Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

Molecular cloning and expression analysis of Ch-penaeidin, an antimicrobial peptide from Chinese shrimp, Fenneropenaeus chinensis

A new member of antimicrobial peptide genes of the penaeidin family, Ch-penaeidin, has been cloned from the haemocytes of Chinese shrimp, Fenneropenaeus chinensis, by reverse transcription PCR (RT-PCR), 3'-rapid amplification of cDNA end (3'-RACE) and smart cDNA methods. The Ch-penaeidin cDNA was 655 bp and the open reading frame of the cDNA encoded a 71 amino acid peptide. Ch-penaeidin contained a putative NH2-terminal signal Sequence (1-19) followed by a mature peptide (20-71). The sequence identify with other penaeidins from Litopenaeus vannamei and Litopenaeus setiferus is between 48% and 71%. The signal sequence of Ch-penaeidin is almost completely identical to that of other penaeidins, while differing relatively in the N-terminal domain of the mature peptide. Ch-penaeidin was designated as a novel member of class penaeidin 3 according to phylogenetic analysis. The Mature peptide. with a predicted molecular weight of 5589.32 Da, and a pI of 9.77, has eight positively charged amino acids and no negatively charged amino acids. The expression and distribution of Ch-penaeidin in Unchallenged shrimps were studied by RT-PCR, Northern blot and in situ hybridisation. The results showed that the Ch-penaeidin transcripts were detected in haemocytes (granular haemocytes), heart, gill, intestine, and subcuticular epithelia of the shrimp. and that Ch-penaeidin was constitutively expressed mainly in haemocytes. (C) 2003 Elsevier Ltd. All rights reserved.

Mapping the news on (social)-media. Methodological considerations for the analysis of local news networks.

info:eu-repo/semantics/nonPublished

Vibrational spectroscopy and crystal structure analysis of two polymorphs of the di-amino acid peptide cyclo(L-Glu-L-Glu)

Cyclo(L-Glu-L-Glu) has been crystallised in two different polymorphic forms. Both polymorphs are monoclinic, but form 1 is in space group P21 and form 2 is in space group C2. Raman scattering and FT-IR spectroscopic studies have been conducted for the N,O-protonated and deuterated derivatives. Raman spectra of orientated single crystals, solid-state and aqueous solution samples have also been recorded. The different hydrogen-bonding patterns for the two polymorphs have the greatest effect on vibrational modes with N&bond;H and C&dbond;O stretching character. DFT (B3-LYP/cc-pVDZ) calculations of the isolated cyclo(L-Glu-L-Glu) molecule predict that the minimum energy structure, assuming C2 symmetry, has a boat conformation for the diketopiperazine ring with the two L-Glu side chains being folded above the ring. The calculated geometry is in good agreement with the X-ray crystallographic structures for both polymorphs. Normal coordinate analysis has facilitated the band assignments for the experimental vibrational spectra. Copyright © 2009 John Wiley & Sons, Ltd.

Pelophylaxins: novel antimicrobial peptide homologs from the skin secretion of the Fukien gold-striped pond frog, Pelophylax plancyi fukienensis: identification by “shotgun” cDNA cloning and sequence analysis.

Amphibian skin secretions are rich in antimicrobial peptides that act as important components of an innate immune system. Here, we describe a novel “shotgun” skin peptide precursor cloning technique that facilitates rapid access to these genetically encoded molecules and effects their subsequent identification and structural characterization from the secretory peptidome. Adopting this approach on a skin secretion-derived library from a hitherto unstudied Chinese species of frog, we identified a family of novel antimicrobial peptide homologs, named pelophylaxins, that belong to previously identified families (ranatuerins, brevinins and temporins) found predominantly in the skin secretions from frogs of the genus Rana. These data further substantiate the scientifically robust nature of applying parallel transcriptome and peptidome analyses on frog defensive skin secretions that can be obtained in a non-invasive, non-destructive manner. In addition, the present data illustrate that rapid structural characterization of frog skin secretion peptides can be achieved from an unstudied species without prior knowledge of primary structures of endogenous peptides.