Three-dimensional folding and functional organization principles of the Drosophila genome

Chromosomes are the physical realization of genetic information and thus form the basis for its readout and propagation. Here we present a high-resolution chromosomal contact map derived from a modified genome-wide chromosome conformation capture approach applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of contact density and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, whereas active domains reach out of the territory to form remote intra- and interchromosomal contacts. Moreover, we systematically identify specific long-range intrachromosomal contacts between Polycomb-repressed domains. Together, these observations allow for quantitative prediction of the Drosophila chromosomal contact map, laying the foundation for detailed studies of chromosome structure and function in a genetically tractable system.     

Plant O-methyltransferases: molecular analysis,common signature and classification

Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32–71% sequence identity, and can be grouped according to the different compounds they utilise as substrates. Five highly conserved regions are proposed as a signature for plant O-methyltransferases, two of which (regions I and IV) are believed to be involved in S-adenosyl-L-methionine and metal binding, respectively. The glycine-rich signature regions include a 36 amino acid domain which is located in the mid-terminal section of the carboxy terminus of most O-methyltransferase sequences. Cladistic analysis of the amino acid sequences suggests that plant O-methyltransferases may have arisen from common ancestral genes that were driven by different structural and/or functional requirements, and whose descendants segregated into different biochemical species. A comprehensive classification of plant O-methyltransferases is proposed following the guidelines of the Commission of Plant Gene Nomenclature.     

Life cycle assessment of nanocomposites made of thermally conductive graphite nanoplatelets

Purpose

Polymers typically have intrinsic thermal conductivity much lower than other materials. Enhancement of this property may be obtained by the addition of conductive fillers. Nanofillers are preferred to traditional ones, due to their low percolation threshold resulting from their high aspect ratio. Beyond these considerations, it is imperative that the development of such new fillers takes place in a safe and sustainable manner. A conventional life cycle assessment (LCA) has been conducted on epoxy-based composites, filled with graphite nanoplatelets (GnP). In particular, this study focuses on energy requirements for the production of such composites, in order to stress environmental hot spots and primary energy of GnP production process (nano-wastes and nanoparticles emissions are not included).

Methods

A cradle-to-grave approach has been employed for this assessment, in an attributional modeling perspective. The data for the LCA have been gathered from both laboratory data and bibliographic references. A technical LCA software package, SimaPro (SimaPro 7.3), which contains Ecoinvent (2010) life cycle inventory (LCI) database, has been used for the life cycle impact assessment (LCIA), studying 13 mid-point indicators. Sensitivity and uncertainty analyses have also been performed.

Results and discussion

One kilogram of GnP filler requires 1,879 MJ of primary energy while the preparation of 1 kg of epoxy composite loaded with 0.058 kg of GnP 303 MJ. Besides energy consumption in the filler preparation, it is shown that the thermoset matrix material has also a non-negligible impact on the life cycle despite the use of GnP: the primary energy required to make epoxy resin is 187 MJ, i.e., 62 % of the total energy to make 1 kg of composite.

Conclusions

Raw material extraction and filler and resin preparation phase exhibit the highest environmental impact while the composite production is negligible. Thermosetting resin remains the highest primary energy demand when used as matrix for GnP fillers. The result of the sensitivity analysis carried out on the electricity mix used during the GnP and the composite production processes does not affect the conclusions.     

Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila

In Drosophila melanogaster, Hox genes are organized in an anterior and a posterior cluster, called Antennapedia complex and bithorax complex, located on the same chromosome arm and separated by 10 Mb of DNA. Both clusters are repressed by Polycomb group (PcG) proteins. Here, we show that genes of the two Hox complexes can interact within nuclear PcG bodies in tissues where they are corepressed. This colocalization increases during development and depends on PcG proteins. Hox gene contacts are conserved in the distantly related Drosophila virilis species and they are part of a large gene interaction network that includes other PcG target genes. Importantly, mutations on one of the loci weaken silencing of genes in the other locus, resulting in the exacerbation of homeotic phenotypes in sensitized genetic backgrounds. Thus, the three-dimensional organization of Polycomb target genes in the cell nucleus stabilizes the maintenance of epigenetic gene silencing.     

Direct evidence for ribonucleolytic activity of a PR-10-like protein from white lupin roots

An abundant 17 kDa protein which was isolated and characterized from 10-day old healthy root tissue of white lupin (Lupinus albus) proved to have a high sequence similarity to pathogenesis-related proteins found in other species. Subsequently, a corresponding clone (LaPR-10) was identified in a cDNA library prepared from the same tissue that exhibited a high amino acid sequence similarity to a number of the PR-10 family proteins. The clone contains an open reading frame encoding a polypeptide of 158 amino acids, with a predicted molecular mass of 16905 Da and an isoelectric point of 4.66. Southern blot analysis indicates that LaPR-10 is likely a single-copy gene, or a member of a small gene family. The clone was expressed in Escherichia coli, and its protein product was purified to near homogeneity. Both the native and the recombinant proteins were immunorecognized by antibodies raised against pea PR-10 proteins, and exhibited a ribonucleolytic activity against several RNA preparations, including lupin root total RNA. Characterization of its enzymatic properties indicates that the LaPR-10 protein belongs to the class II ribonucleases. We present evidence that the white lupin 17 kDa protein is constitutively expressed during all stages of root development and, to a lesser extent, in other plant parts. In addition, we demonstrate the presence, in the LaPR-10 amino acid sequence, of a number of motifs that are common to most PR-10 proteins, as well as a RGD motif that is shared only with the alfalfa SRG1 sequence.     

Uptake of isopentenyl diphosphate by plastids isolated from Vitis vinifera L. cell suspensions

The uptake of [1-¹⁴C]isopentenyl diphosphate by intact plastids purified from cell suspensions of Vitis vinifera L. cv. Muscat de Frontignan was investigated using vacuum-filtration and silicone-oil-filtering techniques. Transport across the plastid envelope which was stimulated by cations, such as Mg²⁺ and Mn²⁺, was characterized by a K _m of approx. 0.5 mM and a V _max of 25 nmol·(mg protein)^-1·-h^-1. The data showed that isopentenyl diphosphate apparently accumulated in the plastid against a concentration gradient. The involvement of a protein carrier was suggested by the strong inhibition of the uptake by compounds which are known to block SH groups. Thus, the saturation kinetics together with the pH optimum (7.5–8), the temperature dependence (maximum incorporation at 37 °C) and the competitive inhibition by a structural analogue of the substrate (aminophenylethyl diphosphate) provided evidence for a mechanism of uptake by facilitated diffusion. The carrier identified may thus play a major role in supplying the plastid compartment with isopentenyl diphosphate for isoprenoid biosynthesis.Abbreviations APP aminophenylethyl diphosphate - DMAPP dimethylallyl diphosphate - GPP geranyl diphosphate - IPP isopentenyl diphosphate - NEM N-ethylmaleïmide - PCMB p-chloromercuribenzoate