The role of the triangle singularity in Λ(1405)\Lambda(1405) production in the π−p→K0πΣ\pi^-p\rightarrow K^0\pi\Sigma and pp→pK+πΣpp\rightarrow pK^+\pi\Sigma processes

We have investigated the cross section for the $\pi^-p\rightarrow K^0\pi\Sigma$ and $pp\rightarrow pK^+\pi\Sigma$ reactions paying attention to a mechanism that develops a triangle singularity. The triangle diagram is realized by the decay of a $N^*$ to $K^*\Sigma$ and the $K^*$ decay into $\pi K$, and the $\pi\Sigma$ finally merges into $\Lambda(1405)$. The mechanism is expected to produce a peak around $2140$ MeV in the $K\Lambda(1405)$ invariant mass. We found that a clear peak appears around $2100$ MeV in the $K\Lambda(1405)$ invariant mass which is about $40$ MeV lower than the expectation, and that is due to the resonance peak of a $N^*$ resonance which plays a crucial role in the $K^*\Sigma$ production. The mechanism studied produces the peak of the $\Lambda(1405)$ around or below 1400 MeV, as is seen in the $pp\rightarrow pK^+\pi\Sigma$ HADES experiment.Comment: 12 pages, 9 figure

Additional file 3: of COGNATE: comparative gene annotation characterizer

Result table. COGNATE results of analyzing exon and intron lengths of Apis mellifera. This data sheet contains the mean and median lengths of exons and introns, which are part of the 10,733 transcripts analyzed by COGNATE (default run, i.e., using the longest of each gene’s alternative transcripts). In total, 76,276 exons and 65,543 introns were taken into account. The data is visualized in Fig. 2. (XLSX 225 kb

Additional file 4: of COGNATE: comparative gene annotation characterizer

The COGNATE package. This archive file contains the COGNATE package, including Perl scripts, Additional file 1: Parameter table, Readme, example data and output, and the GAL library. (ZIP 566 kb

Amplicons_NT.tar

Supplementary File Archive: "Amplicons_NT.tar.gz." Multiple nucleotide sequence alignments in FASTA format of expected amplicons when applying the PCR oligonucleotide primer pairs inferred in our study. Each multiple nucleotide sequence alignment contains the nucleotide sequence of each of the nine species of Hymenoptera whose genomes we analyzed plus the position and nucleotide sequence (with IUPAC ambiguity code; complement sequence of reverse primer) of the inferred forward and reverse PCR oligonucleotide primer. Anatomy of the file names: [Identifier of ortholog group]_[Identifier of oligonucleotide primer pair specific to ortholog group]_[Identifier of recommended pair of sequencing primers].NT.fas For example, the file name "HOG2939_01_B.NT.fas" contains the nucleotide sequences expected to be amplified from the genes belonging to ortholog group "HOG2939" when using the first oligonucleotide primer pair that has been inferred for this ortholog group and the sequencing oligonucleotide primer pair B. HOG stands for "Hymenoptera Ortholog Group"

Rating of obtained polymerase chain reaction (PCR) products.

<p>Rating of the PCR products obtained from using the degenerate oligonucleotide primers shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039826#pone-0039826-t003" target="_blank">Table 3</a> to amplify ten target genes in six apocritan Hymenoptera. ++  =  target PCR product in excess. +  =  target PCR product sufficient for direct sequencing. +/−  =  target PCR product insufficient for direct sequencing. –  =  no target PCR product. (?)  =  unclear whether or not PCR products include amplicon of target gene.</p>*<p>Secondary PCR amplification product likely hampering direct sequencing.</p

Empirically evaluated degenerate oligonucleotide PCR primer pairs.

<p>The ten degenerate oligonucleotide primers were tested with the respective binding sites for sequencing primer HOG-Seq-A (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039826#pone-0039826-t002" target="_blank">Table 2</a>) attached to the 5′ end and used to amplify ten target genes in six apocritan Hymenoptera. <i>d</i>  =  degree of degeneration. <i>T</i>_m  =  approximate melting temperature [°C].</p

Oligonucleotide sequencing primer pairs.

<p>The nucleotide sequences of the sequencing primers were attached as a binding site to the 5′ end of the degenerate oligonucleotide polymerase chain reaction (PCR) primers. Each of the oligonucleotide primers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039826#pone.0039826.s002" target="_blank">Table S1</a> is compatible with at least one of the sequencing primers added to the 5′ end of the PCR primer. <i>T</i>_m  =  approximate melting temperature [°C].</p

Polymerase chain reaction (PCR) products separated on 1.5% agarose gel.

<p>The depicted gel shows the PCR products obtained from using the inferred oligonucleotide primer pair 7229_02_A (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039826#pone-0039826-t003" target="_blank">Table 3</a>) to PCR amplify DNA of <i>Stephanus serrator</i> (Stephanidae, 1), <i>Leucospis dorsigera</i> (Leucospidae, 2), <i>Gasteruption tournieri</i> (Gasteruptiidae, 3), <i>Chrysis mediata</i> (Chrysididae, 4), <i>Lestica alata</i> (Crabronidae, 5), and <i>Episyron albonotatum</i> (Pompilidae, 6). All PCR products were suitable for direct sequencing with the sequencing oligonucleotide primers HOG-Seq-A-F/−R (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039826#pone-0039826-t002" target="_blank">Table 2</a>). –  =  negative control.</p

Hypothesized phylogenetic relationships of apocritan Hymenoptera studied in this investigation [4], [12].

<p>Taxa with sequenced genomes are highlighted in green; their genome sequences were analyzed to identify single-copy genes and to design degenerate oligonucleotide PCR primers. DNA of non-highlighted species was used to assess the functionality of the inferred PCR and sequencing primers.</p