Gene content array of <i>Rickettsia</i> plasmidome obtained from BBH analysis.

<p>The right three columns showed the pRIG references of putative ortholog gene groups, the total number of genes for each pRIG and its corresponding annotation including its COGID form COG database. Each member of the pRIG was annotated as either complete (red), split (yellow), fragment (blue), chimeric (green) and absent (or remnant, violet).</p

Kebijakan Anti Dumping Dan Trade Deflection: Studi Kasus Synthetic Staple Fibre Polyester (PSF)

. This research empirically examines whether a country\u27s anti dumping policy can distort export of another country to third markets. This research tries to explore about trade deflection of Indonesia\u27s export on Synthetic Staple Fibre Polyester (PSF) HS 550320 to non-European Union as the result of European Union\u27s (EU) anti dumping policy on Indonesia. This research uses panel data model (fixed effects) and 20 countries (non-European Union) of Indonesia\u27s PSF export during ten years (1996-2005). We find evidence that trade deflection for Indonesia\u27s export on Synthetic Staple Fibre Polyester (PSF) HS 550320 occurred. Because of European Union had imposed anti dumping duty on Indonesia, Indonesia\u27s export to nonEuropean Union had increased ranged from 25 percent to 44 percent. This result shows that dumping duty from European Union does not fully carry out negative effect for Indonesia, furthermore thisphenomena can be used as ”early warning” for Indonesia both for case of Indonesia as exporting country or third countries

COG functional categories of <i>Rickettsia</i> plasmidome originated from vertical and horizontal evolutions as well as duplications.

<p>COG functional categories of <i>Rickettsia</i> plasmidome originated from vertical and horizontal evolutions as well as duplications.</p

Evolutionary scenario of rickettsial plasmids.

<p>Evolutionary scenario of rickettsial plasmids.</p

Supertree obtained from 10 genes of <i>Rickettsia</i> plasmids as well as <i>Rickettsia</i> and <i>Orientia</i> chromosomes using subtree prune-and-regraft distance (D = 64).

<p><i>Candidatus Midichloria mitochondrii</i> (YP_004679220.1) and <i>Pantoea ananatis</i> (YP_005193440.1) were used as outgroups. The list of genes used are two transposases, patatin-like phospholipase, thymidylate kinase, heat shock protein, <i>dna</i>A-like replication initiator proteins, helix-turn-helix DNA-binding domain, cell surface antigen Sca12, conjugative transfer protein containing <i>tra</i>D domain, and leucine rich-repeat containing protein. In the right, summary of evolutionary events that shaped rickettsial plasmids.</p

Test used at protein level to conclude on putative gene or putative pseudogene.

<p>The species where the protein is tested is highlighted in bold type. Other species have known proteins. <i>D1</i> and <i>D2</i> are age of divergence, in millions of years. Note that all abbreviations concerning species name and their ancestors are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038792#pone-0038792-g006" target="_blank">Figure 6</a> (A) The species in which the protein is analyzed is surrounded by species having different LCAs. If the sequence identity is higher between <i>Mus</i> and <i>Hsa</i> as compared to <i>Mus</i> and <i>Mdo</i> thus, we can conclude on a putative gene; otherwise on a putative pseudogene. (B) If all species with known protein have the same LCA as the species under investigation, a calculation step is necessary. <i>Value1</i> is the percent identity between <i>Mus</i> and <i>Hsa</i>. <i>Value2</i> is the percent identity between <i>Mmu</i> and <i>Hsa</i>. A minimum relative threshold is calculated by multiplying <i>D2</i> distance by the similarity percentage <i>Value2</i> and by dividing the total by the distance <i>D</i>. If the similarity percentage <i>Value1</i> is superior to the minimum relative threshold calculated, we conclude on a putative gene; otherwise, we conclude on a putative pseudogene.</p

Benchmark results of 14 pseudogenes cases described in literature.

<p>The <b><i>Publications</i></b> column indicates references of studies of the literature used as reference for comparison with GLADX results.</p><p>The <b><i>Agree</i></b> column contains yes if the case is consistent with the literature results and no when the result is in contradiction.</p><p>The <b><i>Precision</i></b> column indicates the quality of results obtained: “-” means low precision, “+” means a better precision, “ = ” means we found exactly the same results, and “/” means it can't be interpreted.</p><p>The <b><i>Artifacts</i></b><i> </i><b><i>highlighted</i></b> column indicates cases where artifacts are present: “*” are cases where GLADX found artifacts in databases (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038792#pone.0038792.s004" target="_blank">Text S2</a>); “**” means artifacts caused by tools implemented in GLADX, and “/” means no artifact was observed.</p><p>The <b><i>Comments</i></b> column indicates some particularities, “/” means no particular comment.</p

Frequencies of complete and degraded (split, fragment or chimeric) genes identified in the plasmidome of <i>Rickettsia</i>.

<p>Frequencies of complete and degraded (split, fragment or chimeric) genes identified in the plasmidome of <i>Rickettsia</i>.</p

<i>Rickettsia</i> and <i>Orientia</i> genomes extracted from the National Center for Biotechnology Information (NCBI) database.

<p><i>Rickettsia</i> and <i>Orientia</i> genomes extracted from the National Center for Biotechnology Information (NCBI) database.</p

Processing of an alignment and conservation of informative signal of sequences.

<p>The hatched area is deleted area, blue boxes are exons (exons of retrieved orthologs come from prediction), bold black lines are DNA, and bold dotted lines are gaps.</p