Structural aspects of nucleic acid-sensing Toll-like receptors

Invading pathogens elicit potent immune responses in cells through interactions between structurally conserved molecules derived from the pathogens and specialized innate immune receptors such as the Toll-like receptors (TLRs). Nucleic acid is one of the principal TLR ligands. Nucleic acid-sensing TLRs recognize an array of nucleic acids, including double-stranded RNA, single-stranded RNA, and DNAs with specific sequence motifs. Although ligand-induced dimerization is commonly observed followed by TLR activation, both the specific recognition mechanisms and the ligand–receptor interactions vary among different TLRs. In this review, we highlight our current understanding of how these receptors recognize their cognate ligands based on the recent advances in structural biology.     

Distribution Survey and Threat Assessment of the Yellow-tailed Woolly Monkey (<Emphasis Type="BoldItalic">Oreonax flavicauda;</Emphasis> Humboldt 1812), Northeastern Peru

Peruvian yellow-tailed woolly monkeys (Oreonax flavicauda) are considered Critically Endangered (IUCN Categories A4c). The International Primatological Society also considers them one of the world’s 25 most endangered primate species and therefore a conservation priority. However, there is little concerted conservation action, and the existing protected area network may be inadequate to protect this species from extinction. Until recently this species has been the focus of few studies and its distributional limits remain unknown. I present results of a range-wide survey of Oreonax flavicauda in northeastern Peru. I conducted 53 presence/absence field surveys at 43 sites between March 2007 and March 2010, with data collected for an additional 7 sites from other researchers. I chose sites where the species was previously reported or following suggestions from predictive GIS modeling. Oreonax flavicauda was present at 35 sites, all presence records were in Ficus spp.–dominated cloud forests between 1500 and 2650 m above sea level. I give the geographical limits of this species distribution throughout the north, east, and west of its range; the exact extent of its range to the south requires further investigation. Oreonax flavicauda continues to be threatened throughout its range. The major threats I identified at the survey locations were the continued conversion of forests to cattle pasture, opening of new access routes into virgin areas, and both commercial and subsistence hunting. My results suggest that existing conservation measures may be inadequate at protecting this species but that substantial opportunities do exist. Further surveys need to be made in the southern distribution of this species to determine more accurately extant habitat.     

<Emphasis Type="Italic">Sphedamnocarpus andersonii</Emphasis> (Malpighiaceae), a new species from Madagascar

Sphedamnocarpus andersonii, a new species from the Ihorombe Region of Madagascar, is described and illustrated. The twiggy, white-flowered shrubs are characterized by linear leaves, unique in the genus.     

Genetic linkage of hyper-IgE syndrome to chromosome 4.

The hyper-IgE syndrome (HIES) is a rare primary immunodeficiency characterized by recurrent skin abscesses, pneumonia, and highly elevated levels of serum IgE. HIES is now recognized as a multisystem disorder, with nonimmunologic abnormalities of the dentition, bones, and connective tissue. HIES can be transmitted as an autosomal dominant trait with variable expressivity. Nineteen kindreds with multiple cases of HIES were scored for clinical and laboratory findings and were genotyped with polymorphic markers in a candidate region on human chromosome 4. Linkage analysis showed a maximum two-point LOD score of 3.61 at recombination fraction of 0 with marker D4S428. Multipoint analysis and simulation testing confirmed that the proximal 4q region contains a disease locus for HIES.     

Bioconjugatable porphyrins bearing a compact swallowtail motif for water solubility

A broad range of applications requires access to water-soluble, bioconjugatable porphyrins. Branched alkyl groups attached at the branching site to the porphyrin meso position are known to impart high organic solubility. Such "swallowtail" motifs bearing a polar group (hydroxy, dihydroxyphosphoryl, dihydroxyphosphoryloxy) at the terminus of each branch have now been incorporated at a meso site in trans-AB-porphyrins. The incorporation of the swallowtail motif relies on rational synthetic methods whereby a 1,9-bis(N-propylimino)dipyrromethane (bearing a bioconjugatable tether at the 5-position) is condensed with a dipyrromethane (bearing a protected 1,5-dihydroxypent-3-yl unit at the 5-position). The two hydroxy groups in the swallowtail motif of each of the resulting zinc porphyrins can be transformed to the corresponding diphosphate or diphosphonate product. A 4-(carboxymethyloxy)phenyl group provides the bioconjugatable tether. The six such porphyrins reported here are highly water-soluble (> or =20 mM at room temperature in water at pH 7) as determined by visual inspection, UV-vis absorption spectroscopy, or 1H NMR spectroscopy. Covalent attachment was carried out in aqueous solution with the unprotected porphyrin diphosphonate and a monoclonal antibody against the T-cell receptor CD3epsilon. The resulting conjugate performed comparably to a commercially available fluorescein isothiocyanate-labeled antibody with Jurkat cells in flow cytometry and fluorescence microscopy assays. Taken together, this work enables preparation of useful quantities of water-soluble, bioconjugatable porphyrins in a compact architecture for applications in the life sciences.     

Plant-insect communities and predator-prey ratios in field margin strips,adjacent crop fields,and fallows

The management of field margin strips for the enhancement of biodiversity of plant-insect communities and natural-enemy populations was studied on experimental farms near Göttingen (Germany). Young and old, sown and naturally developed field margin strips were compared and differences to large fallows established. The five types of field margin strips (around cereal fields) were: (1, 2) 1- or 6-year-old naturally developed strips, (3) strips sown with a Phacelia mixture, (4) strips sown with a mixture of 19 wild flower species, and (5) strips sown with winter wheat or oat as a control. The naturally developed vegetation of the field margin strips was dominated by aggressive weeds, presumably due to the intensive farming practices and the fertile soils. Cirsium arvense populations decreased, while Elymus repens populations increased with age of habitat. Sowings were suitable to suppress these aggressive weeds. Potted plants of mugwort (Artemisia vulgaris) and red clover (Trifolium pratense) were exposed in the field margin strips to study arthropod colonization of these experimentally standardized plant patches. Arthropod species richness did not differ between field margin types, reflecting the overall similarity in floristic diversity, but sprayed and strip-free edges of cereal fields had a reduced diversity. Dispersal of insect populations of red clover into the cereal fields decreased with increasing distance, but benefited from adjacent field margin strips. Populations of predators (mainly spiders) as well as predator-prey ratios were significantly larger in 6-year-old than in 1-year-old strips emphasizing the importance of habitat age for natural enemies and possible biological control. Predator-prey ratios were also higher on old than young fallows. Large fallows had greater predator-prey ratios than small field margin strips emphasizing the trophic-level hypothesis of island biogeography in that the relative importance of natural enemies increased with habitat area. Insect species richness was only marginally influenced by area and not by age. As species richness of predators did not increase with area and age, species diversity and the possible biological-control function did not covary.     

The phylogenetic position of taxaceae based on 18S rRNA sequences

The evolutionary position of the yew family, Taxaceae, has been very controversial. Some plant taxonomists strongly advocate excluding Taxaceae from the conifer order and raising its taxonomic status to a new order or even class because of its absence of seed cones, contrary to the case in the majority of conifers. However, other authors believe that the Taxaceae are not fundamentally different from the rest of the conifers except in that they possess the most reduced solitary-ovule cones. To resolve the controversy, we have sequenced the 18S rRNA genes from representative gymnosperms: Taxus mairei (Taxaceae), Podocarpus nakaii (Podocarpaceae), Pinus luchuensis (Pinaceae), and Ginkgo biloba (Ginkgoales). Our phylogenetic analysis of the new sequence data with the published 18S rRNA sequence of Zamia pumila (a cycad) as an outgroup strongly indicates that Taxus, Pinus, and Podocarpus form a monophyletic group with the exclusion of Ginkgo and that Taxus is more closely related to Pinus than to Podocarpus. Therefore, Taxaceae should be classified as a family of Coniferales. Our finding that Taxaceae, Pinaceae, and Podocarpaceae form a clade contradicts both the view that the uniovulate seed of Taxaceae is a primitive character and the view that the Taxaceae are descendants of the Podocarpaceae. Rather, the uniovulate seed of Taxaceae and that of some species of Podocarpus appear to have different origins, probably all reduced from multiovulate cones. Correspondence to: W.-H. Li