Npas4: Linking Neuronal Activity to Memory

Immediate-early genes (IEGs) are rapidly activated after sensory and behavioral experience and are believed to be crucial for converting experience into long-term memory. Neuronal PAS domain protein 4 (Npas4), a recently discovered IEG, has several characteristics that make it likely to be a particularly important molecular link between neuronal activity and memory: it is among the most rapidly induced IEGs, is expressed only in neurons, and is selectively induced by neuronal activity. By orchestrating distinct activity-dependent gene programs in different neuronal populations, Npas4 affects synaptic connections in excitatory and inhibitory neurons, neural circuit plasticity, and memory formation. It may also be involved in circuit homeostasis through negative feedback and psychiatric disorders. We summarize these findings and discuss their implications.National Institutes of Health (U.S.) (Grant MH091220-01

A qRT-PCR method to evaluate viability of potato cyst nematode (<i>Globodera</i> spp.)

<p>Potato cyst nematodes (PCN) – <i>Globodera rostochiensis</i> and <i>G. pallida</i> – cause significant yield losses on potato worldwide. One of the main challenges to PCN management is the ability of PCN to remain dormant in the soil for several decades. For that reason, many countries have strict quarantine regulations for PCN. These regulations, although expensive and restrictive for growers, are necessary to prevent further spread of PCN but should be lifted when no more viable cysts are found. Here, we report a promising qRT-PCR method for the quantification of viable eggs and propose that this method be included in routine testing. The method was successful for quantifying <i>G. ellingtonae, G. rostochiensis</i> and <i>G. pallida</i> and was found to be very sensitive with the systematic detection of a single larva. Intron-flanking probes were used to eliminate the possibility of false positives due to genomic DNA, and an internal control was added to detect failure in PCR due to inhibitors. No amplification occurred during the testing of eggs that had previously received heat treatments or fumigation with methyl bromide. This qRT-PCR assay was used to evaluate the viability of field populations of <i>G. rostochiensis</i> 10 years after the establishment of a quarantine area in Saint-Amable, Quebec, Canada. The number of viable eggs after a decade of regulation was found to be very low and confirmed the effectiveness of the measures put in place. Egg viability was also monitored in microplots following five continuous years of planting resistant potatoes, and no signs of resistance-breaking genotypes were observed.</p

UNEAK PstI-MspI allele frequencies - Validation assay - 28 Quebec populations from 2 fields + 1 outgroup

Allele frequencies calculated from UNEAK exact counts (mnC=1, minCov=20 and MAF=0.01) and used for principal component analysis (PCA) of Globodera rostochiensis populations from two fields of the province of Quebec, Canada and an unrelated population from France

PstI-MspI SNP table - UNEAK - 23 worldwide populations

Generated with mnC=0.8, minCov=1 and a MAF=0.01. Use this file as input to generate the “UNEAK-PstI/MspI” SNP tables with different parameters (mnC, minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software)

Sample description

Details about the origin (Country, province and field) of the samples, which experiment and figures they were used in and accession numbers (bioproject and biosample numbers)

Supplemental Figure 2

Number of SNPs retained by UNEAK and PoPoolation2 pipelines at different parameter values on an ApeKI library from 23 worldwide populations of Globodera rostochiensis. ‘MAF’ is the minimum allele frequency; ‘minCov’ is the minimum number of reads/locus/population required to accept a SNP; ‘mnC’ is the minimum proportion of populations in which a locus must have been scored to be accepted. PoPoolation2 does not allow missing data (mnC = 1.0). *The number of SNPs identified by UNEAK was not influenced by the ‘mnC’ value when the minimum allele frequency was set to 5% (MAF = 0.05)

Supplemental Figure 1

Relationship between the median coverage (median number of reads/locus/population supporting each SNP) and the number of SNPs retained by the two pipelines at a minimum allele frequency of 1% (MAF = 0.01) and 5% (MAF = 0.05)

Supplemental Figure 3

Principal component analyses of 23 worldwide populations of Globodera rostochiensis from different pathotypes (Ro1, Ro2, Ro3, Ro4, Ro5 and a mixed population of Ro2/Ro3). Calculated with the prcomp() function in R. Based on genome-wide allele frequencies of different number of loci obtained from the PstI/MspI library supported by six different minimum coverage values (minCov = 5, 10, 20, 30, 40 or 50 reads/locus/population). Computed by the PoPoolation2 pipeline with a minimum allele frequency of 1% (MAF = 0.01) and no missing data allowed (mnC = 1.0)

Supplemental Figure 4

Principal component analysis of 23 worldwide populations of Globodera rostochiensis. Calculated with the prcomp() function in R. Based on genome-wide allele frequencies of 1,277 loci obtained from the PstI/MspI library, and computed by the PoPoolation2 pipeline with a minimum allele frequency of 1% (MAF = 0.01), no missing data allowed (mnC = 1.0) and a minimum coverage of 20 reads/SNP/population (minCov = 20). Colors represent the different pathotypes: Black = Ro1; Yellow = Ro2; Green = Ro3; Red = Ro4; Blue = Ro5 and Grey is the mixed Ro2/3 sample

Analysis of Putative Apoplastic Effectors from the Nematode, <i>Globodera rostochiensis</i>, and Identification of an Expansin-Like Protein That Can Induce and Suppress Host Defenses

<div><p>The potato cyst nematode, <i>Globodera rostochiensis</i>, is an important pest of potato. Like other pathogens, plant parasitic nematodes are presumed to employ effector proteins, secreted into the apoplast as well as the host cytoplasm, to alter plant cellular functions and successfully infect their hosts. We have generated a library of ORFs encoding putative <i>G. rostochiensis</i> putative apoplastic effectors in vectors for expression <i>in planta</i>. These clones were assessed for morphological and developmental effects on plants as well as their ability to induce or suppress plant defenses. Several CLAVATA3/ESR-like proteins induced developmental phenotypes, whereas predicted cell wall-modifying proteins induced necrosis and chlorosis, consistent with roles in cell fate alteration and tissue invasion, respectively. When directed to the apoplast with a signal peptide, two effectors, an ubiquitin extension protein (<i>Gr</i>UBCEP12) and an expansin-like protein (<i>Gr</i>EXPB2), suppressed defense responses including NB-LRR signaling induced in the cytoplasm. <i>Gr</i>EXPB2 also elicited defense response in species- and sequence-specific manner. Our results are consistent with the scenario whereby potato cyst nematodes secrete effectors that modulate host cell fate and metabolism as well as modifying host cell walls. Furthermore, we show a novel role for an apoplastic expansin-like protein in suppressing intra-cellular defense responses.</p></div