Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, >6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant

Neuroarchitecture of Aminergic Systems in the Larval Ventral Ganglion of Drosophila melanogaster

Biogenic amines are important signaling molecules in the central nervous system of both vertebrates and invertebrates. In the fruit fly Drosophila melanogaster, biogenic amines take part in the regulation of various vital physiological processes such as feeding, learning/memory, locomotion, sexual behavior, and sleep/arousal. Consequently, several morphological studies have analyzed the distribution of aminergic neurons in the CNS. Previous descriptions, however, did not determine the exact spatial location of aminergic neurite arborizations within the neuropil. The release sites and pre-/postsynaptic compartments of aminergic neurons also remained largely unidentified. We here used gal4-driven marker gene expression and immunocytochemistry to map presumed serotonergic (5-HT), dopaminergic, and tyraminergic/octopaminergic neurons in the thoracic and abdominal neuromeres of the Drosophila larval ventral ganglion relying on Fasciclin2-immunoreactive tracts as three-dimensional landmarks. With tyrosine hydroxylase- (TH) or tyrosine decarboxylase 2 (TDC2)-specific gal4-drivers, we also analyzed the distribution of ectopically expressed neuronal compartment markers in presumptive dopaminergic TH and tyraminergic/octopaminergic TDC2 neurons, respectively. Our results suggest that thoracic and abdominal 5-HT and TH neurons are exclusively interneurons whereas most TDC2 neurons are efferent. 5-HT and TH neurons are ideally positioned to integrate sensory information and to modulate neuronal transmission within the ventral ganglion, while most TDC2 neurons appear to act peripherally. In contrast to 5-HT neurons, TH and TDC2 neurons each comprise morphologically different neuron subsets with separated in- and output compartments in specific neuropil regions. The three-dimensional mapping of aminergic neurons now facilitates the identification of neuronal network contacts and co-localized signaling molecules, as exemplified for DOPA decarboxylase-synthesizing neurons that co-express crustacean cardioactive peptide and myoinhibiting peptides

Capturing judgement strategies in risk assessments with improved quality of clinical information: How nurses' strategies differ from the ecological model

Background: Nurses' risk assessments of patients at risk of deterioration are sometimes suboptimal. Advances in clinical simulation mean higher quality information can be used as an alternative to traditional paper-based approaches as a means of improving judgement. This paper tests the hypothesis that nurses' judgement strategies and policies change as the quality of information used by nurses in simulation changes. Methods: Sixty-three student nurses and 34 experienced viewed 25 paper-case based and 25 clinically simulated scenarios, derived from real cases, and judged whether the (simulated) patient was at 'risk' of acute deterioration. Criteria of judgement "correctness" came from the same real cases. Information relative weights were calculated to examine judgement policies of individual nurses. Group comparisons of nurses and students under both paper and clinical simulation conditions were undertaken using non parametric statistical tests. Judgment policies were also compared to the ecological statistical model. Cumulative relative weights were calculated to assess how much information nurses used when making judgements. Receiver operating characteristic (ROC) curves were generated to examine predictive accuracy amongst the nurses. Results: There were significant variations between nurses' judgement policies and those optimal policies determined by the ecological model. Nurses significantly underused the cues of consciousness level, respiration rate, and systolic blood pressure than the ecological model requires. However, in clinical simulations, they tended to make appropriate use of heart rate, with non-significant difference in the relative weights of heart rate between clinical simulations and the ecological model. Experienced nurses paid substantially more attention to respiration rate in the simulated setting compared to paper cases, while students maintained a similar attentive level to this cue. This led to a non-significant difference in relative weights of respiration rate between experienced nurses and students. Conclusions: Improving the quality of information by clinical simulations significantly impacted on nurses' judgement policies of risk assessments. Nurses' judgement strategies also varied with the increased years of experience. Such variations in processing clinical information may contribute to nurses' suboptimal judgements in clinical practice. Constructing predictive models of common judgement situations, and increasing nurses' awareness of information weightings in such models may help improve judgements made by nurses

Sequence and structure of the dopa decarboxylase gene of Drosophila: evidence for novel RNA splicing variants.

In Drosophila, dopa decarboxylase (DDC) serves a dual role in neurotransmitter production and sclerotization of the cuticle. The Ddc gene is under complex hormonal and tissue-specific control and several sizes of Ddc RNA are observed at embryonic hatching, pupariation and adult eclosion. We present here the complete nucleotide sequence of the Drosophila dopa decarboxylase gene and the partial sequence of two corresponding Ddc cDNAs. The sequence allows us to account for the detailed structure of four of the five major Ddc RNA species observed. The cDNA sequence reveals the existence of previously undetected splicing events and provides evidence for two RNA splicing alternatives which appear to encode two protein isoforms. The structure, processing and developmental regulation of the Ddc transcripts and putative protein isoforms are discussed. Interestingly, the pyridoxal-binding peptide of porcine DDC matches the Drosophila sequence perfectly suggesting considerable selective pressure on at least portions of the sequence. This is the first available Ddc gene sequence from any organism and should serve as a basis of comparison for the related proteins of other species