Indirect effects of sea ice loss on summer‐fall habitat and behaviour for sympatric populations of an Arctic marine predator

Aim

Climate change is fundamentally altering habitats, with complex consequences for species across the globe. The Arctic has warmed 2–3 times faster than the global average, and unprecedented sea ice loss can have multiple outcomes for ice‐associated marine predators. Our goal was to assess impacts of sea ice loss on population‐specific habitat and behaviour of a migratory Arctic cetacean.

Location

Arctic Ocean.

Methods

Using satellite telemetry data collected during summer‐fall from sympatric beluga whale (Delphinapterus leucas) populations (“Chukchi” and “Beaufort” belugas), we applied generalized estimating equations to evaluate shifts in sea ice habitat associations and diving behaviour during two periods: 1993–2002 (“early”) and 2004–2012 (“late”). We used resource selection functions to assess changes in sea ice selection as well as predict trends in habitat selection and “optimal” habitat, based on satellite‐derived sea ice data from 1990 to 2014.

Results

Sea ice cover declined substantially between periods, and Chukchi belugas specifically used significantly lower sea ice concentrations during the late than early period. Use of bathymetric features did not change between periods for either population. Population‐specific sea ice selection, predicted habitat and the amount of optimal habitat also generally did not change during 1990–2014. Chukchi belugas tracked during 2007–2012 made significantly more long‐duration and deeper dives than those tracked during 1998–2002.

Main conclusions

Taken together, our results suggest bathymetric parameters are consistent predictors of summer‐fall beluga habitat rather than selection for specific sea ice conditions during recent sea ice loss. Beluga whales were able to mediate habitat change despite their sea ice associations. However, trends towards prolonged and deeper diving possibly indicate shifting foraging opportunities associated with ecological changes that occur in concert with sea ice loss. Our results highlight that responses by some Arctic marine wildlife can be indirect and variable among populations, which could be included in predictions for the future.

     

Are Lithuanian eels fat enough to reach the spawning grounds?

Stocks of the European eel Anguilla anguilla have been in a steep decline since the 1980s. Stocking of water bodies with juvenile eels captured in the wild to establish or enhance local populations has been a common practise in Europe for many decades. However, the degree of contribution by stocked eels to natural spawning capacity is poorly known and extensively debated. There have been suggestions that eels derived from stocking are less likely to contribute to the spawning stock due to a lack of navigational capability and lower fitness related to insufficiency of energetic resources. Results of the current study indicated that eels translocated long distances from the point of capture and released into inland waters in Lithuania are successfully undergoing the silvering process. A proportion of 23.7% (N = 27) among all migrating eels were described to be at the yellow (SI, SFII or SFIII) eel stage and downstream movements of these eels should be attributed to local movements, rather than spawning migration; 76.3% were assigned to the silver eel stage. This study suggests that 36.8% (N = 32) of downstream migrating silver eels of stocked origin had accumulated sufficient energetic resources for spawning migration and gonadal development and should be able to traverse the 7900-km distance to the presumptive spawning grounds in the Sargasso Sea. The rest of migrating silver eels (63.2%, N = 55) had insufficient energetic resources; the average potential swimming range of these eels was estimated to be 6135 ± 683 km.     

Radiosynthesis and in vivo evaluation of [11C]MOV as a PET imaging agent for COX-2

Radiosynthesis and in vivo evaluation of [¹¹C]4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]benzenesulfonamide (methoxy analogue of valdecoxib, [¹¹C]MOV), a COX-2 inhibitor, was conducted in rat and baboon. Synthesis of the reference standard MOV (3), and its desmethyl precursor 2 for radiolabeling were performed using 1,2-diphenylethan-1-one as the starting material in five steps with 15% overall yield. Radiosynthesis of [¹¹C]MOV was accomplished in 40?±?10% yield and?>99% radiochemical purity by reacting the precursor 2 in dimethyl formamide (DMF) with [¹¹C]CH₃I followed by removal of the dimethoxytrityl (DMT) protective group using trifluroacetic acid. PET studies in anesthetized baboon showed very low uptake and homogeneous distribution of [¹¹C]MOV in brain. The radioligand underwent rapid metabolism in baboon plasma. MicroPET studies in male Sprague Dawley rats revealed [¹¹C]MOV binding in lower thorax. The tracer binding in rats was partially blocked in heart and duodenum by the administration of 1?mg/kg oral dose of COX-2 inhibitor valdecoxib.     

Quantification of the catalytic performance of C1-cellulose-specific lytic polysaccharide monooxygenases

Applied Microbiology and Biotechnology - Lytic polysaccharide monooxygenases (LPMOs) have recently been shown to significantly enhance the degradation of recalcitrant polysaccharides and are of...     

Structural basis for the flexible recognition of α‐glucan substrates by Bacteroides thetaiotaomicron SusG

Bacteria that reside in the mammalian intestinal tract efficiently hydrolyze dietary carbohydrates, including starch, that escape digestion in the small intestine. Starch is an abundant dietary carbohydrate comprised of α1,4 and α1,6 linked glucose, yet mammalian intestinal glucoamylases cannot effectively hydrolyze starch that has frequent α1,6 branching as these structures hinder recognition and processing by α1,4‐specific amylases. Here we present the structure of the cell surface amylase SusG from Bacteroides thetaiotaomicron complexed with a mixed linkage amylosaccharide generated from transglycosylation during crystallization. Although SusG is specific for α1,4 glucosidic bonds, binding of this new oligosaccharide at the active site demonstrates that SusG can accommodate α1,6 branch points at subsite ?3 to ?2, and also at subsite+1 adjacent to the site of hydrolysis, explaining how this enzyme may be able to process a wide range of limit dextrins in the intestinal environment. These data suggest that B. thetaiotaomicron and related organisms may have a selective advantage for amylosaccharide scavenging in the gut.     

GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

Background

Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists’ capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter-gene sets association is rarely taken into consideration. Deep learning, an emerging machine learning technique in computational biology, can be used to generate an unbiased combination of gene set, and to determine the biological relevance and analysis consistency of these combining gene sets by leveraging large genomic data sets.

Results

In this study, we proposed a gene superset autoencoder (GSAE), a multi-layer autoencoder model with the incorporation of a priori defined gene sets that retain the crucial biological features in the latent layer. We introduced the concept of the gene superset, an unbiased combination of gene sets with weights trained by the autoencoder, where each node in the latent layer is a superset. Trained with genomic data from TCGA and evaluated with their accompanying clinical parameters, we showed gene supersets’ ability of discriminating tumor subtypes and their prognostic capability. We further demonstrated the biological relevance of the top component gene sets in the significant supersets.

Conclusions

Using autoencoder model and gene superset at its latent layer, we demonstrated that gene supersets retain sufficient biological information with respect to tumor subtypes and clinical prognostic significance. Superset also provides high reproducibility on survival analysis and accurate prediction for cancer subtypes.

     

Glomerular anionic charge in congenital nephrotic syndrome of the Finnish type

Summary Decrease of the anionic charge of the glomerular basement membrane and especially the reduced amount of heparan sulphate proteoglycan in the lamina rara externa has been suggested to be the basic pathogenetic defect in congenital nephrotic syndrome. In the present study the anionic charge of glomeruli was examined in the congenital nephrotic syndrome of the Finnish type and in controls using cationic stains (polyethyleneimine, Ruthenium Red) in electron microscopy. Chondroitinase and heparinase treatments were used to characterize further the anionic elements detected. Scanning electron microscopy (SEM) was used in addition to transmission electron microscopy (TEM) to examine the tridimensional structure and secondary changes of podocytes in this syndrome. The number (mean ± SD) of polyethyleneimine granules per 1 μm length of lamina rara externa of the glomerular basement membrane was 24.9 ± 4.5 in control and 2.32 ± 4.3 in congenital nephrotic syndrome subjects. The Ruthenium Red staining pattern was closely similar in syndrome and control kidneys. The granules evident after staining with either cationic stain were seen after chondroitinase but not after heparinase treatment in control as well as in syndrome patient kidney samples. No denuded areas of basement membrane in 42 glomeruli from four syndrome patients were found in SEM. In conclusion, the amount of anionic sites in the lamina rara externa as detected by either cationic stain was comparable to controls. These results do not support the hypothesis of decreased anionic sites in the lamina rara externa of the glomerular basement membrane in congenital nephrotic syndrome of the Finnish type.