| 1. |
- Dujon, B, et al.
(author)
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The nucleotide sequence of Saccharomyces cerevisiae chromosome XV
- 1997
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 387:6632, s. 98-102
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Journal article (peer-reviewed)abstract
- Chromosome XV was one of the last two chromosomes of Saccharomyces cerevisiae to be discovered(1). It is the third-largest yeast chromosome after chromosomes XII and IV, and is very similar in size to chromosome VII. It alone represents 9% of the yeast genome (8% if ribosomal DNA is included). When systematic sequencing of chromosome XV was started, 93 genes or markers were identified, and most of them were mapped(2). However, very little else was known about chromosome XV which, in contrast to shorter chromosomes, had not been the object of comprehensive genetic or molecular analysis. It was therefore decided to start sequencing chromosome XV only in the third phase of the European Yeast Genome Sequencing Programme, after experience was gained on chromosomes III, XI and II (refs 3-5). The sequence of chromosome XV has been determined from a set of partly overlapping cosmid clones derived from a unique yeast strain, and physically mapped at 3.3-kilobase resolution before sequencing. As well as numerous new open reading frames (ORFs) and genes encoding tRNA or small RNA molecules, the sequence of 1,091,283 base pairs confirms the high proportion of orphan genes and reveals a number of ancestral and successive duplications with other yeast chromosomes.
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| 2. |
- Keune, H., et al.
(author)
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Science-policy challenges for biodiversity, public health and urbanization : examples from Belgium
- 2013
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In: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 8:2, s. 025015-
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Journal article (peer-reviewed)abstract
- Internationally, the importance of a coordinated effort to protect both biodiversity and public health is more and more recognized. These issues are often concentrated or particularly challenging in urban areas, and therefore on-going urbanization worldwide raises particular issues both for the conservation of living natural resources and for population health strategies. These challenges include significant difficulties associated with sustainable management of urban ecosystems, urban development planning, social cohesion and public health. An important element of the challenge is the need to interface between different forms of knowledge and different actors from science and policy. We illustrate this with examples from Belgium, showcasing concrete cases of human-nature interaction. To better tackle these challenges, since 2011, actors in science, policy and the broader Belgian society have launched a number of initiatives to deal in a more integrated manner with combined biodiversity and public health challenges in the face of ongoing urbanization. This emerging community of practice in Belgium exemplifies the importance of interfacing at different levels. (1) Bridges must be built between science and the complex biodiversity/ecosystem-human/public health-urbanization phenomena. (2) Bridges between different professional communities and disciplines are urgently needed. (3) Closer collaboration between science and policy, and between science and societal practice is needed. Moreover, within each of these communities closer collaboration between specialized sections is needed.
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| 3. |
- Leder, Erica H, 1967, et al.
(author)
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Post-glacial establishment of locally adapted fish populations over a steep salinity gradient
- 2021
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In: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 34:1, s. 138-56
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Journal article (peer-reviewed)abstract
- Studies of colonization of new habitats that appear from rapidly changing environments are interesting and highly relevant to our understanding of divergence and speciation. Here, we analyse phenotypic and genetic variation involved in the successful establishment of a marine fish (sand goby,Pomatoschistus minutus) over a steep salinity drop from 35 PSU in the North Sea (NE Atlantic) to two PSU in the inner parts of the post-glacial Baltic Sea. We first show that populations are adapted to local salinity in a key reproductive trait, the proportion of motile sperm. Thereafter, we show that genome variation at 22,190 single nucleotide polymorphisms (SNPs) shows strong differentiation among populations along the gradient. Sequences containing outlier SNPs and transcriptome sequences, mapped to a draft genome, reveal associations with genes with relevant functions for adaptation in this environment but without overall evidence of functional enrichment. The many contigs involved suggest polygenic differentiation. We trace the origin of this differentiation using demographic modelling and find the most likely scenario is that at least part of the genetic differentiation is older than the Baltic Sea and is a result of isolation of two lineages prior to the current contact over the North Sea-Baltic Sea transition zone.
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| 4. |
- Majchrzak, Paulina, et al.
(author)
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Spectroscopic view of ultrafast charge carrier dynamics in single- and bilayer transition metal dichalcogenide semiconductors
- 2021
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In: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 250
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Journal article (peer-reviewed)abstract
- 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 1.9-2.5 eV between our systems. The transient conduction band signals decay on a sub-50 fs timescale on the metals, signifying an efficient removal of photoinduced carriers into the bulk metallic states. On graphene, we instead observe a fast timescale on the order of 170 fs, followed by a slow dynamics for the conduction band decay in MoS2. These 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.
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| 5. |
- Majchrzak, P., et al.
(author)
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Switching of the electron-phonon interaction in 1T-VSe2 assisted by hot carriers
- 2021
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In: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 103:24
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Journal article (peer-reviewed)abstract
- We apply an intense infrared laser pulse in order to perturb the electronic and vibrational states in the three-dimensional charge density wave material 1T-VSe2. Ultrafast snapshots of the light-induced hot carrier dynamics and nonequilibrium quasiparticle spectral function are collected using time- and angle-resolved photoemission spectroscopy. The hot carrier temperature and time-dependent electronic self-energy are extracted from the time-dependent spectral function, revealing that incoherent electron-phonon interactions heat the lattice above the charge density wave critical temperature on a timescale of (200±40) fs. Density functional perturbation theory calculations establish that the presence of hot carriers alters the overall phonon dispersion and quenches efficient low-energy acoustic phonon scattering channels, which results in a new quasiequilibrium state that is experimentally observed.
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| 6. |
- Rostami, Habib, et al.
(author)
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Layer and orbital interference effects in photoemission from transition metal dichalcogenides
- 2019
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In: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 100:23
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Journal article (peer-reviewed)abstract
- In this work, we provide an effective model to evaluate the one-electron dipole matrix elements governing optical excitations and the photoemission process of single-layer (SL) and bilayer (BL) transition metal dichalcogenides. By utilizing a k . p Hamiltonian, we calculate the photoemission intensity as observed in angle-resolved photoemission from the valence bands around the (K) over bar valley of MoS2. In SL MoS2, we find a significant masking of intensity outside the first Brillouin zone, which originates from an in-plane interference effect between photoelectrons emitted from the Mo d orbitals. In BL MoS2, an additional interlayer interference effect leads to a distinctive modulation of intensity with photon energy. Finally, we use the semiconductor Bloch equations to model the optical excitation in a time- and angle-resolved pump-probe photoemission experiment. We find that the momentum dependence of an optically excited population in the conduction band leads to an observable dichroism in both SL and BL MoS2.
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| 7. |
- Vandamme, S., et al.
(author)
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Reconciling seascape genetics and fisheries science in three codistributed flatfishes
- 2021
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In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 14:2, s. 536-552
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Journal article (peer-reviewed)abstract
- Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population-specific information. We conclude that the management of fish stocks has to consider species-specific genetic structures and may benefit from the documentation of the genetic seascape and life-history traits.
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| 8. |
- Volckaert, Klara, et al.
(author)
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Momentum-resolved linear dichroism in bilayer MoS2
- 2019
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In: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 100:24
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Journal article (peer-reviewed)abstract
- 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- and momentum-resolved snapshots of excited electrons by time- and 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.
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