Ribosomes pause at specific sites during synthesis of membrane-bound chloroplast reaction center protein D1

Photosynthetic reaction center protein D1 contains five membrane-spanning alpha-helices which form binding sites for pheophytin, chlorophyll, carotenoids, quinone, Fe2+, and probably Mn2+. D1 translation intermediates of 15 to 28 kD were detected when isolated chloroplasts were pulse-labeled with [35S]methionine. The D1 translation intermediates were associated with membrane polysomes and can be chased into full length D1. The sites of translation pausing were determined by mapping the distribution of ribosomes on D1 mRNA using toeprint analysis. Clusters of toeprint signals were generated by D1 mRNA associated with membranes but not by D1 mRNA in nonpolysomal fractions of the soluble phase or phenol-extracted mRNA. The distribution of ribosomes on D1 mRNA determined by toeprint analysis was consistent with D1 translation intermediates observed with pulse-labeling. Ribosome pausing may facilitate co-translational binding of co-factors such as chlorophyll to D1 and aid the integration of D1 into thylakoid membranes.     

Spatial and temporal population genetic structure of four northeastern Pacific littorinid gastropods: the effect of mode of larval development on variation at one mitochondrial and two nuclear DNA markers

We investigated the effect of development mode on the spatial and temporal population genetic structure of four littorinid gastropod species. Snails were collected from the same three sites on the west coast of Vancouver Island, Canada in 1997 and again in 2007. DNA sequences were obtained for one mitochondrial gene, cytochrome b ( Cyt b ), and for up to two nuclear genes, heat shock cognate 70 ( HSC70 ) and aminopeptidase N intron ( APN54 ). We found that the mean level of genetic diversity and long-term effective population sizes ( N _e) were significantly greater for two species, Littorina scutulata and L. plena , that had a planktotrophic larval stage than for two species, Littorina sitkana and L. subrotundata , that laid benthic egg masses which hatched directly into crawl-away juveniles. Predictably, two poorly dispersing species, L. sitkana and L. subrotundata , showed significant spatial genetic structure at an 11- to 65-km geographical scale that was not observed in the two planktotrophic species. Conversely, the two planktotrophic species had more temporal genetic structure over a 10-year interval than did the two direct-developing species and showed highly significant temporal structure for spatially pooled samples. The greater temporal genetic variation of the two planktotrophic species may have been caused by their high fecundity, high larval dispersal, and low but spatially correlated early survivorship. The sweepstakes-like reproductive success of the planktotrophic species could allow a few related females to populate hundreds of kilometres of coastline and may explain their substantially larger temporal genetic variance but lower spatial genetic variance relative to the direct-developing species.     

Partial protein domains: evolutionary insights and bioinformatics challenges

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.With the rapid expansion in the number of determined protein sequences - over 92 million in UniProt in March 2015 - an ever-increasing number of biologists are using bioinformatics tools for annotation of these sequences. One widely used strategy is to identify occurrences of Pfam families within the sequence of interest [1]. A Pfam family is a multiple sequence alignment of the occurrences of a particular domain both in different species and in different regions of the same protein. The concept underpinning Pfam is that proteins typically comprise one or more domains (regions), each of which is an evolutionary unit that generally has a well-defined biological function. A significant sequence similarity between a query protein and a Pfam family provides the basis for annotations. Two recent articles [2,3] in Genome Biology evaluate the implications of having the query sequence only matching part of a Pfam family, which is an intriguing finding, given that a Pfam family is considered to be an evolutionary unit.     

Cross-National Validation of an Eight-Factor Model of Societal Risk Perception

This study cross-nationally tested an eight-factor model of societal risk perception. The factors in the model were: Common individual hazards, Pollutants, Energy production and public transportation, Outdoor activities, Sex, deviance and addictions, Medical care, Weapons, and Psychotropic drugs. Using confirmatory factor analyses, the model was tested on a sample of Greek students and on a sample of French students, and was shown to satisfactorily account for the data in both samples. This model may be considered as a potentially useful tool for studying cross-national as well as individual differences (e.g., age, gender, worldviews or personality) in risk perception. Future studies are needed to determine: (a) whether this model applies to samples composed of persons of different ages or composed of persons from non-Western countries and (b) whether this model could be usefully expanded with one or more factors.     

Reduction of turgor induces rapid changes in leaf translatable RNA

The turgor of pea (Pisum sativum) leaves was reduced by exposing excised pea shoots to a stream of 23°C air for 20 min. Poly(A)⁺ RNA was isolated from control and wilted shoots, translated in vitro and radiolabeled translation products separated by electrophoresis on two-dimensional (isoelectric focusing-sodium dodecyl sulfate) polyacrylamide gels. This analysis showed that the levels of several poly(A)⁺ RNAs increased in wilted plants. Most of the poly(A)⁺ RNAs induced in wilted plants did not accumulate in response to heat shock or exogenously applied ABA even though endogenous ABA levels were found to increase in shoots 30 min after wilting and by 4 h had increased 50-fold (1 versus 0.02 microgram per gram fresh weight). A λgt10 cDNA library was constructed using poly(A)⁺ RNA from wilted shoots which had been incubated for 4 hours. Differential screening of the library identified four clones corresponding to poly(A)⁺ RNAs which are induced in wilted shoots.