Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics

Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

We have developed a new vector strategy for the insertion of foreign genes into the genomes of gram negative bacteria not closely related to Escherichia coli. The system consists of two components: special E. coli donor strains and derivatives of E. coli vector plasmids. The donor strains (called mobilizing strains) carry the transfer genes of the broad host range IncP–type plasmid RP4 integrated in their chromosomes. They can utilize any gram negative bacterium as a recipient for conjugative DNA transfer. The vector plasmids contain the P–type specific recognition site for mobilization (Mob site) and can be mobilized with high frequency from the donor strains. The mobilizable vectors are derived from the commonly used E. coli vectors pACYC184, pACYC177, and pBR325, and are unable to replicate in strains outside the enteric bacterial group. Therefore, they are widely applicable as transposon carrier replicons for random transposon insertion mutagenesis in any strain into which they can be mobilized but not stably maintained. The vectors are especially useful for site–directed transposon mutagenesis and for site–specific gene transfer in a wide variety of gram negative organisms.

A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria

The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.cazy.org/.

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

Plant transgenes may participate in two types of homology-based gene silencing. One requires transcript homology, is post-transcriptional, and is referred to as cosuppression; the other requires promoter homology, is transcriptional, and is similar to paramutation. This paper uses flower color transgenes to address the hierarchical operation of both mechanisms in plants carrying two transgene copies. It is shown that cosuppression of homologous, endogenous flower color genes by single-copy transgenes requires that the transgene be driven by a strong promoter and that the degree of cosuppression is highly sensitive to increasing transgene dosage. Together, these observations suggest that cosuppression should be a sensitive reporter of epigenetic changes in transgene transcription, such as might be caused by paramutation-like interactions between transgene loci. Intercrosses bringing together two homologous transgene loci, one a known epimutable reporter and the other a transgene inverted repeat, result in complete loss of cosuppression in some outcross progeny and a qualitative change in morphology-based patterns of cosuppression in other outcross progeny. This paramutation-like behavior suggests that the transgenes may be altered at the transcriptional level, eliminating cosuppression altogether or changing the spatial pattern of transgene transcription to produce a new pattern of cosuppression.

Homology-based control of gene expression patterns in transgenic petunia flowers.

Genetic Organization of Tn5

In Arabidopsis thaliana, XIPOTL1 encodes a phosphoethanolamine N-methyltransferase with a central role in phosphatidylcholine biosynthesis via the methylation pathway. To gain further insights into the mechanisms that regulate XIPOTL1 expression, the effect of upstream open reading frame 30 (uORF30) on the translation of the major ORF (mORF) in the presence or absence of endogenous choline (Cho) or phosphocholine (PCho) was analysed in Arabidopsis seedlings. Dose-response assays with Cho or PCho revealed that both metabolites at physiological concentrations are able to induce the translational repression of a mORF located downstream of the intact uORF30, without significantly altering its mRNA levels. PCho profiles showed a correlation between increased endogenous PCho levels and translation efficiency of a uORF30-containing mORF, while no correlation was detectable with Cho levels. Enhanced expression of a uORF30-containing mORF and decreased PCho levels were observed in the xipotl1 mutant background relative to wild type, suggesting that PCho is the true mediator of uORF30-driven translational repression. In Arabidopsis, endogenous PCho content increases during plant development and affects root meristem size, cell division, and cell elongation. Because XIPOTL1 is preferentially expressed in Arabidopsis root tips, higher PCho levels are found in roots than shoots, and there is a higher sensitivity of this tissue to translational uORF30-mediated control, it is proposed that root tips are the main site for PCho biosynthesis in Arabidopsis.

Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30

Germinally transmissible variants that arise by the anomalous imposition of developmental information on the genome are not uncommon in plant genetics, although they are often ignored. Better understanding of such variants is believed to be important because they appear to reflect basic features of developmental control processes. This paper briefly reviews classical genetic studies of such variants in plants, then discusses recent work on the genetic behaviour of plant transgenes, the results of which parallel and extend the classical genetic studies of these phenomena. An attempt is made to explain the molecular basis of these phenomena in terms of modern hypotheses on the dynamic organization of chromatin.

The Germinal Inheritance of Epigenetic Information in Plants

A novel method of producing a plant with a marker closely linked to a target locus, in particular a nuclear male sterile target locus, is described. The method involves transformation of a group of plants in order to introduce a marker into each plant, and isolation of a plant with the marker closely linked to a target locus. The markers include visible markers and dominant conditional lethal markers. The method is of particular use for hybrid seed production where the target locus is a nuclear male sterile locus.

Richard A. Jorgensen

Papers

Homology-based control of gene expression patterns in transgenic petunia flowers.

Genetic Organization of Tn5

Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30

The Germinal Inheritance of Epigenetic Information in Plants

Transformation of plants to introduce closely linked markers