71 research outputs found
Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion
In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.Fil: Vaschetto, Luis Maria Benjamin. Consejo Nacional de Investigaciones CientΓficas y TΓ©cnicas. Centro CientΓfico TecnolΓ³gico Conicet - CΓ³rdoba. Instituto de Diversidad y EcologΓa Animal. Universidad Nacional de CΓ³rdoba. Facultad de Ciencias Exactas FΓsicas y Naturales. Instituto de Diversidad y EcologΓa Animal; Argentina. Universidad Nacional de CΓ³rdoba. Facultad de Ciencias Exactas, FΓsicas y Naturales. CΓ‘tedra de Diversidad Animal I; Argentin
High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity
The RNA-programmable Cas9 endonuclease cleaves double-stranded DNA at sites complementary to a 20-base-pair guide RNA. The Cas9 system has been used to modify genomes in multiple cells and organisms, demonstrating its potential as a facile genome-engineering tool. We used in vitro selection and high-throughput sequencing to determine the propensity of eight Cas9:guide RNA complexes to cleave each of 10^12 potential off-target DNA sequences. The selection results predicted five off-target sites in the human genome that were confirmed to undergo genome cleavage in HEK293T cells upon expression of one of two Cas9:guide RNA complexes. In contrast to previous models, our results show that Cas9:guide RNA specificity extends past a 7- to 12-base pair seed sequence. Our results also suggest a tradeoff between activity and specificity both in vitro and in cells as a shorter, less-active guide RNA is more specific then a longer, more-active guide RNA. High concentrations of Cas9:guide RNA complexes can cleave off-target sites containing mutations near or within the PAM that are not cleaved when enzyme concentrations are limiting
A Preference for Contralateral Stimuli in Human Object- and Face-Selective Cortex
Visual input from the left and right visual fields is processed predominantly in the contralateral hemisphere. Here we investigated whether this preference for contralateral over ipsilateral stimuli is also found in high-level visual areas that are important for the recognition of objects and faces. Human subjects were scanned with functional magnetic resonance imaging (fMRI) while they viewed and attended faces, objects, scenes, and scrambled images in the left or right visual field. With our stimulation protocol, primary visual cortex responded only to contralateral stimuli. The contralateral preference was smaller in object- and face-selective regions, and it was smallest in the fusiform gyrus. Nevertheless, each region showed a significant preference for contralateral stimuli. These results indicate that sensitivity to stimulus position is present even in high-level ventral visual cortex
Age-related delay in information accrual for faces: Evidence from a parametric, single-trial EEG approach
Background: In this study, we quantified age-related changes in the time-course of face processing
by means of an innovative single-trial ERP approach. Unlike analyses used in previous studies, our
approach does not rely on peak measurements and can provide a more sensitive measure of
processing delays. Young and old adults (mean ages 22 and 70 years) performed a non-speeded
discrimination task between two faces. The phase spectrum of these faces was manipulated
parametrically to create pictures that ranged between pure noise (0% phase information) and the
undistorted signal (100% phase information), with five intermediate steps.
Results: Behavioural 75% correct thresholds were on average lower, and maximum accuracy was
higher, in younger than older observers. ERPs from each subject were entered into a single-trial
general linear regression model to identify variations in neural activity statistically associated with
changes in image structure. The earliest age-related ERP differences occurred in the time window
of the N170. Older observers had a significantly stronger N170 in response to noise, but this age
difference decreased with increasing phase information. Overall, manipulating image phase
information had a greater effect on ERPs from younger observers, which was quantified using a
hierarchical modelling approach. Importantly, visual activity was modulated by the same stimulus
parameters in younger and older subjects. The fit of the model, indexed by R2, was computed at
multiple post-stimulus time points. The time-course of the R2 function showed a significantly slower
processing in older observers starting around 120 ms after stimulus onset. This age-related delay
increased over time to reach a maximum around 190 ms, at which latency younger observers had
around 50 ms time lead over older observers.
Conclusion: Using a component-free ERP analysis that provides a precise timing of the visual
system sensitivity to image structure, the current study demonstrates that older observers
accumulate face information more slowly than younger subjects. Additionally, the N170 appears to
be less face-sensitive in older observers
Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs
Abstract
Background
This paper uses simulation to explore how gene drives can increase genetic gain in livestock breeding programs. Gene drives are naturally occurring phenomena that cause a mutation on one chromosome to copy itself onto its homologous chromosome.
Methods
We simulated nine different breeding and editing scenarios with a common overall structure. Each scenario began with 21 generations of selection, followed by 20 generations of selection based on true breeding values where the breeder used selection alone, selection in combination with genome editing, or selection with genome editing and gene drives. In the scenarios that used gene drives, we varied the probability of successfully incorporating the gene drive. For each scenario, we evaluated genetic gain, genetic variance
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, rate of change in inbreeding (
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F
), number of distinct quantitative trait nucleotides (QTN) edited, rate of increase in favourable allele frequencies of edited QTN and the time to fix favourable alleles.
Results
Gene drives enhanced the benefits of genome editing in seven ways: (1) they amplified the increase in genetic gain brought about by genome editing; (2) they amplified the rate of increase in the frequency of favourable alleles and reduced the time it took to fix them; (3) they enabled more rapid targeting of QTN with lesser effect for genome editing; (4) they distributed fixed editing resources across a larger number of distinct QTN across generations; (5) they focussed editing on a smaller number of QTN within a given generation; (6) they reduced the level of inbreeding when editing a subset of the sires; and (7) they increased the efficiency of converting genetic variation into genetic gain.
Conclusions
Genome editing in livestock breeding results in short-, medium- and long-term increases in genetic gain. The increase in genetic gain occurs because editing increases the frequency of favourable alleles in the population. Gene drives accelerate the increase in allele frequency caused by editing, which results in even higher genetic gain over a shorter period of time with no impact on inbreeding
Gadolinium and nephrogenic systemic fibrosis: time to tighten practice
Nephrogenic systemic fibrosis (NSF) is a relatively new entity, first described in 1997. Few cases have been reported, but the disease has high morbidity and mortality. To date it has been seen exclusively in patients with renal dysfunction. There is an emerging link with intravenous injection of gadolinium contrast agents, which has been suggested as a main triggering factor, with a lag time of days to weeks. Risk factors include the severity of renal impairment, major surgery, vascular events and other proinflammatory conditions. There is no reason to believe that children have an altered risk compared to the adult population. It is important that the paediatric radiologist acknowledges emerging information on NSF but at the same time considers the risk:benefit ratio prior to embarking on alternative investigations, as children with chronic kidney disease require high-quality diagnostic imaging
Representing Where along with What Information in a Model of a Cortical Patch
Behaving in the real world requires flexibly combining and maintaining information about both continuous and discrete variables. In the visual domain, several lines of evidence show that neurons in some cortical networks can simultaneously represent information about the position and identity of objects, and maintain this combined representation when the object is no longer present. The underlying network mechanism for this combined representation is, however, unknown. In this paper, we approach this issue through a theoretical analysis of recurrent networks. We present a model of a cortical network that can retrieve information about the identity of objects from incomplete transient cues, while simultaneously representing their spatial position. Our results show that two factors are important in making this possible: A) a metric organisation of the recurrent connections, and B) a spatially localised change in the linear gain of neurons. Metric connectivity enables a localised retrieval of information about object identity, while gain modulation ensures localisation in the correct position. Importantly, we find that the amount of information that the network can retrieve and retain about identity is strongly affected by the amount of information it maintains about position. This balance can be controlled by global signals that change the neuronal gain. These results show that anatomical and physiological properties, which have long been known to characterise cortical networks, naturally endow them with the ability to maintain a conjunctive representation of the identity and location of objects
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