Evaluation of Human Telomeric G-Quadruplexes: The Influence of Overhanging Sequences on Quadruplex Stability and Folding

To date, various G-quadruplex structures have been reported in human telomeric sequences. Human telomeric repeats can form many topological structures depending on conditions and on base modification; parallel, antiparallel, and hybrid forms. The effect of salts and some specific ligands on conformational switches between different conformers is known, but the influence of protruding sequences has rarely been discussed. In this paper, we analyze different quadruplex-forming oligomers derived from human telomeric sequences which contain 3′- and 5′-protruding nucleotides, not usually associated with the G-quadruplex motif. The study was performed using electrophoresis, CD, and UV spectroscopies. The major findings are (i) protruding nucleotides destabilize the G-quadruplex structure, and (ii) overhanging sequences influence the folding of the quadruplex

Felföldy Lajos (1920–2016)

Felföldy Lajos (1920–2016) magyar botanika és hidrobiológia egyik legsokoldalúbb és legeredetibb egyénisége volt. Pályáját Soó Rezső irányításával kezdte, 1938 és 1946 között aktívan részt vett a debreceni és 1941–1942 között a kolozsvári Tudományegyetem Növénytani Tanszékén folyó geobotanikai kutatásokban. Számos tudományterületen maradandót alkotott. A légszennyezésnek az epifiton zuzmókra gyakorolt hatását vizsgáló kutatásai (1942) világviszonylatban is az elsők közé tartoznak. A Raunkiaer-féle növényi életforma-rendszeren belül elkülönítette a kétévesek (Hemitherophyta) életforma-típusát az egyévesekétől (1942). Úttörő szerepet játszott Magyarországon a vadon élő növényfajok citológiai (kariológiai) vizsgálatában (1947–1949). Foglalkozott növényélettannal (1951–1959), vizekben folyó primer produkcióval és algatenyésztéssel (1958–1960). 1972-ban életre hívta és 1990-ig szerkesztette a Vízügyi Hidrobiológia sorozatot. Megalapozta a magyarországi vízminőség-védelmet, amely a mai napig meghatározza a magyar hidrobiológusok szemléletét. 14 és 89 éves kora között legalább tízezer herbáriumi lapot gyűjtött. Nyugdíjba vonulása után a MTM Növénytár és az ELTE Füvészkert herbáriumi anyagának rendezésével, revíziójával foglalkozott, aktívan részt vett az Új Magyar Füvészkönyv elkészítésének munkálataiban. Munkáira egyszerre jellemző a természet iránti mély tisztelet, az elméleti megalapozottság és a gyakorlatiasság.</jats:p

High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response

<p>Abstract</p> <p>Background</p> <p>Rye (<it>Secale cereale </it>L.) is the most frost tolerant cereal species. As an outcrossing species, rye exhibits high levels of intraspecific diversity, which makes it well-suited for allele mining in genes involved in the frost responsive network. For investigating genetic diversity and the extent of linkage disequilibrium (LD) we analyzed eleven candidate genes and 37 microsatellite markers in 201 lines from five Eastern and Middle European rye populations.</p> <p>Results</p> <p>A total of 147 single nucleotide polymorphisms (SNPs) and nine insertion-deletion polymorphisms were found within 7,639 bp of DNA sequence from eleven candidate genes, resulting in an average SNP frequency of 1 SNP/52 bp. Nucleotide and haplotype diversity of candidate genes were high with average values <it>π </it>= 5.6 × 10^-3and <it>Hd </it>= 0.59, respectively. According to an analysis of molecular variance (AMOVA), most of the genetic variation was found between individuals within populations. Haplotype frequencies varied markedly between the candidate genes. <it>ScCbf14</it>, <it>ScVrn1</it>, and <it>ScDhn1 </it>were dominated by a single haplotype, while the other 8 genes (<it>ScCbf2</it>, <it>ScCbf6</it>, <it>ScCbf9b</it>, <it>ScCbf11</it>, <it>ScCbf12</it>, <it>ScCbf15</it>, <it>ScIce2</it>, and <it>ScDhn3</it>) had a more balanced haplotype frequency distribution. Intra-genic LD decayed rapidly, within approximately 520 bp on average. Genome-wide LD based on microsatellites was low.</p> <p>Conclusions</p> <p>The Middle European population did not differ substantially from the four Eastern European populations in terms of haplotype frequencies or in the level of nucleotide diversity. The low LD in rye compared to self-pollinating species promises a high resolution in genome-wide association mapping. SNPs discovered in the promoters or coding regions, which attribute to non-synonymous substitutions, are suitable candidates for association mapping.</p

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To date, various G-quadruplex structures have been reported in human telomeric sequences. Human telomeric repeats can form many topological structures depending on conditions and on base modification; parallel, antiparallel, and hybrid forms. The effect of salts and some specific ligands on conformational switches between different conformers is known, but the influence of protruding sequences has rarely been discussed. In this paper, we analyze different quadruplex-forming oligomers derived from human telomeric sequences which contain 3 -and 5 -protruding nucleotides, not usually associated with the G-quadruplex motif. The study was performed using electrophoresis, CD, and UV spectroscopies. The major findings are (i) protruding nucleotides destabilize the G-quadruplex structure, and (ii) overhanging sequences influence the folding of the quadruplex

Sign of inverse spin Hall voltages generated by ferromagnetic resonance and temperature gradients in yttrium iron garnet|platinum bilayers

We carried out a concerted effort to determine the absolute sign of the inverse spin Hall effect voltage generated by spin currents injected into a normal metal. We focus on yttrium iron garnet (YIG)|platinum bilayers at room temperature, generating spin currents by microwaves and temperature gradients. We find consistent results for different samples and measurement setups that agree with theory. We suggest a right-hand-rule to define a positive spin Hall angle corresponding to with the voltage expected for the simple case of scattering of free electrons from repulsive Coulomb charges.Comment: incorporated additions from the published versio

Transferring Dexterous Manipulation from GPU Simulation to a Remote Real-World TriFinger

We present a system for learning a challenging dexterous manipulation task involving moving a cube to an arbitrary 6-DoF pose with only 3-fingers trained with NVIDIA's IsaacGym simulator. We show empirical benefits, both in simulation and sim-to-real transfer, of using keypoints as opposed to position+quaternion representations for the object pose in 6-DoF for policy observations and in reward calculation to train a model-free reinforcement learning agent. By utilizing domain randomization strategies along with the keypoint representation of the pose of the manipulated object, we achieve a high success rate of 83% on a remote TriFinger system maintained by the organizers of the Real Robot Challenge. With the aim of assisting further research in learning in-hand manipulation, we make the codebase of our system, along with trained checkpoints that come with billions of steps of experience available, at https://s2r2-ig.github.ioComment: International Conference on Intelligent Robots and Systems (IROS 2022