Progressive Mauve: Multiple alignment of genomes with gene flux and rearrangement

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a method to align two or more genomes that have undergone large-scale recombination, particularly genomes that have undergone substantial amounts of gene gain and loss (gene flux). The method utilizes a novel alignment objective score, referred to as a sum-of-pairs breakpoint score. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The progressive genome alignment algorithm demonstrates markedly improved accuracy over previous approaches in situations where genomes have undergone realistic amounts of genome rearrangement, gene gain, loss, and duplication. We apply the progressive genome alignment algorithm to a set of 23 completely sequenced genomes from the genera Escherichia, Shigella, and Salmonella. The 23 enterobacteria have an estimated 2.46Mbp of genomic content conserved among all taxa and total unique content of 15.2Mbp. We document substantial population-level variability among these organisms driven by homologous recombination, gene gain, and gene loss. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve .Comment: Revision dated June 19, 200

Dust sublimation by GRBs and its implications

The prompt optical flash recently detected accompanying GRB990123 suggests that, for at least some GRBs, gamma-ray emission is accompanied by prompt optical-UV emission with luminosity L(1-7.5eV)=10^{49}(\Delta\Omega/4\pi)erg/s, where \Delta\Omega is the solid angle into which gamma-ray and optical-UV emission is beamed. Such an optical-UV flash can destroy dust in the beam by sublimation out to an appreciable distance, approximately 10 pc, and may clear the dust out of as much as 10^7(\Delta\Omega/4\pi)M_sun of molecular cloud material on an apparent time scale of 10 seconds. Detection of time dependent extinction on this time scale would therefore provide strong constraints on the GRB source environment. Dust destruction implies that existing, or future, observations of not-heavily-reddened fireballs are not inconsistent with GRBs being associated with star forming regions. In this case, however, if gamma-ray emission is highly beamed, the expanding fireball would become reddened on a 1 week time scale. If the optical depth due to dust beyond approximately 8 pc from the GRB is 0.2<\tau_V<2, most of the UV flash energy is converted to infra-red, \lambda \sim 1 micron, radiation with luminosity \sim 10^{41} erg/s extending over an apparent duration of \sim 20(1+z)(\Delta\Omega/0.01) day. Dust infra-red emission may already have been observed in GRB970228 and GRB980326, and may possibly explain their unusual late time behavior.Comment: 16 pages, including 1 figure, submitted to Ap

Keragaman Genetik Dari Msp 1, Msp 2, Dan Glurp Pada Plasmodium Falciparum Di Kabupaten Sumba Tengah, Nusa Tenggara Timur

Malaria is still a public health problem in Central Sumba regency, East Nusa Tenggara. Over the past decade, anti malaria drugs resistance has rapidly become a major public health problem in the East Nusa Tenggara, including Central Sumba regency. The problem of malaria control are not only influenced by the anti malaria drugs resistance on P. faciparum and specific genes but also by many variations of allele of Plasmodium malaria. A study is needed especially on molecular epidemiology of P. falciparum using locus gene Merozoites Surface Protein 1 (MSP 1) , Merozoites Surface Protein (MSP2) and Glutamate Rich Protein (GLURP), which aims to identify the genetic diversity marker of Plasmodium falciparum in Central Sumba Regency. The method applied was a nested Polymerase Chain Reaction (PCR) to each locus gen separately. The results of the 50 fresh blood of patients infected with P. falciparum, each gene locus of MSP 1, MSP 2 and GLURP can be identified as muchas 38%, 12% and 10%. The third gene locus was found only in 38 % (19/50) positive samples. It can be identified 7 alleles at each locus genes, three classes'MSP1 allele (15.8 %), four classes of MSP alleles (21.1%) and three classes of GLURP alleles (15.8 %). A multigenotype infection of P. falciparum and MSP 2 deleted was diverse marker of P. falciparum gene locus with varied class of alleles. It can be concluded that multigenotype infections have occurred in research location

Concrete resource analysis of the quantum linear system algorithm used to compute the electromagnetic scattering cross section of a 2D target

We provide a detailed estimate for the logical resource requirements of the quantum linear system algorithm (QLSA) [Phys. Rev. Lett. 103, 150502 (2009)] including the recently described elaborations [Phys. Rev. Lett. 110, 250504 (2013)]. Our resource estimates are based on the standard quantum-circuit model of quantum computation; they comprise circuit width, circuit depth, the number of qubits and ancilla qubits employed, and the overall number of elementary quantum gate operations as well as more specific gate counts for each elementary fault-tolerant gate from the standard set {X, Y, Z, H, S, T, CNOT}. To perform these estimates, we used an approach that combines manual analysis with automated estimates generated via the Quipper quantum programming language and compiler. Our estimates pertain to the example problem size N=332,020,680 beyond which, according to a crude big-O complexity comparison, QLSA is expected to run faster than the best known classical linear-system solving algorithm. For this problem size, a desired calculation accuracy 0.01 requires an approximate circuit width 340 and circuit depth of order $10^{25}$ if oracle costs are excluded, and a circuit width and depth of order $10^8$ and $10^{29}$, respectively, if oracle costs are included, indicating that the commonly ignored oracle resources are considerable. In addition to providing detailed logical resource estimates, it is also the purpose of this paper to demonstrate explicitly how these impressively large numbers arise with an actual circuit implementation of a quantum algorithm. While our estimates may prove to be conservative as more efficient advanced quantum-computation techniques are developed, they nevertheless provide a valid baseline for research targeting a reduction of the resource requirements, implying that a reduction by many orders of magnitude is necessary for the algorithm to become practical.Comment: 37 pages, 40 figure

PERSEPSI DAN PARTISIPASI MASYARAKAT LOKAL TERHADAP KEBERADAAN HUTAN DIKLAT SISIMENI SANAM DI DESA SILLU KECAMATAN FATULEU KABUPATEN KUPANG

Hutan Diklat Sisimeni Sanam merupakan suatu areal hutan yang diperuntukan sebagai&nbsp;sarana dan prasarana praktek dalam rangka mendukung kegiatan diklat kehutanan serta sebagai&nbsp;laboratorium alam untuk mengembangkan ilmu pengetahun dan teknologi (Iptek) di bidang&nbsp;kehutanan. Kawasan Hutan Diklat Sisimeni sanam (RTK.185) Pulau Timor secara keseluruhan&nbsp;telah disahkan sebagai kawasan hutan tetap pada tanggal 25 September 1982 oleh MenteriPertanian u.b. Direktur Jendral Kehutanan dengan fungsi sebagai hutan produksi terbatas,&nbsp;sehingga kawasan hutan tersebut telah mempunyai kekuatan hukum. Dalam Permenhut No. 44&nbsp;tahun 2012, tentang pengukuhan kawasan hutan dilakukan melalui tahapan penunjukan kawasan&nbsp;hutan, penataan batas kawasan hutan serta penetapan kawasan hutan. Kawasan Hutan Dengan&nbsp;Tujuan Khusus (KHDTK) Diklat Sisimeni sanam telah ditetapkan melalui Keputusan MenteriKehutanan No. SK. 367/Menhut-II/2009 dengan luas ± 2.973,20 ha dan panjang 37,94 km.&nbsp;Sebelum ditunjuk sebagai kawasan hutan pendidikan dan pelatihan berstatus sebagai Register&nbsp;Tanah Kehutanan (RTK) 185 kelompok hutan Sisimeni Sanam, dikelola sebagai Hutan Produksi&nbsp;oleh RPH Camplong, BKPH Camplong, CDK Kupang. Kurangnya sosialisasi dan komunikasi&nbsp;dari pihak pengelola dengan masyarakat Desa Sillu, mengakibatkan kurangnya pemahaman danwawasan masyarakat tentang Keberadaan Hutan Diklat Sisimeni Sanam.&nbsp;Tujuan dari penelitian ini adalah untuk mengetahui sikap, persepsi, perilaku mayarakat lokal&nbsp;terhadap keberadaan Hutan Diklat Sisimeni Sanam dan untuk mengetahui bagaimana partisipasi&nbsp;masyarakat dalam pengelolaan Hutan Diklat Sisimeni Sanam. Sampel yang digunakan dalam&nbsp;penelitian ini adalah penduduk sekitar kawasan Hutan Diklat Sisimeni Sanam yang berjumlah 91&nbsp;jiwa, dengan penentuannya menggunakan purposive sampling. Hasil dari penelitian ini&nbsp;menunjukan bahwa sikap dan partisipasi masyarakat terhadap Hutan Diklat Sisimeni Sanam di&nbsp;Desa Sillu, Kecamatan Fatuleu, Kabupaten Kupang, Provinsi Nusa Tenggara Timur tergolong&nbsp;pada kategori baik (60.93% dan 79,08%), sedangkan tingkat persepsi dan perilaku mayarakat&nbsp;lokal terhadap keberadaan Hutan Diklat Sisimeni Sanam tergolong pada kategori netral (50,92%&nbsp;dan 52,59%)

Spin-dependent effective interactions for halo nuclei

We discuss the spin-dependence of the effective two-body interactions appropriate for three-body computations. The only reasonable choice seems to be the fine and hyperfine interactions known for atomic electrons interacting with the nucleus. One exception is the nucleon-nucleon interaction imposing a different type of symmetry. We use the two-neutron halo nucleus 11Li as illustration. We demonstrate that models with the wrong spin-dependence are basically without predictive power. The Pauli forbidden core and valence states must be consistently treated.Comment: TeX file, 6 pages, 3 postscript figure

Temperate and tropical forest canopies are already functioning beyond their thermal thresholds for photosynthesis

Tropical tree species have evolved under very narrow temperature ranges compared to temperate forest species. Studies suggest that tropical trees may be more vulnerable to continued warming compared to temperate species, as tropical trees have shown declines in growth and photosynthesis at elevated temperatures. However, regional and global vegetation models lack the data needed to accurately represent such physiological responses to increased temperatures, especially for tropical forests. To address this need, we compared instantaneous photosynthetic temperature responses of mature canopy foliage, leaf temperatures, and air temperatures across vertical canopy gradients in three forest types: tropical wet, tropical moist, and temperate deciduous. Temperatures at which maximum photosynthesis occurred were greater in the tropical forests canopies than the temperate canopy (30 ± 0.3 °C vs. 27 ± 0.4 °C). However, contrary to expectations that tropical species would be functioning closer to threshold temperatures, photosynthetic temperature optima was exceeded by maximum daily leaf temperatures, resulting in sub-optimal rates of carbon assimilation for much of the day, especially in upper canopy foliage (\u3e10 m). If trees are unable to thermally acclimate to projected elevated temperatures, these forests may shift from net carbon sinks to sources, with potentially dire implications to climate feedbacks and forest community composition