Search results for "MUTATION"
showing 10 items of 2830 documents
On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing
2013
One of the most used techniques to study structural variation at a genome level is paired-end mapping (PEM). PEM has the advantage of being able to detect balanced events, such as inversions and translocations. However, inversions are still quite difficult to predict reliably, especially from high-throughput sequencing data. We simulated realistic PEM experiments with different combinations of read and library fragment lengths, including sequencing errors and meaningful base-qualities, to quantify and track down the origin of false positives and negatives along sequencing, mapping, and downstream analysis. We show that PEM is very appropriate to detect a wide range of inversions, even with …
Why are viral genomes so fragile? The bottleneck hypothesis
2021
If they undergo new mutations at each replication cycle, why are RNA viral genomes so fragile, with most mutations being either strongly deleterious or lethal? Here we provide theoretical and numerical evidence for the hypothesis that genetic fragility is partly an evolutionary response to the multiple population bottlenecks experienced by viral populations at various stages of their life cycles. Modelling within-host viral populations as multi-type branching processes, we show that mutational fragility lowers the rate at which Muller’s ratchet clicks and increases the survival probability through multiple bottlenecks. In the context of a susceptible-exposed-infectious-recovered epidemiolog…
From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses.
2012
Although evolution is a multifactorial process, theory posits that the speed of molecular evolution should be directly determined by the rate at which spontaneous mutations appear. To what extent these two biochemical and population-scale processes are related in nature, however, is largely unknown. Viruses are an ideal system for addressing this question because their evolution is fast enough to be observed in real time, and experimentally-determined mutation rates are abundant. This article provides statistically supported evidence that the mutation rate determines molecular evolution across all types of viruses. Properties of the viral genome such as its size and chemical composition are…
TALPID3/KIAA0586 regulates multiple aspects of neuromuscular patterning during gastrointestinal development in animal models and human
2021
ABSTRACTTALPID3/KIAA0586 is an evolutionary conserved protein, which plays an essential role in protein trafficking. Its role during gastrointestinal (GI) and enteric nervous system (ENS) development has not been studied previously. Here, we analysed chicken, mouse and human embryonic GI tissues with TALPID3 mutations. The GI tract of TALPID3 chicken embryos was shortened and malformed. Histologically, the gut smooth muscle was mispatterned and enteric neural crest cells were scattered throughout the gut wall. Analysis of the Hedgehog pathway and gut extracellular matrix provided causative reasons for these defects. Interestingly, chicken intra-species grafting experiments and a conditional…
Familial Mediterranean Fever and Diet: A Narrative Review of the Scientific Literature
2022
Background: Familial Mediterranean fever (FMF) is an inherited autoinflammatory disease characterized by short acute attacks, with an as yet unknown cause. Several authors have investigated the role of some foods as potential triggers. This narrative review aims to analyze the correlation between diet and FMF clinical outcomes. Methods: The review was carried out following PRISMA statement guidelines, including all cross-sectional, case-crossover, and trial studies written in English and conducted between 1974 and 2022. Results: Overall, 642 records were identified through PubMed/MEDLINE (292) and Scopus (350), and seven studies were included: three out of seven (43%) studies evaluated FMF …
Improving table compression with combinatorial optimization
2002
We study the problem of compressing massive tables within the partition-training paradigm introduced by Buchsbaum et al. [SODA'00], in which a table is partitioned by an off-line training procedure into disjoint intervals of columns, each of which is compressed separately by a standard, on-line compressor like gzip. We provide a new theory that unifies previous experimental observations on partitioning and heuristic observations on column permutation, all of which are used to improve compression rates. Based on the theory, we devise the first on-line training algorithms for table compression, which can be applied to individual files, not just continuously operating sources; and also a new, …
Right-jumps and pattern avoiding permutations
2015
We study the iteration of the process "a particle jumps to the right" in permutations. We prove that the set of permutations obtained in this model after a given number of iterations from the identity is a class of pattern avoiding permutations. We characterize the elements of the basis of this class and we enumerate these "forbidden minimal patterns" by giving their bivariate exponential generating function: we achieve this via a catalytic variable, the number of left-to-right maxima. We show that this generating function is a D-finite function satisfying a nice differential equation of order~2. We give some congruence properties for the coefficients of this generating function, and we sho…
On Block Sensitivity and Fractional Block Sensitivity
2018
We investigate the relation between the block sensitivity bs(f) and fractional block sensitivity fbs(f) complexity measures of Boolean functions. While it is known that fbs(f) = O(bs(f)2), the best known separation achieves $${\rm{fbs}}\left( f \right) = \left( {{{\left( {3\sqrt 2 } \right)}^{ - 1}} + o\left( 1 \right)} \right){\rm{bs}}{\left( f \right)^{3/2}}$$ . We improve the constant factor and show a family of functions that give fbs(f) = (6−1/2 − o(1)) bs(f)3/2.
All Classical Adversary Methods Are Equivalent for Total Functions
2017
We show that all known classical adversary lower bounds on randomized query complexity are equivalent for total functions and are equal to the fractional block sensitivity fbs( f ). That includes the Kolmogorov complexity bound of Laplante and Magniez and the earlier relational adversary bound of Aaronson. This equivalence also implies that for total functions, the relational adversary is equivalent to a simpler lower bound, which we call rank-1 relational adversary. For partial functions, we show unbounded separations between fbs( f ) and other adversary bounds, as well as between the adversary bounds themselves. We also show that, for partial functions, fractional block sensitivity canno…
Quantum lower bound for inverting a permutation with advice
2014
Given a random permutation $f: [N] \to [N]$ as a black box and $y \in [N]$, we want to output $x = f^{-1}(y)$. Supplementary to our input, we are given classical advice in the form of a pre-computed data structure; this advice can depend on the permutation but \emph{not} on the input $y$. Classically, there is a data structure of size $\tilde{O}(S)$ and an algorithm that with the help of the data structure, given $f(x)$, can invert $f$ in time $\tilde{O}(T)$, for every choice of parameters $S$, $T$, such that $S\cdot T \ge N$. We prove a quantum lower bound of $T^2\cdot S \ge \tilde{\Omega}(\epsilon N)$ for quantum algorithms that invert a random permutation $f$ on an $\epsilon$ fraction of…