Latest Articles
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Neuroscience
Functional correlates of immediate early gene expression in mouse visual cortex
10.24072/pcjournal.156 - Peer Community Journal, Volume 2 (2022), article no. e45.
Get full text PDFDuring visual development, response properties of layer 2/3 neurons in visual cortex are shaped by experience. Both visual and visuomotor experience are necessary to coordinate the integration of bottom-up visual input and top-down motor-related input. Whether visual and visuomotor experience engage different plasticity mechanisms, possibly associated with the two separate input pathways, is still unclear. To begin addressing this, we measured the expression level of three different immediate early genes (IEG) (c-fos, egr1 or Arc) and neuronal activity in layer 2/3 neurons of visual cortex before and after a mouse’s first visual exposure in life, and subsequent visuomotor learning. We found that expression levels of all three IEGs correlated positively with neuronal activity, but that first visual and first visuomotor exposure resulted in differential changes in IEG expression patterns. In addition, IEG expression levels differed depending on whether neurons exhibited primarily visually driven or motor-related activity. Neurons with strong motor-related activity preferentially expressed EGR1, while neurons that developed strong visually driven activity preferentially expressed Arc. Our findings are consistent with the interpretation that bottom-up visual input and top-down motor-related input are associated with different IEG expression patterns and hence possibly also with different plasticity pathways.
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Infections
Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV)
10.24072/pcjournal.154 - Peer Community Journal, Volume 2 (2022), article no. e44.
Get full text PDFStructural variations (SVs) constitute a significant source of genetic variability in virus genomes. Yet knowledge about SV variability and contribution to the evolutionary process in large double-stranded (ds)DNA viruses is limited. Cyprinid herpesvirus 3 (CyHV-3), also commonly known as koi herpesvirus (KHV), has the largest dsDNA genome within herpesviruses. This virus has become one of the biggest threats to common carp and koi farming, resulting in high morbidity and mortalities of fishes, serious environmental damage, and severe economic losses. A previous study analyzing CyHV-3 virulence evolution during serial passages onto carp cell cultures suggested that CyHV-3 evolves, at least in vitro, through an assembly of haplotypes that alternatively become dominant or under-represented. The present study investigates the SV diversity and dynamics in CyHV-3 genome during 99 serial passages in cell culture using, for the first time, ultra-deep whole-genome and amplicon-based sequencing. The results indicate that KHV polymorphism mostly involves SVs. These SVs display a wide distribution along the genome and exhibit high turnover dynamics with a clear bias towards inversion and deletion events. Analysis of the pathogenesis-associated ORF150 region in ten intermediate cell passages highlighted mainly deletion, inversion and insertion variations that deeply altered the structure of ORF150. Our findings indicate that SV turnovers and defective genomes represent key drivers in the viral population dynamics and in vitro evolution of KHV. Thus, the present study can contribute to the basic research needed to design safe live-attenuated vaccines, classically obtained by viral attenuation after serial passages in cell culture.
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Zoology
Dopamine pathway characterization during the reproductive mode switch in the pea aphid
10.24072/pcjournal.152 - Peer Community Journal, Volume 2 (2022), article no. e43.
Get full text PDFAphids are major pests of most of the crops worldwide. Such a success is largely explained by the remarkable plasticity of their reproductive mode. They reproduce efficiently by viviparous parthenogenesis during spring and summer generating important damage on crops. At the end of the summer, viviparous parthenogenetic females perceive the photoperiod shortening and transduce this signal to their embryos that change their reproductive fate to produce sexual individuals: oviparous females and males. After mating, those females lay cold-resistant eggs. Earlier studies showed that some transcripts coding for key components of dopamine pathway were regulated between long days and short days conditions suggesting that dopamine might be involved in the transduction of seasonal cues prior to reproductive mode switch. In this study, we aimed at going deeper into the characterization of the expression dynamics of this pathway but also in the analysis of its functional role in this context in the pea aphid Acyrthosiphon pisum. We first analysed the level of expression of ten genes of this pathway in embryos and larval heads of aphids reared under long days (asexual producers) or short days (sexual producers) conditions. We then performed in situ hybridization experiments to localize in embryos the ddc and pale transcripts that are coding for two key enzymes in dopamine synthesis. Finally, Using CRISPR-Cas9 mutagenesis in eggs produced after the mating of sexual individuals, we targeted the ddc gene. We could observe strong melanization defaults in ddc mutated eggs, which confidently mimicked the Drosophila ddc phenotype. Nevertheless, such a lethal phenotype did not allow us to validate the involvement of dopamine as a signaling pathway necessary to trigger the reproductive mode switch in embryos.
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Genomics
Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codons
10.24072/pcjournal.141 - Peer Community Journal, Volume 2 (2022), article no. e42.
Get full text PDFIn ambiguous stop/sense genetic codes, the stop codon(s) not only terminate translation but can also encode amino acids. Such codes have evolved at least four times in eukaryotes, twice among ciliates (Condylostoma magnum and Parduczia sp.). These have appeared to be isolated cases whose next closest relatives use conventional stop codons. However, little genomic data have been published for the Karyorelictea, the ciliate class that contains Parduczia sp., and previous studies may have overlooked ambiguous codes because of their apparent rarity. We therefore analyzed single-cell transcriptomes from four of the six karyorelict families to determine their genetic codes. Reassignment of canonical stops to sense codons was inferred from codon frequencies in conserved protein domains, while the actual stop codon was predicted from full-length transcripts with intact 3’-untranslated regions (3’-UTRs). We found that all available karyorelicts use the Parduczia code, where canonical stops UAA and UAG are reassigned to glutamine, and UGA encodes either tryptophan or stop. Furthermore, a small minority of transcripts may use an ambiguous stop-UAA instead of stop-UGA. Given the ubiquity of karyorelicts in marine coastal sediments, ambiguous genetic codes are not mere marginal curiosities but a defining feature of a globally distributed and diverse group of eukaryotes.
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