Assessing the genetic effects of rehabilitating harbor seals (<Emphasis Type="Italic">Phoca vitulina</Emphasis>) in the Wadden Sea using stochastic simulations

Rehabilitation of marine mammals with the intent of releasing them back into nature is carried out for several species. Rehabilitation can help supporting critically endangered species, increase public awareness, and serve scientific purposes, but rehabilitation also causes concern due to risk of introducing diseases into the wild populations and genetic changes from disruption of natural selection and host-pathogen co-evolution. In this study, we investigate another potential risk from rehabilitation that has not previously been considered, i.e., anthropogenic increase in population inbreeding level. For this purpose, we performed stochastic population viability analyses of the Wadden Sea harbor seal population using VORTEX. In the Wadden Sea, rehabilitation takes place in several rehabilitation centers, and many of the seals suffer from parasitic bronchopneumonia or are orphaned. Several studies have found a correlation between helminth infection and inbreeding level. Moreover, a relation between fitness traits such as pup survival and inbreeding has been demonstrated. On this basis, we assess the effects from rehabilitating relatively inbred seals on population size and genetic diversity. We find that releasing seals significantly affect population inbreeding level and to a lesser extent population size. The effect depends on the level of inbreeding in rehabilitated seals as well as the actual number of inbred seals released.     

Insights into lipid-protein interactions from computer simulations

Lipid-protein interactions play an important direct role in the function of many membrane proteins. We argue they are key players in membrane structure, modulate membrane proteins in more subtle ways than direct binding, and are important for understanding the mechanism of classes of hydrophobic drugs. By directly comparing membrane proteins from different families in the same, complex lipid mixture, we found a unique lipid environment for every protein. Extending this work, we identified both differences and similarities in the lipid environment of GPCRs, dependent on which family they belong to and in some cases their conformational state, with particular emphasis on the distribution of cholesterol. More recently, we have been studying modes of coupling between protein conformation and local membrane properties using model proteins. In more applied approaches, we have used similar methods to investigate specific hypotheses on interactions of lipid and lipid-like molecules with ion channels. We conclude this perspective with some considerations for future work, including a new more sophisticated coarse-grained force field (Martini 3), an interactive visual exploration framework, and opportunities to improve sampling.     

The diet of feral raccoon dog (<Emphasis Type="Italic">Nyctereutes procyonoides</Emphasis>) and native badger (<Emphasis Type="Italic">Meles meles</Emphasis>) and red fox (<Emphasis Type="Italic">Vulpes vulpes</Emphasis>) in Denmark

The raccoon dog (Nyctereutes procyonoides) is an East Asian Canid that has been introduced in Europe. Introduction of alien species is an increasing conservation issue. We examined the diet of a recently established raccoon dog population in Denmark by analysing stomach content in 249 carcasses collected in 2008–2016. Raccoon dog diet was compared to the diet of native badger (Meles meles) and red fox (Vulpes vulpes) in Denmark. The most common food for raccoon dogs were invertebrates (frequency of occurrence, FO 69%), small mammals (FO 68%), birds (FO 41%), fruits (FO 38%), amphibians (FO 36%) and carrions (FO 34%). The occurrence of invertebrates was highest during spring and summer, while fruits, cereals and carrions were eaten most often during autumn and winter. As expected, raccoon dog shared the major food categories with badger and red fox, but generally, it had a wider dietary niche. Overall, dietary overlap between raccoon dog and badger was 0.74 (Pianka index, O_jk). The dietary overlap with red fox was relatively high in all seasons, peaking in summer (O_jk 0.87) and dropping in winter (O_jk 0.79). Despite the dietary overlap between the alien racoon dog and native red fox and badger, the species may coexist due to partitioning of feeding habitats and/or because the red fox is limited by other factors, e.g. diseases and anthropogenic activities. The introduced raccoon dog seems to fit a dietary niche between badger and red foxes in human-dominated landscapes in north-western Europe.     

Proteolytic activity of Oidiodendron kalrai.

The physiochemical characteristics of the intracellular proteolytic enzymes of Oidiodendron kalari, a neuropathogenic fungus, were studied. The organism in the yeast phase was grown in a semisynthetic medium containing 1% tryptone, at 37 degrees C for 48 hr, on a gyrotory shaker. The crude extract was prepared by breaking the cells in a French pressure cell and the proteolytci activity was tested against biological substrates. The cell-free extract hydrolyzed casein, hemoglobin, lactalbumin, gelatin, elastin, collagen and purified rabbit renal basement membrane to various degrees. Optimal proteolytic activity was observed at pH 6 and at 32 degrees C. Calcium and EDTA did not affect the enzymatic activity; however, activity was partially inhibited by sulfhydryl-blocking agents and by heat-inactivated horse, calf, and human serum. The extract was totally inactivated by exposure to a temperature of 70 degrees C for 60 min. Storage at -76 degrees C or -15 degrees C for 6 months or at 4 degrees C for 4 weeks did not affect protease activity.     

Scaling of the mean and variance of population dynamics under fluctuating regimes

Theoretical ecologists have long sought to understand how the persistence of populations depends on the interactions between exogenous (biotic and abiotic) and endogenous (e.g., demographic and genetic) drivers of population dynamics. Recent work focuses on the autocorrelation structure of environmental perturbations and its effects on the persistence of populations. Accurate estimation of extinction times and especially determination of the mechanisms affecting extinction times is important for biodiversity conservation. Here we examine the interaction between environmental fluctuations and the scaling effect of the mean population size with its variance. We investigate how interactions between environmental and demographic stochasticity can affect the mean time to extinction, change optimal patch size dynamics, and how it can alter the often-assumed linear relationship between the census size and the effective population size. The importance of the correlation between environmental and demographic variation depends on the relative importance of the two types of variation. We found the correlation to be important when the two types of variation were approximately equal; however, the importance of the correlation diminishes as one source of variation dominates. The implications of these findings are discussed from a conservation and eco-evolutionary point of view.     

Craniometrical variability and developmental stability. Two useful tools for assessing the population viability of Eurasian otter (Lutra lutra) populations in Europe.

Morphometrical univariate analyses of otter skulls collected over the past hundred years in European countries from presumed healthy populations were compared with skulls from presumed endangered populations. The average degree of sexual dimorphism of die European populations was found to be directly correlated to die skull size of die male otters. Fluctuating asymmetry (FA) in metric skull traits was analysed as an estimator of developmental stability. There was evidence for increased FA in different traits over time in some of the presumed endangered populations, and for a reduction in size of skull traits. In contrast, the healthy populations did not show any significant changes in the same traits during the same period. The reduced sexual dimorphism of the endangered populations is suggested to be a product of relaxed sexual selection and deteriorated habitat conditions. Environmental and genetic forces that may have shaped these patterns are discussed.     

Conformational dynamics of Tetracenomycin aromatase/cyclase regulate polyketide binding and enzyme aggregation propensity

BackgroundThe N-terminal domain of Tetracenomycin aromatase/cyclase (TcmN), an enzyme derived from Streptomyces glaucescens, is involved in polyketide cyclization, aromatization, and folding. Polyketides are a diverse class of secondary metabolites produced by certain groups of bacteria, fungi, and plants with various pharmaceutical applications. Examples include antibiotics, such as tetracycline, and anticancer drugs, such as doxorubicin. Because TcmN is a promising enzyme for in vitro production of polyketides, it is important to identify conditions that enhance its thermal resistance and optimize its function.MethodsTcmN unfolding, stability, and dynamics were evaluated by fluorescence spectroscopy, circular dichroism, nuclear magnetic resonance ¹⁵N relaxation experiments, and microsecond molecular dynamics (MD) simulations.ResultsTcmN thermal resistance was enhanced at low protein and high salt concentrations, was pH-dependent, and denaturation was irreversible. Conformational dynamics on the μs-ms timescale were detected for residues in the substrate-binding cavity, and two predominant conformers representing opened and closed cavity states were observed in the MD simulations.ConclusionBased on the results, a mechanism was proposed in which the thermodynamics and kinetics of the TcmN conformational equilibrium modulate enzyme function by favoring ligand binding and avoiding aggregation.General significanceUnderstanding the principles underlying TcmN stability and dynamics may help in designing mutants with optimal properties for biotechnological applications.     

Depauperate genetic variability detected in the American and European bison using genomic techniques

 

A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip), and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly, they exhibited extremely depauperate genomes, deviations from genetic equilibrium and a genome organization consisting of a mosaic of haplotype blocks: regions with low haplotype diversity and high levels of linkage disequilibrium. No evidence for positive or stabilizing selection was found in EB, WB and PB, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow radical improvements of breeding practices in captive or managed populations, otherwise hampered by the limited availability of polymorphic markers. This result in improved possibilities for 1) estimating genetic relationships among individuals and 2) designing breeding strategies which attempt to preserve or reduce polymorphism in ecologically relevant genes and/or entire blocks.

Reviewers

This article was reviewed by: Fyodor Kondrashov and Shamil Sunyaev     

Outbreeding causes developmental instability in <Emphasis Type=Italic>Drosophila subobscura</Emphasis>

A possible effect of interpopulation hybridization is either outbreeding depression, as a consequence of breakdown of coadapted gene complexes which can increase developmental instability (DI) of the traits, or increased heterozygosity, which can reduce DI. One of the principal methods commonly used to estimate DI is the variability of fluctuating asymmetry (FA). We analysed the effect of interpopulation hybridization in Drosophila subobscura through the variability in the wing size and the FA of wing length and width for both sexes in parental, F1 and F2 generations. The results of the wing size per se in intra- and interpopulation hybrids of D. subobscura do not explicitly reveal the significance of either of the two hypotheses. However, the results of the FA of the wing traits give a different insight. The FA of wing length and width generally increases in interpopulation crosses in F1 with respect to the FA in the parental generation, which suggests the possibility that outbreeding depression occurred in the first generation after the hybridization event. We generally observed that the FA values for the wing length and width of interpopulation hybrids were higher in F1 and F2 generations, compared to intrapopulation hybrids in same generations. These results suggest that the association between coadaptive genes with the same evolutionary history are the most probable mechanism that maintains the developmental homeostasis in Drosophila subobscura populations.