Small-scale clinal variation, genetic diversity and environmental heterogeneity in the marine gobies <i>Pomatoschistus minutus</i> and <i>P. lozanoi</i> (Gobiidae, Teleostei)

Genetic variation was assayed at 14 allozyme loci in estuarine, coastal and offshore samples of Lozano's goby, Pomatoschistus lozanoi and the sand goby, P. minutus. Samples were taken from locations on the Belgian Continental Shelf and in the Schelde estuary with a range of environmental heterogeneity. We evaluate whether any differences in (1) the degree of genetic variation and (2) allele frequencies at the various loci exist within samples occurring in various habitats on the BCS and in the Schelde estuary. No significant differences in levels of genetic diversity were recorded between estuarine, coastal and offshore samples in either species. A temporally stable clinal gradient in allele frequencies at the two-allele locus GPI-A* was observed in P. lozanoi, differentiating the samples in an estuarine, coastal and offshore group. We suggest that these differences might be maintained by balancing selection at locus GPI-A*

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

Abstract Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.Peer Reviewe

Noise-induced distortion of nonequilibrium oscillator mean limit cycle

Under general conditions imposed on an active stochastic oscillator, we study change in the size and shape of its average limit cycle as a function of temperature. Such dynamics occur in a multitude of nonequilibrium systems, including the spontaneous oscillations of hair cells of the inner ear. We demonstrate one of the many mechanisms through which distortion of the mean curve may occur and identify regions in the driven oscillator phase space susceptible to corner-cutting due to noise. This we infer causes rounding of certain sharp features in the noiseless curve given by the underlying complex theoretical model, making them inaccessible under any amount of averaging of the experimentally obtained finite-temperature trajectory.Comment: 8 pages, 10 figure

Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labrax

Background: In fish, the most studied production traits in terms of heritability are body weight or growth, stress or disease resistance, while heritability of cortisol levels, widely used as a measure of response to stress, is less studied. In this study, we have estimated heritabilities of two growth traits (body weight and length) and of cortisol response to confinement stress in the European sea bass. Findings: The F1 progeny analysed (n = 922) belonged to a small effective breeding population with contributions from an unbalanced family structure of just 10 males and 2 females. Heritability values ranged from 0.54 (+/- 0.21) for body weight to 0.65 (+/- 0.22) for standard body length and were low for cortisol response i.e. 0.08 (+/- 0.06). Genetic correlations were positive (0.94) between standard body length and body weight and negative between cortisol and body weight and between cortisol and standard body length (-0.60 and -0.55, respectively). Conclusion: This study confirms that in European sea bass, heritability of growth-related traits is high and that selection on such traits has potential. However, heritability of cortisol response to stress is low in European sea bass and since it is known to vary greatly among species, further studies are necessary to understand the reasons for these differences

Momentum-resolved linear dichroism in bilayer MoS2

In solid state photoemission experiments it is possible to extract information about the symmetry and orbital character of the electronic wave functions via the photoemission selection rules that shape the measured intensity. This approach can be expanded in a pump-probe experiment where the intensity contains additional information about interband excitations induced by an ultrafast laser pulse with tunable polarization. Here, we find an unexpected strong linear dichroism effect (up to 42.4%) in the conduction band of bilayer MoS2, when measuring energy- A nd momentum-resolved snapshots of excited electrons by time- A nd angle-resolved photoemission spectroscopy. We model the polarization-dependent photoemission intensity in the transiently populated conduction band using the semiconductor Bloch equations. Our theoretical analysis reveals a strongly anisotropic momentum dependence of the optical excitations due to intralayer single-particle hopping, which explains the observed linear dichroism

Anisotropic Two-Dimensional Screening at the Surface of Black Phosphorus

Electronic screening can have direct consequences for structural arrangements on the nanoscale, such as on the periodic ordering of adatoms on a surface. So far, such ordering phenomena have been explained in terms of isotropic screening of free electronlike systems. Here, we directly illustrate the structural consequences of anisotropic screening, making use of a highly anisotropic two-dimensional electron gas (2DEG) near the surface of black phosphorous. The presence of the 2DEG and its filling is controlled by adsorbed potassium atoms, which simultaneously serve to probe the electronic ordering. Using scanning tunneling microscopy, we show that the anisotropic screening leads to the formation of potassium chains with a well-defined orientation and spacing. We quantify the mean interaction potential utilizing statistical methods and find that the dimensionality and anisotropy of the screening is consistent with the presence of a band bending-induced 2DEG near the surface. The electronic dispersion of the 2DEG inferred by electronic ordering is consistent with that measured by angle-resolved photoemission spectroscopy. © 2019 American Physical Society

Spectroscopic view of ultrafast charge carrier dynamics in single- and bilayer transition metal dichalcogenide semiconductors

Funding: We gratefully acknowledge funding from VILLUM FONDEN through the Young Investigator Program (Grant. No. 15375) and the Centre of Excellence for Dirac Materials (Grant.No. 11744), the Danish Council for Independent Research, Natural Sciences under the Sapere Aude program (Grant Nos. DFF-9064-00057B and DFF-6108-00409). Access to the Artemis Facility was funded by STFC. I.M. acknowledges financial support by the International Max Planck Research School for Chemistry and Physics of Quantum Materials (IMPRS-CPQM). The authors also acknowledge The Royal Society and The Leverhulme Trust.The quasiparticle spectra of atomically thin semiconducting transition metal dichalcogenides (TMDCs) and their response to an ultrafast optical excitation critically depend on interactions with the underlying substrate. Here, we present a comparative time- and angle-resolved photoemission spectroscopy (TR-ARPES) study of the transient electronic structure and ultrafast carrier dynamics in the single- and bilayer TMDCs MoS2 and WS2 on three different substrates: Au(111), Ag(111) and graphene/SiC. The photoexcited quasiparticle bandgaps are observed to vary over the range of 1.9-2.3 eV between our systems. The transient conduction band signals decay on a sub-100 fs timescale on the metals, signifying an efficient removal of photoinduced carriers into the bulk metallic states. On graphene, we instead observe two timescales on the order of 200 fs and 50 ps, respectively, for the conduction band decay in MoS2. These multiple timescales are explained by Auger recombination involving MoS2 and in-gap defect states. In bilayer TMDCs on metals we observe a complex redistribution of excited holes along the valence band that is substantially affected by interactions with the continuum of bulk metallic states.Publisher PDFPeer reviewe

The T7-Related Pseudomonas putida Phage ϕ15 Displays Virion-Associated Biofilm Degradation Properties

Formation of a protected biofilm environment is recognized as one of the major causes of the increasing antibiotic resistance development and emphasizes the need to develop alternative antibacterial strategies, like phage therapy. This study investigates the in vitro degradation of single-species Pseudomonas putida biofilms, PpG1 and RD5PR2, by the novel phage ϕ15, a ‘T7-like virus’ with a virion-associated exopolysaccharide (EPS) depolymerase. Phage ϕ15 forms plaques surrounded by growing opaque halo zones, indicative for EPS degradation, on seven out of 53 P. putida strains. The absence of haloes on infection resistant strains suggests that the EPS probably act as a primary bacterial receptor for phage infection. Independent of bacterial strain or biofilm age, a time and dose dependent response of ϕ15-mediated biofilm degradation was observed with generally a maximum biofilm degradation 8 h after addition of the higher phage doses (104 and 106 pfu) and resistance development after 24 h. Biofilm age, an in vivo very variable parameter, reduced markedly phage-mediated degradation of PpG1 biofilms, while degradation of RD5PR2 biofilms and ϕ15 amplification were unaffected. Killing of the planktonic culture occurred in parallel with but was always more pronounced than biofilm degradation, accentuating the need for evaluating phages for therapeutic purposes in biofilm conditions. EPS degrading activity of recombinantly expressed viral tail spike was confirmed by capsule staining. These data suggests that the addition of high initial titers of specifically selected phages with a proper EPS depolymerase are crucial criteria in the development of phage therapy