The synaptonemal complex is assembled by a polySUMOylation-driven feedback mechanism in yeast

During meiotic prophase I, proteinaceous structures called synaptonemal complexes (SCs) connect homologous chromosomes along their lengths via polymeric arrays of transverse filaments (TFs). Thus, control of TF polymerization is central to SC formation. Using budding yeast, we show that efficiency of TF polymerization closely correlates with the extent of SUMO conjugation to Ecm11, a component of SCs. HyperSUMOylation of Ecm11 leads to highly aggregative TFs, causing frequent assembly of extrachromosomal structures. In contrast, hypoSUMOylation leads to discontinuous, fragmented SCs, indicative of defective TF polymerization. We further show that the N terminus of the yeast TF, Zip1, serves as an activator for Ecm11 SUMOylation. Coexpression of the Zip1 N terminus and Gmc2, a binding partner of Ecm11, is sufficient to induce robust polySUMOylation of Ecm11 in nonmeiotic cells. Because TF assembly is mediated through N-terminal head-to-head associations, our results suggest that mutual activation between TF assembly and Ecm11 polySUMOylation acts as a positive feedback loop that underpins SC assembly.     

Cameral membranes in prolecanitid and goniatitid ammonoids from the Permian Arcturus Formation, Nevada, USA

We describe cameral membranes in prolecanitid and goniatitid ammonoids from the Lower Permian Arcturus Formation, Nevada, USA. The membranes are preserved as phosphatic sheets and were originally composed of organic material such as conchiolin. Because the phragmocones are filled with micritic calcite, the cameral membranes can be exposed by etching with weak acetic acid. The membranes are associated with the siphuncle and also coat the septal faces and chamber walls. The siphuncular membranes are much more extensive in the prolecanitids than in the goniatites. These membranes appear in the prolecanitids at the beginning of the third whorl, corresponding to a shell diameter of 3-4 mm, and become more complex through ontogeny. Additional membranes, called transverse membranes, appear in some of the septal saddles on the ventrolateral side. The siphuncular membranes in prolecanitids are very similar to those in the Ceratitina plus Mesozoic Ammonoidea, suggesting that such membranes are widely distributed in this group. However, the origin and function of these membranes are unclear. We argue that the siphuncular membranes were sequentially secreted by the rear mantle during forward movement of the body and were not produced by desiccation of cameral liquid after the formation of the chambers. The most compelling arguments for this interpretation are the abrupt appearance of these membranes at a shell diameter of approximately 3-4 mm in prolecanitids, ceratites, and ammonitids, coincident with the end of the neanic stage, and the uniform increase in complexity of the membranes through ontogeny. The shape of the siphuncular membranes in prolecanitids suggests the presence of an invagination on the dorsal side of the siphuncle during part of the chamber formation cycle. Cameral membranes may have served a variety of functions including stabilizing the cameral liquid to reduce rocking motion during swimming, anchoring the siphuncle to the chamber wall, and facilitating cameral liquid removal, permitting a faster rate of growth.     

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.