Comprehensive analysis of lncRNAs and mRNAs in skeletal muscle of rainbow trout (Oncorhynchus mykiss) exposed to estradiol

Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout (Oncorhynchus mykiss), but the mechanisms directing with this response are not fully understood. To better characterize the effects of E2 in muscle, we identified differentially regulated mRNAs and lncRNAs in juvenile rainbow trout exposed to E2. Here, we performed next-generation RNA sequencing and comprehensive bioinformatics analyses to characterize the transcriptome profiles, including mRNAs and long noncoding RNAs (lncRNAs), in skeletal muscle of rainbow trout injected with E2. A total of 226 lncRNAs and 253 mRNAs were identified as differentially regulated. We identified crucial pathways, including several signal transduction pathways, hormone response, oxidative response and protein, carbon and fatty acid metabolism pathways. Subsequently, a functional lncRNA-mRNA co- expression network was constructed, which consisted of 681 co-expression relationships between 164 lncRNAs and 201 mRNAs. Moreover, a lncRNA-pathway network was constructed. A total of 65 key lncRNAs were identified that regulate 20 significantly enriched pathways. Overall, our analysis provides insights into mRNA and lncRNA networks in rainbow trout skeletal muscle and their regulation by E2 while understanding the molecular mechanism of lncRNAs

Maternal and neonatal outcomes of pregnancy at 39 weeks and beyond with mild gestational diabetes mellitus

Objectives: The purpose of this study was to retrospectively analyze maternal and neonatal outcomes in pregnant women with mild gestational diabetes mellitus at 39 weeks compared to 40 weeks. Material and methods: Clinical data of 372 cases of mild gestational diabetes mellitus form First Affiliated Hospital of Sun Yat-sen University were analyzed retrospectively. There were 108 mild GDM patients that delivered at 40–40+6 weeks in our research group, and 264 patients that delivered in 39–39+6 weeks in the control group. Neonatal and maternal outcomes were compared between the two groups. Results: There was no difference between the two groups in the rate of cesarean section (42.6% vs. 45.5%, p = 0.614). The incidence of large for gestational age between the two groups was also not different (11.1% vs. 10.6%, p = 0.887). The rate of postpartum hemorrhage and shoulder dystocia of the two groups was not different either (p > 0.05). There was no significant difference in the incidence of fetal distress, neonatal asphyxia, neonatal pathological jaundice, neonatal hypoglycemia, and neonatal respiratory distress syndrome in the two groups (p > 0.05). Conclusions: There were no significant differences in adverse pregnancy outcomes and neonatal outcomes in women with mild gestational diabetes between deliveries at 39 and 40 weeks

Lhx8 interacts with a novel germ cell-specific nuclear factor containing an Nbl1 domain in rainbow trout (Oncorhynchus mykiss)

Lhx8 is an important transcription factor that is preferentially expressed in germ cells. Lhx8 null mice are infertile due to lack of oocytes and impairment of the transition from primordial follicles to primary follicles. Lhx8 deficiency also affects the expression of many important oocyte-specific genes. In this study, we report the characterization of rainbow trout lhx8 genes and identification of a novel germ cell-specific nuclear factor that interacts with Lhx8. Two lhx8genes, lhx8a and lhx8b, were identified, encoding proteins of 344 and 361 amino acids, respectively. The two proteins share 83% sequence identity and both transcripts are specifically expressed in the ovary. Quantitative real time PCR analysis demonstrated that both genes are expressed highly in pre-vitellogenic ovaries as well as in early stage embryos. Using a yeast two-hybrid screening system, a novel protein (Borealin-2) interacting with Lhx8 was identified. The interaction between either Lhx8a or Lhx8b and Borealin-2 was further confirmed by a bimolecular fluorescence complementation (BiFC) assay. Borealin-2 is a protein of 255 amino acids containing an Nbl1 domain, and its mRNA expression is restricted to the ovary and testis. A GFP reporter assay revealed that Borealin-2 is a nuclear protein. Collectively, results indicate that both Lhx8a and Lhx8b function through interaction with Borealin-2, which may play an important role during oogenesis and early embryogenesis in rainbow trout

A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus)

BACKGROUND: The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine stickleback populations at the phenotypic trait of lateral plate morphology and the underlying candidate gene Ectodysplacin (EDA). Many studies have focused on this trait and candidate gene, although other genes involved in marine-freshwater adaptation may be equally important. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background. RESULTS: RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new. CONCLUSIONS: We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-867) contains supplementary material, which is available to authorized users

Multimodal imaging of congenital pyriform fossa fistula in children

ObjectiveOur aim was to explore the clinical value of multimodal imaging examinations in the diagnosis of congenital pyriform fossa fistula in children, so as to provide clues for the early diagnosis and treatment of congenital pyriform fossa fistula.MethodsThe clinical and imaging data of 55 children with pyriform fossa fistula diagnosed surgically in our hospital from 2015 to 2018 were analyzed retrospectively. All 55 patients underwent a CT scan. Of those patients, contrast enhancement CT was performed in 47 cases, MRI was performed in 2 cases, and barium esophagography was performed in 41 cases.ResultsAmong the 55 cases, there were 24 male patients and 31 female patients. The age ranged from 11 months to 13 years old, and the median age was 3.8 years old. The lesions of 49 cases (89.1%) were located on the left side, and the imaging of CT showed soft tissue mass in the anterior cervical region blurred boundary. There was ipsilateral thyroid involvement in 50 cases (90.9%), trachea and/or carotid sheath extension in 43 cases (78.2%), abscess formation in 39 cases (70.9%), and pneumatosis in 25 cases (45.5%). The CT examination of 22 children after treatment showed a linear or tubular low-density shadow in the thyroid gland, gas accumulation in the anterior cervical region or thyroid, and residual contrast medium, partly. A total of 24 cases underwent barium esophagography during the acute phase, and 15 cases (62.5%) showed sinus formation from the pyriform fossa downward or punctate high-density shadow in the anterior cervical region. The 2 cases where MRI was performed showed abscess formation in one side of the neck and thyroid involvement.ConclusionPyriform fossa fistula is most common in the left anterior cervical region, and it is closely related to the thyroid gland. The plain and enhanced-contrast CT scan can be used as the first choice during the infection stage. It helps to understand the location, extent, and structure of the surrounding tissue. The preliminary diagnosis of pyriform sinus fistula was according to the imaging features. It provided an important basis for clinical diagnosis and reduced the pain caused by repeated infection or surgical incision and drainage

Understanding the Discrepancy between IRX and Balmer Decrement in Tracing Galaxy Dust Attenuation

We compare the infrared excess (IRX) and Balmer decrement (${\rm H\alpha/H\beta }$) as dust attenuation indicators in relation to other galaxy parameters using a sample of $\sim$32 000 local star-forming galaxies (SFGs) carefully selected from SDSS, GALEX and WISE. While at fixed ${\rm H\alpha/H\beta }$, IRX turns out to be independent on galaxy stellar mass, the Balmer decrement does show a strong mass dependence at fixed IRX. We find the discrepancy, parameterized by the color excess ratio $R_{\rm EBV} \equiv E(B-V)_{\rm IRX}/E(B-V)_{\rm H\alpha/H\beta }$, is not dependent on the gas-phase metallicity and axial ratio but on the specific star formation rate (SSFR) and galaxy size ($R_{\rm e}$) following $R_{\rm EBV}=0.79+0.15\log({\rm SSFR}/R_{\rm e}^{2})$. This finding reveals that the nebular attenuation as probed by the Balmer decrement becomes increasingly larger than the global (stellar) attenuation of SFGs with decreasing SSFR surface density. This can be understood in the context of an enhanced fraction of intermediate-age stellar populations that are less attenuated by dust than the HII region-traced young population, in conjunction with a decreasing dust opacity of the diffuse ISM when spreading over a larger spatial extent. Once the SSFR surface density of an SFG is known, the conversion between attenuation of nebular and stellar emission can be well estimated using our scaling relation.Comment: 9 pages, 5 figures, Accepted for publication in Ap

A Universal Relation of Dust Obscuration Across Cosmic Time

We investigate dust obscuration as parameterised by the infrared excess IRX$\equiv$$L_{\rm IR}/L_{\rm UV}$ in relation to global galaxy properties, using a sample of $\sim$32$\,$000 local star-forming galaxies (SFGs) selected from SDSS, GALEX and WISE. We show that IRX generally correlates with stellar mass ($M_\ast$), star formation rate (SFR), gas-phase metallicity ($Z$), infrared luminosity ($L_{\rm IR}$) and the half-light radius ($R_{\rm e}$). A weak correlation of IRX with axial ratio (b/a) is driven by the inclination and thus seen as a projection effect. By examining the tightness and the scatter of these correlations, we find that SFGs obey an empirical relation of the form $IRX$=$10^\alpha\,(L_{\rm IR})^{\beta}\,R_{\rm e}^{-\gamma}\,(b/a)^{-\delta}$ where the power-law indices all increase with metallicity. The best-fitting relation yields a scatter of $\sim$0.17$\,$dex and no dependence on stellar mass. Moreover, this empirical relation also holds for distant SFGs out to $z=3$ in a population-averaged sense, suggesting it to be universal over cosmic time. Our findings reveal that IRX approximately increases with $L_{\rm IR}/R_{\rm e}^{[1.3 - 1.5]}$ instead of $L_{\rm IR}/R_{\rm e}^{2}$ (i.e., surface density). We speculate this may be due to differences in the spatial extent of stars versus star formation and/or complex star-dust geometries. We conclude that not stellar mass but IR luminosity, metallicity and galaxy size are the key parameters jointly determining dust obscuration in SFGs.Comment: 22 pages, 14 figures, accepted for publication in the MNRA

The genome sequence of the wisent (Bison bonasus)

This work was supported by the Youth Science and Technology Innovation Team of Sichuan Province (2014TD003), Shenzhen Industrial Designation Services Cloud Platform (GGJS20150429172906635), International Collaboration 111 Projects of China, Fundamental Research Funds for the Central Universities, 985 and 211 Projects of Sichuan University.The wisent, also known as the European bison, was rescued from extinction approximately 80 years ago through the conservation of 12 individuals. Here, we present the draft genome sequence of a male wisent individual descended from this founding stock. A total of 366 billion base pairs (Gb) of raw reads from whole-genome sequencing of this wisent were generated using the Illumina HiSeq2000 platform. The final genome assembly (2.58 Gb) is composed of 29,074 scaffolds with an N50 of 4.7 Mb. 47.3% of the genome is composed of repetitive elements. We identified 21,542 genes and 58,385 non-coding RNAs. A phylogenetic tree based on nuclear genomes indicated sister relationships between bison and wisent and between the wisent-bison clade and yak. For 75 genes we obtained evidence of positive evolution in the wisent lineage. We provide the first genome sequence and gene annotation for the wisent. The availability of these resources will be of value for the future conservation of this endangered large mammal and for reconstructing the evolutionary history of the Bovini tribe.Publisher PDFPeer reviewe