InDels within caprine IGF2BP1 intron 2 and the 3'-untranslated regions are associated with goat growth traits

Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) is involved in the Hedgehog pathway and has been shown to regulate the RNA stability of several growth-related target genes. It is located in a quantitative trait locus showing a strong association with traits related to body size in ducks. Fibroblast growth factor receptor 1 (FGFR1) also participates in Hedgehog signaling pathways and has been reported to be associated with organic growth and development. FGFR1-knockout mice have been shown to have severe postnatal growth defects, including an approximately 50% reduction in body weight and bone mass. Meanwhile, nonsense-mediated mRNA decay factor (SMG6) can maintain genomic stability, which is associated with organic growth and development. Therefore, we hypothesized that IGF2BP1, FGFR1 and SMG6 genes may play important roles in the growth traits of goats. In this study, the existence of two insertion/deletion (InDel) variants within IGF2BP1, one InDel within FGFR1 and two InDels within SMG6 was verified and their correlation with growth traits was analyzed in 2429 female Shaanbei white cashmere goats. Results showed both the 15 bp InDel in intron 2 and the 5 bp InDel in the 3' regulatory region within IGF2BP1 were significantly associated with growth traits (P < 0.05) and goats with the combinatorial homozygous insertion genotypes of these two loci had the highest body weight (P = 0.046). The other InDels within FGFR1 and SMG6 were not obviously associated with growth traits (P > 0.05). Therefore, the two InDels in IGF2BP1 were vital mutations affecting goat growth traits.

Randomised clinical trial: Tong-Xie-Yao-Fang granules versus placebo for patients with diarrhoea-predominant irritable bowel syndrome

BACKGROUND

Tong-Xie-Yao-Fang (TXYF) is a Chinese herbal formula for treating chronic diarrhoea accompanied by abdominal pain. The results were inconsistent in previous trials examining its effect.

AIM

To study the efficacy of TXYF granules for treating diarrhoea-predominant irritable bowel syndrome (IBS-D).

METHODS

We performed a double-blind, placebo-controlled randomised trial and enrolled 160 participants with IBS-D. The participants had VAS scores ≥3 cm in IBS-D global symptoms and ≥2 days in a week with abdominal pain and loose stools (Bristol score 5, 6 or 7). They were randomly assigned to received TXYF or placebo during a treatment period of 4 weeks, and they were followed up for 8 weeks after treatment. The primary outcome was adequate relief of IBS-D global symptoms for at least 2 of 4 weeks during weeks 1-4. Secondary outcomes included mean weekly VAS scores of IBS-D major symptoms, mean weekly stool frequency, mean weekly Bristol score, and adverse events.

RESULTS

155 of 160 patients completed the trial. We found a significantly higher rate of adequate relief of global symptoms in TXFY group during weeks 1 to 4 (57.5% vs 37.5%, χ² = 5.6391, P = 0.017); logistic regression analysis showed a similar result (OR 2.2, 95% CI 1.2-4.4, P = 0.016). Most of the secondary outcomes showed superiority of TXYF over placebo in weekly assessment from week 3 to week 7. The adverse event rate was low in both groups (3.8% vs 3.8%, P = 1.000).

CONCLUSION

During a 4 week trial, TXFY granules were superior to placebo in controlling symptoms of IBS-D.

The developmental transcriptome landscape of bovine skeletal muscle defined by Ribo-Zero ribonucleic acid sequencing

Ribonucleic acid sequencing (RNA-Seq) libraries are normally prepared with oligo(dT) selection of poly(A)+ mRNA, but it depends on intact total RNA samples. Recent studies have described Ribo-Zero technology, a novel method that can capture both poly(A)+ and poly(A)- transcripts from intact or fragmented RNA samples. We report here the first application of Ribo-Zero RNA-Seq for the analysis of the bovine embryonic, neonatal, and adult skeletal muscle whole transcriptome at an unprecedented depth. Overall, 19,893 genes were found to be expressed, with a high correlation of expression levels between the calf and the adult. Hundreds of genes were found to be highly expressed in the embryo and decreased at least 10-fold after birth, indicating their potential roles in embryonic muscle development. In addition, we present for the first time the analysis of global transcript isoform discovery in bovine skeletal muscle and identified 36,694 transcript isoforms. Transcriptomic data were also analyzed to unravel sequence variations; 185,036 putative SNP and 12,428 putative short insertions-deletions (InDel) were detected. Specifically, many stop-gain, stop-loss, and frameshift mutations were identified that probably change the relative protein production and sequentially affect the gene function. Notably, the numbers of stage-specific transcripts, alternative splicing events, SNP, and InDel were greater in the embryo than in the calf and the adult, suggesting that gene expression is most active in the embryo. The resulting view of the transcriptome at a single-base resolution greatly enhances the comprehensive transcript catalog and uncovers the global trends in gene expression during bovine skeletal muscle development.

Improved Constraints on Global Methane Emissions and Sinks Using δ 13C-CH4

We study the drivers behind the global atmospheric methane (CH4) increase observed after 2006. Candidate emission and sink scenarios are constructed based on proposed hypotheses in the literature. These scenarios are simulated in the TM5 tracer transport model for 1984-2016 to produce three-dimensional fields of CH4 and δ 13C-CH4, which are compared with observations to test the competing hypotheses in the literature in one common model framework. We find that the fossil fuel (FF) CH4 emission trend from the Emissions Database for Global Atmospheric Research 4.3.2 inventory does not agree with observed δ 13C-CH4. Increased FF CH4 emissions are unlikely to be the dominant driver for the post-2006 global CH4 increase despite the possibility for a small FF emission increase. We also find that a significant decrease in the abundance of hydroxyl radicals (OH) cannot explain the post-2006 global CH4 increase since it does not track the observed decrease in global mean δ 13C-CH4. Different CH4 sinks have different fractionation factors for δ 13C-CH4, thus we can investigate the uncertainty introduced by the reaction of CH4 with tropospheric chlorine (Cl), a CH4 sink whose abundance, spatial distribution, and temporal changes remain uncertain. Our results show that including or excluding tropospheric Cl as a 13 Tg/year CH4 sink in our model changes the magnitude of estimated fossil emissions by ∼20%. We also found that by using different wetland emissions based on a static versus a dynamic wetland area map, the partitioning between FF and microbial sources differs by 20 Tg/year, ∼12% of estimated fossil emissions.

Altered microRNA expression in bovine skeletal muscle with age

Age-dependent decline in skeletal muscle function leads to several inherited and acquired muscular disorders in elderly individuals. The levels of microRNAs (miRNAs) could be altered during muscle maintenance and repair. We therefore performed a comprehensive investigation for miRNAs from five different periods of bovine skeletal muscle development using next-generation small RNA sequencing. In total, 511 miRNAs, including one putatively novel miRNA, were identified. Thirty-six miRNAs were differentially expressed between prenatal and postnatal stages of muscle development including several myomiRs (miR-1, miR-206 and let-7 families). Compared with miRNA expression between different muscle tissues, 14 miRNAs were up-regulated and 22 miRNAs were down-regulated in the muscle of postnatal stage. In addition, a novel miRNA was predicted and submitted to the miRBase database as bta-mir-10020. A dual luciferase reporter assay was used to demonstrate that bta-mir-10020 directly targeted the 3'-UTR of the bovine ANGPT1 gene. The overexpression of bta-mir-10020 significantly decreased the DsRed fluorescence in the wild-type expression cassette compared to the mutant type. Using three computational approaches - miranda, pita and rnahybrid - these differentially expressed miRNAs were also predicted to target 3609 bovine genes. Disease and biological function analyses and the KEGG pathway analysis revealed that these targets were statistically enriched in functionality for muscle growth and disease. Our miRNA expression analysis findings from different states of muscle development and aging significantly expand the repertoire of bovine miRNAs now shown to be expressed in muscle and could contribute to further studies on growth and developmental disorders in this tissue type.

Overexpression of angiopoietin 2 promotes the formation of oral squamous cell carcinoma by increasing epithelial-mesenchymal transition-induced angiogenesis

Oral squamous cell carcinoma (OSCC) is the most common cancer of the head and neck and is associated with a high rate of lymph node metastasis. The initial step in the metastasis and transition of tumors is epithelial-mesenchymal transition (EMT)-induced angiogenesis, which can be mediated by angiopoietin 2 (ANG2), a key regulatory factor in angiogenesis. In the present study, immunohistochemistry and real-time quantitative reverse transcriptase (qRT-PCR) were used to measure the expression of ANG2 in OSCC tissues. Plasmids encoding ANG2 mRNA were used for increased ANG2 expression in the OSCC cell line TCA8113. The short interfering RNA (siRNA)-targeting ANG2 mRNA sequences were used to inhibit ANG2 expression in TCA8113 cells. Subsequently, transwell assays were performed to examine the effects of ANG2 on TCA8113 cell migration and invasion. Furthermore, in vivo assays were performed to assess the effect of ANG2 on tumor growth. Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) assays and immunohistochemistry were used to examine cell apoptosis and angiogenesis in tumor tissues, respectively. Finally, western blot analysis was performed to evaluate tumor formation-related proteins in OSCC tissues. We found that protein expression of ANG2 was remarkably upregulated in OSCC tissues. Overexpression of ANG2 increased the migration and invasion of TCA8113 cells by regulating EMT. Further investigations showed that overexpression of ANG2 increased tumor growth in nude mice, and angiogenesis of OSCC tissues increased in the presence of ANG2 overexpression. Overexpression of ANG2 also reduced cell apoptosis in tumor tissue cells. Finally, we found that overexpression of ANG2 resulted in changes in the expression of tumor formation-related proteins including vimentin, E-cadherin, Bim, PUMA, Bcl-2, Bax, Cyclin D1, PCNA and CD31. Our findings show that ANG2 has an important role in the migration and invasion of OSCC. More importantly, further investigations suggested that overexpression of ANG2 might increase OSCC metastasis by promoting angiogenesis in nude mice. This stimulatory effect could be achieved by inducing abnormal EMT and by reducing apoptosis and increasing proliferation of cells.

Maintenance of SOX9 stability and ECM homeostasis by selenium-sensitive PRMT5 in cartilage

OBJECTIVES

Selenium (Se) plays pivotal roles in maintaining optimal health. Nevertheless, how Se influences the metabolism of extracellular matrix (ECM) in cartilage remains unclear. The aim of the present study was to observe protein dimethylation by certain Se-sensitive PRMT and to elucidate its effects on the key transcriptional factor in cartilage.

METHODS

We observed the expression of selenoproteins and markers of ECM metabolism in chondrocytes and articular cartilage of the rats under Se-deficiency by RT-qPCR, immunoblotting and immunohistochemistry. Then, we analyzed the expression of total dimethylated protein by using specific antibody under different Se statuses. After Se sensitive PRMT was identified, we used siRNA or PRMT inhibitor or stably overexpressing vector to intervene in the PRMT expression and identified the key transcriptional factor. Co-immunoprecipitation was applied to verify the interaction between PRMT and the key transcriptional factor. Finally, we measured the half-life time of the key transcriptional factor by immunoblotting after cycloheximide treatment.

RESULTS

In chondrocytes and cartilage of the rats with Se deficiency, we found an aberrant metabolism manifesting decreased expression of Col2a1 and increased expression of Mmp-3. Then, we identified that PRMT5 was the unique type II PRMT, sensitive to Se status. PRMT5 upregulation led to the increased COL2A1 expression but decreased MMP-3 expression in chondrocytes. Furthermore, we revealed that PRMT5 improved SOX9 stability by dimethylating the protein, which contributed to maintain the matrix metabolic homeostasis of the chondrocytes.

CONCLUSIONS

Se-sensitive PRMT5 increases the half-life of SOX9 protein via PTM and helps to maintain ECM homeostasis of the articular cartilage.

Six novel coding SNPs of the nucleophosmin 1 (<i>NPM1</i>) gene and their associations with growth traits in bovine (Brief Report)

Abstract. The Nucleophosmin 1 (NPM1) gene encodes a multifunctional nucleolar phosphoprotein that has crucial roles in the control of different aspects of cell growth and homeostasis, such as ribosome biogenesis, centrosome duplication, cell cycle progression, apoptosis and cell differentiation (GRISENDI et al. 2006, NAOE et al. 2006). As mutants of NPM1 gene impact protein synthesis, NPM1 is an essential protein in mouse development and cell growth (MAGGI et al. 2008). The bovine NPM1 gene contains one exon and locates at chromosome 9. In previous work, the 12-bp deletion was detected in bovine NPM1 gene coding region. (HUANG et al. 2010). In this study, the coding region of bovine NPM1 gene has been scanned by PCR-SSCP, DNA sequencing and forced PCR-RFLP methods for SNPs in 1 032 individuals belonging to four Chinese cattle breeds. Association of six mutations of NPM1 gene with growth traits was analyzed.

Dot-immunogold filtration assay as a screening test for syphilis

A dot-immunogold filtration assay (DIGFA) for the rapid detection of reaginic antibody in the serum of syphilitic patients was developed. The assay was simple, rapid, and reproducible. The test completion time was 2 min, and the assay required no equipment. The positive dot was very obvious, and the results could easily be determined with the naked eye. A total of 350 serum samples were examined by DIGFA, the rapid plasma reagin test, and the fluorescent treponemal antibody-absorption test. The levels of agreement between DIGFA and the rapid reagin test and between DIGFA and the fluorescent treponemal antibody-absorption test were 100 and 98%, respectively. The results of clinical application indicated that DIGFA could be used as a routine screening test for syphilis.

Prevalence, trend and disparities of palliative care utilization among hospitalized metastatic breast cancer patients who received critical care therapies

BACKGROUND

Early integration of palliative care (PC) for patients with advanced cancer has been recommended to improve quality of care. This study aims to describe prevalence, temporal trend and predictors of PC use in metastatic breast cancer (mBCa) patients receiving critical care therapies (CCT; included invasive mechanic ventilation, percutaneous endoscopic gastrostomy tube, total parenteral nutrition, tracheostomy and dialysis).

METHODS

The National Inpatient Sample was queried for mBCa patients receiving CCT between 2005 and 2014. Annual percent changes (APC) were calculated for PC prevalence in the overall cohort and subgroups. Multivariable logistic analysis was used to explore predictors of PC use.

RESULTS

Of 5833 mBCa patients receiving CCT, 880 (15.09%) received PC. Rate of PC use increased significantly from 2.53% in 2005 to 25.96% in 2014 (APC: 35.75%; p < 0.0001). Higher increase in PC use was observed in South (from 0.65% to 27.11%; APC: 59.42%; p < 0.0001), medium bedsize hospitals (from 3.75% to 26.05%; APC: 38.16%; p = 0.0006) and urban teaching hospitals (from 4.13% to 29.86%; APC: 37.33%; p = 0.0005). Multivariable analysis revealed that year interval, urban teaching hospitals, and invasive mechanical ventilation were associated with increased PC use, while primary diagnosis of gastrointestinal disorders, fractures, metastatic sites from lymph nodes and tracheostomy were associated with lower PC use.

CONCLUSIONS

PC use in mBCa patients receiving CCT increases significantly over the period. However, it still remains low. Efforts to illustrate disparities in PC use are needed to improve quality of care for mBCa patients receiving CCT, especially for those hospitalized in rural and nonteaching hospitals.