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

学会抄録

Genome annotation. (XLSX 9 kb

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

Summation of the comprehensive ranking values of gene stability given by RefFinder for RNA-Seq and RT-qPCR variation analyses for 11 candidate reference genes.

<p>Expression variations were calculated on two RNA-Seq replicates and three qRT-PCR replicates for the eight developmental stages of <i>G</i>. <i>rostochiensis</i>.</p

Detailed rankings of 11 candidate reference genes from qRT-PCR data, given by RefFinder in <i>G</i>. <i>pallida</i>.

<p>Detailed rankings of 11 candidate reference genes from qRT-PCR data, given by RefFinder in <i>G</i>. <i>pallida</i>.</p

Description of genes and primers used in this study.

<p>Description of genes and primers used in this study.</p

Transcriptome-wide selection of a reliable set of reference genes for gene expression studies in potato cyst nematodes (<i>Globodera</i> spp.) - Table 2

<p>Comparison of rankings of 11 candidate reference genes from (A) RNA-Seq data and (B) qRT-PCR data, given by RefFinder in <i>G</i>. <i>rostochiensis</i>.</p

Variability of the expression level (span of Cq values) in <i>G. rostochiensis</i> of the 11 candidate reference genes across eight combinations of development stages and time of exposure to potato root diffusate, as measured by qRT-PCR.

<p>The median of three replicates of the eight conditions is represented by the line inside the box, 50% of the values are inside the box, the upper and lower edges represent the 75th and 25th percentiles, respectively, and the circles represent outliers.</p

Transcriptome-wide selection of a reliable set of reference genes for gene expression studies in potato cyst nematodes (<i>Globodera</i> spp.) - Fig 3

<p>Expression of (A) <i>NEP-1</i>, (B) <i>cht-2</i>, and (C) <i>eng</i> assessed by qRT-PCR in dry cysts (DC), water hydrated eggs (W), hydrated eggs exposed to potato root diffusate (PRD) for 1 h, 8 h, 24 h, 48 h, and 7 d, and in J2 larvae. All expression levels were normalized using the geometric mean of <i>aaRS</i>, <i>PMP-3</i>, and <i>GR</i>, <i>our selected reference genes (in black) and Act-1 (in grey)</i>. Dry cyst was used as the calibrator for relative expression calculation. Error bars represent the standard error of the mean, and significant differences among treatments are indicated by different letters (Tukey’s test).</p

Data_Sheet_1_Genome Scans Reveal Homogenization and Local Adaptations in Populations of the Soybean Cyst Nematode.XLSX

<p>Determining the adaptive potential of alien invasive species in a new environment is a key concern for risk assessment. As climate change is affecting local climatic conditions, widespread modifications in species distribution are expected. Therefore, the genetic mechanisms underlying local adaptations must be understood in order to predict future species distribution. The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a major pathogen of soybean that was accidentally introduced in most soybean-producing countries. In this study, we explored patterns of genetic exchange between North American populations of SCN and the effect of isolation by geographical distance. Genotyping-by-sequencing was used to sequence and compare 64 SCN populations from the United States and Canada. At large scale, only a weak correlation was found between genetic distance (Wright's fixation index, F_ST) and geographic distance, but local effects were strong in recently infested states. Our results also showed a high level of genetic differentiation within some populations, allowing them to adapt to new environments and become established in new soybean-producing areas. Bayesian genome scan methods identified 15 loci under selection for climatic or geographic co-variables. Among these loci, two non-synonymous mutations were detected in SMAD-4 (mothers against decapentaplegic homolog 4) and DOP-3 (dopamine receptor 3). High-impact variants linked to these loci by genetic hitchhiking were also highlighted as putatively involved in local adaptation of SCN populations to new environments. Overall, it appears that strong selective pressure by resistant cultivars is causing a large scale homogenization with virulent populations.</p