Towards a computer aided diagnosis system dedicated to virtual microscopy based on stereology sampling and diffusion maps

An original strategy is presented, combining stereological sampling methods based on test grids and data reduction methods based on diffusion maps, in order to build a knowledge image database with no bias introduced by a subjective choice of exploration areas. The practical application of the exposed methodology concerns virtual slides of breast tumors

Thermostable DNA ligases from hyperthermophiles in biotechnology

DNA ligase is an important enzyme ubiquitous in all three kingdoms of life that can ligate DNA strands, thus playing essential roles in DNA replication, repair and recombination in vivo. In vitro, DNA ligase is also used in biotechnological applications requiring in DNA manipulation, including molecular cloning, mutation detection, DNA assembly, DNA sequencing, and other aspects. Thermophilic and thermostable enzymes from hyperthermophiles that thrive in the high-temperature (above 80°C) environments have provided an important pool of useful enzymes as biotechnological reagents. Similar to other organisms, each hyperthermophile harbors at least one DNA ligase. In this review, we summarize recent progress on structural and biochemical properties of thermostable DNA ligases from hyperthermophiles, focusing on similarities and differences between DNA ligases from hyperthermophilic bacteria and archaea, and between these thermostable DNA ligases and non-thermostable homologs. Additionally, altered thermostable DNA ligases are discussed. Possessing improved fidelity or thermostability compared to the wild-type enzymes, they could be potential DNA ligases for biotechnology in the future. Importantly, we also describe current applications of thermostable DNA ligases from hyperthermophiles in biotechnology

Numerical model for granular compaction under vertical tapping

A simple numerical model is used to simulate the effect of vertical taps on a packing of monodisperse hard spheres. Our results are in agreement with an experimantal work done in Chicago and with other previous models, especially concerning the dynamics of the compaction, the influence of the excitation strength on the compaction efficiency, and some ageing effects. The principal asset of the model is that it allows a local analysis of the packings. Vertical and transverse density profiles are used as well as size and volume distributions of the pores. An interesting result concerns the appearance of a vertical gradient in the density profiles during compaction. Furthermore, the volume distribution of the pores suggests that the smallest pores, ranging in size between a tetrahedral and an octahedral site, are not strongly affected by the tapping process, in contrast to the largest pores which are more sensitive to the compaction of the packing.Comment: 8 pages, 15 figures (eps), to be published in Phys. Rev. E. Some corrections have been made, especially in paragraph IV

Membrane homeoviscous adaptation in the piezo-hyperthermophilic archaeon Thermococcus barophilus

International audienceThe archaeon Thermococcus barophilus, one of the most extreme members of hyperthermophilic piezophiles known thus far, is able to grow at temperatures up to 103°C and pressures up to 80MPa. We analyzed the membrane lipids of T. barophilus by HPLC-MS as a function of pressure and temperature. In contrast to previous reports, we show that under optimal growth conditions (40 MPa, 85°C) the membrane spanning tetraether lipid GDGT-0 (sometimes called caldarcheol) is a major membrane lipid of T. barophilus together with archaeol. Increasing pressure and decreasing temperature lead to an increase of the proportion of archaeol. Reversely, a higher proportion of GDGT-0 is observed under low pressure and high temperature conditions. Noticeably, pressure and temperature fluctuations also impact the level of unsaturation of non-polar lipids with an irregular polyisoprenoid carbon skeleton (unsaturated lycopane derivatives), suggesting a structural role for these neutral lipids in the membrane of T. barophilus. Whether these apolar lipids insert in the membrane or not remains to be addressed. However, our results raise questions about the structure of the membrane in this archaeon and other Archaea harboring a mixture of di- and tetraether lipids

In situ Raman and X-ray spectroscopies to monitor microbial activities under high hydrostatic pressure

International audienceUntil recently, monitoring of cells and cellular activities at high hydrostatic pressure (HHP) was mainly limited to ex situ observations. Samples were analyzed prior to and following the depressurization step to evaluate the effect of the pressure treatment. Such ex situ measurements have several drawbacks: (i) it does not allow for kinetic measurements and (ii) the depressurization step often leads to artifactual measurements. Here, we describe recent advances in diamond anvil cell (DAC) technology to adapt it to the monitoring of microbial processes in situ. The modified DAC is asymmetrical, with a single anvil and a diamond window to improve imaging quality and signal collection. Using this novel DAC combined to Raman and X-ray spectroscopy, we monitored the metabolism of glucose by baker's yeast and the reduction of selenite by Agrobacterium tumefaciens in situ under HHP. In situ spectroscopy is also a promising tool to study piezophilic microorganisms

Bradyrhizobium commune sp. nov., isolated from nodules of a wide range of native legumes across the Australian continent

International audienceBradyrhizobia are particularly abundant in Australia, where they nodulate native legumes growing in the acidic and seasonally dry soils that predominate in these environments. They are essential to Australian ecosystems by helping legumes to compensate for nutrient deficiencies and the low fertility of Australian soils. During a survey of Australian native rhizobial communities in 1994–1995, several Bradyrhizobium genospecies were identified, among which genospecies B appeared to be present in various edaphic and climatic conditions and associate with a large range of leguminous hosts across the whole continent. We took advantage of the recent sequencing of the genome of strain BDV5040 T , representative of Bradyrhizobium genospecies B, to re-evaluate the taxonomic status of this lineage. We further characterized strain BDV5040 T based on morpho-physiological traits and determined its phylogenetic relationships with the type strains of all currently described Bradyrhizobium species using both small subunit (SSU) rRNA gene and complete genome sequences. The digital DNA–DNA hybridization relatedness with any type strain was less than 35 % and both SSU rRNA gene and genome phylogenies confirmed the initial observation that this strain does not belong to any formerly described species within the genus Bradyrhizobium . All data thus support the description of the novel species Bradyrhizobium commune sp. nov. for which the type strain is BDV5040 T (=CFBP 9110 T =LMG 32898 T ), isolated from a nodule of Bossiaea ensata in Ben Boyd National Park in New South Wales, Australia

Complete Genome Sequence of the Hyperthermophilic Piezophilic Archaeon Pyrococcus kukulkanii NCB100 Isolated from the Rebecca’s Roost Hydrothermal Vent in the Guaymas Basin

Members of the order Thermococcales are common inhabitants of high-temperature hydrothermal vent systems (black smokers) that are represented in clone libraries mostly by isolates from the Thermococcus genus. We report the complete sequence of a novel species from the Pyrococcus genus, P. kukulkanii strain NCB100, which has been isolated from a flange fragment of the Rebecca’s Roost hydrothermal vent system in the Guaymas Basin

Fractionation of Stable Zinc Isotopes in the Zinc Hyperaccumulator Arabidopsis halleri and Nonaccumulator Arabidopsis petraea

International audienceZn isotope fractionation may provide new insights into Zn uptake, transport and storage mechanisms in plants. It was investigated here in the Zn hyperaccumulator Arabidopsis halleri and the nonaccumulator A. petraea. Plant growth on hydroponic solution allowed us to measure the isotope fractionation between source Zn (with Zn(2+) as dominant form), shoot and root. Zn isotope mass balance yields mean isotope fractionation between plant and source Zn Delta(66)Zn(in-source) of -0.19 +/- 0.20 parts per thousand in the nonaccumulator and of -0.05 +/- 0.12 parts per thousand in-source in the hyperaccurnulator. The isotope fractionation between shoot Zn and bulk Zn incorporated (Delta(66)Zn(shoot-in)) differs between the nonaccumulator and the hyperaccumulator and is function of root-shoot translocation (as given by mass ratio between shoot Zn and bulk plant Zn). The large isotope fractionation associated with sequestration in the root (0.37 parts per thousand) points to the binding of Zn(2+) with a high affinity ligand in the root cell. We conclude that Zn stable isotopes may help to estimate underground and aerial Zn storage in plants and be useful in studying extracellular and cellular mechanisms of sequestration in the root

Molecular Rearrangements in Protomembrane Models Probed by Laurdan Fluorescence

Lipid membranes are a key component of living systems and have been essential to the origin of life. One hypothesis for the origin of life assumes the existence of protomembranes with ancient lipids formed by Fischer–Tropsch synthesis. We determined the mesophase structure and fluidity of a prototypical decanoic (capric) acid-based system, a fatty acid with a chain length of 10 carbons, and a lipid system consisting of a 1:1 mixture of capric acid with a fatty alcohol of equal chain length (C10 mix). To shed light on the mesophase behavior and fluidity of these prebiotic model membranes, we employed Laurdan fluorescence spectroscopy, which reports on the lipid packing and fluidity of membranes, supplemented by small-angle neutron diffraction data. The data are compared with data of the corresponding phospholipid bilayer systems of the same chain length, 1,2-didecanoyl-sn-glycero-3-phosphocholine (DLPC). We demonstrate that the prebiotic model membranes capric acid and the C10 mix show formation of stable vesicular structures needed for cellular compartmentalization at low temperatures only, typically below 20 °C. They reveal the fluid-like lipid dynamic properties needed for optimal physiological function. High temperatures lead to the destabilization of the lipid vesicles and the formation of micellar structures

A novel bacteriophage morphotype with a ribbon-like structure at the tail extremity

7 pagesInternational audienceWe have isolated a novel Siphoviridae phage (named Sol-P11) morphotype from the surface sands of the Sahara Desert with a ribbon-like structure at the tail extremity. Sol-P11 was found to grow on a Bacillus subtilis strain isolated from the same environment and to contain a double stranded DNA genome of approximately 120 kb in length incapable of being hydrolysed by a wide variety of restriction endonucleases. The major constituent proteins of CsCl-purified Sol-P11 virions were 65, 50, 30, and 24 kDa in size, with the 30 kDa polypeptide being the major protein of the 85 nm diameter icosahedral capsid, and the other three proteins comprising the major polypeptides of the tail (320 nm in length) and ribbon-like structure. Moreover, different sized phages displaying a Sol-P11 morphology were observed in phage preparations from the Death Valley and Namib deserts. Sol-P11-like phage morphotypes have been previously described, including PBPI, a flagellum-specific phage that infects B. pumilis and phage BcP15 infecting the marine bacterium, Burkholderia cepacia DR11. We thus propose that Sol-P11 represents a member of a novel morphotype of Siphoviridae phages that use a ribbon-like structure, instead of caudal fibers, to attach to their host cell