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k-word matches, the number of words of length k shared between two sequences, also known as the D2 statistic, are used in alignment-free sequence comparison statistic. The advantages of the use of this statistic over alignment-based methods for nucleotide and amino-acid sequence comparisons are firstly that it does not assume that homologous segments are contiguous, and secondly that the algorithm is computationally extremely fast, the runtime being proportional to the size of the sequence under scrutiny. We summarise our results to date on determing the distributional properties of the D2 statistic for a range of biologically relevant parameters and outline the directions in which the research will proceed. PRIB 2008 proceedings found at: http://dx.doi.org/10.1007/978-3-540-88436-1 Contributors: Monash University. Faculty of Information Technology. Gippsland School of Information Technology ; Chetty, Madhu ; Ahmad, Shandar ; Ngom, Alioune ; Teng, Shyh Wei ; Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB) (3rd : 2008 : Melbourne, Australia) ; Coverage: Rights: Copyright by Third IAPR International Conference on Pattern Recognition in Bioinformatics. All rights reserved.

The phenotype of an animal cannot be explained entirely by its genes. It is now clear that factors other than the genome contribute to the ecology and evolution of animals. Two fundamentally important factors are the associated microbiota and epigenetic regulations. Unlike the genes and regulatory regions of the genome, epigenetics and microbial composition can be rapidly modified, and may thus represent mechanisms for rapid acclimation to a changing environment. At present, the individual functions of epigenetics, microbiomes, and genomic mutations are largely studied in isolation, particularly for species in marine ecosystems. This single variable approach leaves significant questions open for how these mechanisms intersect in the acclimation and adaptation of organisms in different environments. Here, we propose that the starlet sea anemone, Nematostella vectensis, is a model of choice to investigate the complex interplay between adaptation as well as physiological and molecular plasticity in coastal ecosystems. N. vectensis' geographic range spans four distinct coastlines, including a wide thermocline along the Atlantic coast of North America. N. vectensis is a particularly powerful invertebrate model for studying genome-environment interactions due to (1) the availability of a well-annotated genome, including preexisting data on genome methylation, histone modifications and miRNAs, (2) an extensive molecular toolkit including well-developed protocols for gene suppression and transgenesis, and (3) the simplicity of culture and experimentation in the laboratory. Taken together, N. vectensis has the tractability to connect the functional relationships between a host animal, microbes, and genome modifications to determine mechanisms underlying phenotypic plasticity and local adaptation.

Phylogenetic analysis of caspase domains identifed in A. millepora inferred by Maximum Likelihood method. PhyML 3.0 starting from a random tree was used to obtain ML trees under a concatenated model assuming the WAG + G + F (G = 1.523) amino acid substitution matrix model. The ML bootstrap proportion was obtained after 500 bootstraps replicates. Background colouring is as in Fig. 6. (PDF 361 kb)

Phylogenetic analysis of Bcl-2 proteins identifed in A. millepora inferred by the Maximum Likelihood method. PhyML 3.0 starting from a random tree was used to obtain ML trees under a concatenated model assuming the LG + G (G = 1.957) amino acid substitution matrix model. The ML bootstraps proportion was obtained after 1000 bootstrap replicates. (PDF 267 kb)

Plasmid constructs and immunoblot analyses of A. millepora Bcl-2 family proteins. (A) A schematic diagram of the EGFP-fused A. millepora Bcl-2 family proteins. Figures in parentheses are the number of amino acid residues in each construct. (B) Microscopic observation of transfected cells expressing EGFP and mCherry together with or without tX1Bid. Plasmid constructs pEGFP-C1 and pCAG-mCherry were co-transfected into HeLa cells either with pCS2-tX1Bid or control pCS2 empty vector. After 2 days of growth, cultures were washed to remove floating cells, and then fixed. The phase-contrast and both green and red fluorescent images of the remaining attached cells were captured for each field under the microscope. Scale bars represent 100 μm. (C, D) Immunoblot analysis of fusion proteins. Plasmids encoding each fusion protein were transiently transfected into HEK293T cells. In the case of EGFP/AmBax and EGFP/AmBokA proteins, the plasmid construct pCAG-FLAG/XlBclXL was cotransfected to prevent cell death. After culture for 2 days, transgene products were analyzed with control cell extracts by immunoblotting with appropriate antibodies. Arrowheads indicate the positions of immunoreactive proteins. Additional details of reagents and immunoblot analysis are provided as Additional file 8. Abbreviation: MWM, molecular weight marker. (PDF 2361 kb)

Similarity of caspase-X paralogs and immunoblot analysis of A. millepora caspase-X constructs. (A) Alignment of the caspase-X paralogs from A. millepora. The red underlined section is a typical caspase domain, with the catalytic residues (H and C) highlighted. The blue underlined section is an additional caspase-like domain, but lacking the catalytic residues (highlight indicates positions where the catalytic residues should be, based on the alignment). Numbering at left refers to residue position in the caspase-X sequence; note that, in the region shown, the caspase-X sequence (derived from cDNA clone D038-A5, GenBank:KR351289) differs at only one position (V266I) from the genomic prediction AmCaspase Xa. (B) Immunoblot analysis of FLAG/CaspX and its truncated form. Plasmids encoding intact or truncated forms of caspase-X with a FLAG-tag were transiently cotransfected into HEK293T cells together with the pCAG-p35 plasmid. After culture for 2 days, transgene products were analyzed with control cell extracts by immunoblotting with appropriate antibodies. The asterisk indicates a non-specific reaction. Abbreviation: MWM, molecular weight marker. (C) The assignments of α-helix and β-sheet secondary structure elements are based on a previous study [52]. Residues predicted to form H bonds between the two domains are indicated by asterisks. (PDF 1084 kb)