The case for the defense: plants versus Pseudomonas syringae

Incredible progress has been made over the last 20 years in understanding the components and mechanisms governing plant innate immunity. The most important discoveries concern pathogen recognition mechanisms, which divide perception of conserved elicitors at the cell periphery, and recognition of variable elicitors within the host cytoplasm. The underlying mechanisms of immunity post elicitation are complex and poorly defined. This review highlights emergent themes in plant–microbe interactions with a particular focus on the plant immune responses against infection by the bacterium Pseudomonas syringae.     

Phylogenetic approaches to nomenclature: a comparison based on a nemertean case study

Phylogenetic approaches to biological nomenclature are becoming increasingly common. Here I compare the behaviour of two such approaches, the phylogenetic system of definition and the phylogenetic system of reference, when there is a shift in the preference of phylogenetic hypotheses. The comparison is based on a case study from nemertean systematics and is the first to compare two different phylogenetic approaches throughout three stages of change, including two stages of phylogenetic nomenclature. It is concluded that a phylogenetic system of reference in combination with uninomials is superior in conveying phylogenetic information.     

Choice matters: incipient speciation in Gyrodactylus corydori (Monogenoidea: Gyrodactylidae)

We investigated how Gyrodactylus corydoriBueno-Silva and Boeger, 2009 exploits two sympatric host species, Corydoras paleatus (Jenyns, 1842) and Corydoras ehrhardti Steindachner, 1910. Specimens of G. corydori were collected from the Piraquara and Miringuava Rivers, State of Paraná, Brazil, between 2005 and 2006. A total of 167 parasites was measured from both host species. Nine morphometric features of the haptoral sclerites were measured and analyzed by discriminant analysis, cluster analysis and multivariate analysis of variance. A fragment of the mitochondrial cytochrome oxidase I gene (COI) (∼740 bp) and the rDNA internal transcribed spacers (ITS) (∼1200 bp) of G. corydori were sequenced. Bayesian and parsimony analyses of COI recognized two genetically structured clades of G. corydori, which corresponded closely with the two species of Corydoras. Twenty-eight haplotypes were detected (18 were exclusive to C. ehrhardti and seven were exclusive to C. paleatus). The same general pattern between parasites and host species was observed in the morphometric analyses. Nevertheless, poor correlation of genetic and morphometric variation strongly supports the plastic nature of the morphological variation of haptoral sclerites. The existence of two clades with limited gene flow would suggest that G. corydori already represents two cryptic species. However, the morphometric and molecular data showed that there is insufficient evidence to support two valid species. The low COI (0.1-6.2%) and ITS (0.09-3.5%) divergence within G. corydori suggest a recent separation of the lineages between distinct host species (less than 1 million years). As the hypothesis of secondary contact of the parasite demographic history was rejected, our results point to the possibility of sympatric incipient ongoing speciation of G. corydori to form distinct parasite lineages adapted to C. ehrhardti and C. paleatus. This may be a common event within the Gyrodactylidae, adding a yet unreported mode of adaptive speciation that helps to understand its rate of diversification.     

Uniform nomenclature for bacterial plasmids: a proposal

[This corrects the article on p. 168 in vol. 40.].     

The current composition of the subfamily Encotyllabinae (Monogenoidea: Capsalidae)

The historical account and recent taxonomic consideration of the monogenean subfamily Encotyllabinae are given. Main criteria used for diagnostics of the subfamily and its genera are discussed.     

Mesophile versus thermophile: insights into the structural mechanisms of kinetic stability

Obtaining detailed knowledge of folding intermediate and transition state (TS) structures is critical for understanding protein folding mechanisms. Comparisons between proteins adapted to survive extreme temperatures with their mesophilic homologs are likely to provide valuable information on the interactions relevant to the unfolding transition. For kinetically stable proteins such as alpha-lytic protease (alphaLP) and its family members, their large free energy barrier to unfolding is central to their biological function. To gain new insights into the mechanisms that underlie kinetic stability, we have determined the structure and high temperature unfolding kinetics of a thermophilic homolog, Thermobifida fusca protease A (TFPA). These studies led to the identification of a specific structural element bridging the N and C-terminal domains of the protease (the "domain bridge") proposed to be associated with the enhanced high temperature kinetic stability in TFPA. Mutagenesis experiments exchanging the TFPA domain bridge into alphaLP validate this hypothesis and illustrate key structural details that contribute to TFPA's increased kinetic thermostability. These results lead to an updated model for the unfolding transition state structure for this important class of proteases in which domain bridge undocking and unfolding occurs at or before the TS. The domain bridge appears to be a structural element that can modulate the degree of kinetic stability of the different members of this class of proteases.     

Rules and guidelines for genetic nomenclature in mice: excerpted version

The unique identification of genes and mouse strains is critical to their identification in research and in the scientific literature. Rules for genetic nomenclature in mice have existed since the 1940s. The latest complete revision of the rules was approved by the International Committee on Standardized Genetic Nomenclature for Mice in November, 1993. Minor revisions have occurred since. The complete, current rules are available on-line from The Jackson Laboratory's Mouse Genome Database (MGD), URL: http://www.informatics.jax.org. A printed version appeared in Mouse Genome 92 (2), June, 1994, and in Genetic Variants and Strains of the Laboratory Mouse, 3rd edition (Committee on Standardized Genetic Nomenclature for Mice, 1996a,b,c). The excerpted version below gives the general guidelines for naming and symbolizing mouse genes, transgenes and transgenic strains, targeted mutations and DNA markers. More detailed guidelines, including revisions as they are made, may be found at the MGD Web site given above. Subparagraphs are numbered as in the complete guidelines so that the user can refer easily from this excerpted version to the full text. Textual references to paragraphs not included here may be found in the full text as well     

A nomenclature for intestinal in vitro cultures

Many advances have been reported in the long-term culture of intestinal mucosal cells in recent years. A significant number of publications have described new culture media, cell formations, and growth patterns. Furthermore, it is now possible to study, e.g., the capabilities of isolated stem cells or the interactions between stem cells and mesenchyme. However, at the moment there is significant variation in the way these structures are described and named. A standardized nomenclature would benefit the ability to communicate and compare findings from different laboratories using the different culture systems. To address this issue, members of the NIH Intestinal Stem Cell Consortium herein propose a systematic nomenclature for in vitro cultures of the small and large intestine. We begin by describing the structures that are generated by preparative steps. We then define and describe structures produced in vitro, specifically: enterosphere, enteroid, reconstituted intestinal organoid, induced intestinal organoid, colonosphere, colonoid, and colonic organoid.     

Investigating the Barons: narrative and nomenclature in Munchausen syndrome

Recounting stories of the 18th-century Baron von Münchhausen, the unauthorized appropriation of his name into literature, and Richard Asher's subsequent medical use of the name Munchausen 150 years later, this article examines the narratives that are told about and through Munchausen syndrome that create meaning within medicine. By analyzing a half-century debate over the name of the illness, this article discusses how the medical literature invests meaning in names and how names create meaning through narrative with effects on the practice of medicine.