Molecular biology approaches for understanding microbial polycyclic aromatic hydrocarbons (PAHs) degradation

The known or suspected hazards of polycyclic aromatic hydrocarbons (PAHs) have provoked enormous concentration and endeavours to relieve or eliminate these precarious compounds from miscellaneous environments including soil, water and air. Among various interventions, biodegradation is an appealing approach for its comparative high efficiency and preferable safety. Microorganisms played crucial role in biodegradation of PAHs. Traditional access mainly including culture-dependent procedures has discovered and isolated PAHs-degrading microorganisms which could be subsequently applied to specific contaminated locus. Although certain progress has been achieved owing to traditional methods, much details in PAHs bioremedation leave pending because of the complexity nature of this process. As the rapid development of biology, molecular techniques such as PCR, fingerprinting technique (mainly DGGE), DNA hybridization technique and gene reporters technique have been intensively applied to gain further insight into the mechanism of PAHs degradation. These techniques not only proved the existence and role of uncultivable microorganisms in the whole population of PAHs degrading related microbials, but also made it possible to revealed the otherwise undetectable complex relationships between multi-microorganism concerned in PAHs biodegradation. Application of such techniques in the field of PAHs biodegradation were reviewed in this article.     

Occurrence and abundance of a mariner-like element in freshwater and terrestrial planarians (Platyhelminthes, Tricladida) from southern Brazil

Transposable elements are DNA sequences present in all the large phylogenetic groups, both capable of changing position within the genome and constituting a significant part of eukaryotic genomes. The mariner family of transposons is one of the few which occurs in a wide variety of taxonomic groups, including freshwater planarians. Nevertheless, so far only five planarian species have been reported to carry mariner-like elements (MLEs), although several different species have been investigated. Regarding the number of copies of MLEs, Girardia tigrina is the only planarian species in which this has been evaluated, with an estimation of 8,000 copies of the element per haploid genome. Preliminary results obtained in our laboratory demonstrated that MLE is found in a large number of different species of planarians, including terrestrial. With this in mind, the aim was to evaluate the occurrence and estimate the number of MLE copies in different planarian species collected in south Brazil. Twenty-eight individuals from 15 planarian species were analyzed. By using PCR and the hybridization of nucleic acids, it was found that MLE was present in all the analyzed species, the number of copies being high, probably over 10(3) per haploid genome.     

Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure

The p hosphorus up take 1 ( Pup1 ) locus was identified as a major quantitative trait locus (QTL) for tolerance of phosphorus deficiency in rice. Near-isogenic lines with the Pup1 region from tolerant donor parent Kasalath typically show threefold higher phosphorus uptake and grain yield in phosphorus-deficient field trials than the intolerant parent Nipponbare. In this study, we report the fine mapping of the Pup1 locus to the long arm of chromosome 12 (15.31–15.47 Mb). Genes in the region were initially identified on the basis of the Nipponbare reference genome, but did not reveal any obvious candidate genes related to phosphorus uptake. Kasalath BAC clones were therefore sequenced and revealed a 278-kbp sequence significantly different from the syntenic regions in Nipponbare (145 kb) and in the indica reference genome of 93-11 (742 kbp). Size differences are caused by large insertions or deletions (INDELs), and an exceptionally large number of retrotransposon and transposon-related elements (TEs) present in all three sequences (45%–54%). About 46 kb of the Kasalath sequence did not align with the entire Nipponbare genome, and only three Nipponbare genes (fatty acid α-dioxygenase, dirigent protein and aspartic proteinase) are highly conserved in Kasalath. Two Nipponbare genes (expressed proteins) might have evolved by at least three TE integrations in an ancestor gene that is still present in Kasalath. Several predicted Kasalath genes are novel or unknown genes that are mainly located within INDEL regions. Our results highlight the importance of sequencing QTL regions in the respective donor parent, as important genes might not be present in the current reference genomes.     

Epigenetics and its implications for plant biology 2. The 'epigenetic epiphany': epigenetics, evolution and beyond

SCOPE: In the second part of a two-part review, the ubiquity and universality of epigenetic systems is emphasized, and attention is drawn to the key roles they play, ranging from transducing environmental signals to altering gene expression, genomic architecture and defence. KEY ISSUES: The importance of transience versus heritability in epigenetic marks is examined, as are the potential for stable epigenetic marks to contribute to plant evolution, and the mechanisms generating novel epigenetic variation, such as stress and interspecific hybridization. FUTURE PROSPECTS: It is suggested that the ramifications of epigenetics in plant biology are immense, yet unappreciated. In contrast to the ease with which the DNA sequence can be studied, studying the complex patterns inherent in epigenetics poses many problems. Greater knowledge of patterns of epigenetic variation may be informative in taxonomy and systematics, as well as population biology and conservation.     

The backstage of the ABC model: The Antirrhinum majus contribution

At the beginning of the 1990s, a simple genetic model that explained flower development was presented based on Arabidopsis thaliana and Antirrhinum majus floral homeotic mutants. According to this model, which is a milestone in plant development studies, flower development can be explained by three classes of genes (A, B and C), each one controlling the identity of organs in two adjacent whorls. Intriguingly, more than 20 years later, there are still some unanswered questions, in particular regarding the universality of the class A-function genes. Class A genes are well characterised in A. thaliana, but so far no A mutants have been described in other plant species nor in Antirrhinum majus. Here, we retrace the story that led to the proposal of the ABC model focusing on the contribution of A. majus to this model. Although fewer groups are still using A. majus as a model system, this plant was a master contributor to our comprehension of the molecular networks controlling flower development.     

A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors

PIWI proteins and their bound PIWI-interacting RNAs (piRNAs) form the core of a gonad-specific small RNA silencing pathway that protects the animal genome against the deleterious activity of transposable elements. Recent studies linked the piRNA pathway to TUDOR biology as TUDOR domains of various proteins bind symmetrically methylated Arginine residues in PIWI proteins. We systematically analysed the Drosophila TUDOR protein family and identified four previously not characterized TUDOR domain-containing proteins (CG4771, CG14303, CG11133 and CG31755) as essential piRNA pathway factors. We characterized CG4771 (Vreteno) in detail and demonstrate a critical role for this protein in primary piRNA biogenesis. Vreteno physically and/or genetically interacts with the primary pathway components Piwi, Armitage, Yb and Zucchini. Vreteno also interacts with the Tdrd12 orthologues CG11133 (Brother of Yb) and CG31755 (Sister of Yb), which are essential for the primary piRNA pathway in the germline and probably replace the function of the related but soma-specific factor Yb.     

When phage,plasmids, and transposons collide: genomic islands,and conjugative- and mobilizable-transposons as a mosaic continuum

Plasmids and bacteriophage represent the classical vectors for gene transfer within the horizontal gene pool. However, the more recent discovery of an increasing array of other mobile genetic elements (MGE) including genomic islands (GIs), conjugative transposons (CTns), and mobilizable transposons (MTns) which each integrate within the chromosome, offer an increasingly diverse assemblage contributing to bacterial adaptation and evolution. Molecular characterisation of these elements has revealed that they are comprised of functional modules derived from phage, plasmids, and transposons, and further that these modules are combined to generate a continuum of mosaic MGE. In particular, they are comprised of any one of three distinct types of recombinase, together with plasmid-derived transfer and mobilisation gene functions. This review highlights both the similarities and distinctions between these integrating transferable elements resulting from combination of the MGE toolbox.     

综述: 高等植物转座元件功能研究进展

转座元件是指在基因组中能够移动、复制并重新整合到基因组新位点的DNA片段．转座元件一度被视为基因组内的“垃圾”或“自私DNA”,长期以来,转座元件的研究主要集中于阐释转座元件在宿主中的复制或表观沉默机制,而转座元件的调控功能并未得到全面探讨．已有研究表明,转座元件的比例与物种基因组大小存在正相关性,从而为C值悖论的解释提供了依据．近年来,越来越多的证据表明转座元件可以作为宿主基因组的“控制元件”发挥重要的调控作用．在作物中研究发现,转座元件既可以通过顺式或反式作用方式调控基因表达,也可以诱导表观等位基因的产生,从而促使固着生长的植物更好地适应外界环境的变化．本文拟就高等植物转座元件的作用及其对未来作物育种的意义进行总结．     

Transposon Mediated Integration of Plasmid DNA into the Subventricular Zone of Neonatal Mice to Generate Novel Models of Glioblastoma

An urgent need exists to test the contribution of new genes to the pathogenesis and progression of human glioblastomas (GBM), the most common primary brain tumor in adults with dismal prognosis. New potential therapies are rapidly emerging from the bench and require systematic testing in experimental models which closely reproduce the salient features of the human disease. Herein we describe in detail a method to induce new models of GBM with transposon-mediated integration of plasmid DNA into cells of the subventricular zone of neonatal mice. We present a simple way to clone new transposons amenable for genomic integration using the Sleeping Beauty transposon system and illustrate how to monitor plasmid uptake and disease progression using bioluminescence, histology and immuno-histochemistry. We also describe a method to create new primary GBM cell lines. Ideally, this report will allow further dissemination of the Sleeping Beauty transposon system among brain tumor researchers, leading to an in depth understanding of GBM pathogenesis and progression and to the timely design and testing of effective therapies for patients.