1 – <i>Thermococcus prieurii</i> virus 1, and PAV1 – <i>Pyrococcus abyssi</i> virus 1). Our results confirm that viruses can be fossilised, with silica precipitating on the different viral structures (proteins, envelope) over several months in a manner similar to that of other experimentally and naturally fossilised microorganisms. This study thus suggests that viral remains or traces could be preserved in the rock record although their identification may be challenging due to the small size of the viral particles

Hydrodynamics of thermal granular convection

A hydrodynamic theory is formulated for buoyancy-driven ("thermal") granular convection, recently predicted in molecular dynamic simulations and observed in experiment. The limit of a dilute flow is considered. The problem is fully described by three scaled parameters. The convection occurs via a supercritical bifurcation, the inelasticity of the collisions being the control parameter. The theory is expected to be valid for small Knudsen numbers and nearly elastic grain collisions.Comment: 4 pages, 4 EPS figures, some details adde

Determination of cutoff values on computed tomography and magnetic resonance images for the diagnosis of atlantoaxial instability in small-breed dogs.

OBJECTIVE To determine cutoff values for the diagnosis of atlantoaxial instability (AAI) based on cross-sectional imaging in small-breed dogs. STUDY DESIGN Retrospective multicenter study. SAMPLE POPULATION Client-owned dogs (n = 123) and 28 cadavers. METHODS Dogs were assigned to three groups: a control group, a "potentially unstable" group, and an AAI-affected group, according to imaging findings and clinical signs. The ventral compression index (VCI), cranial translation ratio (CTR), C1-C2 overlap, C1-C2 angle, atlantoaxial distance, basion-dens interval, dens-to-axis length ratio (DALR), power ratio, and clivus canal angles were measured on CT or T2-weighted magnetic resonance (MR) images. Receiver operating characteristic (ROC) analysis was performed to define cutoff values in flexed (≥25°) and extended (<25°) head positions. RESULTS Cutoff values for the VCI of ≥0.16 in extended and ≥0.2 in flexed head positions were diagnostic for AAI (sensitivity of 100% and 100%, specificity of 94.54% and 96.67%, respectively). Cutoff values for the other measurements were defined with a lower sensitivity (75%-96%) and specificity (70%-97%). A combination of the measurements did not increase the sensitivity and specificity compared with the VCI as single measurement. CONCLUSION Cutoff values for several imaging measurements were established with good sensitivity and specificity. The VCI, defined as the ratio between the ventral and dorsal atlantodental interval, had the highest sensitivity and specificity in both head positions. CLINICAL SIGNIFICANCE The use of defined cutoff values allows an objective diagnosis of AAI in small-breed dogs. The decision for surgical intervention, however, should remain based on a combination of clinical and imaging findings

Helical Chirality: a Link between Local Interactions and Global Topology in DNA

DNA supercoiling plays a major role in many cellular functions. The global DNA conformation is however intimately linked to local DNA-DNA interactions influencing both the physical properties and the biological functions of the supercoiled molecule. Juxtaposition of DNA double helices in ubiquitous crossover arrangements participates in multiple functions such as recombination, gene regulation and DNA packaging. However, little is currently known about how the structure and stability of direct DNA-DNA interactions influence the topological state of DNA. Here, a crystallographic analysis shows that due to the intrinsic helical chirality of DNA, crossovers of opposite handedness exhibit markedly different geometries. While right-handed crossovers are self-fitted by sequence-specific groove-backbone interaction and bridging Mg2+ sites, left-handed crossovers are juxtaposed by groove-groove interaction. Our previous calculations have shown that the different geometries result in differential stabilisation in solution, in the presence of divalent cations. The present study reveals that the various topological states of the cell are associated with different inter-segmental interactions. While the unstable left-handed crossovers are exclusively formed in negatively supercoiled DNA, stable right-handed crossovers constitute the local signature of an unusual topological state in the cell, such as the positively supercoiled or relaxed DNA. These findings not only provide a simple mechanism for locally sensing the DNA topology but also lead to the prediction that, due to their different tertiary intra-molecular interactions, supercoiled molecules of opposite signs must display markedly different physical properties. Sticky inter-segmental interactions in positively supercoiled or relaxed DNA are expected to greatly slow down the slithering dynamics of DNA. We therefore suggest that the intrinsic helical chirality of DNA may have oriented the early evolutionary choices for DNA topology

Microtubules in Bacteria: Ancient Tubulins Build a Five-Protofilament Homolog of the Eukaryotic Cytoskeleton

Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as “bacterial microtubules” (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening