Taxonomy and redescription of the Fawn Antechinus, Antechinus bellus (Thomas) (Marsupialia: Dasyuridae)

We provide a taxonomic redescription of the Fawn Antechinus, Antechinus bellus (Thomas). A. bellus is the only member of its genus to occur in Australia’s Northern Territory, where it can be found in savannah woodlands of the Top End. It is perhaps the most distinctive antechinus, and clearly distinguishable from the other 10 extant species of antechinus found in Australia: externally, A. bellus has pale body fur, white feet and large ears; A. bellus skulls have large auditory bullae and narrow interorbital width, while broadening abruptly at the molar row; mitochondrial and nuclear genes clearly dis-tinguish A. bellus from all congeners, phylogenetically positioning the Fawn Antechinus as sister to Queensland’s A. leo Van Dyck, 1980, with which it shares a curled supratragus of the external ear and a similar tropical latitudinal range.

Taxonomy and redescription of the Yellow-footed Antechinus, Antechinus flavipes (Waterhouse) (Marsupialia: Dasyuridae)

We provide a taxonomic redescription of the ubiquitous and variable dasyurid marsupial Yellow-footed Antechinus, Antechinus flavipes (Waterhouse), which comprises three currently recognized subspecies whose combined geographic distribution spans almost the length and breadth of Australia. A. flavipes leucogaster Gray is confined to south-west Western Australia; A. flavipes flavipes is distributed in south-eastern Australia across four states—South Australia, Victoria, New South Wales and Queensland; A. flavipes rubeculus Van Dyck is confined to the wet tropics of Queensland. A. flavipes is readily distinguished from all extant congeners based on external morphology by the following combination of features: a grey head; orange-yellow toned flanks/rump, feet and tail base; pale eye-rings and a darkened tail tip. A. flavipes skulls are stout, being broad at the level of the rear upper molars, have small palatal vacuities and small entoconid cusps on the lower molars. However, notable differences among subspecies of A. flavipesprevent any obvious collection of skull characters being diagnostic for species-level discrimination among congeners. A. flavipes rubeculus is the largest of the three subspecies of Yellow-footed Antechinus and most similar in skull morphology to A. leo, A. bellus and A. godmani—all four species are geographically limited to tropical Australia. A. f. rubeculus is notably larger in many characters than its conspecifics: A. f. flavipes, the next largest, and A. f. leucogaster, the smallest of the group. A. f. flavipes and A. f. leucogaster diverge significantly at only a few skull characters, and both subspecies have cranial morphological affinities with the recently discovered A. mysticus, most notably A. f. leucogaster. Phylogenies generated from mt- and nDNA data strongly support Antechinus flavipes as monophyletic with respect to other members of the genus; within A. flavipes, each of the three recognized subspecies form distinctive monophyletic clades.

Eph receptors and their ligands : promising molecular biomarkers and therapeutic targets in prostate cancer

Although at present, there is a high incidence of prostate cancer, particularly in the Western world, mortality from this disease is declining and occurs primarily only from clinically significant late stage tumors with a poor prognosis. A major current focus of this field is the identification of new biomarkers which can detect earlier, and more effectively, clinically significant tumors from those deemed “low risk”, as well as predict the prognostic course of a particular cancer. This strategy can in turn offer novel avenues for targeted therapies. The large family of Receptor Tyrosine Kinases, the Ephs, and their binding partners, the ephrins, has been implicated in many cancers of epithelial origin through stimulation of oncogenic transformation, tumor angiogenesis, and promotion of increased cell survival, invasion and migration. They also show promise as both biomarkers of diagnostic and prognostic value and as targeted therapies in cancer. This review will briefly discuss the complex roles and biological mechanisms of action of these receptors and ligands and, with regard to prostate cancer, highlight their potential as biomarkers for both diagnosis and prognosis, their application as imaging agents, and current approaches to assessing them as therapeutic targets. This review demonstrates the need for future studies into those particular family members that will prove helpful in understanding the biology and potential as targets for treatment of prostate cancer.

Taxonomy and redescription of the Atherton Antechinus, Antechinus godmani (Thomas) (Marsupialia: Dasyuridae)

We provide a taxonomic redescription of the dasyurid marsupial Atherton Antechinus, Antechinus godmani (Thomas). A. godmani is only rarely encountered and limited to wet tropical rainforests of north-east Queensland, Australia, between the towns of Cardwell and Cairns (a distribution spanning 135 kilometres from north to south). The distinctive species occurs at altitudes of over 600 meters asl, in all major rainforest types, and can be found with both the northern subspecies of the Yellow-footed Antechinus, A. flavipes rubeculus Van Dyck and the Rusty Antechinus, A. adustus (Thomas). A. god-mani is clearly separated from all congeners on the basis of both morphometrics and genetics. A. godmani can be distin-guished from all extant congeners based on external morphology by a combination of large size, naked-looking tail and reddish fur on the face and head. A. godmani skulls are characteristically large, with a suite of long features: basicranium, palate, upper premolar tooth row, inter-palatal vacuity distance and dentary. Phylogenies generated from mt- and nDNA data position Antechinus godmani as monophyletic with respect to other members of the genus; A. godmani is strongly supported as the sister-group to a clade containing all other antechinus, but excluding the south-east Australian Dusky An-techinus, A. swainsonii (Waterhouse) and Swamp Antechinus, A. minimus (Geoffroy). Antechinus godmani are genetically very divergent compared to all congeners (mtDNA: range 12.9–16.3%).

Product feature taxonomy learning based on user reviews

In recent years, the Web 2.0 has provided considerable facilities for people to create, share and exchange information and ideas. Upon this, the user generated content, such as reviews, has exploded. Such data provide a rich source to exploit in order to identify the information associated with specific reviewed items. Opinion mining has been widely used to identify the significant features of items (e.g., cameras) based upon user reviews. Feature extraction is the most critical step to identify useful information from texts. Most existing approaches only find individual features about a product without revealing the structural relationships between the features which usually exist. In this paper, we propose an approach to extract features and feature relationships, represented as a tree structure called feature taxonomy, based on frequent patterns and associations between patterns derived from user reviews. The generated feature taxonomy profiles the product at multiple levels and provides more detailed information about the product. Our experiment results based on some popularly used review datasets show that our proposed approach is able to capture the product features and relations effectively.

Tensile properties of graphene nanotube hybrid structures : a molecular dynamics study

Graphene has been reported with record-breaking properties which have opened up huge potential applications. A considerable research has been devoted to manipulate or modify the properties of graphene to target a more smart nanoscale device. Graphene and carbon nanotube hybrid structure (GNHS) is one of the promising graphene derivates, while their mechanical properties have been rarely discussed in literature. Therefore, such a studied is conducted in this paper basing on the large-scale molecular dynamics simulation. The target GNHS is constructed by considering two separate graphene layers that being connected by single-wall carbon nanotubes (SWCNTs) according to the experimental observations. It is found that the GNHSs exhibit a much lower yield strength, Young’s modulus, and earlier yielding comparing with a bilayer graphene sheet. Fracture of studied GNHSs is found to fracture located at the connecting region between carbon nanotubes (CNTs) and graphene. After failure, monatomic chains are normally observed at the front of the failure region, and the two graphene layers at the failure region without connecting CNTs will adhere to each other, generating a bilayer graphene sheet scheme (with a layer distance about 3.4 Å). This study will enrich the current understanding of the mechanical performance of GNHS, which will guide the design of GNHS and shed lights on its various applications.

Strategies and challenges for systematically mapping biologically significant molecular pathways regulating carcinoma epithelial-mesenchymal transition

Enormous progress has been made towards understanding the role of specific factors in the process of epithelial-mesenchymal transition (EMT); however, the complex underlying pathways and the transient nature of the transition continues to present significant challenges. Targeting tumour cell plasticity underpinning EMT is an attractive strategy to combat metastasis. Global gene expression profiling and high-content analyses are among the strategies employed to identify novel EMT regulators. In this review, we highlight several approaches to systematically interrogate key pathways involved in EMT, with particular emphasis on the features of multiparametric, high-content imaging screening strategies that lend themselves to the systematic discovery of highly significant modulators of tumour cell plasticity.

Molecular mechanisms of cisplatin resistance in lung cancer

Cisplatin is one of the most potent anticancer agents, displaying significant clinical activity against a variety of solid tumours. To date, cisplatin-based combination treatment remains the most effective systemic chemotherapy for non-small cell lung cancer (NSCLC) patients. Unfortunately, the outcome of cisplatin therapy in NSCLC has reached a plateau due to the development of both intrinsic and acquired resistance that have become a major obstacle in the use of cisplatin in the clinical setting. The molecular mechanisms that underlie chemoresistance are largely unknown. Mechanisms of acquired resistance to cisplatin include reduced intracellular accumulation of the drug, enhanced drug inactivation by metallothionine and glutathione, increased repair activity of DNA damage, and altered expression of oncogenes and regulatory proteins. Cisplatin-induced cytotoxicity is mediated through the induction of apoptosis and cell cycle arrest as a result of cisplatin-DNA adduct formation, which in turn, activates multiple signaling pathways and mediators. These include p53, Bcl-2 family, caspases, cyclins, CDKs, MAPK and PI3K/Akt. Increased expression of anti-apoptotic genes and mutations in the intrinsic apoptotic pathway may also contribute to the inability of cells to detect DNA damage or to induce apoptosis. This chapter will provide an insight into the mechanisms involved in cisplatin resistance and a better understanding of the molecular basis of the cellular response to cisplatin-based chemotherapy in lung cancer.

Molecular characterization of "Candidatus Parilichlamydia carangidicola," a novel Chlamydia-like epitheliocystis agent in yellowtail kingfish, Seriola lalandi (Valenciennes), and the proposal of a new family, "Candidatus Parilichlamydiaceae" fam. nov. (order Chlamydiales).

Three cohorts of farmed yellowtail kingfish (Seriola lalandi) from South Australia were examined for Chlamydia-like organisms associated with epitheliocystis. To characterize the bacteria, 38 gill samples were processed for histopathology, electron microscopy, and 16S rRNA amplification, sequencing, and phylogenetic analysis. Microscopically, the presence of membrane-enclosed cysts was observed within the gill lamellae. Also observed was hyperplasia of the epithelial cells with cytoplasmic vacuolization and fusion of the gill lamellae. Transmission electron microscopy revealed morphological features of the reticulate and intermediate bodies typical of members of the order Chlamydiales. A novel 1,393-bp 16S chlamydial rRNA sequence was amplified from gill DNA extracted from fish in all cohorts over a 3-year period that corresponded to the 16S rRNA sequence amplified directly from laser-dissected cysts. This sequence was only 87% similar to the reported "Candidatus Piscichlamydia salmonis" (AY462244) from Atlantic salmon and Arctic charr. Phylogenetic analysis of this sequence against 35 Chlamydia and Chlamydia-like bacteria revealed that this novel bacterium belongs to an undescribed family lineage in the order Chlamydiales. Based on these observations, we propose this bacterium of yellowtail kingfish be known as "Candidatus Parilichlamydia carangidicola" and that the new family be known as "Candidatus Parilichlamydiaceae."

Molecular characterization of "Candidatus Similichlamydia latridicola" gen. nov., sp. nov. (Chlamydiales: "Candidatus Parilichlamydiaceae"), a novel Chlamydia-like epitheliocystis agent in the striped trumpeter, Latris lineata (Forster)

Histological analysis of gill samples taken from individuals of Latris lineata reared in aquaculture in Tasmania, Australia, and those sampled from the wild revealed the presence of epitheliocystis-like basophilic inclusions. Subsequent morphological, in situ hybridization, and molecular analyses were performed to confirm the presence of this disease and discovered a Chlamydia-like organism associated with this condition, and the criteria set by Fredericks and Relman's postulates were used to establish disease causation. Three distinct 16S rRNA genotypes were sequenced from 16 fish, and phylogenetic analyses of the nearly full-length 16S rRNA sequences generated for this bacterial agent indicated that they were nearly identical novel members of the order Chlamydiales. This new taxon formed a well-supported clade with "Candidatus Parilichlamydia carangidicola" from the yellowtail kingfish (Seriola lalandi). On the basis of sequence divergence over the 16S rRNA region relative to all other members of the order Chlamydiales, a new genus and species are proposed here for the Chlamydia-like bacterium from L. lineata, i.e., "Candidatus Similichlamydia latridicola" gen. nov., sp. nov.

Multilocus sequence analysis provides insights into molecular epidemiology of Chlamydia pecorum infections in Australian sheep, cattle and koalas

Chlamydia pecorum is a significant pathogen of domestic livestock and wildlife. We have developed a C. pecorum-specific multilocus sequence analysis (MLSA) scheme to examine the genetic diversity of and relationships between Australian sheep, cattle, and koala isolates. An MLSA of seven concatenated housekeeping gene fragments was performed using 35 isolates, including 18 livestock isolates (11 Australian sheep, one Australian cow, and six U.S. livestock isolates) and 17 Australian koala isolates. Phylogenetic analyses showed that the koala isolates formed a distinct clade, with limited clustering with C. pecorum isolates from Australian sheep. We identified 11 MLSA sequence types (STs) among Australian C. pecorum isolates, 10 of them novel, with koala and sheep sharing at least one identical ST (designated ST2013Aa). ST23, previously identified in global C. pecorum livestock isolates, was observed here in a subset of Australian bovine and sheep isolates. Most notably, ST23 was found in association with multiple disease states and hosts, providing insights into the transmission of this pathogen between livestock hosts. The complexity of the epidemiology of this disease was further highlighted by the observation that at least two examples of sheep were infected with different C. pecorum STs in the eyes and gastrointestinal tract. We have demonstrated the feasibility of our MLSA scheme for understanding the host relationship that exists between Australian C. pecorum strains and provide the first molecular epidemiological data on infections in Australian livestock hosts.

Improved molecular tools for sugar cane biotechnology

Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology.

Structures of life : the role of molecular structures in scientists' work

The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions and to better understand cellular processes. Combining results from two field studies, we explore the role of molecular structures in life scientists’ current work from a humanfactors perspective. Our main conclusion is that different representations of molecular structures, due to their visual nature, are important for supporting collaboration, constructing new knowledge and supporting scientists’ professional activities in general.