On the Uniform Random Generation of Non Deterministic Automata Up to Isomorphism

In this paper we address the problem of the uniform random generation of non deterministic automata (NFA) up to isomorphism. First, we show how to use a Monte-Carlo approach to uniformly sample a NFA. Secondly, we show how to use the Metropolis-Hastings Algorithm to uniformly generate NFAs up to isomorphism. Using labeling techniques, we show that in practice it is possible to move into the modified Markov Chain efficiently, allowing the random generation of NFAs up to isomorphism with dozens of states. This general approach is also applied to several interesting subclasses of NFAs (up to isomorphism), such as NFAs having a unique initial states and a bounded output degree. Finally, we prove that for these interesting subclasses of NFAs, moving into the Metropolis Markov chain can be done in polynomial time. Promising experimental results constitute a practical contribution.Comment: Frank Drewes. CIAA 2015, Aug 2015, Umea, Sweden. Springer, 9223, pp.12, 2015, Implementation and Application of Automata - 20th International Conferenc

Synthetic biology tools for engineering Yarrowia lipolytica

The non-conventional oleaginous yeast Yarrowia lipolytica shows great industrial promise. It naturally produces certain compounds of interest but can also artificially generate non-native metabolites, thanks to an engineering process made possible by the significant expansion of a dedicated genetic toolbox. In this review, we present recently developed synthetic biology tools that facilitate the manipulation of Y. lipolytica, including 1) DNA assembly techniques, 2) DNA parts for constructing expression cassettes, 3) genome-editing techniques, and 4) computational tools

The association of telomere length with paternal history of premature myocardial infarction in the European Atherosclerosis Research Study II

Inter-individual variability in telomere length is highly heritable and has been correlated with risk of coronary heart disease (CHD). Our aim was to determine the association of mean leukocyte telomere length with paternal history of premature myocardial infarction (MI). Mean leukocyte telomere length was measured with real-time polymerase chain reactions in 369 male students (18–28 years) with a paternal history of MI before the age of 55, recruited from 14 European universities, serving as cases and 396 age-matched controls with no paternal history of CHD. Overall, cases had borderline significantly shorter mean length (~550 bp), adjusted for age and geographical region, than controls (p = 0.05). A significant difference in telomere length across the geographical regions of Europe was observed (p < 0.0001), with shorter mean length in the Baltic and South and the longest in the Middle. The case–control difference (∼2.24 kb) in mean length was highly significant only in the Baltic region (p < 0.0001). There is suggestive evidence that, in young men, the biological expression of a paternal history of premature MI is at least in part mediated through inherited short telomeres. The association with paternal history of MI is strongly seen only in the Baltic compared to the rest of Europe, but this is not explained by shorter telomere length in this region

Synchronizing Random Almost-Group Automata

In this paper we address the question of synchronizing random automata in the critical settings of almost-group automata. Group automata are automata where all letters act as permutations on the set of states, and they are not synchronizing (unless they have one state). In almost-group automata, one of the letters acts as a permutation on $n-1$ states, and the others as permutations. We prove that this small change is enough for automata to become synchronizing with high probability. More precisely, we establish that the probability that a strongly connected almost-group automaton is not synchronizing is $\frac{2^{k-1}-1}{n^{2(k-1)}}(1+o(1))$, for a $k$-letter alphabet.Comment: full version prepared for CIAA 201

The T allele of the hepatic lipase promoter variant C-480T is associated with increased fasting lipids and HDL and increased preprandial and postprandial LpCIII:B : European Atherosclerosis Research Study (EARS) II

The common C-480T transition in the hepatic lipase (HL) promoter has been shown to be associated with lower HL activity and increased high density lipoprotein (HDL) cholesterol. We examined the frequency and lipid associations of this HL polymorphism in 385 healthy, young (18- to 28-year-old) men whose fathers had had a premature myocardial infarction (designated cases) and 405 age-matched controls. These individuals were participants in the European Atherosclerosis Research Study II postprandial trial, who had been recruited from 11 European countries in 4 regions (the Baltic; United Kingdom; and central and southern Europe). Overall, the frequency of the T allele was 0.207 in controls and 0.244 in cases (P=0.08). The T allele was associated with higher fasting plasma total cholesterol (P<0.01), triglycerides (P<0.01), and HDL cholesterol (P<0.01). The strongest association was found with apolipoprotein (apo) A-I concentration, which was 10% higher in individuals homozygous for the T allele compared with those homozygous for the C allele (P<0.001). This polymorphism had no effect on the rise in plasma triglyceride levels after a fatty meal. However, before and after the fat load was ingested, levels of particles containing both apoC-III and apoB (LpC-III:B) were higher in carriers of the T allele, with homozygotes having 23% and 27% higher levels preprandially and postprandially, respectively, than those homozygous for the C allele (P<0.05). Thus, our results demonstrate that the C-480T polymorphism in the HL promoter is associated with alterations in plasma lipids and lipoproteins and the accumulation of atherogenic LpC-III:B particles

Engineering Yarrowia lipolytica to enhance lipid production from lignocellulosic materials

Background: Yarrowia lipolytica is a common biotechnological chassis for the production of lipids, which are the pre‑ ferred feedstock for the production of fuels and chemicals. To reduce the cost of microbial lipid production, inexpen‑ sive carbon sources must be used, such as lignocellulosic hydrolysates. Unfortunately, lignocellulosic materials often contain toxic compounds and a large amount of xylose, which cannot be used by Y. lipolytica. Results: In this work, we engineered this yeast to efciently use xylose as a carbon source for the production of lipids by overexpressing native genes. We further increased the lipid content by overexpressing heterologous genes to facilitate the conversion of xylose-derived metabolites into lipid precursors. Finally, we showed that these engineered strains were able to grow and produce lipids in a very high yield (lipid content = 67%, titer = 16.5 g/L, yield = 3.44 g/g sugars, productivity 1.85 g/L/h) on a xylose-rich agave bagasse hydrolysate in spite of toxic compounds. Conclusions: This work demonstrates the potential of metabolic engineering to reduce the costs of lipid production from inexpensive substrates as source of fuels and chemicals

A New Technique for Reachability of States in Concatenation Automata

We present a new technique for demonstrating the reachability of states in deterministic finite automata representing the concatenation of two languages. Such demonstrations are a necessary step in establishing the state complexity of the concatenation of two languages, and thus in establishing the state complexity of concatenation as an operation. Typically, ad-hoc induction arguments are used to show particular states are reachable in concatenation automata. We prove some results that seem to capture the essence of many of these induction arguments. Using these results, reachability proofs in concatenation automata can often be done more simply and without using induction directly.Comment: 23 pages, 1 table. Added missing affiliation/funding informatio

Genetic engineering of the β-oxidation pathway in the yeast Yarrowia lipolytica to increase the production of aroma compounds

peer reviewedThe yeast Yarrowia lipolytica possesses five acyl-CoA oxidases (Aox1p to 5), the enzyme catalysing the first reaction of β-oxidation. The understanding of the specific role of each acyl-CoA oxidase is important to construct a yeast strain growing at a good rate and able to produce without degrading the aroma compound γ-decalactone. In this study we observed that Aox4p exhibits a slight activity on a broad spectrum of substrates and that it is involved in lactone degradation. We constructed a strain lacking this activity. Its growth was only slightly altered and it produced 10 times more lactone than the wild type in 48h. © 2004 Elsevier B.V. All rights reserved