We observe a narrow enhancement near 2m(p) in the invariant mass spectrum of pp pairs from radiative J/psi-->gammapp decays. No similar structure is seen in J/psi-->pi(0)pp decays. The results are based on an analysis of a 58 x 10(6) event sample of J/psi decays accumulated with the BESII detector at the Beijing electron-positron collider. The enhancement can be fit with either an S- or P-wave Breit-Wigner resonance function. In the case of the S-wave fit, the peak mass is below 2m(p) at M=1859(+3)(-10) (stat)+5-25(syst) MeV/c(2) and the total width is Gamma<30 MeV/c(2) at the 90% confidence level. These mass and width values are not consistent with the properties of any known particle.

BackgroundThe green mud crab (Scylla paramamosain) is the most prevalent crustacean on the southeast coast of China. The molecular regulatory mechanism of sex determination and gonadal differentiation in this species has received considerable attention in recent years because of the huge differences—both biological and economic—between male and female crabs. In this study, next-generation sequencing technology was used to develop deep-coverage transcriptomic sequencing data for the testis and ovary of S. paramamosain.ResultsA total of 365,116 reads (testis 171,962, ovary 193,154) with an average sequence length of 285 bp were produced from testis and ovary cDNA libraries. After filtering out contaminating reads, the clean reads were assembled, producing a total of 21,791 isotigs and leaving 22,814 reads as singlets. Using the BLASTX program, 3,471 unique sequences (2,275 isotigs and 1,196 singletons) were annotated with known protein sequences from the NCBI non-redundant (Nr) protein sequence database. The Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses allowed the 224 unique sequences that were annotated with enzyme code (EC) numbers to be mapped into 174 KEGG pathways. After comparing the ovary and testis libraries, 4,021 gonad-differentially, 10,522 ovary-specifically, and 19,013 testis-specifically expressed genes were identified. Moreover, 33 ovary-specific, 14 testis-specific, and 34 gonad-differential transcripts were confirmed by semi-quantitative PCR and quantitative real-time PCR. In addition, 8,610 putative simple sequence repeats (SSRs) and 23,879 potential single nucleotide polymorphisms (SNPs) were identified.ConclusionThis is the first large-scale RNA sequencing of S. paramamosain to be reported. We have identified many important functional genes and made a preliminary attempt to construct the regulatory network involved in the gonadal development of crustaceans. The annotated transcriptome data will provide fundamental support for future research into the reproduction biology of S. paramamosain. A large number of candidate SSRs and SNPs were detected, which could be used as genetic markers for population genetics and functional genomics in this species.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-585) contains supplementary material, which is available to authorized users.

The decays of J/psi --> etaphif(0)(980)[eta --> gammagamma, phi --> K(+) K(-), f(0)(980) --> pi(+)pi(-)] are analyzed using a sample of 5.8 x 10(7) J/psi events collected with the BESII detector at the Beijing Electron-Positron Collider. A structure at around 2.18 GeV/c(2) with about 5 sigma significance is observed in the phif(0)(980) invariant mass spectrum. A fit with a Breit-Wigner function gives the peak mass and width of m = 2.186+/-0.010(stat)+/-0.006(syst) GeV/c(2) and Gamma = 0.065+/-0.023(stat)+/-0.017(syst) GeV/c(2), respectively, which are consistent with those of Y(2175), observed by the BABAR Collaboration in the initial-state radiation process e(+)e(-) --> gamma(ISR) phif(0)(980). The production branching ratio is determined to be Br(J/psi --> etaY(2175))Br(Y(2175)- -> phif(0)(980))Br(f(0)(980) --> pi(+)pi(-)) = [3.23+/-0.75(stat)+/-0.73(syst)] x 10(-4), assuming that the Y(2175) is a 1(--) state.

Background: In gnathostomes, chemosensory receptors (CR) expressed in olfactory epithelia are encoded by evolutionarily dynamic gene families encoding odorant receptors (OR), trace amineassociated receptors (TAAR), V1Rs and V2Rs. A limited number of OR-like sequences have been found in invertebrate chordate genomes. Whether these gene families arose in basal or advanced vertebrates has not been resolved because these families have not been examined systematically in agnathan genomes.

BackgroundDe novo assembly of non-model organism’s transcriptomes has recently been on the rise in concert with the number of de novo transcriptome assembly software programs. There is a knowledge gap as to what assembler software or k-mer strategy is best for construction of an optimal de novo assembly. Additionally, there is a lack of consensus on which evaluation metrics should be used to assess the quality of de novo transcriptome assemblies.ResultSix different assembly strategies were evaluated from four different assemblers. The Trinity assembly was used in its default 25 single k-mer value while Bridger, Oases, and SOAPdenovo-Trans were performed with multiple k-mer strategies. Bridger, Oases, and SOAPdenovo-Trans used a small multiple k-mer (SMK) strategy consisting of the k-mer lengths of 21, 25, 27, 29, 31, and 33. Additionally, Oases and SOAPdenovo-Trans were performed using a large multiple k-mer (LMK) strategy consisting of k-mer lengths of 25, 35, 45, 55, 65, 75, and 85. Eleven metrics were used to evaluate each assembly strategy including three genome related evaluation metrics (contig number, N50 length, Contigs >1 kb, reads) and eight transcriptome evaluation metrics (mapped back to transcripts (RMBT), number of full length transcripts, number of open reading frames, Detonate RSEM-EVAL score, and percent alignment to the southern platyfish, Amazon molly, BUSCO and CEGMA databases). The assembly strategy that performed the best, that is it was within the top three of each evaluation metric, was the Bridger assembly (10 of 11) followed by the Oases SMK assembly (8 of 11), the Oases LMK assembly (6 of 11), the Trinity assembly (4 of 11), the SOAP LMK assembly (4 of 11), and the SOAP SMK assembly (3 of 11).ConclusionThis study provides an in-depth multi k-mer strategy investigation concluding that the assembler itself had a greater impact than k-mer size regardless of the strategy employed. Additionally, the comprehensive performance transcriptome evaluation metrics utilized in this study identified the need for choosing metrics centered on user defined research goals. Based on the evaluation metrics performed, the Bridger assembly was able to construct the best assembly of the testis transcriptome in Fundulus heteroclitus.

We report values of R = sigma(e(+)e(-)-->hadrons)/sigma(e(+)e(-)-->mu(+)mu(-)) for 85 center-of-mass energies between 2 and 5 GeV measured with the upgraded Beijing Spectrometer at the Beijing Electron-Positron Collider.

Variations in gene expression are essential for the evolution of novel phenotypes and for speciation. Studying allelic specific gene expression (ASGE) within interspecies hybrids provides a unique opportunity to reveal underlying mechanisms of genetic variation. Using Xiphophorus interspecies hybrid fishes and high-throughput next generation sequencing technology, we were able to assess variations between two closely related vertebrate species, X. maculatus and X. couchianus, and their F1 interspecies hybrids. We constructed transcriptome-wide SNP polymorphism sets between two highly inbred X. maculatus lines (JP 163 A and B), and between X. maculatus and a second species, X. couchianus. The X. maculatus JP 163 A and B parental lines have been separated in the laboratory for ≈ 70 years and we were able to identify SNPs at a resolution of 1 SNP per 49 kb of transcriptome. In contrast, SNP polymorphisms between X. couchianus and X. maculatus species, which diverged ≈ 5–10 million years ago, were identified about every 700 bp. Using 6,524 transcripts with identified SNPs between the two parental species (X. maculatus and X. couchianus), we mapped RNA-seq reads to determine ASGE within F1 interspecies hybrids. We developed an in silico X. couchianus transcriptome by replacing 90,788 SNP bases for X. maculatus transcriptome with the consensus X. couchianus SNP bases and provide evidence that this procedure overcomes read mapping biases. Employment of the insilico reference transcriptome and tolerating 5 mismatches during read mapping allow direct assessment of ASGE in the F1 interspecies hybrids. Overall, these results show that Xiphophorus is a tractable vertebrate experimental model to investigate how genetic variations that occur during speciation may affect gene interactions and the regulation of gene expression.

Glucose transporters (GLUTs) have been implicated in adaptive and survival responses to hypoxic stress in mammals. In fish, the expression and regulation of GLUT in relation to hypoxia remains unexplored. Here we describe the identification of a hypoxia-responsive glucose transporter gene (gcGLUT) and the corresponding full-length cDNA from the grass carp. The gene spans 11 kb of genomic sequence and consists of 12 exons and 11 introns, and an open reading frame (ORF) of 1599 bp encoding a polypeptide of 533 amino acids, with a predicted molecular mass of 57 kDa and a pI of 8.34. BLASTX analysis showed that the ORF shared high sequence identity with the GLUT1 (57-59%), GLUT3 (59-60%) and GLUT4 (55-59%) proteins from different vertebrates. Comparative analysis of GLUT genomic structures showed that the arrangement of exons and position of split codons are highly conserved amongst members of the class I GLUTs suggesting that these genes share a common ancestor. Phylogenetic analysis indicated that gcGLUT is most closely related to the GLUT3 proteins. Northern blot analysis showed that the 3.1-kb gcGLUT transcript was most abundantly expressed and responsive to hypoxia in kidney. Up-regulated expression by hypoxia was also evident in eye and gill, but differential patterns of expression were observed. Low expression levels detected in brain, heart, liver and muscle were not responsive to hypoxic stress.