Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees

Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least one horizontal transfer event. As a natural generalization, we consider symmetrized Fitch maps, that is, symmetric maps $\varepsilon$ that assign a subset of colors to each pair of vertices in $X$ and that can be explained by a tree $T$ with edges that are labeled with subsets of colors in the sense that the color $m$ appears in $\varepsilon(x,y)$ if and only if $m$ appears in a label along the unique path between $x$ and $y$ in $T$. We first give an alternative characterization of the monochromatic case and then give a characterization of symmetrized Fitch maps in terms of compatibility of a certain set of quartets. We show that recognition of symmetrized Fitch maps is NP-complete. In the restricted case where $|\varepsilon(x,y)|\leq 1$ the problem becomes polynomial, since such maps coincide with class of monochromatic Fitch maps whose graph-representations form precisely the class of complete multi-partite graphs

Generalized Fitch Graphs II: Sets of Binary Relations that are explained by Edge-labeled Trees

Fitch graphs $G=(X,E)$ are digraphs that are explained by $\{\emptyset, 1\}$-edge-labeled rooted trees $T$ with leaf set $X$: there is an arc $(x,y) \in E$ if and only if the unique path in $T$ that connects the last common ancestor $\mathrm{lca}(x,y)$ of $x$ and $y$ with $y$ contains at least one edge with label "1". In practice, Fitch graphs represent xenology relations, i.e., pairs of genes $x$ and $y$ for which a horizontal gene transfer happened along the path from $\mathrm{lca}(x,y)$ to $y$. In this contribution, we generalize the concept of Fitch graphs and consider trees $T$ that are equipped with edge-labeling $\lambda: E\to \mathcal{P}(M)$ that assigns to each edge a subset $M'\subseteq M$ of colors. Given such a tree, we can derive a map $\varepsilon_{(T,\lambda)}$ (or equivalently a set of not necessarily disjoint binary relations), such that $i\in \varepsilon_{(T,\lambda)}(x,y)$ (or equivalently $(x,y)\in R_i$) with $x,y\in X$, if and only if there is at least one edge with color $i$ from $\mathrm{lca}(x,y)$ to $y$. The central question considered here: Is a given map $\varepsilon$ a Fitch map, i.e., is there there an edge-labeled tree $(T,\lambda)$ with $\varepsilon_{(T,\lambda)} = \varepsilon$, and thus explains $\varepsilon$? Here, we provide a characterization of Fitch maps in terms of certain neighborhoods and forbidden submaps. Further restrictions of Fitch maps are considered. Moreover, we show that the least-resolved tree explaining a Fitch map is unique (up to isomorphism). In addition, we provide a polynomial-time algorithm to decide whether $\varepsilon$ is a Fitch map and, in the affirmative case, to construct the (up to isomorphism) unique least-resolved tree $(T^*,\lambda^*)$ that explains $\varepsilon$

Production of negative-emissions steel using a reducing gas derived from dfb gasification

A dual fluidized bed (DFB) gasification process is proposed to produce sustainable reducing gas for the direct reduction (DR) of iron ore. This novel steelmaking route is compared with the established process for DR, which is based on natural gas, and with the emerging DR technology using electrolysis-generated hydrogen as the reducing gas. The DFB-DR route is found to produce reducing gas that meets the requirement of the DR reactor, based on existing MIDREX plants, and which is produced with an energetic efficiency comparable with the natural gas route. The DFB-DR path is the only route considered that allows negative CO2 emissions, enabling a 145% decrease in emissions relative to the traditional blast furnace–basic oxygen furnace (BF–BOF) route. A reducing gas cost between 45–60 EUR/MWh is obtained, which makes it competitive with the hydrogen route, but not the natural gas route. The cost estimation for liquid steel production shows that, in Sweden, the DFB-DR route cannot compete with the natural gas and BF–BOF routes without a cost associated with carbon emissions and a revenue attributed to negative emissions. When the cost and revenue are set as equal, the DFB-DR route becomes the most competitive for a carbon price >60 EUR/tCO2

Detection of RNA structures in porcine EST data and related mammals

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background Non-coding RNAs (ncRNAs) are involved in a wide spectrum of regulatory functions. Within recent years, there have been increasing reports of observed polyadenylated ncRNAs and mRNA like ncRNAs in eukaryotes. To investigate this further, we examined the large data set in the Sino-Danish PigEST resource http://pigest.ku.dk which also contains expression information distributed on 97 non-normalized cDNA libraries. Results We constructed a pipeline, EST2ncRNA, to search for known and novel ncRNAs. The pipeline utilises sequence similarity to ncRNA databases (blast), structure similarity to Rfam (RaveNnA) as well as multiple alignments to predict conserved novel putative RNA structures (RNAz). EST2ncRNA was fed with 48,000 contigs and 73,000 singletons available from the PigEST resource. Using the pipeline we identified known RNA structures in 137 contigs and single reads (conreads), and predicted high confidence RNA structures in non-protein coding regions of additional 1,262 conreads. Of these, structures in 270 conreads overlap with existing predictions in human. To sum up, the PigEST resource comprises trans-acting elements (ncRNAs) in 715 contigs and 340 singletons as well as cis-acting elements (inside UTRs) in 311 contigs and 51 singletons, of which 18 conreads contain both predictions of trans- and cis-acting elements. The predicted RNAz candidates were compared with the PigEST expression information and we identify 114 contigs with an RNAz prediction and expression in at least ten of the non-normalised cDNA libraries. We conclude that the contigs with RNAz and known predictions are in general expressed at a much lower level than protein coding transcripts. In addition, we also observe that our ncRNA candidates constitute about one to two percent of the genes expressed in the cDNA libraries. Intriguingly, the cDNA libraries from developmental (brain) tissues contain the highest amount of ncRNA candidates, about two percent. These observations are related to existing knowledge and hypotheses about the role of ncRNAs in higher organisms. Furthermore, about 80% porcine coding transcripts (of 18,600 identified) as well as less than one-third ORF-free transcripts are conserved at least in the closely related bovine genome. Approximately one percent of the coding and 10% of the remaining matches are unique between the PigEST data and cow genome. Based on the pig-cow alignments, we searched for similarities to 16 other organisms by UCSC available alignments, which resulted in a 87% coverage by the human genome for instance. Conclusion Besides recovering several of the already annotated functional RNA structures, we predicted a large number of high confidence conserved secondary structures in polyadenylated porcine transcripts. Our observations of relatively low expression levels of predicted ncRNA candidates together with the observations of higher relative amount in cDNA libraries from developmental stages are in agreement with the current paradigm of ncRNA roles in higher organisms and supports the idea of polyadenylated ncRNAs.Published versio

Generation of integration free induced pluripotent stem cells from fibrodysplasia ossificans progressiva (FOP) patients from urine samples

Fibrodysplasia ossificans progressiva (FOP) is an extremely rare, autosomal dominant transmitted genetic disease. Patients experience progressive bone formation replacing tendons, ligaments, muscle and soft tissue. Cause of FOP are gain-of-function mutations in the Bone Morphogenetic Protein (BMP) receptor Activin A receptor type 1 (ACVR1) ( Kaplan et al., 2008). The most common mutation is R206H, which leads to the substitution of codon 206 from arginine to histidine (Shore et al., 2006). Here, we describe the derivation and characterization of two hiPSC lines from two FOP patients, both carrying the mutation R206H. Cells were isolated from urine and reprogrammed using integration free Sendai virus vectors under defined conditions

INFluENCE OF VESSEl TypE, phySICal STaTE OF MEdIuM aNd TEMpOrary IMMErSION ON ThE MICrOprOpagaTION OF ThrEE Rhodophiala SpECIES

aBSTraCT Rhodophiala C. Presl (Amaryllidaceae) is a genus of attractive flowering geophytes native to South America. They have ornamental value, but most species are not well-known and have conservation problems. The objective of this study was to optimize a micropropagation process to support the use and preservation of three Chilean native species, R. montana (Phil.) Traub, R. splendens (Rengifo) Traub., and R. ananuca (Phil.) Traub. The research evaluated the feasibility of implementing liquid medium culture and assessed the influence of different tissue culture systems on the shoot production and biomass increment of small bulbs. Three experiments were carried out. The first one determined the influences of flask size and volume of media; the second compared liquid and solid media, and in the third experiment, a temporary immersion system (TIS), and conventional culture in static liquid, shaken liquid and gelled Murashige and Skoog (MS) media were compared. By using larger (350 mL) flasks with higher (50 mL) media volume, 100% more fresh weight of microbulb was obtained that treatment with smaller flasks (45 mL) and media volume (10 mL). In gelled medium, hyperhydricity affected only 5% of explants, while in liquid medium was 16-40%. Survival to acclimatization reached 87-94% for plants from gelled medium; from liquid medium only 38-69%. TIS yielded higher propagation rate (1.9 shoots in 30 d) compared with shaken liquid medium (1.0) (P < 0.05) in R. ananuca only. Current procedures are appropriate for the support of ex situ conservation and germplasm bank establishment

Origin of the highest energy cosmic rays observed

Introducing a simple Galactic wind model patterned after the solar wind we show that back-tracing the orbits of the highest energy cosmic events suggests that they may all come from the Virgo cluster, and so probably from the active radio galaxy M87. This confirms a long standing expectation. Those powerful radio galaxies that have their relativistic jets stuck in the interstellar medium of the host galaxy, such as 3C147, will then enable us to derive limits on the production of any new kind of particle, expected in some extensions of the standard model in particle physics. New data from HIRES will be crucial in testing the model proposed here.Comment: At TAUP99, the 6th international workshop on topics in Astroparticle Physics and Underground Physics, College de France, Eds. J. Dumarchez, M. Froissart, D. Vignaud, (Sep 1999

Deciphering the genetic basis for polyketide variation among mycobacteria producing mycolactones.

BACKGROUND: Mycolactones are immunosuppressive and cytotoxic polyketides, comprising five naturally occurring structural variants (named A/B, C, D, E and F), produced by different species of very closely related mycobacteria including the human pathogen, Mycobacterium ulcerans. In M. ulcerans strain Agy99, mycolactone A/B is produced by three highly homologous type I polyketide megasynthases (PKS), whose genes (mlsA1: 51 kb, mlsA2: 7.2 kb and mlsB: 42 kb) are found on a 174 kb plasmid, known as pMUM001. RESULTS: We report here comparative genomic analysis of pMUM001, the complete DNA sequence of a 190 kb megaplasmid (pMUM002) from Mycobacterium liflandii 128FXT and partial sequence of two additional pMUM replicons, combined with liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis. These data reveal how PKS module and domain differences affecting MlsB correlate with the production of mycolactones E and F. For mycolactone E these differences from MlsB in M. ulcerans Agy99 include replacement of the AT domain of the loading module (acetate to propionate) and the absence of an entire extension module. For mycolactone F there is also a reduction of one extension module but also a swap of ketoreductase domains that explains the characteristic stereochemistry of the two terminal side-chain hydroxyls, an arrangement unique to mycolactone F CONCLUSION: The mycolactone PKS locus on pMUM002 revealed the same large, three-gene structure and extraordinary pattern of near-identical PKS domain sequence repetition as observed in pMUM001 with greater than 98.5% nucleotide identity among domains of the same function. Intra- and inter-strain comparisons suggest that the extreme sequence homogeneity seen among the mls PKS genes is caused by frequent recombination-mediated domain replacement. This work has shed light on the evolution of mycolactone biosynthesis among an unusual group of mycobacteria and highlights the potential of the mls locus to become a toolbox for combinatorial PKS biochemistry.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are