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

Non-minimal Einstein-Yang-Mills-Higgs theory: Associated, color and color-acoustic metrics for the Wu-Yang monopole model

We discuss a non-minimal Einstein-Yang-Mills-Higgs model with uniaxial anisotropy in the group space associated with the Higgs field. We apply this theory to the problem of propagation of color and color-acoustic waves in the gravitational background related to the non-minimal regular Wu-Yang monopole.Comment: 14 pages, no figure

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

Effects of Biochar Amendment and Arbuscular Mycorrhizal Fungi Inoculation on Availability of Soil Phosphorus and Growth of Maize

A glasshouse experiment was conducted to study the interactive effects of biochar amendment and arbuscular mycorrhizal fungi (AMF) inoculation on phosphorus uptake by maize (Zea mayze L.) grown on a calcareous soil of Kupang, East Nusa Tenggara. The biochar was made of cow dung. Twelve treatment combinations (three biochars levels of 0, 5 and 7.5 g/kg of soil, and four AMF inoculation levels of 0, 5, 10 and 15 spores / kg of soil) were arranged in a completely randomized block design with three replicates. Results of the study showed that at 8 weeks after transplanting, the biochar and mycorrhizal treatments increased the availability soil phosphorus and phosphorus uptake by maize. Application 4.5 and 7.5 g biochar/kg of soil combined with inoculation of 10-15 AMF spores / kg of soil provided to high value of phosphorus uptake by maize. Application of biochar alone, however, did not significantly improve maize growth and phosphorus uptake by maize

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%)

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli

BACKGROUND: Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites. RESULTS: Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility. CONCLUSION: We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events