Automated categorisation of patent claims that reference human genome sequences

Debates on gene patents have necessitated the analysis of patents that disclose and reference human sequences. In this study, we built an automated classifier that assigns sequences to one of nine predefined categories according to their functional roles in patent claims by applying natural language processing and supervised learning techniques. To improve its correctness, we experimented with various feature mappings, resulting in the maximal accuracy of 79%.

Mapping the regulatory sequences controlling 93 breast cancer-associated miRNA genes leads to the identification of two functional promoters of the Hsa-mir-200b cluster, methylation of which is associated with metastasis or hormone receptor status in advanced breast cancer

MicroRNAs (miRNAs) are small non-coding RNAs of 20 nt in length that are capable of modulating gene expression post-transcriptionally. Although miRNAs have been implicated in cancer, including breast cancer, the regulation of miRNA transcription and the role of defects in this process in cancer is not well understood. In this study we have mapped the promoters of 93 breast cancer-associated miRNAs, and then looked for associations between DNA methylation of 15 of these promoters and miRNA expression in breast cancer cells. The miRNA promoters with clearest association between DNA methylation and expression included a previously described and a novel promoter of the Hsa-mir-200b cluster. The novel promoter of the Hsa-mir-200b cluster, denoted P2, is located 2 kb upstream of the 5′ stemloop and maps within a CpG island. P2 has comparable promoter activity to the previously reported promoter (P1), and is able to drive the expression of miR-200b in its endogenous genomic context. DNA methylation of both P1 and P2 was inversely associated with miR-200b expression in eight out of nine breast cancer cell lines, and in vitro methylation of both promoters repressed their activity in reporter assays. In clinical samples, P1 and P2 were differentially methylated with methylation inversely associated with miR-200b expression. P1 was hypermethylated in metastatic lymph nodes compared with matched primary breast tumours whereas P2 hypermethylation was associated with loss of either oestrogen receptor or progesterone receptor. Hypomethylation of P2 was associated with gain of HER2 and androgen receptor expression. These data suggest an association between miR-200b regulation and breast cancer subtype and a potential use of DNA methylation of miRNA promoters as a component of a suite of breast cancer biomarkers.

Draft genome and plasmid sequences of Chlamydia pneumoniae strain B21 from an Australian endangered marsupial, the western barred bandicoot

Chlamydia pneumoniae is a ubiquitous intracellular pathogen, first associated with human respiratory disease and subsequently detected in a range of mammals, amphibians, and reptiles. Here we report the draft genome sequence for strain B21 of C. pneumoniae, isolated from the endangered Australian marsupial the western barred bandicoot.

Public disclosure of biological sequences in global patent practice

Biological sequences are an important part of global patenting, with unique challenges for their effective and equitable use in practice and in policy. Because their function can only be determined with computer-aided technology, the form in which sequences are disclosed matters greatly. Similarly, the scope of patent rights sought and granted requires computer readable data and tools for comparison. Critically, the primary data provided to the national patent offices and thence to the public, must be comprehensive, standardized, timely and meaningful. It is not yet. The proposed global Patent Sequence (PatSeq) Data platform can enable national and regional jurisdictions meet the desired standards.

DNA sequences and austral taxa indicate generic synonymy of Paratrichocladius Santos-Abreu with Cricotopus Wulp (Diptera: Chironomidae)

In the century since the description of the orthoclad genus Paratrichocladius Santos-Abreu (Diptera: Chironomidae), separation in any life stage from the cosmopolitan, diverse Cricotopus Wulp has been problematic. Molecular analysis reveals the presence of two species in Australia that conform in morphology to Paratrichocladius and which form a well-supported clade including Paratrichocladius micans (Kieffer) from Africa and a distinct southern African larva. This clade clusters with taxa allied with Cricotopus albitibia (Walker), in turn nested within all other sampled Australian Cricotopus. Relevant nodes strongly support Cricotopus as nonmonophyletic without inclusion of Paratrichocladius. We synonymize Paratrichocladius with Cricotopus syn.n, treating Paratrichocladius as a subgenus. Cricotopus (Paratrichocladius) australiensis Cranston sp.n. is described for Trichocladius pluriserialis Freeman from Australia, which is not the same species under that name in New Zealand. Cricotopus (Paratrichocladius) bifenestrus Cranston sp.n. from Australia is described, also in all life stages. The many new combinations, listed in an Appendix, include three replacement names for new secondary homonyms, namely: Cricotopus (Paratrichocladius) sinobicinctus Cranston & Krosch nom.n. for Paratrichocladius bicinctus Fu, Sæther & Wang, Cricotopus draysoni Cranston & Krosch nom.n. for Cricotopus brevicornis Drayson, Krosch & Cranston, and Cricotopus (Paratrichocladius) sikhotealinus Makarchenko & Makarchenko nom.n. for Cricotopus orientalis Kieffer. We conclude with comments on wider issues in the taxonomy of Paratrichocladius, especially concerning New Zealand species.

Human action recognition from video sequences

This PhD research has proposed new machine learning techniques to improve human action recognition based on local features. Several novel video representation and classification techniques have been proposed to increase the performance with lower computational complexity. The major contributions are the construction of new feature representation techniques, based on advanced machine learning techniques such as multiple instance dictionary learning, Latent Dirichlet Allocation (LDA) and Sparse coding. A Binary-tree based classification technique was also proposed to deal with large amounts of action categories. These techniques are not only improving the classification accuracy with constrained computational resources but are also robust to challenging environmental conditions. These developed techniques can be easily extended to a wide range of video applications to provide near real-time performance.

Complete genome sequences of seven Helicoverpa armigera SNPV-AC53-derived strains

Wild-type baculovirus isolates typically consist of multiple strains. We report the full genome sequences of seven alphabaculovirus strains derived by passage through tissue culture from Helicoverpa armigera SNPV-AC53 (KJ909666).