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

Saying it with genes: molecular flower breeding

A new paradigm for intercellular signaling in vascular plants is emerging that offers to revolutionize our understanding of these deceptively simple organisms and reveal the true level of their sophistication in information processing. The new conceptual understanding is based on directed trafficking of information-rich macromolecular signals (transcription factors and RNA molecules) between cells and systemically throughout the plant (for review, see ref. 1). Intercellular and systemic movement occurs via two specialized structures: (i) intercellular organelles known as plasmodesmata, which provide continuity of cytoplasm and endoplasmic reticulum between adjacent cells; and (ii) the phloem, which is responsible for translocation of photoassimilates from source leaves to sink tissues and, together with the xylem, forms the vascular system of higher plants. 

siRNAs can trigger RNA silencing in plants, just as in animals.

https://www.pnas.org/content/pnas/99/18/11561.full.pdf

RNA traffics information systemically in plants

Do unintended antisense transcripts contribute to sense cosuppression in plants

/pdf/restructuring-the-genome-in-response-to-adaptive-challenge-36eoveyob8.pdf

Restructuring the genome in response to adaptive challenge: McClintock's bold conjecture revisited.

Developmental and physiological factors can impose heritable metastable changes on the plant genome, a fact that was established by maize geneticists during the 1950s and 1960s, largely through the efforts of R. Alexander Brink and Barbara McClintock. This paper describes a transgenic reporter system that monitors genomic impositions as changes in morphogenetically-determined flower color patterns. The observations reported here on the metastable properties of plant transgenes illustrate the proposals of Brink and McClintock that chromosomal impositions occur during normal development as ordered sequences of events which contribute to the elaboration of complex developmental patterns. The relationship between this process and some recent findings about the control of gene expression in transgenic plants is also discussed. © 1994 Wiley-Liss, Inc.

Richard A. Jorgensen

Papers

Saying it with genes: molecular flower breeding

RNA traffics information systemically in plants

Do unintended antisense transcripts contribute to sense cosuppression in plants

Restructuring the genome in response to adaptive challenge: McClintock's bold conjecture revisited.

Developmental significance of epigenetic impositions on the plant genome: A paragenetic function for chromosomes