Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes

The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.This work has been supported by Australian Research Council grants to MJP (DP07745015) and MB (FT0991741). The website for the funder is www.arc.gov.au. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Stochastic Simulation of Process Calculi for Biology

Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot rely on standard reaction-based simulation methods, which require fixed numbers of species and reactions. Rather than implementing custom stochastic simulation algorithms for each process calculus, we propose to use a generic abstract machine that can be instantiated to a range of process calculi and a range of reaction-based simulation algorithms. The abstract machine functions as a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. In this short paper we give a brief summary of the generic abstract machine, and show how it can be instantiated with the stochastic simulation algorithm known as Gillespie's Direct Method. We also discuss the wider implications of such an abstract machine, and outline how it can be used to simulate multiple calculi simultaneously within a common framework.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Geometric Entropy for Lead vs Top-Rope Rock Climbing

International Journal of Exercise Science 9(2): 168-174, 2016. The complexity of movement of a rock climber’s center of mass during an ascent has been described as geometric entropy (GE). It has been proposed that lower geometric entropy could represent more fluid and economical movement during climbing. The purpose of the present study was to measure GE during rock climbing ascents under a lead condition (LD), where the climber connects a safety rope to several intermediate anchors during the ascent and under a top-rope condition (TR), where the safety rope is always anchored above the climber. Six experienced rock climbers volunteered to participate in the study. Each participant ascended a route on natural rock outdoors under three conditions. The first ascent was performed in a top-rope condition as an accommodation trial. The two remaining ascents were performed as LD and top-rope (TR2) in random order. Each LD and TR2 ascent was recorded via digital video at 30 Hz. A single point at the back center of each climber’s waist harness was manually digitized from the video images at 6 Hz and interpreted as the climber’s center of mass (CM). The displacement of CM was expressed as the line of motion (LM). Geometric Entropy (GE) was calculated as GE = ln((2∙LM)/CH)), where CH was the value of the convex hull about the LM. A within subjects, repeated measures ANOVA with Bonferroni post hoc testing was utilized to test for differences among ascent conditions with significance set at P \u3c0.05. Mean (±s.d) values for LM and GE were 81.5±11.3 m vs 77.6±7.3 m and 1.021±0.133 vs 0.924±0.062 for LD and TR2 respectively. There were no significant differences for LM and GE between ascent conditions. It was concluded that LM and GE do not vary between LD and TR ascent conditions

Pre-clinical evaluation of a novel chloroethylating agent, Clomesone.

The in vitro activity of the novel chloroethylating agent, Clomesone, was investigated in a panel of established murine and human tumour cell lines. In vivo anti-tumour activity was examined against three transplantable adenocarcinomas of the mouse colon and in vivo bone marrow toxicity was assessed using a spleen colony forming unit assay. The pharmacokinetic behaviour of the drug in vivo and drug stability in vitro was analysed by gas chromatography with electron capture detection. Clomesone exhibited no activity in vitro against the majority of cell lines derived from solid human colorectal carcinomas. Anti-tumour activity against the murine tumours in vivo was not impressive and was accompanied by myelosuppression. Pharmacokinetic data suggested that the lack of in vivo activity was due to the failure to achieve effective anti-neoplastic drug concentrations at the tumour site. It was concluded that this study found no evidence to suggest that Clomesone was toxicologically more selective than the chloroethylnitrosoureas

A 275–425-GHz Tunerless Waveguide Receiver Based on AlN-Barrier SIS Technology

We report on a 275–425-GHz tunerless waveguide receiver with a 3.5–8-GHz IF. As the mixing element, we employ a high-current-density Nb–AlN–Nb superconducting–insulating– superconducting (SIS) tunnel junction. Thanks to the combined use of AlN-barrier SIS technology and a broad bandwidth waveguide to thin-film microstrip transition, we are able to achieve an unprecedented 43% instantaneous bandwidth, limited by the receiver's corrugated feedhorn. The measured double-sideband (DSB) receiver noise temperature, uncorrected for optics loss, ranges from 55 K at 275 GHz, 48 K at 345 GHz, to 72 K at 425 GHz. In this frequency range, the mixer has a DSB conversion loss of 2.3 1 dB. The intrinsic mixer noise is found to vary between 17–19 K, of which 9 K is attributed to shot noise associated with leakage current below the gap. To improve reliability, the IF circuit and bias injection are entirely planar by design. The instrument was successfully installed at the Caltech Submillimeter Observatory (CSO), Mauna Kea, HI, in October 2006

Social competence in pediatric brain tumor survivors: application of a model from social neuroscience and developmental psychology.

Pediatric brain tumor (BT) survivors are at risk for psychosocial late effects across many domains of functioning, including neurocognitive and social. The literature on the social competence of pediatric BT survivors is still developing and future research is needed that integrates developmental and cognitive neuroscience research methodologies to identify predictors of survivor social adjustment and interventions to ameliorate problems. This review discusses the current literature on survivor social functioning through a model of social competence in childhood brain disorder and suggests future directions based on this model. Interventions pursuing change in survivor social adjustment should consider targeting social ecological factors

Global and Local Conformation of Human IgG Antibody Variants Rationalizes Loss of Thermodynamic Stability.

Immunoglobulin G (IgG) monoclonal antibodies (mAbs) are a major class of medicines, with high specificity and affinity towards targets spanning many disease areas. The antibody Fc (fragment crystallizable) region is a vital component of existing antibody therapeutics, as well as many next generation biologic medicines. Thermodynamic stability is a critical property for the development of stable and effective therapeutic proteins. Herein, a combination of ion-mobility mass spectrometry (IM-MS) and hydrogen/deuterium exchange mass spectrometry (HDX-MS) approaches have been used to inform on the global and local conformation and dynamics of engineered IgG Fc variants with reduced thermodynamic stability. The changes in conformation and dynamics have been correlated with their thermodynamic stability to better understand the destabilising effect of functional IgG Fc mutations and to inform engineering of future therapeutic proteins.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/anie.20150722