The use of historical environmental monitoring data to test predictions on cross-scale ecological responses to alterations in river flows

Determination of ecological responses to river flows is fundamental to understanding how flow-dependent ecosystems have been altered by regulation, water diversions and climate change, and how to effect river restoration. Knowledge of ecohydrological relationships can support water management and policy, but this is not always the case. Management rules have tended to be developed ahead of scientific knowledge. The lag between practice and knowledge could be addressed by using historical monitoring data on ecological responses to changes in flows to determine significant empirical ecohydrological relationships, as an adjunct to investigating responses prospectively. This possibility was explored in the Murray–Darling Basin, Australia. We assessed 359 data sets collected during monitoring programs across the basin. Of these, only 32 (9%) were considered useful, based on a match between the scale at which sampling was done and ecological responses are likely to occur, and used to test flow–ecology predictions for phytoplankton, macroinvertebrates, fishes, waterbirds, floodplain trees, basin-scale vegetation and estuarine biota. We found relationships between flow and ecological responses were likely to be more strongly supported for large, long-lived, widespread biota (waterbirds, basin-scale vegetation, native fishes), than for more narrowly distributed (e.g. estuarine fishes) or smaller, short-lived organisms (e.g. phytoplankton, macroinvertebrates). This pattern is attributed to a mismatch between the design of monitoring programs and the response time frames of individual biota and processes, and to the use of local river discharge as a primary predictor variable when, for many biotic groups, other predictors need to be considered.     

Behavioural responses of an Australian colubrid snake (<Emphasis Type="Italic">Dendrelaphis punctulatus</Emphasis>) to a novel toxic prey item (the Cane Toad <Emphasis Type="Italic">Rhinella marina</Emphasis>)

The invasion of a toxic prey type can differentially affect closely related predator species. In Australia, the invasive Cane Toad (Rhinella marina) kills native anurophagous predators that cannot tolerate the toad’s toxins; but predators that are physiologically resistant (i.e., belong to lineages that entered Australia recently from Asia, where toads of other species are common) have been more resilient. In the current study, we examine the case of an Asian-derived predator lineage that relies on behavioural not physiological adaptations to deal with toads. Despite their Asian origins, Common Tree Snakes (Dendrelaphis punctulatus) are highly sensitive to toad toxins; yet this snake has not declined in abundance due to toads. We exposed captive (field-collected) snakes to toads of different sizes and ontogenetic stages, to quantify feeding responses and outcomes. Tree Snakes were less likely to attack toads than to attack native frogs, and rarely retained their hold on large toads. Tree Snakes ingested frogs of a wide range of body sizes but only ingested very small toads (<?1 g vs. up to 30 g for frogs). Behavioural responses were virtually identical between Tree Snakes from invaded versus yet-to-be-invaded areas, suggesting that preadaptation (from Asia) rather than adaptation (within Australia) is the key to successful utilisation of this novel but potentially toxic prey resource. Nonetheless, a previously-documented shift in relative head sizes of Tree Snakes coincident with toad invasion suggests that the ancestral behavioural tactic may have been reinforced by a recent morphological shift that further reduces maximal prey size, and hence the risk of fatal poisoning.     

Identification of usual interstitial pneumonia pattern using RNA-Seq and machine learning: challenges and solutions

Background

We developed a classifier using RNA sequencing data that identifies the usual interstitial pneumonia (UIP) pattern for the diagnosis of idiopathic pulmonary fibrosis. We addressed significant challenges, including limited sample size, biological and technical sample heterogeneity, and reagent and assay batch effects.

Results

We identified inter- and intra-patient heterogeneity, particularly within the non-UIP group. The models classified UIP on transbronchial biopsy samples with a receiver-operating characteristic area under the curve of ~?0.9 in cross-validation. Using in silico mixed samples in training, we prospectively defined a decision boundary to optimize specificity at ≥85%. The penalized logistic regression model showed greater reproducibility across technical replicates and was chosen as the final model. The final model showed sensitivity of 70% and specificity of 88% in the test set.

Conclusions

We demonstrated that the suggested methodologies appropriately addressed challenges of the sample size, disease heterogeneity and technical batch effects and developed a highly accurate and robust classifier leveraging RNA sequencing for the classification of UIP.

     

Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIα and IIβ

Etoposide is an anticancer drug that acts by inducing topoisomerase II-mediated DNA cleavage. Despite its wide use, etoposide is associated with some very serious side-effects including the development of treatment-related acute myelogenous leukemias. Etoposide targets both human topoisomerase IIα and IIβ. However, the contributions of the two enzyme isoforms to the therapeutic vs. leukemogenic properties of the drug are unclear. In order to develop an etoposide-based drug with specificity for cancer cells that express an active polyamine transport system, the sugar moiety of the drug has been replaced with a polyamine tail. To analyze the effects of this substitution on the specificity of hybrid molecules toward the two enzyme isoforms, we analyzed the activity of a series of etoposide-polyamine hybrids toward human topoisomerase IIα and IIβ. All of the compounds displayed an ability to induce enzyme-mediated DNA cleavage that was comparable to or higher than that of etoposide. Relative to the parent drug, the hybrid compounds displayed substantially higher activity toward topoisomerase IIβ than IIα. Modeling studies suggest that the enhanced specificity may result from interactions with Gln778 in topoisomerase IIβ. The corresponding residue in the α isoform is a methionine.     

Not the End of the World? Post-Classical Decline and Recovery in Rural Anatolia

Between the foundation of Constantinople as capital of the eastern half of the Roman Empire in 330 CE and its sack by the Fourth Crusade in 1204 CE, the Byzantine Empire underwent a full cycle from political-economic stability, through rural insecurity and agrarian decline, and back to renewed prosperity. These stages plausibly correspond to the phases of over-extension (K), subsequent release (Ω) and recovery (α) of the Adaptive Cycle in Socio-Ecological Systems. Here we track and partly quantify the consequences of those changes in different regions of Anatolia, firstly for rural settlement (via regional archaeological surveys) and secondly for land cover (via pollen analysis). We also examine the impact of climate changes on the agrarian system. While individual histories vary, the archaeological record shows a major demographic decline between ca .650 and ca. 900 CE in central and southwestern Anatolia, which was then a frontier zone between Byzantine and Arab armies. In these regions, and also in northwest Anatolia, century-scale trends in pollen indicate a substantial decline in the production of cereal and tree crops, and a smaller decline in pastoral activity. During the subsequent recovery (α) phase after 900 CE there was strong regional differentiation, with central Anatolia moving to a new economic system based on agro-pastoralism, while lowland areas of northern and western Anatolia returned to the cultivation of commercial crops such as olive trees. The extent of recovery in the agrarian economy was broadly predictable by the magnitude of its preceding decline, but the trajectories of recovery varied between different regions.     

Mean-field models for non-Markovian epidemics on networks

Journal of Mathematical Biology - This paper introduces a novel extension of the edge-based compartmental model to epidemics where the transmission and recovery processes are driven by general...     

Evidence for genetic allopolyploidy in <Emphasis Type="Italic">Eutrema edwardsii</Emphasis> (Brassicaceae): implications for conservation

Eutrema edwardsii R.Br. (Brassicaceae) is an arctic-alpine mustard with a circumpolar distribution. Its closest relative, Eutrema penlandii Rollins, is a federally listed, threatened species that is endemic to the Mosquito Range in the Southern Rocky Mountains of Colorado, USA. As part of a larger project addressing the systematics of this species complex in North America, we conducted chromosome counts, flow cytometry, and allozyme analysis to test the hypothesis that these taxa comprise an autopolyploid complex. Within that context, it should be noted that a chromosome count has not been reported previously for E. penlandii. Results obtained from mitotic counts obtained for two populations of E. penlandii reveal this taxon to be diploid. Diploidy was confirmed using flow cytometry for an additional 15 individuals representing four populations. Previously published chromosome counts for E. edwardsii reveal a polyploid complex of tetraploid, hexaploid, and octaploid populations for which an autopolyploid origin has been presumed. However, allozyme analysis revealed an allopolyploid origin for E. edwardsii, as evidenced from fixed heterozygosity at six loci. Although our data suggest that E. penlandii is a close relative of one of the progenitors of E. edwardsii, the taxonomic identity of the other progenitor(s) cannot be elucidated from these data. The data reported herein support the recognition of E. penlandii as taxonomically distinct, which has implications for conservation, and reveal cryptic variation within E. edwardsii.