Biology subjects

Simon, A.

Publications and source records attributed to Simon, A..

4 recordsLinked to original sources

bioRxiv2018

First natural crossover recombination of intact ORFs between two distinct species of the family Closteroviridae

Lettuce chlorosis virus-SP (LCV-SP) (family Closteroviridae, genus Crinivirus), is a new strain of LCV which is able to infect green bean plants and incapable of infecting lettuce crops. In the present study, high throughput and Sanger sequencing of RNA was used to obtain the LCV-SP full-length sequence. The LCV-SP genome comprises 8825 nt and 8672 nt equivalent with RNA1 and RNA2 respectively. RNA1 of LCV-SP contains four ORFs, the proteins encoded by the ORF1a and ORF1b are closely related to LCV RNA1 from California (FJ380118) whereas the 3{acute} end encodes proteins which share high amino acid sequence identity with RNA1 of BnYDV (EU191904). The genomic sequence of RNA2 consists of 8 ORFs, instead of 10 ORFs contained in LCV-California isolate. The distribution of vsiRNA (virus-derived small interfering RNA) along the LCV-SP genome suggested the presence of subgenomic RNAs corresponding with HSP70, P6.4 and P60. Results of the analysis using RDP4 and Simplot programs are the proof of the evidence that LCV-SP is the first recombinant of the family Closteroviridae by crossover recombination of intact ORFs, being the LCV RNA1 (FJ380118) and BnYDV RNA1 (EU191904) the origin of the new LCV strain. Genetic diversity values of virus isolates in the recombinant region obtained after sampling LCV-SP infected green bean between 2011 and 2017 might suggest that the recombinant virus event occurred in the area before this period. The presence of LCV-SP shows the role of recombination as a driving force of evolution within the genus Crinivirus, a globally distributed, emergent genus.

plant biology↗

bioRxiv2018

An optimized toolkit for precision base editing

CRISPR base editing is a potentially powerful technology that enables the creation of genetic mutations with single base pair resolution. By re-engineering both DNA and protein sequences, we developed a collection of constitutive and inducible base editing vector systems that dramatically improve the ease and efficiency by which single nucleotide variants can be created. This new toolkit is effective in a wide range of model systems, and provides a means for efficient in vivo somatic base editing.

bioengineering↗

bioRxiv2018

Cross-fostering in rodents causes region-specific alterations in entorhinal cortical gamma rhythms associated with NMDA receptor dysfunction

There has recently been a large increase in the number of children placed in foster care in the United States and Europe. While this is the least worst scenario for those with a lack of appropriate biological care, it is recognised that these children are exposed to major stressors correlated with behavioural changes, particularly in the realm of social cognition into adulthood. Here we model foster care in rodents: rat pups are removed from their biological mother and placed with a non-genetically related dam. This prevented the entorhinal cortex from generating patterns of gamma rhythms required for normal parahippocampal function relevant to social interaction. These changes correlated with a reduction in NMDA receptor-mediated excitation, and changes in parvalbumin expression in interneurons. These data suggest that early life care delivered by a non-biological parent may disrupt social behaviour but, in contrast, generate neurobiological changes antagonistic to those currently associated with psychosis.\n\nSignificance StatementCross fostering is an effective approach for delineating the effect of environment from genetic influences upon behavior. This involves removal of pups from one mother and transfer to another lactating dam. This manipulation is considered as a mild form of early life stress, producing neurobehavioral changes such as alterations in social interaction. We demonstrate that cross fostering produces changes in the ability of cortical microcircuits to generate oscillatory rhythms, in particular the gamma rhythm, in brain regions important for social cognition. This reduction in gamma rhythmogenesis is related to a reduction in synaptic drive provided by the NMDA receptor. One implication of this work is that the modulation of NMDA receptors offers a potential therapeutic strategy for disorders involving impaired sociability.

neuroscience↗

bioRxiv2017

Coadapted genomes and selection on hybrids: Fisher’s geometric model explains a variety of empirical patterns

Natural selection plays a variety of roles in hybridization, speciation and admixture. Most research has focused on two extreme cases: crosses between closely-related inbred lines, where hybrids are fitter than their parents, or crosses between effectively isolated species, where hybrids suffer severe breakdown. Many natural populations must fall into intermediate regimes, with multiple types of gene interaction, but these are more difficult to study. Here, we develop a simple fitness landscape model, and show that it naturally interpolates between previous modeling approaches, involving mildly deleterious recessives, or discrete hybrid incompatibilities. The model yields several new predictions, which we test with genomic data from Mytilus mussels, and published data from plants (Zea, Populus and Senecio) and animals (Mus, Teleogryllus and Drosophila). The predictions are generally supported, and the model explains surprising empirical patterns that have been observed in both extreme regimes. Our approach enables novel and complementary uses of genome-wide datasets, which do not depend on identifying outlier loci, or \"speciation genes\" with anomalous effects. Given its simplicity and flexibility, and its predictive successes with a wide range of data, the approach should be readily extendable to other outstanding questions in the study of hybridization.

evolutionary biology↗