Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis

Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3) that were isolated from blades of Porphyra umbilicalis (P.um.1). These three Operational Taxonomic Units (OTUs) belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators) and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes) or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases) that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase) and stress responses (e.g., efflux pump, amino acid transporter). Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.     

In Vivo,In Vitro,and In Silico Characterization of Peptoids as Antimicrobial Agents

Bacterial resistance to conventional antibiotics is a global threat that has spurred the development of antimicrobial peptides (AMPs) and their mimetics as novel anti-infective agents. While the bioavailability of AMPs is often reduced due to protease activity, the non-natural structure of AMP mimetics renders them robust to proteolytic degradation, thus offering a distinct advantage for their clinical application. We explore the therapeutic potential of N-substituted glycines, or peptoids, as AMP mimics using a multi-faceted approach that includes in silico, in vitro, and in vivo techniques. We report a new QSAR model that we developed based on 27 diverse peptoid sequences, which accurately correlates antimicrobial peptoid structure with antimicrobial activity. We have identified a number of peptoids that have potent, broad-spectrum in vitro activity against multi-drug resistant bacterial strains. Lastly, using a murine model of invasive S. aureus infection, we demonstrate that one of the best candidate peptoids at 4 mg/kg significantly reduces with a two-log order the bacterial counts compared with saline-treated controls. Taken together, our results demonstrate the promising therapeutic potential of peptoids as antimicrobial agents.     

An optimum estimator of body size to relate to behavioural and physiological parameters in field studies

Body size is an essential variable in many behavioural and physiological studies. Previous methods for body size estimation present two conflicting drawbacks. They either (1) consider variation in only one dimension through linear measurements or (2) they are time and resource consuming, hard to apply in field conditions and/or stressful to the animal. We present a method for estimating body size, an ellipsoid approximation, which requires simple linear measurements and incorporates variation in three dimensions. The method is tested on two species of teleost fish and one species of insect. The amount of variance in mass explained by the proposed method exceeds that of previous reported methods, including the most accurate ones, that usually require expensive digitising procedures and/or stressful handling.     

Diet and Dietary Preferences of the Southern Cassowary (Casuarius casuarius) in North Queensland, Australia

We investigated the diet of the southern cassowary (Casuarius casuarius) by identifying the seeds and fruits in fecal droppings encountered on a set of transects over 2 yr in upland rain forest in the wet tropics of North Queensland. A total of 198 droppings containing 56 plant species were found. We surveyed fleshy fruit availability over the subsequent 68 mo on transects in the same area to ascertain fruiting patterns in the study area. The number of droppings found each month did not correspond to the pattern of available fruit biomass. There was no relationship between the fruit traits of moisture content, flesh to seed mass ratio, color, or crop size to contribution of a species to the diet. During the lean fruiting season (May–July) cassowaries relied more on species that fruited continuously throughout the year as they were significantly over‐represented in droppings, while annual fruiting species were under‐represented. During months of high fruit availability (October–December), continuously fruiting species were still over‐represented in the diet but became less important while annual and biennial species became more important. Significantly more species with large fruit and large seeds appeared in the diet than expected and we confirm that the cassowary contributes to the continued dispersal of these species over long distances and in large quantities.     

Genetics of mating and sex determination in the parasitic nematode Haemonchus contortus

Genetic analysis of parasitic nematodes has been a neglected area of research and the basic genetics of this important group of pathogens are poorly understood. Haemonchus contortus is one of the most economically significant livestock parasites worldwide and is a key experimental model for the strongylid nematode group that includes many important human and animal pathogens. We have undertaken a study of the genetics and the mode of mating of this parasite using microsatellite markers. Inheritance studies with autosomal markers demonstrated obligate dioecious sexual reproduction and polyandrous mating that are reported here for the first time in a parasitic helminth and provide the parasite with a mechanism of increasing genetic diversity. The karyotype of the H. contortus, MHco3(ISE) isolate was determined as 2n = 11 or 12. We have developed a panel of microsatellite markers that are tightly linked on the X chromosome and have used them to determine the sex chromosomal karyotype as XO male and XX female. Haplotype analysis using the X-chromosomal markers also demonstrated polyandry, independent of the autosomal marker analysis, and enabled a more direct estimate of the number of male parental genotypes contributing to each brood. This work provides a basis for future forward genetic analysis on H. contortus and related parasitic nematodes.