Metal-ion induced FRET in macrocyclic dynamic tweezers

International audienceAbstract We report here about effective FRET process (73-99%) in mono-Mg2+ complexes of symmetrical crown ether bis(styryl) dyes. The FRET process has not been observed in the free state and in binuclear complexes. The formation of mononuclear complex provides two styrylic fragments with appropriate positions of absorption and emission bands for FRET. The other important parameter for FRET is the proper geometric orientation of both chromophores, which attain sandwich conformation with close positioning of complexed and free styryl fragments induced by ion-modulated geometry reorganization of the bis-dye

Study of the thermal conductivity of natural carbonates

The thermal conductivity of natural monoliths of calcite, dolomite marble, and limestone from various deposits was measured using the absolute stationary method of longitudinal heat flow in the temperature range of 50–300 K and the dynamic method in the range of 323–573 K. A majority of calcite marbles were inferior in thermal conductivity to dolomite marbles. At room temperature, the thermal conductivity coefficients of all studied samples were lower k = 5 W/(m K). The obtained data were compared with the literature data. The diversity of experimental data from different authors on the thermal conductivity of carbonates is associated with qualitative differences in the samples studie

Substrate distortion and the catalytic reaction mechanism of 5-carboxyvanillate decarboxylase

5-Carboxyvanillate decarboxylase (LigW) catalyzes the conversion of 5-carboxyvanillate to vanillate in the biochemical pathway for the degradation of lignin. This enzyme was shown to require Mn2+ for catalytic activity and the kinetic constants for the decarboxylation of 5-carboxyvanillate by the enzymes from Sphingomonas paucimobilis SYK-6 (kcat = 2.2 s–1 and kcat/Km = 4.0 × 104 M–1 s–1) and Novosphingobium aromaticivorans (kcat = 27 s–1 and kcat/Km = 1.1 × 105 M–1 s–1) were determined. The three-dimensional structures of both enzymes were determined in the presence and absence of ligands bound in the active site. The structure of LigW from N. aromaticivorans, bound with the substrate analogue, 5-nitrovanillate (Kd = 5.0 nM), was determined to a resolution of 1.07 Å. The structure of this complex shows a remarkable enzyme-induced distortion of the nitro-substituent out of the plane of the phenyl ring by approximately 23°. A chemical reaction mechanism for the decarboxylation of 5-carboxyvanillate by LigW was proposed on the basis of the high resolution X-ray structures determined in the presence ligands bound in the active site, mutation of active site residues, and the magnitude of the product isotope effect determined in a mixture of H2O and D2O. In the proposed reaction mechanism the enzyme facilitates the transfer of a proton to C5 of the substrate prior to the decarboxylation step

Demonstration of a parity-time symmetry breaking phase transition using superconducting and trapped-ion qutrits

Scalable quantum computers hold the promise to solve hard computational problems, such as prime factorization, combinatorial optimization, simulation of many-body physics, and quantum chemistry. While being key to understanding many real-world phenomena, simulation of non-conservative quantum dynamics presents a challenge for unitary quantum computation. In this work, we focus on simulating non-unitary parity-time symmetric systems, which exhibit a distinctive symmetry-breaking phase transition as well as other unique features that have no counterpart in closed systems. We show that a qutrit, a three-level quantum system, is capable of realizing this non-equilibrium phase transition. By using two physical platforms - an array of trapped ions and a superconducting transmon - and by controlling their three energy levels in a digital manner, we experimentally simulate the parity-time symmetry-breaking phase transition. Our results indicate the potential advantage of multi-level (qudit) processors in simulating physical effects, where additional accessible levels can play the role of a controlled environment.Comment: 14 pages, 9 figure

Population dynamics and demographic history of Eurasian collared lemmings.

BACKGROUND: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. RESULTS: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene. CONCLUSIONS: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene

Ancient DNA suggests modern wolves trace their origin to a late Pleistocene expansion from Beringia.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a dataset of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.L.L., K.D. and G.L. were supported by the Natural Environment Research Council, UK (grant numbers NE/K005243/1, NE/K003259/1); LL was also supported by the European Research Council grant (339941‐ADAPT); A.M. and A.E. were supported by the European Research Council Consolidator grant (grant number 647787‐LocalAdaptation); L.F. and G.L. were supported by the European Research Council grant (ERC‐2013‐StG 337574‐UNDEAD); T.G. was supported by a European Research Council Consolidator grant (681396‐Extinction Genomics) & Lundbeck Foundation grant (R52‐5062); O.T. was supported by the National Science Center, Poland (2015/19/P/NZ7/03971), with funding from EU's Horizon 2020 programme under the Marie Skłodowska‐Curie grant agreement (665778) and Synthesys Project (BETAF 3062); V.P., E.P. and P.N. were supported by the Russian Science Foundation grant (N16‐18‐10265 RNF); A.P. was supported by the Max Planck Society; M.L‐G. was supported by a Czech Science Foundation grant (GAČR15‐06446S)

Ancient DNA suggests modern wolves trace their origin to a late Pleistocene expansion from Beringia.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a dataset of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.L.L., K.D. and G.L. were supported by the Natural Environment Research Council, UK (grant numbers NE/K005243/1, NE/K003259/1); LL was also supported by the European Research Council grant (339941‐ADAPT); A.M. and A.E. were supported by the European Research Council Consolidator grant (grant number 647787‐LocalAdaptation); L.F. and G.L. were supported by the European Research Council grant (ERC‐2013‐StG 337574‐UNDEAD); T.G. was supported by a European Research Council Consolidator grant (681396‐Extinction Genomics) & Lundbeck Foundation grant (R52‐5062); O.T. was supported by the National Science Center, Poland (2015/19/P/NZ7/03971), with funding from EU's Horizon 2020 programme under the Marie Skłodowska‐Curie grant agreement (665778) and Synthesys Project (BETAF 3062); V.P., E.P. and P.N. were supported by the Russian Science Foundation grant (N16‐18‐10265 RNF); A.P. was supported by the Max Planck Society; M.L‐G. was supported by a Czech Science Foundation grant (GAČR15‐06446S)

Grey wolf genomic history reveals a dual ancestry of dogs

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canisfamiliaris) lived(1-8). Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT8840,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.Peer reviewe

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)