65 research outputs found
The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima
Genotype-phenotype (GP) maps specify how the random mutations that change
genotypes generate variation by altering phenotypes, which, in turn, can
trigger selection. Many GP maps share the following general properties: 1) The
number of genotypes is much larger than the number of selectable
phenotypes; 2) Neutral exploration changes the variation that is accessible to
the population; 3) The distribution of phenotype frequencies ,
with the number of genotypes mapping onto phenotype , is highly
biased: the majority of genotypes map to only a small minority of the
phenotypes. Here we explore how these properties affect the evolutionary
dynamics of haploid Wright-Fisher models that are coupled to a simplified and
general random GP map or to a more complex RNA sequence to secondary structure
map. For both maps the probability of a mutation leading to a phenotype
scales to first order as , although for the RNA map there are further
correlations as well. By using mean-field theory, supported by computer
simulations, we show that the discovery time of a phenotype similarly
scales to first order as for a wide range of population sizes and
mutation rates in both the monomorphic and polymorphic regimes. These
differences in the rate at which variation arises can vary over many orders of
magnitude. Phenotypic variation with a larger is therefore be much more
likely to arise than variation with a small . We show, using the RNA
model, that frequent phenotypes (with larger ) can fix in a population
even when alternative, but less frequent, phenotypes with much higher fitness
are potentially accessible. In other words, if the fittest never `arrive' on
the timescales of evolutionary change, then they can't fix. We call this highly
non-ergodic effect the `arrival of the frequent'.Comment: full paper plus supplementary material
Epistasis can lead to fragmented neutral spaces and contingency in evolution
In evolution, the effects of a single deleterious mutation can sometimes be
compensated for by a second mutation which recovers the original phenotype.
Such epistatic interactions have implications for the structure of genome space
- namely, that networks of genomes encoding the same phenotype may not be
connected by single mutational moves. We use the folding of RNA sequences into
secondary structures as a model genotype-phenotype map and explore the neutral
spaces corresponding to networks of genotypes with the same phenotype. In most
of these networks, we find that it is not possible to connect all genotypes to
one another by single point mutations. Instead, a network for a phenotypic
structure with bonds typically fragments into at least neutral
components, often of similar size. While components of the same network
generate the same phenotype, they show important variations in their
properties, most strikingly in their evolvability and mutational robustness.
This heterogeneity implies contingency in the evolutionary process.Comment: 21 pages, 21 figure
Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability.
Mutational neighbourhoods in genotype-phenotype (GP) maps are widely believed to be more likely to share characteristics than expected from random chance. Such genetic correlations should strongly influence evolutionary dynamics. We explore and quantify these intuitions by comparing three GP maps-a model for RNA secondary structure, the HP model for protein tertiary structure, and the Polyomino model for protein quaternary structure-to a simple random null model that maintains the number of genotypes mapping to each phenotype, but assigns genotypes randomly. The mutational neighbourhood of a genotype in these GP maps is much more likely to contain genotypes mapping to the same phenotype than in the random null model. Such neutral correlations can be quantified by the robustness to mutations, which can be many orders of magnitude larger than that of the null model, and crucially, above the critical threshold for the formation of large neutral networks of mutationally connected genotypes which enhance the capacity for the exploration of phenotypic novelty. Thus neutral correlations increase evolvability. We also study non-neutral correlations: Compared to the null model, i) If a particular (non-neutral) phenotype is found once in the 1-mutation neighbourhood of a genotype, then the chance of finding that phenotype multiple times in this neighbourhood is larger than expected; ii) If two genotypes are connected by a single neutral mutation, then their respective non-neutral 1-mutation neighbourhoods are more likely to be similar; iii) If a genotype maps to a folding or self-assembling phenotype, then its non-neutral neighbours are less likely to be a potentially deleterious non-folding or non-assembling phenotype. Non-neutral correlations of type i) and ii) reduce the rate at which new phenotypes can be found by neutral exploration, and so may diminish evolvability, while non-neutral correlations of type iii) may instead facilitate evolutionary exploration and so increase evolvability.This work was funded under EP/P504287/1 by the Engineering and Physical Sciences Research Council (https://www.epsrc.ac.uk). SEA is supported by The Royal Society (https://royalsociety.org/).This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pcbi.100477
A new method to prevent carry-over contaminations in two-step PCR NGS library preparations
Two-step PCR procedures are an efficient and well established way to generate
amplicon libraries for NGS sequencing. However, there is a high risk of cross-
contamination by carry-over of amplicons from first to second amplification
rounds, potentially leading to severe misinterpretation of results. Here we
describe a new method able to prevent and/or to identify carry-over
contaminations by introducing the K-box, a series of three synergistically
acting short sequence elements. Our K-boxes are composed of (i) K1 sequences
for suppression of contaminations, (ii) K2 sequences for detection of possible
residual contaminations and (iii) S sequences acting as separators to avoid
amplification bias. In order to demonstrate the effectiveness of our method we
analyzed two-step PCR NGS libraries derived from a multiplex PCR system for
detection of T-cell receptor beta gene rearrangements. We used this system
since it is of high clinical relevance and may be affected by very low amounts
of contaminations. Spike-in contaminations are effectively blocked by the
K-box even at high rates as demonstrated by ultra-deep sequencing of the
amplicons. Thus, we recommend implementation of the K-box in two-step PCR-
based NGS systems for research and diagnostic applications demanding high
sensitivity and accuracy
Influence of natural killer cells and perforin-mediated cytolysis on the development of chemically induced lung cancer in A/J mice
One alternative approach for the treatment of lung cancer might be the activation of the immune system using vaccination strategies. However, most of clinical vaccination trials for lung cancer did not reach their primary end points, suggesting that lung cancer is of low immunogenicity. To provide additional experimental information about this important issue, we investigated which type of immune cells contributes to the protection from lung cancer development. Therefore, A/J mice induced for lung adenomas/adenocarcinomas by the tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) were depleted of CD4+ or CD8+ T cells, CD11b+ macrophages, Gr-1+ neutrophils and asialo GM1+ natural killer (NK) cells. Subsequent analysis of tumour growth showed an increase in tumour number only in mice depleted of NK cells. Further asking by which mechanism NK cells suppressed tumour development, we neutralized several death ligands of the tumour necrosis factor (TNF) family known to be involved in NK cell-mediated cytotoxicity. However, neither depletion of TNF-α, TNF-related apoptosis-inducing ligand, TNF-like weak inducer of apoptosis or FasL alone nor in combination induced an augmentation of tumour burden. To show whether an alternative cell death pathway is involved, we next generated A/J mice deficient for perforin. After challenging with NNK, mice deficient for perforin showed an increase in tumour number and volume compared to wild-type A/J mice. In summary, our data suggest that NK cells and perforin-mediated cytolysis are critically involved in the protection from lung cancer giving promise for further immunotherapeutic strategies for this disease
Severe infections of Panton-Valentine leukocidin positive Staphylococcus aureus in children
Infections caused by Panton-Valentine leukocidin-positive Staphylococcus aureus (PVL-SA) mostly present as recurrent skin abscesses and furunculosis. However, life-threatening infections (eg, necrotizing pneumonia, necrotizing fasciitis, and osteomyelitis) caused by PVL-SA have also been reported.We assessed the clinical phenotype, frequency, clinical implications (surgery, length of treatment in hospitals/intensive care units, and antibiotic treatments), and potential preventability of severe PVL-SA infections in children.Total, 75 children treated for PVL-SA infections in our in- and outpatient units from 2012 to 2017 were included in this retrospective study.Ten out of 75 children contracted severe infections (PVL-methicillin resistant S aureus n = 4) including necrotizing pneumonia (n = 4), necrotizing fasciitis (n = 2), pyomyositis (n = 2; including 1 patient who also had pneumonia), mastoiditis with cerebellitis (n = 1), preorbital cellulitis (n = 1), and recurrent deep furunculosis in an immunosuppressed patient (n = 1). Specific complications of PVL-SA infections were venous thrombosis (n = 2), sepsis (n = 5), respiratory failure (n = 5), and acute respiratory distress syndrome (n = 3). The median duration of hospital stay was 14 days (range 5-52 days). In 6 out of 10 patients a history suggestive for PVL-SA colonization in the patient or close family members before hospital admission was identified.PVL-SA causes severe to life-threatening infections requiring lengthy treatments in hospital in a substantial percentage of symptomatic PVL-SA colonized children. More than 50% of severe infections might be prevented by prompt testing for PVL-SA in individuals with a history of abscesses or furunculosis, followed by decolonization measures
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