Biology subjects

Wright, S.

Publications and source records attributed to Wright, S..

4 recordsLinked to original sources

bioRxiv2018

CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus

The rice blast fungus Magnaporthe oryzae is the most serious pathogen of cultivated rice and a significant threat to global food security. To accelerate targeted mutation and specific gene editing in this species, we have developed a rapid plasmid-free CRISPR-Cas9-based gene editing method. It has previously been reported in M. oryzae that transformation with plasmids expressing Cas9 can generate specific mutations using sgRNAs, directing the endonuclease to specific genes. We show, however, that expression of Cas9 is highly toxic to M. oryzae, rendering this approach impractical. We demonstrate that using purified Cas9 pre-complexed to RNA guides to form ribonucleoproteins (RNPs), provides an alternative and very effective gene editing procedure. When used in combination with oligonucleotide or PCR-generated donor DNAs, generation of strains with specific base pair edits, in-locus gene replacements, or multiple gene edits, is very rapid and straightforward. Additionally, we report a novel counterselection strategy which allows creation of precisely edited fungal strains that contain no foreign DNA and are completely isogenic to the wild type. Together, these developments represent a scalable improvement in the precision and speed of genetic manipulation in M. oryzae and are likely to be broadly applicable to other fungal species.

microbiology↗

bioRxiv2018

Local adaptation and maladaptation during the worldwide range expansion of a self-fertilizing plant

Species having experienced rapid range expansion represent unique opportunities to evaluate the dynamics of adaptation during colonization of new environments. We investigated the consequences of range expansion on local adaptation of a successful worldwide colonizer, the shepherds purse Capsella bursa-pastoris. This species is an annual weed that originated recently in Eurasia and has now broadly colonized both temperate and subtropical areas. We assessed the performance, genetic diversity, and phenology of field-collected accessions belonging to three distinct genetic clusters of decreasing age (Middle East, Europe and Asia) in three common gardens in Europe, Asia and North America. To understand the genetic basis of local adaptation in this species, we also tested for correlation between SNP allele frequencies and environmental factors in Europe and Asia. Overall, we showed that patterns of local adaptation depended on population history: some older populations were weakly adapted to local conditions while those closer to the front of the colonization wave, far from the origin of the species, were maladapted whatever the common gardens. Altogether, our results have important consequences for the understanding of the evolution and adaptation of self-fertilizing plant during range expansion.

evolutionary biology↗

bioRxiv2017

The Facultative Sex Coalescent with Crossing Over Recombination and Multi-Site Gene Conversion

Under neutrality, linkage disequilibrium (LD) results from physically linked sites having non-independent coalescent histories. In obligately sexual organisms, meiotic recombination is the dominant force separating linked variants from one another, and thus in determining the decay of LD with physical distance. In facultatively sexual diploid organisms that principally reproduce clonally, mechanisms of mitotic exchange are expected to become relatively more important in shaping LD. Here we outline mathematical and computational models of a facultative-sex coalescent process that includes meiotic and mitotic recombination, via both crossovers and gene conversion, to determine how LD is affected with facultative sex. We demonstrate that the degree to which LD is broken down by meiotic recombination simply scales with the probability of sex if it is sufficiently high (much greater than 1/N for N the population size). However, with very rare sex (occurring with frequency on the order of 1/N), mitotic gene conversion plays a particularly important and complicated role because it both breaks down associations between sites and removes within-individual diversity. Strong population structure under rare sex leads to lower average LD values than in panmictic populations, due to the influence of low-frequency polymorphisms created by allelic sequence divergence acting in individual subpopulations. These analyses provide information on how to interpret observed LD patterns in facultative sexuals, and determine what genomic forces are likely to shape them.

evolutionary biology↗

bioRxiv2017

NMDA-receptor antibodies alter cortical microcircuit dynamics

NMDA-receptor antibodies (NMDAR-Ab) cause an autoimmune encephalitis with a diverse range of electroencephalographic (EEG) abnormalities. NMDAR-Ab are believed to disrupt receptor function, but how blocking this excitatory neurotransmitter can lead to paroxysmal EEG abnormalities - or even seizures - is poorly understood. Here, we show that NMDAR-Ab change intrinsic cortical connections and neuronal population dynamics to alter the spectral composition of spontaneous EEG activity, and predispose to paroxysmal EEG abnormalities. Based on local field potential recordings in a mouse model, we first validate a dynamic causal model of NMDAR-Ab effects on cortical microcircuitry. Using this model, we then identify the key synaptic parameters that best explain EEG paroxysms in paediatric patients with NMDAR-Ab encephalitis. Finally, we use the mouse model to show that NMDAR-Ab- related changes render microcircuitry critically susceptible to overt EEG paroxysms, when these key parameters are changed. These findings offer mechanistic insights into circuit-level dysfunction induced by NMDAR-Ab.

neuroscience↗