Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition,bi-directionally from the primed protospacer

Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arrays as spacers. This adaptation process is the least characterized step in CRISPR-Cas immunity. Here, we used Pectobacterium atrosepticum to investigate adaptation in Type I-F CRISPR-Cas systems. Pre-existing spacers that matched plasmids stimulated hyperactive primed acquisition and resulted in the incorporation of up to nine new spacers across all three native CRISPR arrays. Endogenous expression of the cas genes was sufficient, yet required, for priming. The new spacers inhibited conjugation and transformation, and interference was enhanced with increasing numbers of new spacers. We analyzed ∼350 new spacers acquired in priming events and identified a 5′-protospacer-GG-3′ protospacer adjacent motif. In contrast to priming in Type I-E systems, new spacers matched either plasmid strand and a biased distribution, including clustering near the primed protospacer, suggested a bi-directional translocation model for the Cas1:Cas2–3 adaptation machinery. Taken together these results indicate priming adaptation occurs in different CRISPR-Cas systems, that it can be highly active in wild-type strains and that the underlying mechanisms vary.     

Development of Eye Position Dependency of Slow Phase Velocity during Caloric Stimulation

The nystagmus in patients with vestibular disorders often has an eye position dependency, called Alexander’s law, where the slow phase velocity is higher with gaze in the fast phase direction compared with gaze in the slow phase direction. Alexander’s law has been hypothesized to arise either due to adaptive changes in the velocity-to-position neural integrator, or as a consequence of processing of the vestibular-ocular reflex. We tested whether Alexander’s law arises only as a consequence of non-physiologic vestibular stimulation. We measured the time course of the development of Alexander’s law in healthy humans with nystagmus caused by three types of caloric vestibular stimulation: cold (unilateral inhibition), warm (unilateral excitation), and simultaneous bilateral bithermal (one side cold, the other warm) stimulation, mimicking the normal push-pull pattern of vestibular stimulation. Alexander’s law, measured as a negative slope of the velocity versus position curve, was observed in all conditions. A reversed pattern of eye position dependency (positive slope) was found <10% of the time. The slope often changed with nystagmus velocity (cross-correlation of nystagmus speed and slope was significant in 50% of cases), and the average lag of the slope with the speed was not significantly different from zero. Our results do not support the hypothesis that Alexander’s law can only be observed with non-physiologic vestibular stimulation. Further, the rapid development of Alexander’s law, while possible for an adaptive mechanism, is nonetheless quite fast compared to most other ocular motor adaptations. These results suggest that Alexander’s law may not be a consequence of a true adaptive mechanism.     

SuperSAGE analysis of the <Emphasis Type="Italic">Nicotiana attenuata</Emphasis> transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses

Background  

Plants trigger and tailor defense responses after perception of the oral secretions (OS) of attacking specialist lepidopteran larvae. Fatty acid-amino acid conjugates (FACs) in the OS of the Manduca sexta larvae are necessary and sufficient to elicit the herbivory-specific responses in Nicotiana attenuata, an annual wild tobacco species. How FACs are perceived and activate signal transduction mechanisms is unknown.     

Energy-dependent changes in the conformation of the epsilon subunit of the chloroplast ATP synthase

Rabbit antiserum raised against the isolated native epsilon subunit of the chloroplast coupling factor 1 activated the ATPase activity of coupling factor 1 in solution by removing the epsilon subunit. Incubation of thylakoid membranes with the antiserum in the dark had no effect on photophosphorylation or on the dithiothreitol-induced Mg2+-ATPase activity. Incubation with the antiserum during illumination, however, strongly inhibited both activities and caused the membranes to become leaky to protons. The results indicate that the formation of a proton gradient across the thylakoid membrane induces a change in conformation of the epsilon subunit of the ATP synthase such that it becomes susceptible to attack and removal by the antibodies. This change may be a part of the mechanism that results in energy-dependent activation of the ATP synthase.     

The evolutionary transformation of phyllopodous to stenopodous limbs in the Branchiopoda (Crustacea)--is there a common mechanism for early limb development in arthropods?

Arthropods and in particular crustaceans show a great diversity concerning their limb morphology. This makes the homologization of limbs and their parts and our understanding of evolutionary transformations of these limb types problematical. To address these problems we undertook a comparative study of the limb development of two representatives of branchiopod crustaceans, one with phyllopodous the other with stenopodous trunk limbs. The trunk limb ontogeny of a 'larger branchiopod', Cyclestheria hislopi ('Conchostraca') and the raptorial cladoceran Leptodora kindtii (Haplopoda) has been examined by various methods such as SEM, Hoechst fluorescent stain and expression of the Distal-less gene. The early ontogeny of the trunk limbs in C. hislopi and L. kindtii is similar. In both species the limbs are formed as ventrally placed, elongate, subdivided limb buds. However, in C. hislopi, the portions of the early limb bud end up constituting the endites and the endopod of the phyllopodous filtratory limb in the adult, whereas in L. kindtii, similar limb bud portions end up constituting the actual segments in the segmented, stenopodous, and raptorial trunk limbs of the adults. Hence, the portions of the limbs corresponding to the endites of the phyllopodous trunk limbs in C. hislopi (and other 'larger branchiopods') are homologous to the segments of the stenopodous trunk limbs in L. kindtii. It is most parsimonious to assume that the segmented trunk limbs in L. kindtii have developed from phyllopodous limbs with endites and not vice versa. This study has demonstrated at least one way in which segmented limbs have been derived from phyllopodous, multi-lobate limbs during evolution. Similar pathways can be assumed for the evolution of stenopodous, segmented and uniramous limbs in other crustaceans. Irrespective of the differences in the adult limb morphology, the early patterning of arthropod limbs seems to follow a similar principle.