Collapsing granular suspensions

A 2D contact dynamics model is proposed as a microscopic description of a collapsing suspension/soil to capture the essential physical processes underlying the dynamics of generation and collapse of the system. Our physical model is compared with real data obtained from in situ measurements performed with a natural collapsing/suspension soil. We show that the shear strength behavior of our collapsing suspension/soil model is very similar to the behavior of this collapsing suspension soil, for both the unperturbed and the perturbed phases of the material.Comment: 7 pages, 5 figures, accepted for publication in EPJ

Growth response of Heritiera simplicifolia (Mast.) Kosterm. and Scaphium macropodum (Miq.) Beumée ex Heyne due to abiotic factors in the nursery

In the earliest stage of development, non-dipterocarp wildlings require specific environmental conditions; they are only able to acclimate to harsher environmental conditions after this stage. As such, the environment acts as a limiting factor of early-stage development in non-dipterocarp shade-tolerant species. We examined the survival rates and growth rates of Heritiera simplicifolia and Scaphium macropodum from the family Malvaceae in the different sets of abiotic conditions. Three abiotic environmental factors medium type, greenhouse technique, and light intensity were varied. The experiment was conducted for six months in an area near Hulu Terengganu Hydroelectric Dam, at the edge of the Tembat Forest Reserve. Height, diameter, leaves numbers, and leaf area was recorded. Our results indicate that the wildlings preferred higher daytime relative humidity and natural air ventilation at night, and they grew more quickly under SN50 (358.74 Photosynthetically Active Radiation; PAR) than under SN70 (101.41 PAR). Subsoil supplemented with vermicompost improved wildling growth more consistently than subsoil supplemented with compost or burned mesocarp. The wildling’s height relative growth rate (HRGR) and survival were affected by all treatments. These results indicate that restoration efforts using young indigenous tree species at degraded sites, supply better growth environments and organic nutrients to the rhizosphere

Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton

Growth response of Heritiera simplicifolia (Mast.) kosterm. and Scaphium macropodum (Miq.) Beumée ex Heyne due to abiotic factors in the nursery

In the earliest stage of development, non-dipterocarp wildlings require specific environmental conditions; they are only able to acclimate to harsher environmental conditions after this stage. As such, the environment acts as a limiting factor of early-stage development in non-dipterocarp shade-tolerant species. We examined the survival rates and growth rates of Heritiera simplicifolia and Scaphium macropodum from the family Malvaceae in the different sets of abiotic conditions. Three abiotic environmental factors medium type, greenhouse technique, and light intensity were varied. The experiment was conducted for six months in an area near Hulu Terengganu Hydroelectric Dam, at the edge of the Tembat Forest Reserve. Height, diameter, leaves numbers, and leaf area was recorded. Our results indicate that the wildlings preferred higher daytime relative humidity and natural air ventilation at night, and they grew more quickly under SN50 (358.74 Photosynthetically Active Radiation; PAR) than under SN70 (101.41 PAR). Subsoil supplemented with vermicompost improved wildling growth more consistently than subsoil supplemented with compost or burned mesocarp. The wildling’s height relative growth rate (HRGR) and survival were affected by all treatments. These results indicate that restoration efforts using young indigenous tree species at degraded sites, supply better growth environments and organic nutrients to the rhizosphere

Heterogeneous catalysis based on supramolecular association

[EN] Heterogeneous catalysis is based mostly on materials built with strong covalent bonds. However, supramolecular aggregation in which individual components self-assemble due to non-covalent interactions to create a larger entity offers also considerable potential for the preparation of materials with application in catalysis. The present article provides a perspective on the use of supramolecular aggregation for the development of heterogeneous catalysts. One of the main advantages of this approach is that the preparation procedure based on spontaneous self-assembly is frequently simpler than those that require the formation of covalent bonds. The emphasis in this article has been placed on the use in the preparation of heterogeneous catalysts of not only carbon materials, particularly graphene and carbon nanotubes, but also dendrimers and organic capsules. 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Importance of Spin-Orbit Coupling in Hybrid Organic/Inorganic Perovskites for Photovoltaic Applications

International audienceThree-dimensional (3D) hybrid perovskites CH3NH3PbX3 (X = Br, I) have recently been suggested as new key materials for dye-sensitized solar cells (DSSC) leading to a new class of hybrid semiconductor photovoltaic cells (HSPC). Thanks to density functional theory calculations, we show that the band gap of these compounds is dominated by a giant spin-orbit coupling (SOC) in the conduction-band (CB). At room temperature, direct and isotropic optical transitions are associated to a spin-orbit split-off band related to the triply degenerated CB of the cubic lattice without SOC. Due to the strong SOC, the electronic states involved in the optical absorption are only slightly perturbed by local distortions of the lattice. In addition, band offset calculations confirm that CH3NH3PbX3/TiO2 is a reference material for driving electrons toward the electrode in HSPC. Two-dimensional (2D) hybrids are also suggested to reach further flexibility for light conversion efficiency. Our study affords the basic concepts to reach the level of knowledge already attained for optoelectronic properties of conventional semiconductors

MicroRNA-96 Directly Inhibits γ-Globin Expression in Human Erythropoiesis

Fetal hemoglobin, HbF (α2γ2), is the main hemoglobin synthesized up to birth, but it subsequently declines and adult hemoglobin, HbA (α2β2), becomes predominant. Several studies have indicated that expression of the HbF subunit γ-globin might be regulated post-transcriptionally. This could be confered by ∼22-nucleotide long microRNAs that associate with argonaute proteins to specifically target γ-globin mRNAs and inhibit protein expression. Indeed, applying immunopurifications, we found that γ-globin mRNA was associated with argonaute 2 isolated from reticulocytes that contain low levels of HbF (<1%), whereas association was significantly lower in reticulocytes with high levels of HbF (90%). Comparing microRNA expression in reticulocytes from cord blood and adult blood, we identified several miRNAs that were preferentially expressed in adults, among them miRNA-96. The overexpression of microRNA-96 in human ex vivo erythropoiesis decreased γ-globin expression by 50%, whereas the knock-down of endogenous microRNA-96 increased γ-globin expression by 20%. Moreover, luciferase reporter assays showed that microRNA-96 negatively regulates expression of γ-globin in HEK293 cells, which depends on a seedless but highly complementary target site located within the coding sequence of γ-globin. Based on these results we conclude that microRNA-96 directly suppresses γ-globin expression and thus contributes to HbF regulation

Decoding the Epigenetic Language of Plant Development

Epigenetics refers to the study of heritable changes in gene expression or cellular phenotype without changes in DNA sequence. Epigenetic regulation of gene expression is accomplished by DNA methylation, histone modifications, histone variants, chromatin remodeling, and may involve small RNAs. DNA methylation at cytosine is carried out by enzymes called DNA Methyltransferases and is involved in many cellular processes, such as silencing of transposable elements and pericentromeric repeats, X-chromosome inactivation and genomic imprinting, etc. Histone modifications refer to posttranslational covalent attachment of chemical groups onto histones such as phosphorylation, acetylation, and methylation, etc. Histone variants, the non-canonical histones with amino acid sequences divergent from canonical histones, can have different epigenetic impacts on the genome from canonical histones. Higher-order chromatin structures maintained or modified by chromatin remodeling proteins also play important roles in regulating gene expression. Small non-coding RNAs play various roles in the regulation of gene expression at pre- as well as posttranscriptional levels. A special issue of Molecular Plant on ‘Epigenetics and Plant Development’ (Volume 4, Number 2, 2009) published a variety of articles covering many aspects of epigenetic regulation of plant development. We have tried here to present a bird's-eye view of these credible efforts towards understanding the mysterious world of epigenetics. The majority of the articles are about the chromatin modifying proteins, including histone modifiers, histone variants, and chromatin remodeling proteins that regulate various developmental processes, such as flowering time, vernalization, stem cell maintenance, and response to hormonal and environmental stresses, etc. Regulation of expression of seed transcriptome, involvement of direct tandem repeat elements in the PHE1 imprinting in addition to PcG proteins activity, paramutation, and epigenetic barriers in species hybridization are described well. The last two papers are about the Pol V-mediated heterochromatin formation independent of the 24nt-siRNA and the effect of genome position and tissue type on epigenetic regulation of gene expression. These findings not only further our current understanding of epigenetic mechanisms involved in many biological phenomena, but also pave the path for the future work, by raising many new questions that are discussed in the following lines