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Background The enzymatic conversion of plant biomass has been recently revolutionized by the discovery of lytic polysaccharide monooxygenases (LPMO) that catalyze oxidative cleavage of polysaccharides. These powerful enzymes are secreted by a large number of fungal saprotrophs and are important components of commercial enzyme cocktails used for industrial biomass conversion. Among the 33 AA9 LPMOs encoded by the genome of Podospora anserina, the PaLPMO9H enzyme catalyzes mixed C1/C4 oxidative cleavage of cellulose and cello-oligosaccharides. Activity of PaLPMO9H on several hemicelluloses has been suggested, but the regioselectivity of the cleavage remained to be determined. Results In this study, we investigated the activity of PaLPMO9H on mixed-linkage glucans, xyloglucan and glucomannan using tandem mass spectrometry and ion mobility-mass spectrometry. Structural analysis of the released products revealed that PaLPMO9H catalyzes C4 oxidative cleavage of mixed-linkage glucans and mixed C1/C4 oxidative cleavage of glucomannan and xyloglucan. Gem-diols and ketones were produced at the non-reducing end, while aldonic acids were produced at the reducing extremity of the products. Conclusion The ability of PaLPMO9H to target polysaccharides, differing from cellulose by their linkages, glycosidic composition and/or presence of sidechains, could be advantageous for this coprophilous fungus when catabolizing highly variable polysaccharides and for the development of optimized enzyme cocktails in biorefineries.

1. Energy expenditure is an important component of foraging ecology, but is extremely difficultto estimate in free-ranging animals and depends on how animals partition their timebetween different activities during foraging. Acceleration data have emerged as a new way todetermine energy expenditure at a fine scale but this needs to be tested and validated in wildanimals.2. This study investigated whether vectorial dynamic body acceleration (VeDBA) could accuratelypredict the energy expended by marine predators during a full foraging trip. We alsoaimed to determine whether the accuracy of predictions of energy expenditure derived fromacceleration increased when partitioned by different types of at-sea activities (i.e. diving, transiting,resting and surface activities).3. To do so, we equipped 20 lactating northern (Callorhinus ursinus) and 20 lactating Antarcticfur seals (Arctocephalus gazella) with GPS, time-depth recorders and tri-axial accelerometersand obtained estimates of field metabolic rates using the doubly labelled water (DLW)method. VeDBA was derived from tri-axial acceleration, and at-sea activities (diving, transiting,resting and surface activities) were determined using dive depth, tri-axial acceleration andtravelling speed.4. We found that VeDBA did not accurately predict the total energy expended by fur sealsduring their full foraging trips (R2 = 036). However, the accuracy of VeDBA as a predictorof total energy expenditure increased significantly when foraging trips were partitioned byactivity and when activity-specific VeDBA was paired with time-activity budgets (R2 = 070).Activity-specific VeDBA also accurately predicted the energy expenditures of each activityindependent of each other (R2 > 085).5. Our study confirms that acceleration is a promising way to estimate energy expenditures offree-ranging marine mammals at a fine scale never attained before. However, it shows that itneeds to be based on the time-activity budgets that make up foraging trips rather than beingderived as a single measure of VeDBA applied to entire foraging trips. Our activity-basedmethod provides a cost-effective means to accurately calculate energy expenditures of fur sealsusing acceleration and time-activity budgets, that can be transfered to studies on other species.

The efficiency with which individuals extract energy from their environment defines their survival and reproductive success, and thus their selective contribution to the population. Individuals that forage more efficiently (i.e., when energy gained exceeds energy expended) are likely to be more successful at raising viable offspring than individuals that forage less efficiently. Our goal was to test this prediction in large long-lived mammals under free-ranging conditions. To do so, we equipped 20 lactating Antarctic fur seals (Arctocephalus gazella) breeding on Kerguelen Island in the Southern Ocean with tags that recorded GPS locations, depth and tri-axial acceleration to determine at-sea behaviours and detailed time-activity budgets during their foraging trips. We also simultaneously measured energy spent at sea using the doubly-labeled water (DLW) method, and estimated the energy acquired while foraging from 1) type and energy content of prey species present in scat remains, and 2) numbers of prey capture attempts determined from head acceleration. Finally, we followed the growth of 36 pups from birth until weaning (of which 20 were the offspring of our 20 tracked mothers), and used the relative differences in body mass of pups at weaning as an index of first year survival and thus the reproductive success of their mothers. Our results show that females with greater foraging efficiencies produced relatively bigger pups at weaning. These mothers achieved greater foraging efficiency by extracting more energy per minute of diving rather than by reducing energy expenditure. This strategy also resulted in the females spending less time diving and less time overall at sea, which allowed them to deliver higher quality milk to their pups, or allowed their pups to suckle more frequently, or both. The linkage we demonstrate between reproductive success and the quality of individuals as foragers provides an individual-based quantitative framework to investigate how changes in the availability and accessibility of prey can affect fitness of animals.

Flipper strokes have been proposed as proxies to estimate the energy expended by marine vertebrateswhile foraging at sea, but this has never been validated on free-ranging otariids (fur seals and sea lions).Our goal was to investigate how well flipper strokes correlate with energy expenditure in 33 foragingnorthern and Antarctic fur seals equipped with accelerometers, GPS, and time-depth recorders. Weconcomitantly measured field metabolic rates with the doubly-labelled water method and derivedactivity-specific energy expenditures using fine-scale time-activity budgets for each seal. Flipper strokeswere detected while diving or surface transiting using dynamic acceleration. Despite some inter-speciesdifferences in flipper stroke dynamics or frequencies, both species of fur seals spent 3.79 ± 0.39 J/kg perstroke and had a cost of transport of ~1.6–1.9 J/kg/m while diving. Also, flipper stroke counts were goodpredictors of energy spent while diving (R2 = 0.76) and to a lesser extent while transiting (R2 = 0.63).However, flipper stroke count was a poor predictor overall of total energy spent during a full foragingtrip (R2 = 0.50). Amplitude of flipper strokes (i.e., acceleration amplitude × number of strokes) predictedtotal energy expenditure (R2 = 0.63) better than flipper stroke counts, but was not as accurate as otheracceleration-based proxies, i.e. Overall Dynamic Body Acceleration.

Many species facing climate change have complex life cycles, with individuals in different stages differing in their sensitivity to a changing climate and their contribution to population growth. We use a quantitative genetics model to predict the dynamics of adaptation in a stage-structured population confronted with a steadily changing environment. Our model assumes that different optimal phenotypic values maximize different fitness components, consistent with many empirical observations. In a constant environment, the population evolves toward an equilibrium phenotype, which represents the best compromise given the trade-off between vital rates. In a changing environment, however, the mean phenotype in the population will lag behind this optimal compromise. We show that this lag may result in a shift along the trade-off between vital rates, with negative consequences for some fitness components but, less intuitively, improvements in some others. Complex eco-evolutionary dynamics can emerge in our model due to feedbacks between population demography and adaptation. Because of such feedback loops, selection may favor further shifts in life history in the same direction as those caused by maladaptive lags. These shifts in life history could be wrongly interpreted as adaptations to the new environment, while in reality they only reflect the inability of the population to adapt fast enough.

Time and energy are the two most important currencies in animal bioenergetics. Howmuch time animals spend engaged in different activities with specific energetic costsultimately defines their likelihood of surviving and successfully reproducing. However,it is extremely difficult to determine the energetic costs of independent activities forfree-ranginganimals. In this study, we developed a new method to calculate activity-specificmetabolic rates, and applied it to female fur seals. We attached biologgers(that recorded GPS locations, depth profiles, and triaxial acceleration) to 12 northern(Callorhinus ursinus) and 13 Antarctic fur seals (Arctocephalus gazella), and used a hierarchicaldecision tree algorithm to determine time allocation between diving, transiting,resting, and performing slow movements at the surface (grooming, etc.). Weconcomitantly measured the total energy expenditure using the doubly-labelled watermethod. We used a general least-square model to establish the relationship betweentime–activity budgets and the total energy spent by each individual during their foragingtrip to predict activity-specificmetabolic rates. Results show that both species allocatedsimilar time to diving (~29%), transiting to and from their foraging grounds(~26–30%), and resting (~8–11%). However, Antarctic fur seals spent significantlymore time grooming and moving slowly at the surface than northern fur seals (36% vs.29%). Diving was the most expensive activity (~30 MJ/day if done non-stop for 24 hr),followed by transiting at the surface (~21 MJ/day). Interestingly, metabolic rates weresimilar between species while on land or while slowly moving at the surface (~13 MJ/day). Overall, the average field metabolic rate was ~20 MJ/day (for all activities combined).The method we developed to calculate activity-specificmetabolic rates can beapplied to terrestrial and marine species to determine the energetic costs of daily activities,as well as to predict the energetic consequences for animals forced to changetheir time allocations in response to environmental shifts.

Biological invasions represent an increasing threat to ecosystems worldwide, with negative ecological and socioeconomic impacts, whereas risk assessment and management remain challenging. The development of decision support systems (DSS) has the potential to help decision-makers and managers mitigate invasive species, but few DSS exist for forest invasive alien species (FIAS). The use of DSS in forestry is not new but they represent an asset in decision making in times of increasing complexity of issues foresters face and factors to consider. Yet, few forest DSS address the problem of FIAS. In this review, we identify key elements of the FIAS risk-assessment and management decision-making process, discuss these elements with a model-based DSS development perspective, and summarize outstanding challenges and opportunities for FIAS DSS development. FIAS DSS should not only estimate the probability of FIAS invasion but also consider forest vulnerability and quantify exposure (i.e., value at risk), while allowing different threat scenarios and possible solutions to be compared. Such a complete risk assessment and management calls for integrative modelling approaches that explicitly link different components of FIAS invasion, management, and impact assessment into a DSS. Such integrative modelling is challenging and may require collaboration among experts of different domains. International collaboration is also needed to facilitate data exchange, as the lack of data is one of the main challenges. In many cases, data and ecological knowledge of invasive species are too limited (in quantity or quality) to constitute useful input to DSS or their components (e.g., species distribution model). Another challenge is to better consider the multiple sources of uncertainties inherent to modelling invasions (e.g., host preferences and behavior, forest vulnerability, potential impacts, and cost and benefits of mitigation actions) when assessing FIAS risk and communicating results from risk assessment. Communication with stakeholders and DSS end-users, in fact, appears as one of the keys to successful DSS development and appropriation, not only to ensure that they correspond to end-users' needs but also to ensure ease of use, functionality, and good visualization of DSS outputs.

Cell-to-cell adhesion is essential for establishment of multicellularity. In plants, such adhesion is mediated through a middle lamella composed primarily of pectic polysaccharides. The molecular interactions that influence cell-to-cell adhesion are not fully understood. We have used Arabidopsis (Arabidopsis thaliana) seed coat mucilage as a model system to investigate interactions between cell wall carbohydrates. Using a forward-genetic approach, we have discovered a gene, RUBY PARTICLES IN MUCILAGE (RUBY), encoding a protein that is annotated as a member of the Auxiliary Activity 5 (AA5) family of Carbohydrate-Active Enzymes (Gal/glyoxal oxidases) and is secreted to the apoplast late in the differentiation of seed coat epidermal cells. We show that RUBY is required for the Gal oxidase activity of intact seeds; the oxidation of Gal in side-chains of rhamnogalacturonan-I (RG-I) present in mucilage-modified2 (mum2) mucilage, but not in wild-type mucilage; the retention of branched RG-I in the seed following extrusion; and the enhancement of cell-to-cell adhesion in the seed coat epidermis. These data support the hypothesis that RUBY is a Gal oxidase that strengthens pectin cohesion within the middle lamella, and possibly the mucilage of wild-type seed coat epidermal cells, through oxidation of RG-I Gal side-chains.

Remnants of ancient transposable elements (TEs) are abundant in mammalian genomes. These sequences harbor multiple regulatory motifs and hence are capable of influencing expression of host genes. In response to environmental changes, TEs are known to be released from epigenetic repression and to become transcriptionally active. Such activation could also lead to lineage-inappropriate activation of oncogenes, as one study described in Hodgkin lymphoma. However, little further evidence for this mechanism in other cancers has been reported. Here, we reanalyzed whole transcriptome data from a large cohort of patients with diffuse large B-cell lymphoma (DLBCL) compared with normal B-cell centroblasts to detect genes ectopically expressed through activation of TE promoters. We have identified 98 such TE-gene chimeric transcripts that were exclusively expressed in primary DLBCL cases and confirmed several in DLBCL-derived cell lines. We further characterized a TE-gene chimeric transcript involving a fatty acid-binding protein gene (LTR2-FABP7), normally expressed in brain, that was ectopically expressed in a subset of DLBCL patients through the use of an endogenous retroviral LTR promoter of the LTR2 family. The LTR2-FABP7 chimeric transcript encodes a novel chimeric isoform of the protein with characteristics distinct from native FABP7. In vitro studies reveal a dependency for DLBCL cell line proliferation and growth on LTR2-FABP7 chimeric protein expression. Taken together, these data demonstrate the significance of TEs as regulators of aberrant gene expression in cancer and suggest that LTR2-FABP7 may contribute to the pathogenesis of DLBCL in a subgroup of patients.

This study investigated prey captures in free-ranging adult female Australian fur seals (Arctocephalus pusillus doriferus) using head-mounted 3-axis accelerometers and animal-borne video cameras. Acceleration data was used to identify individual attempted prey captures (APC), and video data were used to independently verify APC and prey types. Results demonstrated that head-mounted accelerometers could detect individual APC but were unable to distinguish among prey types (fish, cephalopod, stingray) or between successful captures and unsuccessful capture attempts. Mean detection rate (true positive rate) on individual animals in the testing subset ranged from 67-100%, and mean detection on the testing subset averaged across 4 animals ranged from 82-97%. Mean False positive (FP) rate ranged from 15-67% individually in the testing subset, and 26-59% averaged across 4 animals. Surge and sway had significantly greater detection rates, but also conversely greater FP rates compared to heave. Video data also indicated that some head movements recorded by the accelerometers were unrelated to APC and that a peak in acceleration variance did not always equate to an individual prey item. The results of the present study indicate that head-mounted accelerometers provide a complementary tool for investigating foraging behaviour in pinnipeds, but that detection and FP correction factors need to be applied for reliable field application.