Neural Coding and Synaptic Transmission: Participation Exercises for Introductory Psychology

We present two simulations of neural transmission for use in an Introductory Psychology class. These simulations illustrate the complex coding properties of a single neuron, especially how excitatory and inhibitory postsynaptic potentials accumulate to produce an action potential. A follow-up exercise, using the framework of the simple children's game Musical Chairs, illustrates synaptic transmission, including the effects of psychoactive drugs at the synapse.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

ASRP: the Arabidopsis Small RNA Project Database

Eukaryotes produce functionally diverse classes of small RNAs (20–25 nt). These include microRNAs (miRNAs), which act as regulatory factors during growth and development, and short-interfering RNAs (siRNAs), which function in several epigenetic and post-transcriptional silencing systems. The Arabidopsis Small RNA Project (ASRP) seeks to characterize and functionally analyze the major classes of endogenous small RNAs in plants. The ASRP database provides a repository for sequences of small RNAs cloned from various Arabidopsis genotypes and tissues. Version 3.0 of the database contains 1920 unique sequences, with tools to assist in miRNA and siRNA identification and analysis. The comprehensive database is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu

Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense

[EN] The mechanisms underlying induction and suppression of RNA silencing in the ongoing plant-virus arms race are poorly understood. We show here that virus-derived small RNAs produced by Arabidopsis Dicer-like 4 (DCL4) program an effector complex conferring antiviral immunity. Inhibition of DCL4 by a viral-encoded suppressor revealed the subordinate antiviral activity of DCL2. Accordingly, inactivating both DCL2 and DCL4 was necessary and sufficient to restore systemic infection of a suppressor-deficient virus. The effects of DCL2 were overcome by increasing viral dosage in inoculated leaves, but this could not surmount additional, non - cell autonomous effects of DCL4 specifically preventing viral unloading from the vasculature. These findings define a molecular framework for studying antiviral silencing and defense in plants.We thank members of the Voinnet laboratory for discussions and Z. Xie for dcl seeds. Funded by CNRS grant to A.D.; NSF grant MCB-0209836, NIH grant AI43288, and U.S. Department of Agriculture grant NRI 2005-35319-15280 to J.C.; and Pao Schloarship (Zhejiang University, China) to J.B. This work is dedicated to the memory of M. and G. Voinnet.Deleris, A.; Gallego Bartolomé, J.; Bao, J.; Kasschau, KD.; Carrinton, JC.; Voinnet, O. (2006). Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science. 313(5783):68-71. https://doi.org/10.1126/science.11282146871313578

Preparation of multiplexed small RNA libraries from plants

[EN] High-throughput sequencing is a powerful tool for exploring small RNA populations in plants. The ever-increasing output from an Illumina Sequencing System allows for multiplexing multiple samples while still obtaining sufficient data for small RNA discovery and characterization. Here we describe a protocol for generating multiplexed small RNA libraries for sequencing up to 12 samples in one lane of an Illumina HiSeq System single-end, 50 base pair run. RNA ligases are used to add the 3¿ and 5¿ adaptors to purified small RNAs; ligation products that lack a small RNA molecule (adaptor-adaptor products) are intentionally depleted. After cDNA synthesis, a linear PCR step amplifies the DNA fragments. The 3¿ PCR primers used here include unique 6- nucleotide sequences to allow for multiplexing up to 12 samples.The original version of this protocol was described in Carbonell et al. (2012). The updated version of the protocol was described in Carbonell et al. (2014). This work was supported by grants from the National Science Foundation (MCB-0956526, MCB-1231726) and National Institutes of Health (AI043288)Gilbert, KB.; Fahlgren, N.; Kasschau, KD.; Chapman, EJ.; Carrington, JC.; Carbonell, A. (2014). Preparation of multiplexed small RNA libraries from plants. Bio-protocol. 4(21):1-17. https://doi.org/10.21769/BioProtoc.1275S11742

Genome-wide profiling of Populus small RNAs

<p>Abstract</p> <p>Background</p> <p>Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced <it>Populus trichocarpa </it>using a concatenation strategy in combination with 454 sequencing.</p> <p>Results</p> <p>The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of <it>NBS-LRR </it>genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and <it>NBS-LRR </it>disease resistance genes, classes of genes that have been significantly expanded in <it>Populus</it>. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).</p> <p>Conclusions</p> <p>The short RNA population of <it>P. trichocarpa </it>is at least as complex as that of <it>Arabidopsis thaliana</it>. We provide a first genome-wide view of short RNA production for <it>P. trichocarpa </it>and identify new, non-conserved miRNAs.</p

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants with defects in three RNA-dependent RNA polymerase (RDR) and four Dicer-like (DCL) genes. The profiling involved direct analysis using a multiplexed, parallel-sequencing strategy. Small RNA-generating loci, especially those producing predominantly 24-nt siRNAs, were found to be highly correlated with repetitive elements across the genome. These were found to be largely RDR2- and DCL3-dependent, although alternative DCL activities were detected on a widespread level in the absence of DCL3. In contrast, no evidence for RDR2-alternative activities was detected. Analysis of RDR2- and DCL3-dependent small RNA accumulation patterns in and around protein-coding genes revealed that upstream gene regulatory sequences systematically lack siRNA-generating activities. Further, expression profiling suggested that relatively few genes, proximal to abundant 24-nt siRNAs, are regulated directly by RDR2- and DCL3-dependent silencing. We conclude that the widespread accumulation patterns for RDR2- and DCL3-dependent siRNAs throughout the Arabidopsis genome largely reflect mechanisms to silence highly repeated sequences

Genetic and Functional Diversification of Small RNA Pathways in Plants

Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense