Comparative and evolutionary studies of mammalian arylsulfatase and sterylsulfatase genes and proteins encoded on the X-chromosome

At least 19 sulfatase genes have been reported on the human genome, including four arylsulfatase (ARS) genes (ARSD; ARSE; ARSF; ARSH) and a sterylsulfatase (STS) gene located together on the X-chromosome. Bioinformatic analyses of mammalian genomes were undertaken using known human STS and ARS amino acid sequences to study the evolution of these genes and proteins encoded on eutherian and marsupial genomes. Several domain regions and key residues were conserved including signal peptides, active site residues, metal (Ca²⁺) and substrate binding sequences, transmembranes and N-glycosylation sites. Phylogenetic analyses describe the relationships and potential origins of these genes during mammalian evolution. Primate ARSH enzymes lacked signal peptide sequences which may influence their biological functions. CpG117 and CpG92 were detected within the 5′ region of the human STS and ARSD genes, respectively, and miR-205 within the 3′-UTR for the human STS gene, using bioinformatic methods A proposal is described for a primordial invertebrate STS-like gene serving as an ancestor for unequal cross over events generating the gene complex on the eutherian mammalian X-chromosome.     

Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration

The Blueline Rasbora (Rasbora sarawakensis) is a small ray-finned fish categorized under the genus Rasbora in the Cyprinidae family. In this study, the complete mitogenome sequence of R. sarawakensis was sequenced using four primers targeting overlapping regions. The mitogenome is 16,709 bp in size, accommodating 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other genus counterparts. The heavy strand houses 28 genes while the light strand stores the other nine genes. Most protein-coding genes employ ATG as start codon, excluding COI gene, which utilizes GTG instead. The central conserved sequence blocks (CSB-F, CSB-E and CSB-D), variable sequence blocks (CSB-3, CSB-2 and CSB-1) as well as the terminal associated sequence (TAS) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of R. sarawakensis from the basal region of the Rasbora clade, where its evolutionary relationships with R. maculatus and R. pauciperforata are poorly resolved as indicated by the low bootstrap values. This work acts as steppingstone towards further molecular evolution and population genetics studies of Rasbora genus in future.     

Screening of fluorinated materials degrading microbes

Isolation of bacterial strains capable of degrading fluorinated materials was described. 8 strains of Actinobacteria exhibited degradability of ethyl difluoroacetate (DFAc) was accumulated by bacteria, giving difluoroacetic acid and then fluoride ion. Further, 13 strains of Actinobacteria exhibited degradability of fluorobenzene and/or benzotrifluoride. In batch culture, growth of strains on fluorinated materials led to the release of fluoride ion.     

Ecological interaction and phylogeny, studying functionality on composed networks

We study a class of composed networks that are formed by two tree networks, T_P and T_A, whose end points touch each other through a bipartite network B_PA. We explore this network using a functional approach. We are interested in how much the topology, or the structure, of T_X (X=A or P) determines the links of B_PA. This composed structure is a useful model in evolutionary biology, where T_P and T_A are the phylogenetic trees of plants and animals that interact in an ecological community. We make use of ecological networks of dispersion of fruits, which are formed by frugivorous animals and plants with fruits; the animals, usually birds, eat fruits and disperse their seeds. We analyse how the phylogeny of T_X determines or is correlated with B_PA using a Monte Carlo approach. We use the phylogenetic distance among elements that interact with a given species to construct an index κ that quantifies the influence of T_X over B_PA. The algorithm is based on the assumption that interaction matrices that follows a phylogeny of T_X have a total phylogenetic distance smaller than the average distance of an ensemble of Monte Carlo realisations. We find that the effect of phylogeny of animal species is more pronounced in the ecological matrix than plant phylogeny.     

Computing bounded-degree phylogenetic roots of disconnected graphs

The Phylogenetic kth Root Problem (PRk) is the problem of finding a (phylogenetic) tree T from a given graph G=(V,E) such that (1) T has no degree-2 internal nodes, (2) the external nodes (i.e., leaves) of T are exactly the elements of V, and (3) (u,v)E if and only if the distance between u and v in tree T is at most k, where k is some fixed threshold k. Such a tree T, if exists, is called a phylogenetic kth root of graph G. The computational complexity of PRk is open, except for k4. Recently, Chen et al. investigated PRk under a natural restriction that the maximum degree of the phylogenetic root is bounded from above by a constant. They presented a linear-time algorithm that determines if a given connected G has such a phylogenetic kth root, and if so, demonstrates one. In this paper, we supplement their work by presenting a linear-time algorithm for disconnected graphs.     

Random walks and Brownian motion on cubical complexes

Cubical complexes are metric spaces constructed by gluing together unit cubes in an analogous way to the construction of simplicial complexes. We construct Brownian motion on such spaces, define random walks, and prove that the transition kernels of the random walks converge to that for Brownian motion. The proof involves pulling back onto the complex the distribution of Brownian sample paths on a single cube, combined with a distribution on walks between cubes. The main application lies in analysing sets of evolutionary trees: several tree spaces are cubical complexes and we briefly describe our results and applications in this context.     

Integer linear programming as a tool for constructing trees from quartet data

The task of the quartet puzzling problem is to find a best-fitting binary X-tree for a finite n-set from confidence values for the 3n4 binary trees with exactly four leaves from X, its fitness being measured by the sum of the confidence values of all "induced" four-leaves subtrees. We describe a method for finding an exact solution of this problem by integer linear programming. Similar procedures can also be used for finding, e.g. best-fitting "circular" networks. A crucial problem in this context is, of course, how to obtain the input confidence values for the quartet trees. We propose to use inner products of rate-matrix diagonals calculated for pairs of taxa and present the trees resulting from applying our approach to two data sets of up to 36 mitochondrial sequences of mammals including an outgroup.     

Molecular identification of pathogenic house dust mites using 12S rRNA sequences

House dust mites are microarthropods implicated in the cause of allergic diseases. Currently, there is no phylogenetic analysis of dust mites based on genomic or mitochondrial DNA (mtDNA) evidence. For the first time, we report evolutionary relationships based on partial mtDNA 12S rRNA sequences among the four dust mite families Pyroglyphidae (Dermatophagoides pteronyssinus), Glycyphagoidea (Glycyphagus privatus), Acaridae (Aleuroglyphus ovatus), and Echimyopodidae (Blomia tropicalis). Thirteen sequence variants were obtained and phylogenetic analysis showed two monophyletic clades composed of two species each. Contrary to current taxonomic classification, the Acaridae clustered in a monophyletic group with the Pyroglyphidae. Considering the current difficulties in identifying these medically important species for the purpose of eradication and treatment, it is significant that sequence data are capable of discriminating between species belonging to different families of dust mites.     

Lateral gene transfer in phylogeny of azoreductase enzyme

This paper attempts to reconstruct the phylogeny of azoreductase enzyme from different organisms and compare it with the small subunit rRNA-based phylogeny of the organisms. The two phylogenies were found to be incongruent, indicating several events of lateral transfer of azoreductase gene between phylogenetically diverse organisms. However, the phylogenetic analysis methods have several limitations and a single method may not give the true pattern. Hence, it is necessary to corroborate the results with other complementary analysis tools. We used several tools to test our hypothesis of lateral transfer and found that it was supported not only by the analysis of the whole sequences, but also by the conserved motifs detected in these sequences. There were ample evidences for lateral transfer of azoreductase gene among enteric bacteria. There were also indications that azoreductase probably evolved in prokaryotes and then it was laterally transferred to eukaryotes in multiple events, resulting in some sequence variation among eukaryotic azoreductases. Finally, profile HMMs and conserved motifs extracted from these azoreductase sequences were found to provide sensitive tools for identifying potential azoreductases from the database. The analysis techniques used in this study can be extended to other gene trees to verify their evolutionary histories.     

Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo

Abstract

Using a stochastic model for the evolution of discrete characters among a group of organisms, we derive a Markov chain that simulates a Bayesian posterior distribution on the space of dendograms. A transformation of the tree into a canonical cophenetic matrix form, with distinct entries along its superdiagonal, suggests a simple proposal distribution for selecting candidate trees “close” to the current tree in the chain. We apply the consequent Metropolis algorithm to published restriction site data on nine species of plants. The Markov chain mixes well from random starting trees, generating reproducible estimates and confidence sets for the path of evolution.