DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair's skink (Leiolopisma telfairii)

Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration

Study of polytopic membrane protein topological organization as a function of membrane lipid composition.

A protocol is described using lipid mutants and thiol-specific chemical reagents to study lipid-dependent and host-specific membrane protein topogenesis by the substituted-cysteine accessibility method as applied to transmembrane domains (SCAM). SCAM is adapted to follow changes in membrane protein topology as a function of changes in membrane lipid composition. The strategy described can be adapted to any membrane system

A survey on feature weighting based K-Means algorithms

This is a pre-copyedited, author-produced PDF of an article accepted for publication in Journal of Classification [de Amorim, R. C., 'A survey on feature weighting based K-Means algorithms', Journal of Classification, Vol. 33(2): 210-242, August 25, 2016]. Subject to embargo. Embargo end date: 25 August 2017. The final publication is available at Springer via http://dx.doi.org/10.1007/s00357-016-9208-4 © Classification Society of North America 2016In a real-world data set there is always the possibility, rather high in our opinion, that different features may have different degrees of relevance. Most machine learning algorithms deal with this fact by either selecting or deselecting features in the data preprocessing phase. However, we maintain that even among relevant features there may be different degrees of relevance, and this should be taken into account during the clustering process. With over 50 years of history, K-Means is arguably the most popular partitional clustering algorithm there is. The first K-Means based clustering algorithm to compute feature weights was designed just over 30 years ago. Various such algorithms have been designed since but there has not been, to our knowledge, a survey integrating empirical evidence of cluster recovery ability, common flaws, and possible directions for future research. This paper elaborates on the concept of feature weighting and addresses these issues by critically analysing some of the most popular, or innovative, feature weighting mechanisms based in K-Means.Peer reviewedFinal Accepted Versio

Impacts of herbivory by ecological replacements on an island ecosystem

The use of ecological replacements (analogue species to replace extinct taxa) to restore ecosystem functioning is a promising conservation tool. However, this approach is controversial, in part due to a paucity of data on interactions between analogue species and established taxa in the ecosystem. We conducted ecological surveys, comprehensively DNA barcoded an ecosystem's flora and inferred the diet of the introduced Aldabra giant tortoise, acting as an ecological replacement, to understand how it might have modified island plant communities on a Mauritian islet. Through further dietary analyses, we investigated consequential effects on the threatened endemic Telfair's skink. Dietary overlap between tortoises and skinks was greater than expected by chance. However, there was a negative correlation between tortoise and skink preferences in herbivory and minimal overlap in the plants most frequently consumed by the reptiles. Changes in the plant community associated with 7 years of tortoise grazing were characterised by a decrease in the percentage cover of native herbs and creepers, and an increase in the cover of an invasive herb when compared to areas without tortoises. However, tortoise dietary preferences themselves did not directly drive changes in the plant community. Tortoises successfully dispersed the seeds of an endemic palm, which in time may increase the extent of unique palm-rich habitat. We found no evidence that tortoises have increased the extent of plant species hypothesised to be part of a lost Mauritian tortoise grazed community. Synthesis and applications. Due to a negative correlation in tortoise and skink dietary preferences and minimal overlap in the most frequently consumed taxa, the presence of tortoises is unlikely to have detrimental impacts on Telfair's skinks. Tortoise presence is likely to be beneficial to skinks in the long term by increasing the extent of palm-rich habitat. Although tortoises are likely to play a role in controlling invasive plants, they are not a panacea for this challenge. After 7 years, tortoises have not resurrected a lost tortoise grazed community that we hypothesise might have existed in limited areas on the islet, indicating that further interventions may be required to restore this plant community

Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase

Little is known about quality control of proteins that aberrantly or persistently engage the endoplasmic reticulum (ER)-localized translocon en route to membrane localization or the secretory pathway. Hrd1 and Doa10, the primary ubiquitin ligases that function in ER-associated degradation (ERAD) in yeast, target distinct subsets of misfolded or otherwise abnormal proteins based primarily on degradation signal (degron) location. We report the surprising observation that fusing Deg1, a cytoplasmic degron normally recognized by Doa10, to the Sec62 membrane protein rendered the protein a Hrd1 substrate. Hrd1-dependent degradation occurred when Deg1-Sec62 aberrantly engaged the Sec61 translocon channel and underwent topological rearrangement. Mutations that prevent translocon engagement caused a reversion to Doa10-dependent degradation. Similarly, a variant of apolipoprotein B, a protein known to be cotranslocationally targeted for proteasomal degradation, was also a Hrd1 substrate. Hrd1 therefore likely plays a general role in targeting proteins that persistently associate with and potentially obstruct the translocon

Acute escitalopram treatment inhibits REM sleep rebound and activation of MCH-expressing neurons in the lateral hypothalamus after long term selective REM sleep deprivation.

RATIONALE: Selective rapid eye movement sleep (REMS) deprivation using the platform-on-water ("flower pot") method causes sleep rebound with increased REMS, decreased REMS latency, and activation of the melanin-concentrating hormone (MCH) expressing neurons in the hypothalamus. MCH is implicated in the pathomechanism of depression regarding its influence on mood, feeding behavior, and REMS. OBJECTIVES: We investigated the effects of the most selective serotonin reuptake inhibitor escitalopram on sleep rebound following REMS deprivation and, in parallel, on the activation of MCH-containing neurons. METHODS: Escitalopram or vehicle (10 mg/kg, intraperitoneally) was administered to REMS-deprived (72 h) or home cage male Wistar rats. During the 3-h-long "rebound sleep", electroencephalography was recorded, followed by an MCH/Fos double immunohistochemistry. RESULTS: During REMS rebound, the time spent in REMS and the number of MCH/Fos double-labeled neurons in the lateral hypothalamus increased markedly, and REMS latency showed a significant decrease. All these effects of REMS deprivation were significantly attenuated by escitalopram treatment. Besides the REMS-suppressing effects, escitalopram caused an increase in amount of and decrease in latency of slow wave sleep during the rebound. CONCLUSIONS: These results show that despite the high REMS pressure caused by REMS deprivation procedure, escitalopram has the ability to suppress REMS rebound, as well as to diminish the activation of MCH-containing neurons, in parallel. Escitalopram caused a shift from REMS to slow wave sleep during the rebound. Furthermore, these data point to the potential connection between the serotonergic system and MCH in sleep regulation, which can be relevant in depression and in other mood disorders

Compartment-Restricted Biotinylation Reveals Novel Features of Prion Protein Metabolism in Vivo

A selective tagging method for detecting minor alternatively-localized populations of a protein is used to study a disease-associated transmembrane form of prion protein. The analysis reveals key features of transmembrane prion protein metabolism and one way this is altered by human disease-causing mutants

Destabilization of light NREM sleep by thalamic PLC beta 4 deletion impairs sleep-dependent memory consolidation

Sleep abnormality often accompanies the impairment of cognitive function. Both rapid eye movement (REM) and non-REM (NREM) sleep have associated with improved memory performance. However, the role of composition in NREM sleep, consisting of light and deep NREM, for memory formation is not fully understood. We investigated how the dynamics of NREM sleep states influence memory consolidation. Thalamocortical (TC) neuron-specific phospholipase C beta 4 (PLC beta 4) knockout (KO) increased the total duration of NREM sleep, consisting of destabilized light NREM and stabilized deep NREM. Surprisingly, the longer NREM sleep did not improve memory consolidation but rather impaired it in TC-specific PLC beta 4 KO mice. Memory function was positively correlated with the stability of light NREM and spindle activity occurring in maintained light NREM period. Our study suggests that a single molecule, PLC beta 4, in TC neurons is critical for tuning the NREM sleep states and thus affects sleep-dependent memory formation