RNA sequencing analysis of the longissimus dorsi to identify candidate genes underlying the intramuscular fat content in Anqing Six-end-white pigs.

Intramuscular fat (IMF) is a significant marker for pork quality. The Anqing Six-end-white pig has the characteristics of high meat quality and IMF content. Owing to the influence of European commercial pigs and a late start in resource conservation, the IMF content within local populations varies between individuals. This study analyzed the longissimus dorsi transcriptome of purebred Anqing Six-end-white pigs with varying IMF content to recognize differentially expressed genes. We identified 1528 differentially expressed genes between the pigs with high (H) and low (L) IMF content. Based on these data, 1775 Gene Ontology terms were significantly enriched, including lipid metabolism, modification and storage, and regulation of lipid biosynthesis. Pathway analysis revealed 79 significantly enriched pathways, including the Peroxisome proliferator-activated receptor and mitogen-activated protein kinase signaling pathways. Moreover, gene set enrichment analysis indicated that the L group had increased the expression of genes related to ribosome function. Additionally, the protein-protein interaction network analyses revealed that VEGFA, KDR, LEP, IRS1, IGF1R, FLT1 and FLT4 were promising candidate genes associated with the IMF content. Our study identified the candidate genes and pathways involved in IMF deposition and lipid metabolism and provides data for developing local pig germplasm resources.

AK5, a novel prognosis marker, inhibits apoptosis and promotes autophagy as well as proliferation in human gastric cancer.

OBJECTIVE: To explore the relationship between AK5 and gastric cancer. MATERIALS AND METHODS: The in situ levels of AK5 in the GC tissues from 255 patients were detected by immunohistochemistry (IHC). The correlation between AK5 expression and the clinicopathological parameters was analyzed by Pearson correlation, and the prognostic factors were identified by Cox regression analysis. The transcriptome data of 14 human GC cell lines deposited in the CCLE database were analyzed, and two lines were selected for functional studies. AK5 was knocked down in the AZ521 and MKN74 cells using siRNA, and their proliferation and apoptosis were evaluated by Cell Counting Kit-8 (CCK-8) assay and Annexin-V staining, respectively. In addition, the apoptosis and autophagy of the markers were detected by Western blotting. RESULTS: Patients expressing high AK5 levels in the tumor tissues had significantly shorter survival compared to low-expressing group. In addition, AK5 expression was associated with T stage and N stage and was an independent prognostic factor. AK5 knockdown in the AZ521 and MKN74 cells significantly inhibited proliferation and autophagy, and increased apoptosis. CONCLUSIONS: AK5 is a potential prognostic marker and therapeutic target for GC.

Increased CD4+CD25-Foxp3+ T cells in Chinese systemic lupus erythematosus: correlate with disease activity and organ involvement.

OBJECTIVE: The increment of CD4+CD25-Foxp3+T cells has been reported in systemic lupus erythematosus (SLE) patients. However, the exact identity of this T cell subset is still unclear. Thus, we analyzed CD4+CD25-Foxp3+T cells and Treg cells (CD4+CD25+Foxp3+ T cells) in a large sample of Chinese SLE patients in different disease states. METHODS: A total of 280 SLE patients and 38 healthy volunteers were enrolled, which included 21 patients with untreated new-onset lupus (UNOL), 13 patients with drug withdrawal more than 6 months and 246 patients with treatments. Phenotypic and functional analysis of peripheral blood CD4+CD25-Foxp3+ T cells and Treg cells were performed by flow cytometry. The correlation of CD4+CD25-Foxp3+T cells and Treg cells with disease activity, clinical indicators and organ involvement were analyzed. RESULTS: CD4+CD25-Foxp3+ T cells and Treg cells were significantly increased in SLE patients and showed significantly positive correlations with disease activity. CD4+CD25-Foxp3+ T cells were significantly increased in patients with skin and hematologic involvement as well as arthritis. Diverse changes between CD4+CD25-Foxp3+ T cells and Treg cells when faced with different medications, especially HCQ and MMF. CD4+CD25-Foxp3+ T cells expressed more IFN-γ and less CTLA-4 than CD4+CD25+Foxp3+ T cells, which were similar to CD4+CD25+Foxp3- T cells, and expressed similar IL-17, ICOS and Helios to CD4+CD25+Foxp3+ T cells. The synthesis capacity of IL-10 of CD4+CD25-Foxp3+ T cells and the expression of GITR on CD4+CD25-Foxp3+ T cells were between CD4+CD25+Foxp3+ and CD4+CD25+Foxp3- T cells. CONCLUSIONS: Our results indicate that increased CD4+CD25-Foxp3+ T cells in lupus patients, which combined the features of suppression and pro-inflammatory, may serve as a biomarker for disease activity and organ involvement in SLE.

A new dispersion interferometer on HL-2A.

In order to avoid a fringe jump caused by high plasma density and pellet injection [Y. Zhou et al., Rev. Sci. Instrum. 87, 11E107 (2016)], a new CO2 dispersion interferometer is designed and commissioned on HL-2A for average line-density measurement and density feedback control. The second harmonic technology in this system eliminates the phase shift caused by mechanical vibration. Signals are processed by a digital phase comparator and can be monitored in real time. A series of experiments are conducted to study the characteristics of the system such as a second harmonic coefficient and long-term stability. The resolution of density measurement is less than 8 × 1017/m3, and the experiment result on HL-2A demonstrates the interferometer's capability to track plasma density evolution with rapid change. The system also shows good stability against mechanical vibrations.

Genome-wide identification and expression analysis of CIPK genes in diploid cottons.

Calcineurin B-like protein-interacting protein kinase (CIPK) plays a key regulatory role in the growth, development, and stress resistance of plants by combining with phosphatase B subunit-like protein. In the present study, CIPK genes were identified in the whole genomes of diploid cottons and their sequences were subjected to bioinformatic analyses. The results demonstrated that the CIPK gene family was unevenly distributed in two diploid cotton genomes. Forty-one CIPKs were identified in the D genome, mainly located on chromosomes 9 and 10, whereas thirty-nine CIPKs were identified in the A genome, mainly located on chromosomes 8 and 11. Based on the gene structures, CIPKs in cotton could be classified into two types: one that is intron-rich and the other that has few introns. Phylogenetic analysis revealed that the CIPK gene family members in cotton had close evolutionary relationships with those of the dicotyledonous plants, such as Arabidopsis thaliana and poplar. The analysis of transcriptome sequence data demonstrated that there were differences in gene expression in different tissues, indicating that the expression of the CIPKs in cotton had spatio-temporal specificity. The expression analysis of CIPKs under abiotic stresses (drought, salt, and low temperature) in different tissues at trefoil stage demonstrated that these stresses induced the expression of CIPKs.

Identification and differential expression of microRNAs in the ovaries of pigs (Sus scrofa) with high and low litter sizes.

Litter size affects profitability in the swine industry. Mammalian ovaries play important roles during reproduction, including ovulation and hormone secretion, which are tightly regulated by specific microRNAs (miRNAs). In this study, we investigated the effects of specific miRNAs on porcine litter size. We compared the ovarian miRNAs of Yorkshire pigs with high (YH) and low (YL) litter sizes using Solexa sequencing technology. We identified 327 and 320 miRNAs in the ovaries of YH and YL pigs respectively. A total of 297 miRNAs were co-expressed; 30 and 23 miRNAs respectively were specifically expressed in the two libraries. A total of 83 novel miRNAs were predicted; 37 specific miRNAs were obtained, of which 21 miRNAs were upregulated and 16 miRNAs were downregulated in YH compared with YL. Additionally, 19 628 and 19 250 target genes were predicted in the two libraries respectively. The results revealed that specific miRNAs (i.e., miR-224, miR-99a, let-7c, miR-181c, miR-214 and miR-21) may affect porcine litter size. The results of this study will help in gaining understanding of the role of miRNAs in porcine litter size regulation.

Association between ADSL, GARS-AIRS-GART, DGAT1, and DECR1 expression levels and pork meat quality traits.

In this study, meat quality traits were compared between Chinese lard- and European lean-type pigs. The association between expression of four genes (ADSL, GARS-AIRS-GART, DGAT1, and DECR1) and meat quality traits was also investigated. Meat quality traits were found to differ significantly between pig breeds. Meat color parameter values (a* and b*) and intramuscular fat content in Anqingliubai were significantly higher than those in Landrace (P < 0.01). Meat pH at 1 and 24 h following slaughter was significantly higher in Landrace than in Wei pigs, and meat inosine monophosphate (IMP) content was significantly higher in Landrace than in Wei and Anqingliubai pigs (both P < 0.01). Expression levels of ADSL, GARS-AIRS-GART, and DGAT1 were higher in longissimus lumborum muscle than in heart or liver tissues. ADSL and GARS-AIRS-GART expression levels were correlated with meat IMP content and pH levels. The results of this study will contribute to the understanding of meat quality traits in Chinese lard- and European lean-type pigs.

Sequence and phylogenetic analyses of the M and N genes of porcine epidemic diarrhea virus (PEDV) strains in Anhui Province, China.

To assess the homology and phylogenetic relationship between porcine epidemic diarrhea virus (PEDV) Anhui strains and other PEDV strains, molecular homology and phylogenetic analyses of Anhui PEDV field strains were compared with those of reference strains. The results revealed that the M and N genes of PEDV were 681 and 1326 bp long, respectively. The nucleotide sequences of the N genes of Anhui PEDV strains were 95.9-99.9% homologous with each other, and the deduced amino acid sequences were 92.5-99.8% homologous. Compared with the PEDV reference strains, the Anhui PEDV field strains had 94.1-99.5% nucleotide sequence homology in the N gene and 91.2-97.5% amino acid mutation homology in the N protein. The nucleotide sequences of the M genes of Anhui PEDV were 98.3-100% homologous, and the deduced amino acid sequences were 96.5-99.6% homologous. Compared with the PEDV reference strains, the Anhui PEDV field strains had 96.9-100% nucleotide sequence homology in the M gene and 96.5-99.6% amino acid homology in the M protein. The Anhui strains were genetically similar to USA strains (USA/Iowa/16465/2013 and USA/Indiana/17846/2013) but different from European (CV777;Br1/7), Korean (Chinju99), and Japanese (83p-5) strains.

Functional and association studies of the cholesteryl ester transfer protein (CETP) gene in a Wannan Black pig model.

Some polymorphisms of the human CETP gene are causally and significantly associated with serum lipids levels; however, the information regarding this gene in pigs is sparse. To evaluate the effects of CETP on blood lipid traits and fat deposition in pig, porcine CETP tissue expression patterns were observed by quantitative real-time polymerase chain reaction (qPCR) first. High expression was detected in liver, spleen, gluteus medius (GM) muscle and backfat. A de novo polymorphism (AF333037:g.795C>T) in the intron 1 region of porcine CETP was identified. This polymorphism was further genotyped by direct sequencing of the PCR products of 390 Wannan Black pigs, a Chinese native breed population. Association analyses at 45 and 300 days of age revealed highly significant associations between CETP genotypes and serum lipid traits. Furthermore, this polymorphism was proved to be associated with differences in liver CETP mRNA levels: pigs at 300 days of age with the TT genotype had higher levels than did those with other genotypes (P = 0.021). Additionally, analysis at 300 days of age showed that GM CETP mRNA expression correlated positively with serum lipids levels as well as with carcass backfat thickness and intramuscular fat content in GM. These results indicate that CETP is involved in serum, adipose and muscle lipid metabolism in pigs. The mechanisms underlying such relationships and their functional implications are worthy of further research.

Relationship between polymorphisms in exon 10 of FSHR gene and litter size in swine.

Follicle-stimulating hormone (FSH), a glycoprotein secreted by the anterior pituitary, can regulate ovarian function through the FSH receptor (FSHR). To evaluate the effects of the FSHR gene on reproductive traits in pigs, polymorphisms in exon 10 of the FSHR gene were observed by polymerase chain reaction-single-strand conformation polymorphism, and 3 single nucleotide polymorphisms (C1491T, G1885A, and C1977T) in exon 10 of the porcine FSHR gene, and 3 genotypes (AA, AB, and BB) for C1491T and 2 haplotypes (D and E) for G1885A and C1977T were identified. Further analysis of single nucleotide polymorphism genotypes associated with reproductive traits including total number born (TNB) and number born alive (NBA) was carried out in 3 pig populations including Berkshire, Wannan Black (a Chinese indigenous pig breed), and BW pigs (two-way crossbred pigs produced from Berkshire ♂ and Wannan Black pig ♀). The results showed that the TNB and NBA of Wannan Black pigs with the AB genotype were significantly higher than in AA genotype sows (P < 0.01) in multiparity sows and all parities. The TNB and NBA of Berkshire pigs with the DE genotype were significantly higher than the DD and EE genotype sows (P < 0.01) in gilts, sows and all parities. Overall, TNB and NBA from the 3 identified genotypes was DE > DD > EE. The results showed that polymorphisms in exon 10 of the FSHR gene had a significant effect on litter size traits of Wannan Black and Berkshire pigs. These results can be applied for marker-assisted selection in the 2 swine breeds.

Evaluation of Virtual Noncontrast Images Obtained from Dual-Energy CTA for Diagnosing Subarachnoid Hemorrhage.

BACKGROUND AND PURPOSE: The virtual noncontrast images generated with iodine subtraction from dual-energy CTA images are expected to replace the true noncontrast images for radiation-dose reduction. This study assessed the feasibility of virtual noncontrast images for diagnosing SAH. MATERIALS AND METHODS: Eighty-four patients with or without SAH underwent true noncontrast brain CT (the criterion standard for diagnosing SAH). Among them, 37 patients underwent an additional head dual-energy angiography, and the other patients underwent head and neck dual-energy angiography. Virtual noncontrast images were produced on a dedicated dual-energy postprocessing workstation and reconstructed in orientation and section width identical to those in true noncontrast images. The findings on the virtual noncontrast and true noncontrast images were compared at both the individual level and the lesion level. Image noise of the virtual noncontrast and true noncontrast images was also measured and compared. The volume CT dose index and dose-length product were recorded for the radiation-dose analysis. RESULTS: The sensitivity, specificity, positive predictive value, and negative predictive value of virtual noncontrast images at the individual level and the lesion level were 94.5%, 100%, 100%, 90.6% and 86.7%, 96.9%, 91.8%, 94.8%, respectively. The agreement in the diagnosis of SAH on true noncontrast and virtual noncontrast images reached 92.3% at the individual level and 85.1% at the lesion level. The virtual noncontrast images showed a higher image noise level. The volume CT dose index and dose-length product were obviously reduced without the true noncontrast brain CT scan. CONCLUSIONS: Virtual noncontrast images are a reliable tool for diagnosing SAH, with the advantage of reducing the radiation dose.

Detection of a novel single nucleotide polymorphism and imprinted status analysis of the Ras protein-specific guanine nucleotide-releasing factor 1 gene in domestic pigs.

The aim of this study was to determine the imprinting status of the Ras protein-specific guanine nucleotide-releasing factor 1 (Rasgrf1) gene in domestic pigs. In this study, a 228-bp partial sequence located in exon 14 and a 193-bp partial sequence located in exon 1 of the Rasgrf1 gene in domestic pigs were obtained. A novel single nucleotide polymorphism, a G/A transition, was identified in Rasgrf1 exon 14, and then the reciprocal Berkshire x Wannan black F1 hybrid model and the reverse transcription-polymerase chain reaction-restriction fragment length polymorphism method were used to detect the imprinting status of the porcine Rasgrf1 gene at the 1-day-old developmental stage. Imprinting analysis showed that, compared to the imprinted expression of the Rasgrf1 gene in mouse and rat, a variable imprinting status was observed in domestic pigs. In principle, the porcine Rasgrf1 gene was maternally expressed in the liver and small intestine, paternally expressed in the lung, and biallelically expressed in brain, heart, spleen, kidney, stomach, pancreas, fat, testis, ovary, longissimus dorsi, and pituitary tissues. In conclusion, our results indicated that the Rasgrf1 gene shows both species- and tissue-specific variation in imprinted expression.

Diagnostics for energetic particle studies on the HL-2A tokamak.

About 13 kinds of diagnostics for energetic particle physics studied on the HuanLiuqi-2A (commonly referred to as HL-2A) tokamak are described in this paper. Their measurement ranges, resolutions, and arrangement are presented. Three under-construction diagnostics including imaging fast ion D-alpha, scintillator matrix (for hard X-ray detection), and bundle fission chamber are described in detail.

Genetically elevated levels of circulating triglycerides and brachial-ankle pulse wave velocity in a Chinese population.

Elevated levels of circulating triglycerides and increased arterial stiffness are associated with cardiovascular disease. Numerous studies have reported an association between levels of circulating triglycerides and arterial stiffness. We used Mendelian randomization to test whether this association is causal. We investigated the association between circulating triglyceride levels, the apolipoprotein A-V (ApoA5) -1131T>C single nucleotide polymorphism and brachial-ankle pulse wave velocity (baPWV) by examining data from 4421 subjects aged 18-74 years who were recruited from the Chinese population. baPWV was significantly associated with the levels of circulating triglycerides after adjusting for age, sex, body mass index (BMI), systolic blood pressure, heart rate, waist-to-hip ratio, antihypertensive treatment and diabetes mellitus status. The -1131C allele was associated with a 5% (95% confidence interval 3-8%) increase in circulating triglycerides (adjusted for age, sex, BMI, waist-to-hip ratio, diabetes mellitus and antihypertensive treatment). Instrumental variable analysis showed that genetically elevated levels of circulating triglycerides were not associated with increased baPWV. These results do not support the hypothesis that levels of circulating triglycerides have a causal role in the development of arterial stiffness.

Bayesian methods for estimating GEBVs of threshold traits.

Estimation of genomic breeding values is the key step in genomic selection (GS). Many methods have been proposed for continuous traits, but methods for threshold traits are still scarce. Here we introduced threshold model to the framework of GS, and specifically, we extended the three Bayesian methods BayesA, BayesB and BayesCπ on the basis of threshold model for estimating genomic breeding values of threshold traits, and the extended methods are correspondingly termed BayesTA, BayesTB and BayesTCπ. Computing procedures of the three BayesT methods using Markov Chain Monte Carlo algorithm were derived. A simulation study was performed to investigate the benefit of the presented methods in accuracy with the genomic estimated breeding values (GEBVs) for threshold traits. Factors affecting the performance of the three BayesT methods were addressed. As expected, the three BayesT methods generally performed better than the corresponding normal Bayesian methods, in particular when the number of phenotypic categories was small. In the standard scenario (number of categories=2, incidence=30%, number of quantitative trait loci=50, h² = 0.3), the accuracies were improved by 30.4%, 2.4%, and 5.7% points, respectively. In most scenarios, BayesTB and BayesTCπ generated similar accuracies and both performed better than BayesTA. In conclusion, our work proved that threshold model fits well for predicting GEBVs of threshold traits, and BayesTCπ is supposed to be the method of choice for GS of threshold traits.

Identification and characterization of conserved microRNAs and their target genes in wheat (Triticum aestivum).

MicroRNAs (miRNAs) are non-coding small RNAs that regulate gene expression by translational repression or transcript degradation. A large number of miRNAs have been identified from model plant species; however, the character of conserved miRNAs is poorly understood. We studied 42 miRNA families that are conserved within the plant kingdom, using the miRBase database. Some conserved miRNA families were found to be preferentially expressed in dicots relative to monocots, especially miR403, miR472 and miR479. Using an improved homology search-based approach and the conserved miRNAs as the query set, 34 conserved miRNAs and the miR482 family were identified in wheat. Forty-six wheat mRNAs were predicted as their putative target genes. Most conserved wheat miRNAs were found to retain homologous target interactions and have analogous molecular functions. The miR172 displayed a wheat-specific function and was found to have an additional target interaction with succinyl-CoA ligase. We concluded that although miRNAs are conserved, the expression and function of some have drifted during long periods of plant evolution.

Optimal low dosage of acetylsalicylic acid (ASA) for the prevention and treatment of ischemic cerebrovascular disease in geriatric patients.

A series of 108 geriatric patients with ischemic cerebrovascular disease were treated with low dose aspirin (acetylsalicylic acid, ASA). Daily doses of 100 mg, 50 mg and 25 mg were administered to three groups of 36 patients. Changes in platelet aggregation responses were dynamically observed in 64 (22 normal subjects, 42 patients). Monitoring of 22 normal subjects revealed inhibition of platelet aggregation at a dose of 300 mg or 100 mg which could last as long as 7 days. This suggests that 100 mg or less could be clinically effective. Satisfactory inhibitory effects on platelet aggregation were observed in all three groups, with 14 patients in each group given daily doses of 100 mg, 50 mg and 25 mg during four weeks' observation. The most effective inhibition was obtained in the 50 mg group. Therefore, the authors recommend 50 mg/d as the optimal dosage for low dose aspirin therapy in geriatric patients.

Mechanism of the therapeutic effect of anisodamine in disseminated intravascular coagulation: study of platelet adhesion and aggregation, malondialdehyde, thromboxane B2, 6-keto-prostaglandin F1 alpha, and microcirculation.

Acute disseminated intravascular coagulation (DIC) is a life-threatening condition that may be encountered in many situations, especially in cases of shock with uncontrollable hemorrhage. Anisodamine, an alkaloid extracted from a Chinese herb, is well known for its dramatic therapeutic effect on DIC. Sixty male rabbits were used to establish an acute DIC model. A total of 240 blood samples were taken for laboratory assays of changes in blood coagulation factors, platelet count, platelet adhesion, platelet aggregation, malondialdehyde (MDA), thromboxane B2 (TXB2), and 6-keto-prostaglandin F1 alpha (6-keto-PGF1 alpha). Changes of the microcirculatory status and the rate of the blood flow in the conjunctival capillaries of 60 rabbits were observed with WXS-II microcirculation microscope. Pathological sections of the lungs and kidneys were studied. Our investigation showed the presence of microthrombi in the microvasculature. After treatment with anisodamine, the prothrombin time stayed in the normal range, fibrinogen consumption was lessened, adenosine-diphosphate-induced platelet aggregation was inhibited, thromboxane B2 and malondialdehyde concentrations were significantly lower than in the control group, and the elevated quantity of 6-keto-PGF1 alpha was spared. We concluded that the anti-platelet-aggregating, microcirculation-facilitating, thromboxane-B2-inhibiting, malondialdehyde-inhibiting, and 6-keto-PGF1 alpha-sparing effects of anisodamine are the important mechanisms of its dramatic therapeutic effect on DIC.