Quantum Rabi model for N-state atoms

A tractable N-state Rabi Hamiltonian is introduced by extending the parity symmetry of the two-state model. The single-mode case provides a few-parameter description of a novel class of periodic systems, predicting that the ground state of certain four-state atom-cavity systems will undergo parity change at strong coupling. A group-theoretical treatment provides physical insight into dynamics and a modified rotating wave approximation obtains accurate analytical energies. The dissipative case can be applied to study excitation energy transfer in molecular rings or chains.Comment: 5 pages, 3 figures + supplement (2 pages); to appear in Phys. Rev. Let

Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid

<p>Abstract</p> <p>Background</p> <p><it>Paphiopedilum </it>is a horticulturally and ecologically important genus of ca. 80 species of lady's slipper orchids native to Southeast Asia. These plants have long been of interest regarding their chromosomal evolution, which involves a progressive aneuploid series based on either fission or fusion of centromeres. Chromosome number is positively correlated with genome size, so rearrangement processes must include either insertion or deletion of DNA segments. We have conducted Fluorescence <it>In Situ </it>Hybridization (FISH) studies using 5S and 25S ribosomal DNA (rDNA) probes to survey for rearrangements, duplications, and phylogenetically-correlated variation within <it>Paphiopedilum</it>. We further studied sequence variation of the non-transcribed spacers of 5S rDNA (5S-NTS) to examine their complex duplication history, including the possibility that concerted evolutionary forces may homogenize diversity.</p> <p>Results</p> <p>5S and 25S rDNA loci among <it>Paphiopedilum </it>species, representing all key phylogenetic lineages, exhibit a considerable diversity that correlates well with recognized evolutionary groups. 25S rDNA signals range from 2 (representing 1 locus) to 9, the latter representing hemizygosity. 5S loci display extensive structural variation, and show from 2 specific signals to many, both major and minor and highly dispersed. The dispersed signals mainly occur at centromeric and subtelomeric positions, which are hotspots for chromosomal breakpoints. Phylogenetic analysis of cloned 5S rDNA non-transcribed spacer (5S-NTS) sequences showed evidence for both ancient and recent post-speciation duplication events, as well as interlocus and intralocus diversity.</p> <p>Conclusions</p> <p><it>Paphiopedilum </it>species display many chromosomal rearrangements - for example, duplications, translocations, and inversions - but only weak concerted evolutionary forces among highly duplicated 5S arrays, which suggests that double-strand break repair processes are dynamic and ongoing. These results make the genus a model system for the study of complex chromosomal evolution in plants.</p

Penerapan Resource Allocation Dan Levelling Tenaga Kerja Dengan Menggunakan Microsoft Project 2010 Pada Suatu Proyek Konstruksi

Dalam menerapkan allocation dan levelling digunakan software Microsoft project 2010. Metode ini diterapkan pada suatu proyek konstruksi dengan resource yang ada. Sumber daya yang di bahas pada penelitian ini adalah tenaga kerja. Kemudian kita dapat menentukan tenaga kerja yang dibutuhkan pada proyek tersebut sehingga penjadwalan dapat terpenuhi. Pada penelitian ini perhitungan tenaga kerja yang dibutuhkan dilakukan secara manual menggunakan SNI. Kemudian hasilnya diinputkan pada Microsoft Project. Setelah itu melakukan levelling pada Microsoft Project secara otomatis. Hasil penelitian menunjukkan bahwa dengan tenaga kerja yang ada yaitu 1 mandor, 21 pekerja, 3 tukang batu, 10 tukang kayu, jadwal yang awalnya di rencanakan 10 bulan menjadi 20 bulan. Apabila jadwal proyek tetap 10 bulan maka pekerja yang harus disediakan menjadi rata-rata 40 orang tetapi pada akhir bulan September 2014 dan bulan Mei 2015 harus disediakan 65 orang, tukang batu rata-rata 2 orang tetapi pada bulan Desember 2014 dan Januari 2015 harus disediakan 4 orang, tukang kayu rata-rata 8 orang tetapi pada bulan Oktober 2014, Desember 2014 dan Januari 2015 harus disediakan 12 orang. Oleh karena itu pada saat perencanaan jadwal proyek harus memperhitungkan jumlah tenaga kerja yang tersedia sehingga jadwal yang direncanakan dapat realistis sesuai dengan Kenyataan di lapangan

Symmetric Rotating Wave Approximation for the Generalized Single-Mode Spin-Boson System

The single-mode spin-boson model exhibits behavior not included in the rotating wave approximation (RWA) in the ultra and deep-strong coupling regimes, where counter-rotating contributions become important. We introduce a symmetric rotating wave approximation that treats rotating and counter-rotating terms equally, preserves the invariances of the Hamiltonian with respect to its parameters, and reproduces several qualitative features of the spin-boson spectrum not present in the original rotating wave approximation both off-resonance and at deep strong coupling. The symmetric rotating wave approximation allows for the treatment of certain ultra and deep-strong coupling regimes with similar accuracy and mathematical simplicity as does the RWA in the weak coupling regime. Additionally, we symmetrize the generalized form of the rotating wave approximation to obtain the same qualitative correspondence with the addition of improved quantitative agreement with the exact numerical results. The method is readily extended to higher accuracy if needed. Finally, we introduce the two-photon parity operator for the two-photon Rabi Hamiltonian and obtain its generalized symmetric rotating wave approximation. The existence of this operator reveals a parity symmetry similar to that in the Rabi Hamiltonian as well as another symmetry that is unique to the two-photon case, providing insight into the mathematical structure of the two-photon spectrum, significantly simplifying the numerics, and revealing some interesting dynamical properties.Comment: 11 pages, 5 figure

Polyglutamine variation in a flowering time protein correlates with island age in a Hawaiian plant radiation

<p>Abstract</p> <p>Background</p> <p>A controversial topic in evolutionary developmental biology is whether morphological diversification in natural populations can be driven by expansions and contractions of amino acid repeats in proteins. To promote adaptation, selection on protein length variation must overcome deleterious effects of multiple correlated traits (pleiotropy). Thus far, systems that demonstrate this capacity include only ancient or artificial morphological diversifications. The Hawaiian Islands, with their linear geological sequence, present a unique environment to study recent, natural radiations. We have focused our research on the Hawaiian endemic mints (Lamiaceae), a large and diverse lineage with paradoxically low genetic variation, in order to test whether a direct relationship between coding-sequence repeat diversity and morphological change can be observed in an actively evolving system.</p> <p>Results</p> <p>Here we show that in the Hawaiian mints, extensive polyglutamine (CAG codon repeat) polymorphism within a homolog of the pleiotropic flowering time protein and abscisic acid receptor FCA tracks the natural environmental cline of the island chain, consequent with island age, across a period of 5 million years. CAG expansions, perhaps following their natural tendency to elongate, are more frequent in colonists of recently-formed, nutrient-rich islands than in their forebears on older, nutrient-poor islands. Values for several quantitative morphological variables related to reproductive investment, known from Arabidopsis <it>fca </it>mutant studies, weakly though positively correlate with increasing glutamine tract length. Together with protein modeling of FCA, which indicates that longer polyglutamine tracts could induce suboptimally mobile functional domains, we suggest that CAG expansions may form slightly deleterious alleles (with respect to protein function) that become fixed in founder populations.</p> <p>Conclusion</p> <p>In the Hawaiian mint <it>FCA </it>system, we infer that contraction of slightly deleterious CAG repeats occurred because of competition for resources along the natural environmental cline of the island chain. The observed geographical structure of <it>FCA </it>variation and its correlation with morphologies expected from Arabidopsis mutant studies may indicate that developmental pleiotropy played a role in the diversification of the mints. This discovery is important in that it concurs with other suggestions that repetitive amino acid motifs might provide a mechanism for driving morphological evolution, and that variation at such motifs might permit rapid tuning to environmental change.</p

Effects of Thermocycles on Body Weight Gain and Gonadal Growth in the Goldfish, Carassius auratus

Goldfish subjected to increased temperatures at one of six different times of day had significant differences in weight gain and testicular growth depending on the time of treatment. Depending on the time of day the thermocycle was initiated, weight gain and testicular growth could be either stimulated, inhibited, or equal to that in fishes subjected to constant heat or constant cold. Heat applied during the last 4 h of darkness was particularly conducive to weight gain and testicular growth. The results of this study may have important implications for aquaculture

Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants

BACKGROUND: The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases (GSKs) are non-receptor serine/threonine protein kinases that are involved in a variety of biological processes. In contrast to the two members of the GSK3 family in mammals, plants appear to have a much larger set of divergent GSK genes. Plant GSKs are encoded by a multigene family; analysis of the Arabidopsis genome revealed the existence of 10 GSK genes that fall into four major groups. Here we characterized the structure of Arabidopsis and rice GSK genes and conducted the first broad phylogenetic analysis of the plant GSK gene family, covering a taxonomically diverse array of algal and land plant sequences. RESULTS: We found that the structure of GSK genes is generally conserved in Arabidopsis and rice, although we documented examples of exon expansion and intron loss. Our phylogenetic analyses of 139 sequences revealed four major clades of GSK genes that correspond to the four subgroups initially recognized in Arabidopsis. ESTs from basal angiosperms were represented in all four major clades; GSK homologs from the basal angiosperm Persea americana (avocado) appeared in all four clades. Gymnosperm sequences occurred in clades I, III, and IV, and a sequence of the red alga Porphyra was sister to all green plant sequences. CONCLUSION: Our results indicate that (1) the plant-specific GSK gene lineage was established early in the history of green plants, (2) plant GSKs began to diversify prior to the origin of extant seed plants, (3) three of the four major clades of GSKs present in Arabidopsis and rice were established early in the evolutionary history of extant seed plants, and (4) diversification into four major clades (as initially reported in Arabidopsis) occurred either just prior to the origin of the angiosperms or very early in angiosperm history

Functional characterization and expression of GASCL1 and GASCL2, two anther-specific chalcone synthase like enzymes from Gerbera hybrida

The chalcone synthase superfamily consists of type III polyketidesynthases (PKSs), enzymes responsible for producing plant secondary metabolites with various biological and pharmacological activities. Anther-specific chalcone synthase-like enzymes (ASCLs) represent an ancient group of type III PKSs involved in the biosynthesis of sporopollenin, the main component of the exine layer of moss spores and mature pollen grains of seed plants. In the latter, ASCL proteins are localized in the tapetal cells of the anther where they participate in sporopollenin biosynthesis and exine formation within the locule. It is thought that the enzymes responsible for sporopollenin biosynthesis are highly conserved, and thus far, each angiosperm species with a genome sequenced has possessed two ASCL genes, which in Arabidopsis thaliana are PKSA and PKSB. The Gerbera hybrida (gerbera) PKS protein family consists of three chalcone synthases (GCHS1, GCHS3 and GCHS4) and three 2-pyrone synthases (G2PS1, G2PS2 and G2PS3). In previous studies we have demonstrated the functions of chalcone synthases in flavonoid biosynthesis, and the involvement of 2-pyrone synthases in the biosynthesis of antimicrobial compounds found in gerbera. In this study we expanded the gerbera PKS-family by functionally characterizing two gerbera ASCL proteins. In vitro enzymatic studies using purified recombinant proteins showed that both GASCL1 and GASCL2 were able to use medium and long-chain acyl-CoA starters and perform two to three condensation reactions of malonyl-CoA to produce tri- and tetraketide 2-pyrones, usually referred to as alpha-pyrones in sporopollenin literature. Both GASCL1 and GASCL2 genes were expressed only floral organs, with most expression observed in anthers. In the anthers, transcripts of both genes showed strict tapetum-specific localization. (C) 2016 Elsevier Ltd. All rights reserved.Peer reviewe

Scaffold filling, contig fusion and comparative gene order inference

<p>Abstract</p> <p>Background</p> <p>There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes?</p> <p>Results</p> <p>Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes <it>Ricinus communis </it>and <it>Vitis vinifera</it>.</p> <p>Conclusions</p> <p>The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.</p

Coordinated dispersal and pre-isthmian assembly of the central American ichthyofauna

© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. We document patterns of coordinated dispersal over evolutionary time frames in heroine cichlids and poeciliine live-bearers, the two most species-rich clades of freshwater fishes in the Caribbean basin. Observed dispersal rate (DO) values were estimated from time-calibrated molecular phylogenies in LAGRANGE+, a modified version of the ML-based parametric biogeographic program LAGRANGE. DO is measured in units of wallaces (wa) as the number of biogeographic range-expansion events per million years. DO estimates were generated on a dynamic paleogeographic landscape of five areas over three time intervals from Upper Cretaceous to Recent. Expected dispersal rate (DE) values were generated from alternative paleogeographic models, with dispersal rates proportional to target area and source-river discharge volume, and inversely proportional to paleogeographic distance. Correlations between DO and DE were used to assess the relative contributions of these three biogeographic parameters. DO estimates imply a persistent dispersal corridor across the Eastern (Antillean) margin of the Caribbean plate, under the influence of prevailing and perennial riverine discharge vectors such as the Proto-Orinoco-Amazon river. Ancestral area estimation places the earliest colonizations of the Greater Antilles and Central America during the Paleocene-Eocene (ca. 58-45 Ma), potentially during the existence of an incomplete Paleogene Arc (∼59 Ma) or Lesser Antilles Arc (∼45 Ma), but predating the GAARlandia land bridge (∼34-33 Ma). Paleogeographic distance is the single best predictor of DO. The Western (Central American) platemargin did not serve as a dispersal corridor until the LateNeogene (12-0 Ma), and contributed relatively little to the formation of modern distributions