Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We introduce the NOISeq R-package for quality control and analysis of count data. We show how the available diagnostic tools can be used to monitor quality issues, make pre-processing decisions and improve analysis. We demonstrate that the non-parametric NOISeqBIO efficiently controls false discoveries in experiments with biological replication and outperforms state-of-the-art methods. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression.     

Regional differences in foraging behaviour of invasive green crab (<Emphasis Type="Italic">Carcinus maenas</Emphasis>) populations in Atlantic Canada

Invasive green crab populations initially established in Canada within the Bay of Fundy, New Brunswick in the 1950s and were present in all five Atlantic provinces by 2007. Genetic evidence suggests that the Atlantic Canadian populations originated from two separate introductions with differences in time of establishment among regions and possible population-level behavioural differences. In this study, we examine intraspecific foraging behaviour among crabs from different populations, and interspecific foraging behaviour between genetically similar crabs and juvenile lobsters. Both sets of foraging experiments involved competition for a limited food source over a 1-h period. In intraspecific match-ups, recent invaders from Newfoundland (NL) were significantly superior foragers than long-established invaders from Nova Scotia (NS) and New Brunswick (NB) populations; however, we found no differences between NL and Prince Edward Island (PE) invaders. Crabs from PE were better competitors than those from NS and NB, but these differences were not significant. Interspecific competition experiments indicated that the feeding behaviour of recent invaders (NL) and genetically similar, but long-established invaders (NS), differed in the presence of juvenile lobsters. Our study documents striking behavioural differences among populations of green crab from a small geographic region, which may reflect a combination of both genetic differences and time since establishment. These differences may result in varying impacts on newly invaded habitats.     

An Additional Baurusuchid from the Cretaceous of Brazil with Evidence of Interspecific Predation among Crocodyliformes

A new Baurusuchidae (Crocodyliformes, Mesoeucrocodylia), Aplestosuchus sordidus, is described based on a nearly complete skeleton collected in deposits of the Adamantina Formation (Bauru Group, Late Cretaceous) of Brazil. The nesting of the new taxon within Baurusuchidae can be ensured based on several exclusive skull features of this clade, such as the quadrate depression, medial approximation of the prefrontals, rostral extension of palatines (not reaching the level of the rostral margin of suborbital fenestrae), cylindrical dorsal portion of palatine bar, ridge on the ectopterygoid-jugal articulation, and supraoccipital with restricted thin transversal exposure in the caudalmost part of the skull roof. A newly proposed phylogeny of Baurusuchidae encompasses A. sordidus and recently described forms, suggesting its sixter-taxon relationship to Baurusuchus albertoi, within Baurusuchinae. Additionally, the remains of a sphagesaurid crocodyliform were preserved in the abdominal cavity of the new baurusuchid. Direct fossil evidence of behavioral interaction among fossil crocodyliforms is rare and mostly restricted to bite marks resulting from predation, as well as possible conspecific male-to-male aggression. This is the first time that a direct and unmistaken evidence of predation between different taxa of this group is recorded as fossils. This discovery confirms that baurusuchids were top predators of their time, with sphagesaurids occupying a lower trophic position, possibly with a more generalist diet.     

Erythrina mulungu Alkaloids Are Potent Inhibitors of Neuronal Nicotinic Receptor Currents in Mammalian Cells

Crude extracts and three isolated alkaloids from Erythrina mulungu plants have shown anxiolytic effects in different animal models. We investigated whether these alkaloids could affect nicotinic acetylcholine receptors and if they are selective for different central nervous system (CNS) subtypes. Screening experiments were performed using a single concentration of the alkaloid co-applied with acetylcholine in whole cell patch-clamp recordings in three different cell models: (i) PC12 cells natively expressing α3* nicotinic acetylcholine receptors; (ii) cultured hippocampal neurons natively expressing α7* nicotinic acetylcholine receptors; and (iii) HEK 293 cells heterologoulsy expressing α4β2 nicotinic acetylcholine receptors. For all three receptors, the percent inhibition of acetylcholine-activated currents by (+)-11á-hydroxyerysotrine was the lowest, whereas (+)-erythravine and (+)-11á-hydroxyerythravine inhibited the currents to a greater extent. For the latter two substances, we obtained concentration-response curves with a pre-application protocol for the α7* and α4β2 nicotinic acetylcholine receptors. The IC₅₀ obtained with (+)-erythravine and (+)-11á-hydroxyerythravine were 6 µM and 5 µM for the α7* receptors, and 13 nM and 4 nM for the α4β2 receptors, respectively. Our data suggest that these Erythrina alkaloids may exert their behavioral effects through inhibition of CNS nicotinic acetylcholine receptors, particularly the α4β2 subtype.     

Dispersal ability rather than ecological tolerance drives differences in range size between lentic and lotic water beetles (Coleoptera: Hydrophilidae)

Aim In aquatic ecosystems, standing (lentic) and running (lotic) waters differ fundamentally in their stability and persistence, shaping the comparative population genetic structure, geographical range size and speciation rates of lentic versus lotic lineages. While the drivers of this pattern remain incompletely understood, the suite of traits making up the ability of a species to establish new populations is instrumental in determining such differences. Here we explore the degree to which the association between habitat type and geographical range size results from differences in dispersal ability or fundamental niche breadth in the members of the Enochrus bicolor complex, an aquatic beetle clade with species across the lentic–lotic divide. Location Western Mediterranean, with a special focus on North Africa, the Iberian Peninsula and Sicily. Methods DNA sequences for four loci were obtained from species of the E. bicolor complex and analysed using phylogenetic inference. Dispersal and establishment abilities were assessed in lentic–lotic species pairs of the complex, using flight wing morphometrics and thermal tolerance ranges as surrogates, respectively. Results There were clear differences in range size between the lotic and lentic taxa of the complex, which appears to have had a lotic origin with two transitions to standing waters. Only small differences were observed in temperature tolerance and acclimation ability between the two lotic–lentic sister species studied. By contrast, wing morphometrics revealed clear, consistent differences between lotic and lentic Enochrus species pairs, the latter having a higher dispersal capacity. Main conclusions We hypothesize that there have been two habitat shifts from lotic to lentic waters, which have allowed marked expansions in geographical range size in western Mediterranean species of the E. bicolor complex. Differences in dispersal rather than in establishment ability appear to underlie differences in geographical range extent, as transitions to lentic waters were associated with changes in wing morphology, but not in thermal tolerance range. In this lineage of water beetles, selection for dispersal in geologically short‐lived lentic systems has driven the evolution of larger range sizes in lentic taxa compared with those of their lotic relatives.     

Can Wide Consultation Help with Setting Priorities for Large-Scale Biodiversity Monitoring Programs?

Climate and other global change phenomena affecting biodiversity require monitoring to track ecosystem changes and guide policy and management actions. Designing a biodiversity monitoring program is a difficult task that requires making decisions that often lack consensus due to budgetary constrains. As monitoring programs require long-term investment, they also require strong and continuing support from all interested parties. As such, stakeholder consultation is key to identify priorities and make sound design decisions that have as much support as possible. Here, we present the results of a consultation conducted to serve as an aid for designing a large-scale biodiversity monitoring program for the province of Québec (Canada). The consultation took the form of a survey with 13 discrete choices involving tradeoffs in respect to design priorities and 10 demographic questions (e.g., age, profession). The survey was sent to thousands of individuals having expected interests and knowledge about biodiversity and was completed by 621 participants. Overall, consensuses were few and it appeared difficult to create a design fulfilling the priorities of the majority. Most participants wanted 1) a monitoring design covering the entire territory and focusing on natural habitats; 2) a focus on species related to ecosystem services, on threatened and on invasive species. The only demographic characteristic that was related to the type of prioritization was the declared level of knowledge in biodiversity (null to high), but even then the influence was quite small.     

Neurocognitive Function in Acromegaly after Surgical Resection of GH-Secreting Adenoma versus Na?ve Acromegaly

Patients with active untreated acromegaly show mild to moderate neurocognitive disorders that are associated to chronic exposure to growth hormone (GH) and insulin-like growth factor (IGF-I) hypersecretion. However, it is unknown whether these disorders improve after controlling GH/IGF-I hypersecretion. The aim of this study was to compare neurocognitive functions of patients who successfully underwent GH-secreting adenoma transsphenoidal surgery (cured patients) with patients with naive acromegaly. In addition, we wanted to determine the impact of different clinical and biochemical variables on neurocognitive status in patients with active disease and after long-term cure. A battery of six standardized neuropsychological tests assessed attention, memory and executive functioning. In addition, a quantitative electroencephalography with Low-Resolution Electromagnetic Tomography (LORETA) solution was performed to obtain information about the neurophysiological state of the patients. Neurocognitive data was compared to that of a healthy control group. Multiple linear regression analysis was also conducted using clinical and hormonal parameters to obtain a set of independent predictors of neurocognitive state before and after cure. Both groups of patients scored significantly poorer than the healthy controls on memory tests, especially those assessing visual and verbal recall. Patients with cured acromegaly did not obtain better cognitive measures than naïve patients. Furthermore memory deficits were associated with decreased beta activity in left medial temporal cortex in both groups of patients. Regression analysis showed longer duration of untreated acromegaly was associated with more severe neurocognitive complications, regardless of the diagnostic group, whereas GH levels at the time of assessment was related to neurocognitive outcome only in naïve patients. Longer duration of post-operative biochemical remission of acromegaly was associated with better neurocognitive state. Overall, this data suggests that the effects of chronic exposure to GH/IGF-I hypersecretion could have long-term effects on brain functions.