An evolutionary tree represents the relationship among a group of species, DNA or protein sequences, and play fundamental roles in biological lineage research. A high quality tree construction relies heavily on optimal multiple sequence alignment (MSA), which aligns three or more sequence simultaneously to derive the similarity. On the other hand, a good tree can also be used to guide the MSA process. Due to the high computational cost to conduct both the MSA and tree construction, parallel approaches are exploited to utilize the enormous amount of computing power and memory housed in a supercomputer or Linux cluster. In this paper, first of all, a divide and conquer based parallel algorithm is designed and implemented to perform optimal three sequence alignment using reduced memory cost. Secondly, all internal nodes of a phylogenetic tree resulting from a parallel Maximum-likelihood inference software are labeled using the parallel MSA. Such tree node labeling process is carried out from top down and is also parallelized to fully utilize the numerous cores and nodes in a high performance computing facility.

An experiment involving two treatment groups compared whole wheat diet and refined wheat diet on different sets of mice. Of interest were the differences by treatment of the levels of hundreds of bacteria in the guts of the mice. It was desired to determine the statistical significance of not only the individual bacteria, but also the families of bacteria. These family relationships are represented in a phylogenetic tree, and it was determined helpful to color the branches of bacteria based on the significance of their corresponding families. Calculating these p-values and coloring the branches by hand would not be a quick process. An automated method would greatly increase the efficiency of these calculations. To handle this problem, SigTree, an R package, was written. The p-values for individual bacteria (tips) are combined up the tree using meta-analysis methods, and significance is visualized on a color scale in a revised phylogenetic tree plot. SigTree is able to handle not only the motivating mouse diet experiment, but also experiments that fall into the general framework of having significance tests (and resulting p-values) on each tip in a phylogenetic tree.

In this study the composition of the denitrifying bacterial community among constructed wetlands in agricultural areas was investigated. Thirty-two constructed wetlands located in Southern Sweden were surveyed, and biofilm samples from each were analyzed by applying denaturing gradient gel electrophoresis, to investigate the community composition of the three denitrifying bacterial enzyme genes nirK, nirS and nosZ. The DNA sequences of the enzyme genes were compared to known DNA sequences in GeneBank using BLAST. The results of the denitrifying bacterial enzyme genes indicated that these habitats may harbour a heterogeneous denitrifying bacterial community. Individual analysis of the enzyme genes revealed that nirS was more heterogeneous than both nirK and nosZ. Most sequences from the present study clustered with known sequences from species belonging to the group of α-Proteobacteria, and to a lesser extent with β- Proteobacteria and γ-Proteobacteria, and only nirS clustered with a member of gram-positive bacteria. / <p>Included in doctoral thesis: Milenkovski, Susann. Structure and Function of Microbial Communities in Constructed Wetlands - Influence of environmental parameters and pesticides on denitrifying bacteria. Lund University 2009.</p>

The Acentropinae represents a species-rich crambid group with more than 700 species distributed in all the zoogeographic regions except Antarctica, and the highest diversity occurs in the Oriental, Indo-Autralian and Neotropical regions. Most caterpillars of Acentropinae are widely adapted to feed on vegetation in different types of aquatic environments, such as ponds, streams and rivers. However, some of them are known to utilize mosses on land. Therefore the evolutionary relationships between the terrestrial and aquatic lineage become intriguing. The genus Paracymoriza Warren, 1890, is a moderate-sized acentropine genus comprising 39 species ranging throughout southeast and east Asia. Historically the genus was often confused with many unrelated genera due to the superficial resemblance in wing maculation, which is termed the ¡§nymphuliform wing pattern¡¨. The genus is currently divided into 8 species groups, with 5 of them known having aquatic immature stages, while the others having terrestrial immatures. The fact that Paracymoriza includes both truly aquatic and terrestrial species represents a unique case for the Lepidoptera, thus making the monophyly of the genus doubtful. In the present study, a phylogenetic hypothesis Paracymoriza was reconstructed by using morphological characters including wing pattern and immature stage characters obtained from 63 species representing 25 acentropine genera. The results suggest that Paracymoriza is monophyletic. The genus is composed of two major clades: one aquatic, and the other terrestrial. It suggests that Paracymoriza represents a unique example with amphibious immature stage in the Lepidoptera although the tree support values of this phylogenetic hypothesis remains relatively weak due to large amount of homoplasious characters.

MicroRNAs are important biomolecules for regulating biological processes. Moreover, the secondary structure of microRNA is important for its activity and has been used previously as a mean for finding unknown microRNAs. A phylogenetic study of the microRNA secondary structure reveals more information than its primary sequence, because the primary sequence can undergo mutations that give rise to different phylogenetic relationships, whereas the secondary structure is more robust against mutations and therefore sometimes  more informative. Here we constructed a phylogenetic tree entirely based on microRNA secondary structures using tools PHYLIP (Felsenstein, 1995) and RNAforester (Matthias Höchsmann, 2003, Hochsmann et al., 2004), and compared the overall topology and clusters with the phylogenetic tree constructed using microRNA sequence. The purpose behind this comparison was to investigate the sequence and structure similarity in phylogenetic context and also to investigate if functionally similar microRNA genes are closer in their structure-derived phylogenetic tree. Our phylogenetic comparison shows that the sequence similarity has hardly any effect on the structure similarity in the phylogenetic tree. MicroRNAs that have similar function are closer in the phylogenetic tree based on secondary structure than its respective sequence phylogeny. Hence, this approach can be very useful in predicting the functions of the new microRNAs whose function is yet to be known, since the function of the miRNAs heavily relies on its secondary structure.

The expressed sequence tags, derived from the developing tilapia brain, were established in our laboratory. An unique gene, high mobility group proteins 2 (HMG2), were investigated. HMG2 is a non-histone chromatin protein. HMG2 cloned from tilapia, Oreochromis mossambicus, is a gene with open reading frame 642bps, and deduced as 213 amino acid protein sequence. NCBI Conserved Domain search, the Gene Ontology, NEBcutter restrict enzyme analysis, NCBI blastx, and neighbor phylogenetic tree were used for the bioinformatic analysis. In the present study, the protein expression of HMG2 in the BL21 E.coli system, a prokaryotic system, and purified with 6X His Tag NI-NTA affinity chromatography.

Recently, the stochastic approximation Monte Carlo algorithm has been proposed by Liang et al. (2005) as a general-purpose stochastic optimization and simulation algorithm. An annealing version of this algorithm was developed for real small protein folding problems. The numerical results indicate that it outperforms simulated annealing and conventional Monte Carlo algorithms as a stochastic optimization algorithm. We also propose one method for the use of secondary structures in protein folding. The predicted protein structures are rather close to the true structures. Phylogenetic trees have been used in biology for a long time to graphically represent evolutionary relationships among species and genes. An understanding of evolutionary relationships is critical to appropriate interpretation of bioinformatics results. The use of the sequential structure of phylogenetic trees in conjunction with stochastic approximation Monte Carlo was developed for phylogenetic tree reconstruction. The numerical results indicate that it has a capability of escaping from local traps and achieving a much faster convergence to the global likelihood maxima than other phylogenetic tree reconstruction methods, such as BAMBE and MrBayes.

A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for the reconstruction of trees, it is crucial to understand the size and structure of neighbourhoods of trees under tree rearrangement operations. The diameter and size of the immediate neighbourhood of a tree has been well-studied, however little is known about the number of trees at distance two, three or (more generally) k from a given tree. In this thesis we explore previous results on the size of these neighbourhoods under common tree rearrangement operations (NNI, SPR and TBR). We obtain new results concerning the number of trees at distance k from a given tree under the Robinson-Foulds (RF) metric and the Nearest Neighbour Interchange (NNI) operation, and the number of trees at distance two from a given tree under the Subtree Prune and Regraft (SPR) operation. We also obtain an exact count for the number of pairs of binary phylogenetic trees that share a first RF or NNI neighbour.

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