A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes.

A set of high-quality pan-genomes would help identify important genes that are still hidden/incomplete in bird reference genomes. In an attempt to address these issues, we have assembled a de novo chromosome-level reference genome of the Silkie (Gallus gallus domesticus), which is an important avian model for unique traits, like fibromelanosis, with unclear genetic foundation. This Silkie genome includes the complete genomic sequences of well-known, but unresolved, evolutionarily, endocrinologically, and immunologically important genes, including leptin, ovocleidin-17, and tumor-necrosis factor-α. The gap-less and manually annotated MHC (major histocompatibility complex) region possesses 38 recently identified genes, with differentially regulated genes recovered in response to pathogen challenges. We also provide whole-genome methylation and genetic variation maps, and resolve a complex genetic region that may contribute to fibromelanosis in these animals. Finally, we experimentally show leptin binding to the identified leptin receptor in chicken, confirming an active leptin ligand-receptor system. The Silkie genome assembly not only provides a rich data resource for avian genome studies, but also lays a foundation for further functional validation of resolved genes.

Selection on the promoter regions plays an important role in complex traits during duck domestication.

BACKGROUND: Identifying the key factors that underlie complex traits during domestication is a great challenge for evolutionary and biological studies. In addition to the protein-coding region differences caused by variants, a large number of variants are located in the noncoding regions containing multiple types of regulatory elements. However, the roles of accumulated variants in gene regulatory elements during duck domestication and economic trait improvement are poorly understood. RESULTS: We constructed a genomics, transcriptomics, and epigenomics map of the duck genome and assessed the evolutionary forces that have been in play across the whole genome during domestication. In total, 304 (42.94%) gene promoters have been specifically selected in Pekin duck among all selected genes. Joint multi-omics analysis reveals that 218 genes (72.01%) with selected promoters are located in open and active chromatin, and 267 genes (87.83%) with selected promoters were highly and differentially expressed in domestic trait-related tissues. One important candidate gene ELOVL3, with a strong signature of differentiation on the core promoter region, is known to regulate fatty acid elongation. Functional experiments showed that the nearly fixed variants in the top selected ELOVL3 promoter in Pekin duck decreased binding ability with HLF and increased gene expression, with the overexpression of ELOVL3 able to increase lipid deposition and unsaturated fatty acid enrichment. CONCLUSIONS: This study presents genome resequencing, RNA-Seq, Hi-C, and ATAC-Seq data of mallard and Pekin duck, showing that selection of the gene promoter region plays an important role in gene expression and phenotypic changes during domestication and highlights that the variants of the ELOVL3 promoter may have multiple effects on fat and long-chain fatty acid content in ducks.

Exploring the effect of the microbiota on the production of duck striped eggs.

The microbiota has received plenty of attention in recent years due to its influence on host health and productivity. The striped eggs have reduced hatching performance and resulted in economic loss. The reasons are still unknown. Microbiota is one of the potentially important factors contributing to striped egg formation. This study investigates the relationship between the microbiota and striped eggs. The litter samples, feed samples, and cloacal swab samples of female ducks that produce striped eggs and normal eggs were performed for microbial diversity and composition using 16S rRNA sequencing. The results showed that there was no significant difference between feed microbiota and cloacal swab microbiota by alpha diversity, whereas, the number of microorganisms in the litter samples of female ducks that produced striped eggs was less than those of female ducks with normal eggs. There were compositional differences in litter microbiota of female ducks between the striped egg and the normal eggs. Among them, the abundance of Staphylococcus, Corynebacterium, and Brevibacterium in the litter of female ducks that produced striped eggs was significantly higher than that produced normal eggs. And these differential bacteria maybe affect the health of female ducks and cause abnormalities in the formation process of duck eggs. Therefore, the reduction of harmful bacteria may protect the reproductive health of female ducks and decrease the proportion of striped eggs. It provides an important reference to explore why female ducks produce striped eggs.

Genome-wide association study identified the candidate genes associated with angel wing trait in Pekin duck.

Angel wing is a developmental wing deformity that can influence breeding and reproduction in the commercial duck industry. The nutrition foundation of angel wing trait was initially explored, but the genetic basic remains poorly understood. In this study, we identified candidate genes and single-nucleotide polymorphisms (SNPs) associated with angel wing trait in Pekin ducks using a genome-wide association study (GWAS) and selective sweep analysis. The GWAS results showed that nine SNPs across five chromosomes were significantly correlated with the angel wing trait. In total, 468 selection signals were shown between the angel wing ducks and normal ducks, and these signals harbored 154 genes, which were enriched in the nervous system and metabolism. This study provides the new insights into the genetic factors that may influence duck angel wing.

Transplantation of Gut Microbiota From High-Fat-Diet-Tolerant Cynomolgus Monkeys Alleviates Hyperlipidemia and Hepatic Steatosis in Rats.

Emerging evidence has been reported to support the involvement of the gut microbiota in the host's blood lipid and hyperlipidemia (HLP). However, there remains unexplained variation in the host's blood lipid phenotype. Herein a nonhuman primate HLP model was established in cynomolgus monkeys fed a high-fat diet (HFD) for 19 months. At month 19%, 60% (3/5) of the HFD monkeys developed HLP, but surprisingly 40% of them (2/5) exhibited strong tolerance to the HFD (HFD-T) with their blood lipid profiles returning to normal levels. Metagenomic analysis was used to investigate the compositional changes in the gut microbiota in these monkeys. Furthermore, the relative abundance of Megasphaera remarkably increased and became the dominant gut microbe in HFD-T monkeys. A validation experiment showed that transplantation of fecal microbiota from HFD-T monkeys reduced the blood lipid levels and hepatic steatosis in HLP rats. Furthermore, the relative abundance of Megasphaera significantly increased in rats receiving transplantation, confirming the successful colonization of the microbe in the host and its correlation with the change of the host's blood lipid profiles. Our results thus suggested a potentially pivotal lipid-lowering role of Megasphaera in the gut microbiota, which could contribute to the variation in the host's blood lipid phenotype.

Bibliometric analysis of glaucoma-related literature based on SCIE database: a 10-year literature analysis from 2009 to 2018.

AIM: To explore the global trends and focus of glaucoma research from 2009 to 2018. METHODS: Searching for glaucoma-related articles published in Science Citation Index Expanded (SCIE) database during 2009-2018, and describing the distribution of the published year, countries, authors, institutions, funding agencies, journals, impact factor, citation and hot research topic of articles by using bibliometric methods. Meanwhile, we compared some of these indicators over two five-year periods, from 2009 to 2013 and from 2014 to 2018. RESULTS: A total of 19 609 glaucoma-related articles were retrieved and the global SCIE articles have increased yearly from 2009 to 2018. The USA was the pioneer which has made great contributions. China kept the second place and the number of publications has increased rapidly between 2014 and 2018. The author with the highest number of publications was Weinreb, RN. Co-occurrence maps were built amongst the top 50 authors or the top 50 institutions with the most articles, which visualize the closer collaboration of international authors or institutions. The journal Investigative Ophthalmology & Visual Science has published the most papers. Glaucoma literature with an impact factor of 3-5 points accounted for the largest proportion (28.96%). The most frequently cited paper had 798 citations. The top three hot areas on glaucoma were intraocular pressure, optical coherence tomography (OCT) and retinal ganglion cells. And trabecular meshwork, primary angle-closure glaucoma and Spectral-domain OCT have become new hot research topics in recent five years during 2014-2018. CONCLUSION: Bibliometric analysis is an effective method to describe the global literature on glaucoma. In a 10-year literature survey from 2009 to 2018, global glaucoma research has developed in a balanced manner, and the cooperation between various institutions and teams has become closer. Glaucoma-related pathogenesis research, imaging examinations of OCT and surgery therapy have attracted most attention.

One-year efficacy of intravitreal conbercept injection for macular oedema secondary to central retinal vein occlusion in Chinese patients.

PURPOSE: To evaluate intravitreal conbercept injection for treatment of macular oedema secondary to central retinal vein occlusion (CRVO) in Chinese patients during 1-year follow-up in the real-world setting. METHODS: Twenty-seven eyes of 27 patients with macular oedema associated with CRVO were retrospectively reviewed. The eyes received monthly intravitreal conbercept injection (0.5 mg in 50 µl) for 3 months. From then on, the patients were followed up every month and received injection pro re nata (PRN) up to 12 months. The primary outcome measurements included changes of best-corrected visual acuity (BCVA) and central retinal thickness (CRT) from baseline to month 3 and month 12. Other outcome measurements included proportion of patients gaining ≥15 letters in BCVA at month 3 and 12, the mean number of injections and safety concerns. RESULTS: The mean BCVA gain from baseline was 12.7 ± 7.6 letters at month 3 and 14.8 ± 9.6 letters at month 12. The mean CRT reduction from baseline was 374.5 ± 280.7 µm at month 3 and 428.2 ± 241.3 µm at month 12. The proportion of patients who gained ≥15 letters in BCVA was 45.1% at month 3 and 52.9% at month 12. The mean number of injections was 7.6 ± 1.5. No severe local and systemic complications occurred following injection. CONCLUSIONS: Intravitreal conbercept injection by three monthly loading doses followed by PRN treatment regimen was safe and efficacious for patients with macular oedema secondary to CRVO through 1-year follow-up.

Longitudinal observation of intraocular pressure variations with acute altitude changes.

BACKGROUND: Higher intraocular pressure (IOP) is a major risk factor for developing glaucoma, and the leading cause of irreversible blindness worldwide. High altitude (HA) may be involved in IOP, but the reported results were conflicting. Ascent to HA directly by plane from low altitude regions is an acute, effortless exposure. However, the effects of such exposure to different altitudes on IOP have rarely been reported. AIM: To investigate changes in IOP after rapid effortless exposure to HA in stages and compare it with systemic parameters. METHODS: Fifty-eight healthy subjects (116 eyes) were divided into three groups: 17 low-altitude (LA) residents [44 m above sea level (ASL)], 22 HA residents (2261 m ASL) and 19 very HA (VHA) residents (3750 m ASL). The LA group flew to HA first. Three days later, they flew with the HA group to VHA where both groups stayed for 2 d. Then, the LA group flew back to HA and stayed for 1 d before flying back to 44 m. IOP, oxygen saturation (SpO2) and pulse rate were measured. The linear mixed model was used to compare repeated measurements. RESULTS: IOP in the LA group significantly decreased from 18.41 ± 2.40 mmHg at 44 m to 13.60 ± 3.68 mmHg at 2261 m ASL (P < 0.001), and then to 11.85 ± 2.48 mmHg at 3750 m ASL (P = 0.036 compared to IOP at 2261 m ASL) and partially recovered to 13.47 ± 2.57 mmHg upon return to 44 m. IOP in the LA group at HA and VHA was comparable to that in the local residents (12.2 ± 2.4 mmHg for HA,11.5 ± 1.8 mmHg for VHA). IOP was positively associated with SpO2. CONCLUSION: IOP in the LA group gradually reduced as altitude elevated in stages and became comparable to IOP in local residents. Hypoxia may be associated with IOP, which deserves further study.

Comparison of gene expression in cynomolgus monkeys with preclinical type II diabetes induced by different high energy diets.

BACKGROUND: Cynomolgus disease models that are similar to the preclinical stage of human type 2 diabetes mellitus (T2DM) were established by feeding middle-aged cynomolgus monkeys different high energy diets to study the differential expression of diabetes-related genes. METHODS: A total of 36 male monkeys were randomly divided into four groups and fed human diets with high sugar, high fat, double high sugar and fat, and a normal diet. The preclinical diabetes phase was determined by monitoring the metabolic characteristic indices and the results of oral glucose tolerance tests (OGTT). The mRNA expression of 45 diabetes-related genes in peripheral blood leukocytes was analyzed using real-time PCR. RESULTS: A total of 22, 25, and 21 genes were significantly up-regulated (P < 0.05) and 5, 7, and 5 genes were significantly down-regulated (P < 0.05) in the above three induced groups, respectively, compared with the control group. Of the 45 tested genes, the expression profiles of 21 genes were consistent. Most of the expression levels in the double high sugar-and-fat individuals were slightly lower than those in the high glucose and high fat groups, although the expression patterns of the three groups were essentially similar. CONCLUSION: The different high energy diets all induced diabetes and shared some phenotypic properties with human T2DM. Most of the expression patterns of the related genes were identical. The gene expression profiles could be used as references for the study of early diagnostic indicators and T2DM pathogenesis.

miR-33a-5p enhances the sensitivity of lung adenocarcinoma cells to celastrol by regulating mTOR signaling.

MicroRNAs (miRNAs or miRs) have recently become a popular focus of cancer research due to their ability to act as oncogenes or tumor suppressors. In the present study, miR­33a­5p expression was identified to be downregulated in lung adenocarcinoma samples compared with normal, which suggested that miR­33a­5p may serve as a tumor suppressor gene. Transfection with miR­33a­5p mimics inhibited the proliferation and migration of A549 and LTEP­a­2 cells and increased cellular apoptosis. A luciferase reporter assay confirmed that miR­33a­5p targets the 3'­untranslated region of the mechanistic target of rapamycin (mTOR) gene. mTOR expression was decreased in A549 and LTEP­a­2 cells treated with miR­33a­5p mimics, as well as the expression of its downstream effectors phosphorylated (p)­p70 ribosomal protein S6 kinase (p70S6K) and p­eukaryotic translation initiation factor 4E binding protein 1 (4EBP1). Following treatment with celastrol, miR­33a­5p expression was upregulated, and miR­33a­5p could enhance cellular sensitivity to celastrol. Western blot analysis revealed that the expression of mTOR, p­p70S6K and p­4EBP1 decreased following celastrol treatment. These results suggested that mTOR was involved in the mechanism by which miR­33a­5p enhanced the sensitivity of lung adenocarcinoma cells to celastrol. Furthermore, LTEP­a­2 cells were xenografted subcutaneously into nude mice, to examine the effect of celastrol and miR­33a­5p on the growth of LTEP­a­2 cells in vivo. The results demonstrated that tumor growth in the celastrol­treated or miR­33a­5p­treated group was attenuated compared with the control group. Notably, tumor growth in the combination treatment group was almost arrested after 2 weeks. In addition, celastrol upregulated the expression of miR­33a­5p, and high expression of miR­33a­5p inhibited mTOR and its downstream effectors. In summary, miR­33a­5p inhibited the proliferation of lung adenocarcinoma cells, enhanced the antitumor effect of celastrol, and improved sensitivity to celastrol by targeting mTOR in lung adenocarcinoma in vitro and in vivo.

Reproducibility of Perfusion Parameters of Optic Disc and Macula in Rhesus Monkeys by Optical Coherence Tomography Angiography.

BACKGROUND: Optical coherence tomography (OCT) angiography is a novel technique by which we can detect the local perfusion of fundus directly. The aim of this study was to evaluate the reproducibility of optic disc and macular flow perfusion parameters in rhesus monkeys using OCT angiography. METHODS: Eighteen healthy monkeys (18 eyes) were subjected to optic disc and macula flow index measurements via a high-speed and high-resolution spectral-domain OCT XR Avanti with a split-spectrum amplitude de-correlation angiography algorithm. Right eye was imaged 3 times during the first examination and once during each of the two following examinations. The intra-visit and inter-visit intraclass correlation coefficients (ICCs) were both determined. RESULTS: The average flow indices of the four optic disc area layers were 0.171 ± 0.009 (optic nerve head), 0.015 ± 0.004 (vitreous), 0.052 ± 0.009 (radial peripapillary capillary), and 0.167 ± 0.011 (choroid). Average flow indices of the four macula area layers were 0.044 ± 0.011 (superficial retina), 0.036 ± 0.011 (deep retina), 0.016 ± 0.009 (outer retina), and 0.155 ± 0.013 (choroid). Intra-visit (ICC value: 0.821-0.954) and inter-visit (ICC value: 0.844-0.899) repeatability were both high. CONCLUSIONS: The study is about the reproducibility of optic disc and macular perfusion parameters as measured by OCT angiography in healthy rhesus monkeys. Flow index measurement reproducibility is high for both the optic disc and macula of normal monkey eyes. OCT angiography might be a useful technique to assess changes when examining monkeys with experimental ocular diseases.

Cisplatin regulates SH-SY5Y cell growth through downregulation of BDNF via miR-16.

Brain-derived neurotropic factor (BDNF) is a member of the neurotropin family. High levels of BDNF are associated with more aggressive malignant behavior in human cancer. In the present study, we observed the effect of cisplatin on BDNF expression in SH-SY5Y cells and investigated the mechanism of cisplatin in inducing the apoptosis of SH-SY5Y cells. Our results revealed that the expression of BDNF was obviously decreased in cisplatin-treated SH-SY5Y cells. In addition, the 3'-untranslated region of BDNF was found to be targeted by miR-16 using microRNA analysis software. After miR-16 was synthesized chemically, SH-SY5Y cells were transfected with miR-16 to investigate the regulatory role of miR-16 in regards to BDNF. The results showed that the expression of BDNF was markedly decreased in the miR­16-transfected cells when compared with that in the control cultures as determined by western blotting. Moreover, miR-16 expression was obviously upregulated in the cisplatin-treated cells when compared with the untreated controls. Furthermore, SH-SY5Y cells were xenografted subcutaneously in nude mice to study the effect of cisplatin on the growth of SH-SY5Y cells in vivo. The results further showed that cisplatin inhibited the proliferation of SH-SY5Y cells in the cisplatin-treated mice when compared with the saline-treated control. The expression of miR-16 was increased, while the expression of BDNF was decreased in the cisplatin-treated mice. Our results demonstrated that cisplatin downregulated the expression of BDNF through miR-16 to inhibit SH-SY5Y cell proliferation in vitro and in vivo. These findings provide the basis for new targets for drug design or cancer therapy.

Let-7c inhibits A549 cell proliferation through oncogenic TRIB2 related factors.

MicroRNAs have tumor suppressive or oncogenic roles in carcinogenesis. This study aimed to investigate the mechanism of let-7c in suppressing lung cancer cell proliferation. First, let-7c was revealed to be able to inhibit lung adenocarcinoma cell proliferation significantly. TRIB2 was further demonstrated to be a novel target and negatively regulated by let-7c. As downstream signals of TRIB2, the activities of C/EBP-α and phosphorylated p38MAPK were increased obviously in let-7c-treated cells compared with controls. Our results demonstrate that, through regulating the expression of TRIB2 and its downstream factors, let-7c can effectively inhibit A549 cell proliferation in vitro and in vivo.

[Comparison of gene expression between naturally occurring and diet-induced T2DM in cynomolgus monkeys].

To explore pathological alteration of T2DM in cynomolgus monkeys, gene expression profiles of peripheral blood leukocytes from spontaneous and diet-induced T2DM models was analyzed using quantitative real-time PCR. Among 36 T2DM associated genes tested, 19 genes (including G6PC, CCR2B, CTLA4) displayed a similar expression pattern in both spontaneous and diet-induced T2DM models and were significantly up-regulated or down-regulated compared to controls. Interestingly, expression abundance of all up-regulated genes in the diet-induced T2DM was stronger, although not significantly, than spontaneous models, indicating diet-induced T2DM in monkeys should be a reliable research model for changes in gene expression. The characteristic gene expression pattern obtained here may be useful for the clinical diagnosis of T2DM.

[Correlation between cardiovascular risk factors and the expression of cardiovascular disease related genes in cynomolgus monkeys].

The correlation between cardiovascular risk factors and cardiovascular disease related genes plays an important role in early-warning risk and early diagnosis. Thirty middle-aged male crab-eating macaques were fed a moderately atherogenic diet (0.053 mg cholesterol/kJ and 40% of calories as saturated fat) for twelve months. According to cardiovascular risk factors, we selected low-risk and high-risk crab-eating macaques, then analyzed the expression of 113 cardiovascular related genes by real-time PCR. A total of 65 genes were detected in peripheral blood leukocytes by real-time PCR. Sixteen up-regulated genes and nineteen down-regulated genes were detected in low-risk and high-risk crab-eating macaques compared to normal crab-eating macaques (P<0.05), in addition to fifteen genes that showed unique expression patterns (P<0.05). We also detected 42 genes in human peripheral blood leukocytes. The expression patterns of 22 genes were consistent between human and crab-eating macaques. These results narrowed the scope of genes for further research.