The genomes and history of domestic animals

This paper reviews how mammalian genomes are utilized in modern genetics for the detection of genes and polymorphisms (mutations) within domesticated animal (mostly livestock) genomes that are related to traits of economic importance to humans. Examples are given of how genetic analysis allows to determine key genes associated with the quality and quantity of milk in cattle and key genes for meat production. Various questions are reviewed, such as how contemporary methods of genome sequencing allow to maximise the effective detection of coding and regulatory DNA polymorphisms within the genomes of major domesticated mammals (cattle, sheep and pigs) and the history of their formation from the standpoint of genetics

Insights into genomic DNA sampling by prokaryotic Argonaute proteins

Prokaryotic Argonaute proteins (pAgos) are endonucleases that bind small DNA or RNA guides and mediate cleavage of complementary targets. They are encoded in a variety of bacterial and archaeal genomes and supposedly participate in cell defence against foreign DNA. Previous biochemical and structural studies have elucidated the mechanistic aspects of guide binding, target search and cleavage by pAgos. pAgos have been shown to interfere with plasmid uptake in vivo and to autonomously produce guides from double-stranded DNA substrates in vitro. However, the principles underlying self/nonself discrimination remain unknown. Here we characterize in vivo guide biogenesis by pAgos from mesophilic bacteria Limnothrix rosea (LrAgo) and Clostridium butyricum (CbAgo). LrAgo and CbAgo are DNA-guided DNA endonucleases that copurify with small DNAs upon heterologous expression in E. coli. Such guide production depends on their catalytic activity and is abolished when pAgos are rendered inactive. Small DNAs originate from both the expression plasmid and the bacterial chromosome and are enriched for plasmid-derived sequences. Well-defined guide acquisition hotspots are observed within the host chromosome that likely correspond to the preferable sites of DNA processing by pAgos. The hotspots may presumably arise at sites of frequent DNA damage and repair and do not correlate with transcription levels at corresponding regions. Our observations suggest that pAgos may sample genomic DNA in a way similar to the CRISPR adaptation apparatus. As such the DNA repair machinery may orchestrate the action of prokaryotic defence systems by facilitating nonself targeting and guide acquisition

Catalytically active Argonaute proteins from mesophilic bacteria

Argonaute proteins are an integral part of eukaryotic RNA interference machinery. They bind small noncoding RNAs and utilize them for guided cleavage of complementary RNA targets or indirect gene silencing by recruiting additional factors. Argonaute proteins are also encoded in many bacterial and archaeal genomes (pAgos). pAgos from thermophilic bacteria were initially studied to gain structural insight into eukaryotic RNA interference. They were later shown to cleave DNA substrates in a guided manner employing small RNAs or DNAs, which appear to be generated autonomously by pAgos. Thus, pAgos might be considered as means of prokaryotic defense against invasive genetic elements. Here we characterize pAgos from noncultivable or pathogenic mesophilic bacteria. Candidate proteins were selected through bioinformatic screening of genomic databases. Corresponding pAgo genes were chemically synthesized and used for expression in a heterologous system. Upon expression in E. coli these proteins have been shown to associate with short (1425 nt) 5’phosphorylated DNA molecules. Such short DNA loading relies on the catalytic activity of pAgos and is abolished in catalytically dead protein variants, which bear amino acid substitutions in the DEDX catalytic tetrad. Further in vitro assays have shown that purified pAgos cleave various DNA substrates in a guidedependent manner. They display high activity at temperatures ranging from 30 to 45 °C, with the efficiency of cleavage being greatly affected by ionic strength, supplied divalent cations and guide molecules. This suggests that all studied pAgos act as DNA dependent DNA nucleases which may subsequently be used as means of targeted genome editing in eukaryotic organisms

Optical Lattice Polarization Effects on Hyperpolarizability of Atomic Clock Transitions

The light-induced frequency shift due to the hyperpolarizability (i.e. terms of second-order in intensity) is studied for a forbidden optical transition, $J$=0$\to$$J$=0. A simple universal dependence on the field ellipticity is obtained. This result allows minimization of the second-order light shift with respect to the field polarization for optical lattices operating at a magic wavelength (at which the first-order shift vanishes). We show the possibility for the existence of a magic elliptical polarization, for which the second-order frequency shift vanishes. The optimal polarization of the lattice field can be either linear, circular or magic elliptical. The obtained results could improve the accuracy of lattice-based atomic clocks.Comment: 4 pages, RevTeX4, 2 eps fig

Spin-orbit torques in a Rashba honeycomb antiferromagnet

Recent experiments on switching antiferromagnetic domains by electric current pulses have attracted a lot of attention to spin-orbit torques in antiferromagnets. In this work, we employ the tight-binding model solver, kwant, to compute spin-orbit torques in a two-dimensional antiferromagnet on a honeycomb lattice with strong spin-orbit interaction of Rashba type. Our model combines spin-orbit interaction, local s-d-like exchange, and scattering of conduction electrons on on-site disorder potential to provide a microscopic mechanism for angular momentum relaxation. We consider two versions of the model: one with preserved and one with broken sublattice symmetry. A non-equilibrium staggered polarization, that is responsible for the so-called Neel spin-orbit torque, is shown to vanish identically in the symmetric model but may become finite if sublattice symmetry is broken. Similarly, anti-damping spin-orbit torques vanish in the symmetric model but become finite and anisotropic in a model with broken sublattice symmetry. As expected, anti-damping torques also reveal a sizable dependence on impurity concentration. Our numerical analysis also confirms symmetry classification of spin-orbit torques and strong torque anisotropy due to in-plane confinement of electron momenta.Comment: 14 pages, 12 figure

Pure superposition states of atoms generated by a bichromatic elliptically polarized filed

We find specific polarizations of components of a bichromatic field, which allow one to prepare pure superposition states of atoms, using the coherent population trapping effect. These $m$$-$$m$ states are prepared in the system of Zeeman substates of the ground-state hyperfine levels with arbitrary angular momenta $F_1$ and $F_2$. It is established that, in general case $m\ne 0$, the use of waves with elliptical polarizations ($\epsilon_1$$\perp$$\epsilon_2$ field configuration for alkali metal atoms) is necessary for the pure state preparation. We analytically show an unique advantage of the D1 line of alkali metal atoms, which consists in the possibility to generate pure $m$$-$$m$ states even in the absence of spectral resolution of the excited-state hyperfine levels, contrary to the D2 line.Comment: revtex4, 6 pages including 2 eps figure