Investigating the Effect and Relationship of Life-History Genetics and Population Density on Juvenile Atlantic Salmon (Salmo salar) Food Acquisition

Life-history decisions, and trade-offs, are affected by resource acquisition, which can vary among individuals, and during the life cycle of an individual. In Atlantic salmon (Salmo salar) many life-history decisions, such as age-of-maturity, are strongly associated with two genomic regions, vgll3 and six6. Previously, these genomic regions have been associated with food acquisition in adult sea-run Atlantic salmon; however, this has not yet been studied in juvenile salmon. Furthermore, population density strongly affects the food availability of juvenile salmon through resource competition. Here, using controlled crosses reared in semi-natural stream conditions, I investigated the effect and relationship of life-history genetics and population density on juvenile Atlantic salmon food acquisition. Stomach contents from 148 juvenile Atlantic salmon were quantified for their prey item composition, total number of prey items and dry weight, and environmental and genetic basis of food acquisition were analysed using mixed effects models. Late maturing six6 genotype fish had higher stomach-content dry weights and fuller stomachs than early maturing individuals, in low densities. Furthermore, low density fish were of better condition and had higher growth rates than high density fish. There was no association between six6 and vgll3 genotypes and food acquisition in high densities. The results support the existing knowledge of the negative effect of increasing population density on juvenile Atlantic salmon growth and condition. Furthermore, the density dependent association of six6 and food acquisition suggest a trade-off between early maturation and maximised food acquisition

In silico evidence for functional specialization after genome duplication in yeast

A fairly recent whole-genome duplication (WGD) event in yeast enables the effects of gene duplication and subsequent functional divergence to be characterized. We examined 15 ohnolog pairs (i.e. paralogs from a WGD) out of c. 500 Saccharomyces cerevisiae ohnolog pairs that have persisted over an estimated 100 million years of evolution. These 15 pairs were chosen for their high levels of asymmetry, i.e. within the pair, one ohnolog had evolved much faster than the other. Sequence comparisons of the 15 pairs revealed that the faster evolving duplicated genes typically appear to have experienced partially – but not fully – relaxed negative selection as evidenced by an average nonsynonymous/synonymous substitution ratio (dN/dSavg=0.44) that is higher than the slow-evolving genes' ratio (dN/dSavg=0.14) but still <1. Increased number of insertions and deletions in the fast-evolving genes also indicated loosened structural constraints. Sequence and structural comparisons indicated that a subset of these pairs had significant differences in their catalytically important residues and active or cofactor-binding sites. A literature survey revealed that several of the fast-evolving genes have gained a specialized function. Our results indicate that subfunctionalization and even neofunctionalization has occurred along with degenerative evolution, in which unneeded functions were destroyed by mutations

Retinal Temperature Determination Based on Photopic Porcine Electroretinogram

Objective: Subthreshold retinal laser therapy (SLT) is a treatment modality where the temperature of the retinal pigment epithelium (RPE) is briefly elevated to trigger the therapeutic benefits of sublethal heat shock. However, the temperature elevation induced by a laser exposure varies between patients due to individual differences in RPE pigmentation and choroidal perfusion. This study describes an electroretinography (ERG)-based method for controlling the temperature elevation during SLT. Methods: The temperature dependence of the photopic ERG response kinetics were investigated both ex vivo with isolated pig retinas and in vivo with anesthetized pigs by altering the temperature of the subject and recording ERG in different temperatures. A model was created for ERG-based temperature estimation and the feasibility of the model for controlling SLT was assessed through computational simulations. Results: The kinetics of the photopic in vivo flash ERG signaling accelerated between 3.6 and 4.7%/degrees C, depending on the strength of the stimulus. The temperature dependence was 5.0%/degrees C in the entire investigated range of 33 to 44 degrees C in ex vivo ERG. The simulations showed that the method is suitable for determining the steady-state temperature elevation in SLT treatments with a sufficiently long laser exposure and large spot size, e.g., during > 30 s laser exposures with > 3 mm stimulus spot diameter. Conclusions: The described ERG-based temperature estimation model could be used to control SLT treatments such as transpupillary thermotherapy. Significance: The introduced ERG-based method for controlling SLT could improve the repeatability, safety, and efficacy of the treatment of various retinal disorders.Peer reviewe

Enhanced activity of hyperthermostable Pyrococcus horikoshii endoglucanase in superbase ionic liquids

Objectives Ionic liquids (ILs) that dissolve biomass are harmful to the enzymes that degrade lignocellulose. Enzyme hyperthermostability promotes a tolerance to ILs. Therefore, the limits of hyperthemophilic Pyrococcus horikoschii endoglucanase (PhEG) to tolerate 11 superbase ILs were explored. Results PhEG was found to be most tolerant to 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc) in soluble 1% carboxymethylcellulose (CMC) and insoluble 1% Avicel substrates. At 35% concentration, this IL caused an increase in enzyme activity (up to 1.5-fold) with CMC. Several ILs were more enzyme inhibiting with insoluble Avicel than with soluble CMC. K-m increased greatly in the presence ILs, indicating significant competitive inhibition. Increased hydrophobicity of the IL cation or anion was associated with the strongest enzyme inhibition and activation. Surprisingly, PhEG activity was increased 2.0-2.5-fold by several ILs in 4% substrate. Cations exerted the main role in competitive inhibition of the enzyme as revealed by their greater binding energy to the active site. Conclusions These results reveal new ways to design a beneficial combination of ILs and enzymes for the hydrolysis of lignocellulose, and the strong potential of PhEG in industrial, high substrate concentrations in aqueous IL solutions.Peer reviewe

Inhibition of hyperthermostable xylanases by superbase ionic liquids

The use of enzymes in aqueous solutions of ionic liquids (ILs) could be useful for the enzymatic treatment of lignocellulose. Hydrophilic ILs that dissolve lignocellulose are harmful to enzymes. The toleration limits and enzyme-friendly superbase IL combinations were investigated for the hyperthermophilic Thermopolyspora flexuosa GH10 xylanase (endo-1,4-beta-xylanase EC 3.2.1.8) TfXYN10A and Dictyoglomus thermophilum GH11 xylanase DtXYN11B. TfXYN10A was more tolerant than DtXYN11B to acetate or propionate-based ILs. However, when the anion of the ILs was bigger (guaiacolate), GH11 xylanase showed higher tolerance to ILs. 1-Ethyl-3-methylimidazolium acetate ([EMIM]OAc), followed by 1,1,3,3-tetramethylguanidine acetate ([TMGH]OAc), were the most enzyme-friendly ILs for TfXYN10A and [TMGH](+)-based ILs were tolerated best by DtXYN11B. Double-ring cations and a large size anion were associated with the strongest enzyme inhibition. Competitive inhibition appears to be a general factor in the reduction of enzyme activity. However, with guaiacolate ILs, the denaturation of proteins may also contribute to the reduction in enzyme activity. Molecular docking with IL cations and anions indicated that the binding mode and shape of the active site affect competitive inhibition, and the cobinding of cations and anions to separate active site positions caused the strongest enzyme inhibition.Peer reviewe

Environmental DNA reveals the temporal and spatial extent of spawning migrations of European shad in a highly fragmented river basin

1. Anthropogenic barriers on lowland rivers impede the spawning migrations of anadromous fishes, preventing access to historical spawning areas. In the cryptic European shads Alosa alosa and Alosa fallax (‘shad’ hereafter), this has resulted in population declines across their range. Conservation programmes aim to facilitate the passage of migrators over these barriers and so require baseline knowledge on spatial and temporal extent of current migrations. 2. Here, a shad-specific environmental DNA (eDNA) assay was used to quantify the spatial extent of shad spawning migrations in the River Severn basin, Western England. This basin is characterised by the presence of multiple anthropogenic barriers in the lower catchment. In 2017, the eDNA assay was piloted in the River Teme, an important shad spawning tributary, and then applied in 2018 and 2019 across the lower Severn basin. 3. In all years, shad DNA was detected between mid-May and mid-June, with the maximum spatial extent of shad distribution being in early June when shad eDNA was detected upstream of weirs that were generally considered as impassable. In 2018, this included the detection of shad above the most upstream weir on the main River Severn that required individual fish to have passed six weirs. 4. Although anthropogenic barriers inhibit the spawning migrations of shad, this eDNA assay revealed some highly vagile individuals might be able to ascend these barriers and migrate considerable distances upstream. This suggests that efforts to increase the permeability of these barriers could result in relatively high numbers of migrating shad reaching upstream spawning areas. These results demonstrate that this eDNA assay could be also utilised across their range, outside the study system, to further quantify the spatial extent of their spawning, including in highly fragmented rivers and those where shad are believed to only spawn occasionally and are rarely observed

Hijacking the human complement inhibitor C4b-binding protein by the sporozoite stage of the Plasmodium falciparum parasite

The complement system is considered the first line of defense against pathogens. Hijacking complement regulators from blood is a common evasion tactic of pathogens to inhibit complement activation on their surfaces. Here, we report hijacking of the complement C4b-binding protein (C4bp), the regulator of the classical and lectin pathways of complement activation, by the sporozoite (SPZ) stage of the Plasmodium falciparum parasite. This was shown by direct binding of radiolabeled purified C4bp to live SPZs as well as by binding of C4bp from human serum to SPZs in indirect immunofluorescence assays. Using a membrane-bound peptide array, peptides from the N-terminal domain (NTD) of P. falciparum circumsporozoite protein (CSP) were found to bind C4bp. Soluble biotinylated peptide covering the same region on the NTD and a recombinantly expressed NTD also bound C4bp in a dose-dependent manner. NTD-binding site on C4bp was mapped to the CCP1-2 of the C4bp alpha-chain, a common binding site for many pathogens. Native CSP was also co-immunoprecipitated with C4bp from human serum. Preventing C4bp binding to the SPZ surface negatively affected the SPZs gliding motility in the presence of functional complement and malaria hyperimmune IgG confirming the protective role of C4bp in controlling complement activation through the classical pathway on the SPZ surface. Incorporating the CSP-C4bp binding region into a CSP-based vaccine formulation could induce vaccine-mediated immunity that neutralizes this immune evasion region and increases the vaccine efficacy.Peer reviewe

Screening of glycoside hydrolases and ionic liquids for fibre modification

BACKGROUNDThis study elaborates the possibility to apply combined ionic liquid (IL) and enzyme treatments for pulp fibre modification. The approach involves swelling of fibre surfaces with IL followed by enzymatic modification of the disrupted fibre surface using carbohydrate active enzymes. RESULTSThe capacity of seven cellulose-dissolving or cellulose-swelling ionic liquids to swell pulp fibres was compared. In addition, thirteen cellulases and five xylanases were screened for their IL tolerance, which determines their applicability in combined or sequential IL-enzyme treatments of fibres. Among the studied ionic liquids, 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DMP) and 1,3-dimethylimidazolium dimethylphosphate ([DMIM]DMP) had the strongest effect on fibre swelling. These solvents were also found to be the least inactivating for the studied enzymes. CONCLUSIONEnzyme compatibility and cellulose-dissolving capability are not two conflicting properties of an ionic liquid. (c) 2017 Society of Chemical IndustryPeer reviewe

The cultivation of oak seedlings inoculated with Tuber aestivum Vittad. in the boreal region of Finland

Despite recent findings, truffles are rarely found in Finland. In 2006, we began to explore the cultivation potential of Tuber aestivum/uncinatum in Finland. In 2006–2008, roughly 1,200 Quercus robur seedlings and 200 Q. pubescens seedlings were planted in 20 orchards. We aimed to challenge the Southern European (France) tree provenances of oak seedlings in a boreal climate. Additional winter coverings made up of fabric or plastic and twigs prevented the seedlings’ mortality even when the air temperature was below −30 °C during the second winter. The results showed that the top soil temperature at 15 cm depth has to be above −5 °C to guarantee the survival of seedlings. Q. pubescens was more sensitive to low soil temperatures than Q. robur. Morphological and PCR analysis of root samples collected over 2007–2010 confirmed the presence of T. aestivum in all orchards despite unfavorable temperatures during the winter time. The first T. aestivum sporocarps were found under Q. robur in October 2012 in the orchards established in 2006 on old agricultural land, showing truffle cultivation to be successful in the boreal climate