Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence

<p>Abstract</p> <p>Background</p> <p>Histone methylation can dramatically affect chromatin structure and gene expression and was considered irreversible until recent discoveries of two families of histone demethylases, the KDM1 (previously LSD1) and JmjC domain-containing proteins. These two types of proteins have different functional domains and distinct substrate specificities. Although more and more KDM1 and JmjC proteins have been shown to have histone demethylase activity, our knowledge about their evolution history is limited.</p> <p>Results</p> <p>We performed systematic phylogenetic analysis of these histone demethylase families and uncovered different evolutionary patterns. The <it>KDM1 </it>genes have been maintained with a stable low copy number in most organisms except for a few duplication events in flowering plants. In contrast, multiple genes for JmjC proteins with distinct domain architectures were present before the split of major eukaryotic groups, and experienced subsequent birth-and-death evolution. In addition, distinct evolutionary patterns can also be observed between animal and plant histone demethylases in both families. Furthermore, our results showed that some <it>JmjC </it>subfamilies contain only animal genes with specific demethylase activities, but do not have plant members.</p> <p>Conclusion</p> <p>Our study improves the understanding about the evolutionary history of <it>KDM1 </it>and <it>JmjC </it>genes and provides valuable insights into their functions. Based on the phylogenetic relationship, we discussed possible histone demethylase activities for several plant JmjC proteins. Finally, we proposed that the observed differences in evolutionary pattern imply functional divergence between animal and plant histone demethylases.</p

Hydrodynamic Coefficients of Yawed Square Cylinder in Oscillating Flow

Experimental and Computational Hydraulic

Quantum phases of the biased two-chain-coupled Bose-Hubbard Ladder

We investigate the quantum phases of bosons in a two-chain-coupled ladder. This bosonic ladder is generally in a biased configuration, meaning that the two chains of the ladder can have dramatically different on-site interactions and potential energies. Adopting the numerical density-matrix renormalization-group method, we analyze the phase transitions in various parameter spaces. We find signatures of both insulating-to-superfluid and superfluid-to-insulating quantum phase transitions as the interchain tunnelling is increased. Interestingly, tunning the interaction to some intermediate values, the system can exhibit a reentrant quantum phase transition between insulating and superfluid phases. We show that for infinite interaction bias, the model is amenable to some analytical treatments, whose prediction about the phase boundary is in great agreement with the numerical results. We finally clarify some critical parameters which separate the system into regimes with distinct phase behaviours, and briefly compare typical properties of the biased and unbiased bosonic ladder systems. Our work enriches the Bose-Hubbard physics.Comment: 10 pages, 7 figure

Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality.

Eusocial insects, mostly Hymenoptera, have evolved unique colonial lifestyles that rely on the perception of social context mainly through pheromones, and chemoreceptors are hypothesized to have played important adaptive roles in the evolution of sociality. However, because chemoreceptor repertoires have been characterized in few social insects and their solitary relatives, a comprehensive examination of this hypothesis has not been possible. Here, we annotate ∼3,000 odorant and gustatory receptors in recently sequenced Hymenoptera genomes and systematically compare &gt;4,000 chemoreceptors from 13 hymenopterans, representing one solitary lineage (wasps) and three independently evolved eusocial lineages (ants and two bees). We observe a strong general tendency for chemoreceptors to expand in Hymenoptera, whereas the specifics of gene gains/losses are highly diverse between lineages. We also find more frequent positive selection on chemoreceptors in a facultative eusocial bee and in the common ancestor of ants compared with solitary wasps. Our results suggest that the frequent expansions of chemoreceptors have facilitated the transition to eusociality. Divergent expression patterns of odorant receptors between honeybee and ants further indicate differential roles of chemoreceptors in parallel trajectories of social evolution

Spin-tensor Meissner currents of ultracold bosonic gas in an optical lattice

We investigate the Meissner currents of interacting bosons subjected to a staggered artificial gauge field in a three-leg ribbon geometry, realized by spin-tensor--momentum coupled spin-1 atoms in a 1D optical lattice. By calculating the current distributions using the state-of-the-art density-matrix renormalization-group method, we find a rich phase diagram containing interesting Meissner and vortex phases, where the currents are mirror symmetric with respect to the {\color{red}middle leg} (i.e., they flow in the same direction on the two boundary legs opposite to that on the middle leg), leading to the spin-tensor type Meissner currents, which is very different from previously observed chiral edge currents under uniform gauge field. The currents are uniform along each leg in the Meissner phase and form vortex-antivortex pairs in the vortex phase. Besides, the system also support a polarized phase that spontaneously breaks the mirror symmetry, whose ground states are degenerate with currents either uniform or forming vortex-antivortex pairs. We also discuss the experimental schemes for probing these phases. Our work provides useful guidance to ongoing experimental research on synthetic flux ribbons and paves the way for exploring novel many-body phenomena therein.Comment: 10 pages, 9 figure