Micromotion-Synchronized Pulsed Doppler Cooling of Trapped Ions

We propose and demonstrate a new method for Doppler cooling trapped-ion crystals where the distribution of micromotion amplitudes may be large and uneven. The technique uses pulses of Doppler cooling light synchronized with the trap RF that selectively target ions when their velocity is near a node, leading to more uniform cooling across a crystal by a single tone of cooling light. We lay out a theoretical framework that describes where this technique is practical, and provide a simple experimental demonstration

Composition Conditions for Classes of Analytic Functions

We prove that for classes of analytic functions tree composition condition and composition condition coincide.Comment: 13 page

Dynamic Model of Privatization

The paper develops a simple theoretical framework in which the efficiency of industrial restructuring due to privatization process can be analysed. The dynamic model is based on the approach recently proposed by B. Gibson and A. Dutt (1993). This model is extended through inclusion the assumption of increasing efficiency of workers in state enterprises because of competition with the growing number of private firms. This paper attempts to analyse the optimality of time path of privatization in Ukraine as a country with mixed economy.Economic Dynamics, Transition Economies, Privatization

Sobemovirus genome appears to encode a serine protease related to cysteine proteases of picornaviruses

AbstractA putative serine protease was identified among non-structural proteins of southern bean mosaic virus (SBMV) by sequence comparison with cellular and viral proteases. The predicted SBMV proteased is played a significant similarity to cysteine proteases of picornaviruses, providing a possible evolutionary link between the two enzyme classes. It is suggested that SBMV follows the general expression strategy characteristic of other positive-strand RNA viruses containing 5′-terminal covalently linked proteins (VPg), i.e. generation of functional proteins by polyprotein processing

Molecular characterization of vernalization loci VRN1 in wild and cultivated wheats

<p>Abstract</p> <p>Background</p> <p>Variability of the <it>VRN1 </it>promoter region of the unique collection of spring polyploid and wild diploid wheat species together with diploid goatgrasses (donor of B and D genomes of polyploid wheats) were investigated. Accessions of wild diploid (<it>T. boeoticum</it>, <it>T. urartu</it>) and tetraploid (<it>T. araraticum, T. timopheevii</it>) species were studied for the first time.</p> <p>Results</p> <p>Sequence analysis indicated great variability in the region from -62 to -221 nucleotide positions of the <it>VRN1 </it>promoter region. Different indels were found within this region in spring wheats. It was shown that <it>VRN1 </it>promoter region of B and G genome can also contain damages such as the insertion of the transposable element.</p> <p>Some transcription factor recognition sites including hybrid C/G-box for TaFDL2 protein known as the <it>VRN1 </it>gene upregulator were predicted inside the variable region. It was shown that deletions leading to promoter damage occurred in diploid and polyploid species independently. DNA transposon insertions first occurred in polyploid species. At the same time, the duplication of the promoter region was observed in A genomes of polyploid species.</p> <p>Conclusions</p> <p>We can conclude that supposed molecular mechanism of the <it>VRN1 </it>gene activating in cultivated diploid wheat species <it>T. monococcum </it>is common also for wild <it>T. boeoticum </it>and was inherited by <it>T. monococcum</it>. The spring polyploids are not related in their origin to spring diploids. The spring <it>T. urartu </it>and goatgrass accessions have another mechanism of flowering activation that is not connected with indels in <it>VRN1 </it>promoter region. All obtained data may be useful for detailed insight into origin of spring wheat forms in evolution and domestication process.</p

CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission

<p>Abstract</p> <p>Background</p> <p>Non-long terminal repeat (non-LTR) retrotransposons are mobile genetic elements that propagate themselves by reverse transcription of an RNA intermediate. Non-LTR retrotransposons are known to evolve mainly via vertical transmission and random loss. Horizontal transmission is believed to be a very rare event in non-LTR retrotransposons. Our knowledge of distribution and diversity of insect non-LTR retrotransposons is limited to a few species – mainly model organisms such as dipteran genera <it>Drosophila</it>, <it>Anopheles</it>, and <it>Aedes</it>. However, diversity of non-LTR retroelements in arthropods seems to be much richer. The present study extends the analysis of non-LTR retroelements to CR1 clade from four butterfly species of genus <it>Maculinea </it>(Lepidoptera: Lycaenidae).</p> <p>The lycaenid genus <it>Maculinea</it>, the object of interest for evolutionary biologists and also a model group for European biodiversity studies, possesses a unique, specialized myrmecophilous lifestyle at larval stage. Their caterpillars, after three weeks of phytophagous life on specific food plants drop to the ground where they are adopted to the ant nest by <it>Myrmica </it>foraging workers.</p> <p>Results</p> <p>We found that the genome of <it>Maculinea </it>butterflies contains multiple CR1 lineages of non-LTR retrotransposons, including those from MacCR1A, MacCR1B and T1Q families. A comparative analysis of RT nucleotide sequences demonstrated an extremely high similarity among elements both in interspecific and intraspecific comparisons. CR1A-like elements were found only in family Lycaenidae. In contrast, MacCR1B lineage clones were extremely similar to CR1B non-LTR retrotransposons from Bombycidae moths: silkworm <it>Bombyx mori </it>and <it>Oberthueria caeca</it>.</p> <p>Conclusion</p> <p>The degree of coding sequence similarity of the studied elements, their discontinuous distribution, and results of divergence-versus-age analysis make it highly unlikely that these sequences diverged at the same time as their host taxa. The only reasonable alternative explanation is horizontal transfer. In addition, phylogenetic markers for population analysis of <it>Maculinea </it>could be developed based on the described non-LTR retrotransposons.</p

Evolution and origin of merlin, the product of the Neurofibromatosis type 2 (NF2) tumor-suppressor gene

BACKGROUND: Merlin, the product of the Neurofibromatosis type 2 (NF2) tumor suppressor gene, belongs to the ezrin-radixin-moesin (ERM) subgroup of the protein 4.1 superfamily, which links cell surface glycoproteins to the actin cytoskeleton. While merlin's functional activity has been examined in mammalian and Drosophila models, little is understood about its evolution, diversity, and overall distribution among different taxa. RESULTS: By combining bioinformatic and phylogenetic approaches, we demonstrate that merlin homologs are present across a wide range of metazoan lineages. While the phylogenetic tree shows a monophyletic origin of the ERM family, the origin of the merlin proteins is robustly separated from that of the ERM proteins. The derivation of merlin is thought to be in early metazoa. We have also observed the expansion of the ERM-like proteins within the vertebrate clade, which occurred after its separation from Urochordata (Ciona intestinalis). Amino acid sequence alignment reveals the absence of an actin-binding site in the C-terminal region of all merlin proteins from various species but the presence of a conserved internal binding site in the N-terminal domain of the merlin and ERM proteins. In addition, a more conserved pattern of amino acid residues is found in the region containing the so-called "Blue Box," although some amino acid substitutions in this region exist in the merlin sequences of worms, fish, and Ciona. Examination of sequence variability at functionally significant sites, including the serine-518 residue, the phosphorylation of which modulates merlin's intra-molecular association and function as a tumor suppressor, identifies several potentially important sites that are conserved among all merlin proteins but divergent in the ERM proteins. Secondary structure prediction reveals the presence of a conserved α-helical domain in the central to C-terminal region of the merlin proteins of various species. The conserved residues and structures identified correspond to the important sites highlighted by the available crystal structures of the merlin and ERM proteins. Furthermore, analysis of the merlin gene structures from various organisms reveals the increase of gene length during evolution due to the expansion of introns; however, a reduction of intron number and length appears to occur in the merlin gene of the insect group. CONCLUSION: Our results demonstrate a monophyletic origin of the merlin proteins with their root in the early metazoa. The overall similarity among the primary and secondary structures of all merlin proteins and the conservation of several functionally important residues suggest a universal role for merlin in a wide range of metazoa

Numerical simulation and investigation of induction through-heaters in dynamic operation mode

Purpose - Because of their widespread use in industry, induction through-heaters of various metal products must be of high effectiveness not only in "quasi" steady-state operation but in different transient modes as well. Nowadays, they are usually designed to provide the required characteristics in "quasi" steady-state operation mode mainly. The purpose of this paper is to examine numerical simulation of transient processes in induction through-heating lines generally and investigate dynamic temperature fields during the first start of the heaters particularly. Design/methodology/ approach - The research methodology is based on coupled numerical electromagnetic and thermal analyses using FEM approach. ANSYS simulations are supported with the developed tools for imitation of mass transfer effects in continuous induction heating lines. Findings - The results show that transient temperature fields in the heated strip or slab significantly differ from their "quasi" steady-state descriptions. Local temperature variations acquired in longitudinal as well as transverse flux induction heaters during the first start have been predicted. Practical implications - The received results can be used for design of induction through-heaters and improvement of their characteristics in dynamic operation modes. Originality/value - Investigation of dynamic characteristics of the heaters in dynamic modes can be only done by numerical modelling based on special algorithms providing a time loop additional to coupling between electromagnetic and thermal analyses. Such algorithms have been developed and used for investigation of two types of induction installations: through-heaters of cylindrical billets for forging and heating lines of strip or thin slab for rolling mills. © 2011 Emerald Group Publishing Limited. All rights reserved