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

Transgenes designed to overexpress anthocyanin genes An6 (encoding dihydroflavonol-4-reductase) or Hf1 (encoding flavonoid-3',5'-hydroxylase) in Petunia hybrida L. produced flower colour phenotypes similar to those caused by sense cosuppression of chalcone synthase (Chs) genes. However, unlike Chs, sense cosuppression of An6 and Hf1 resulted in female infertility in transgenotes exhibiting complete phenotypic suppression of anthocyanins. Female sterility appeared to be due to embryo abortion, with discolouration of ovules first appearing about 4 d post-fertilization, followed by gradual collapse of the ovule. Pollen from cosuppressed, female-sterile transgenotes placed on wild-type stigmas produced normal seed set, indicating that sterility of cosuppressed plants was maternally controlled. We suggest an hypothesis that cosuppression of An6 and Hf1 leads to accumulation of dihydroflavonols in the seed coat, a maternal tissue, and that this accumulation inhibits embryo growth, either directly or indirectly. In this hypothesis, direct inhibition of embryo growth would require that dihydroflavonols diffuse from the seed coat into the embryo and act there, whereas indirect inhibition would require that dihydroflavonols interfere with some capacity of the seed coat to promote embryo growth.

Maternally-controlled ovule abortion results from cosuppression of dihydroflavonol-4-reductase or flavonoid-3',5'-hydroxylase genes in Petunia hybrida.

Most land plants possess the capacity to protect themselves from UV light, and do so by producing pigments that absorb efficiently in the UV-A and UV-B regions of the spectrum while allowing transmission of nearly all photosynthetically useful wavelengths.1,2 These UV-absorbing pigments are mainly phenylpropanoids and flavonoids. This chapter summarizes current understanding of the mechanism of UV protection in higher land plants, evaluates the information available from lower land plants and their green-algal relatives, and then considers the possible evolutionary origins of this use of chemical filters for selectively screening UV light from solar radiation. It is proposed that photocontrol over the biosynthesis of UV-absorbing phenylpropanoids and flavonoids may have evolved in concert with the evolution of the high biosynthetic activity necessary for UV protection. The toxicity of phenylpropanoids and flavonoids has been postulated to have been a barrier to the evolution of an effective chemical UV screen, and that some means for sequestering these compounds and/or for controlling their synthesis probably evolved prior to, or in concert with, the evolution of high rates of biosynthesis. The original photoreceptor and signal transduction system is speculated to have been based on photoisomerization of a phenylpropanoid ester and a pre-existing product feedback mechanism for controlling phenylpropanoid biosynthesis. Understanding the original mechanism for photocontrol of the chemical UV screen of land plants could be valuable for understanding the adaptability of extant land plants to rising levels of solar UV-B radiation and may suggest genetic strategies for engineering improved UV tolerance in crop plants.

The Genetic Origins of Biosynthesis and Light-Responsive Control of the Chemical UV Screen of Land Plants

With the complete sequence of the rice nuclear genome nearing completion, plant biologists have begun to wonder, discuss, and debate what genome is our next, best target? Although it is easy to list many worthwhile candidates among the angiosperms, the clear favorite for the next complete genome

/pdf/sequencing-maize-just-sample-the-salsa-or-go-for-the-whole-htvkffv2i4.pdf

Sequencing maize: just sample the salsa or go for the whole enchilada?

Plant transgenes can suppress the expression of homologous genes in at least two ways. One is a phenomenon known as epigene conversion,whereby one copy of a gene causes the transcriptional silencing of another copy, and the altered expression state of the silenced gene is heritable after loss of the gene causing the silencing (as in paramutation). The other mode of homology-dependent gene silencing is best referred to as sense suppression, a posttranscriptional phenomenon usually resulting in the cosuppression of homologous transgenes and endogenes. The homology required for sense suppression can be limited to the transcribed regions of the genes. Sense suppression is observed frequently in transgenic plants, generally as a paradoxical outcome of attempts to increase expression of an endogenous gene by the introduction of a chimeric transgene comprised of a strong promoter fused to a copy of the endogene’s coding sequence in the sense orientation. The varied observations and possible mechanisms for homology-dependent transgene silencing phenomena in plants have been much discussed in the literature, citations to which may be found in Matzke and Matzke (1995), de Carvahlo Niebel et al. (1995), and Jorgensen (1995).

A Responsive Regulatory System is Revealed by Sense Suppression of Pigment Genes in Petunia Flowers

Stadler’s definition and exclusions still apply today: genes are clearly not single molecules; chromosomes are. Chromosomes are collections of many genes, and delimiting genes from neighboring genes on a chromosome remains a tremendous, unsolved challenge, even with the complete sequence of a chromosome in hand. Moreover, epigenetics has shown that phenotypically defined “mutations” can have a physical basis other than the alteration of DNA sequence; rather, they may sometimes turn out be “epimutations” based on modification states of DNA and chromatin proteins. Thus, just as in Stadler’s day, “questions concerning the undetermined properties” of the gene remain “the all-important questions that we hope ultimately to answer by the interpretation of the experimental evidence and by the development of new experimental operations.” Importantly, Stadler distinguished between the operationally defined gene and the hypothetical gene, pointing out that use of the term “gene” in the literature sometimes referred to the operational gene, sometimes the hypothetical gene, and sometimes “a curious conglomeration of the two,” an observation that applies to today’s literature as much as it did in 1954. The difference between the two concepts is straightforward: “The operational definition merely represents the properties of the actual gene, so far as they may be established from experimental evidence by present methods. The inferences from this evidence provide a tentative model of the hypothetical gene, a model that will be somewhat different in the minds of different students of the problem and will be further modified in the light of further investigation.”

/pdf/of-genes-and-genomes-challenges-for-the-twenty-first-century-hu3y7qlh9w.pdf

Richard A. Jorgensen

Papers

Maternally-controlled ovule abortion results from cosuppression of dihydroflavonol-4-reductase or flavonoid-3',5'-hydroxylase genes in Petunia hybrida.

The Genetic Origins of Biosynthesis and Light-Responsive Control of the Chemical UV Screen of Land Plants

Sequencing maize: just sample the salsa or go for the whole enchilada?

A Responsive Regulatory System is Revealed by Sense Suppression of Pigment Genes in Petunia Flowers

Of genes and genomes: challenges for the twenty-first century.