A computational method to predict carbonylation sites in yeast proteins.

Several post-translational modifications (PTM) have been discussed in literature. Among a variety of oxidative stress-induced PTM, protein carbonylation is considered a biomarker of oxidative stress. Only certain proteins can be carbonylated because only four amino acid residues, namely lysine (K), arginine (R), threonine (T) and proline (P), are susceptible to carbonylation. The yeast proteome is an excellent model to explore oxidative stress, especially protein carbonylation. Current experimental approaches in identifying carbonylation sites are expensive, time-consuming and limited in their abilities to process proteins. Furthermore, there is no bioinformational method to predict carbonylation sites in yeast proteins. Therefore, we propose a computational method to predict yeast carbonylation sites. This method has total accuracies of 86.32, 85.89, 84.80, and 86.80% in predicting the carbonylation sites of K, R, T, and P, respectively. These results were confirmed by 10-fold cross-validation. The ability to identify carbonylation sites in different kinds of features was analyzed and the position-specific composition of the modification site-flanking residues was discussed. Additionally, a software tool has been developed to help with the calculations in this method. Datasets and the software are available at https://sourceforge.net/projects/hqlstudio/ files/CarSpred.Y/.

miR-204 suppresses non-small-cell lung carcinoma (NSCLC) invasion and migration by targeting JAK2.

Aberrant expression of microRNA is associated with the development and progression of cancers. MicroRNA-204 (miR-204) down-regulation has been previously demonstrated in non-small-cell lung carcinoma (NSCLC); however, the underlying mechanism by which miR-204 suppresses tumorigenesis in NSCLC remains elusive. In this study, miR-204 expression was found to be down-regulated, and that of Janus kinase 2 (JAK2) was found to be up-regulated in four NSCLC cell lines (A549, H1299, H1650, and H358) compared to the normal lung cell line. The overexpression of miR-204 suppressed the invasive and migratory capacities of H1299 cells. A luciferase assay confirmed that the binding of miR-124 to the -untranslated region of JAK2 inhibited the expression of JAK2 proteins in H1299 cells. JAK-2 overexpression effectively reversed miR-204-repressed NSCLC metastasis. Taken together, our findings revealed that miR-204 functions as a tumor suppressor in NSCLC by targeting JAK2, and that miR-204 may therefore serve as a biomarker for the diagnosis and treatment of NSCLC.

Genetic analysis of floral organ size in broccoli × cabbage via a mixed inheritance model of a major gene plus polygene.

Broccoli and cabbage are important vegetable crops that produce hybrid seeds after insect pollination; the size of floral organs is crucial for this process. To investigate the genetic characteristics of floral organ sizes (corolla width, petal length and width, and lengths of stamen, anther, style, and stigma) and to improve the flower size and breeding efficiency of broccoli, we used multi-generation analysis of a major gene plus polygene model. Six populations obtained from a broccoli inbred line 93219 (small floral organs) and cabbage inbred line 195 (large floral organs) were used for the analysis. Corolla and petal width and stamen and anther length were controlled by the additive-dominance-epistasis polygene model. The heritability of these traits in BC1, BC2, and F2 generations was high (72.80-93.76%). Petal and stigma length were governed by the two major genes of additive-dominance-epistasis effects plus additive-dominance polygene model; the major gene heritability in the F2 generation were 79.17 and 65.77%, respectively. Style length was controlled by one major gene of additive-dominance effects plus additive-dominance-epistasis polygene model; the major gene heritability in BC1, BC2, and F2 were 40.60, 10.35, and 38.44%, respectively; the polygene heritability varied from 41.85 to 68.44%. Our results provide important genetic information for breeding, which could guide improvement of flower-related traits and lay the foundation for quantitative trait loci mapping of the flower-size traits in Brassica.

Association of MMP3 genotype with susceptibility to frozen shoulder: a case-control study in a Chinese Han population.

Genetic factors may play an important role in frozen shoulder etiology, which may involve matrix metalloproteinase-3 (MMP3) gene polymorphisms. In this study, we examined single nucleotide polymorphisms in MMP3 for their association with frozen shoulder susceptibility in a Chinese Han population. The rs591058, rs650108, and rs679620 polymorphisms in the MMP3 gene were genotyped in 112 subjects diagnosed as having frozen shoulder and in 143 healthy controls. rs650108 was found to be significantly associated with an increased risk of frozen shoulder. For other single nucleotide polymorphisms, no statistically significant associations with frozen shoulder were found. In conclusion, our data demonstrated that the MMP3 rs650108 variant was significantly associated with increased frozen shoulder susceptibility in a Chinese Han population.

Association between XRCC3 Thr241Met polymorphism and risk of osteosarcoma in a Chinese population.

Osteosarcoma is one of the most common bone malignancies in adolescents, and hereditary factors may influence its susceptibility. We assessed the association between XRCC3 Thr241Met polymorphism and susceptibility to osteosarcoma in a Chinese population. Between May 2012 and May 2014, a total of 136 osteosarcoma patients and 136 healthy control subjects were included in our study. The XRCC3 Thr241Met polymorphism was analyzed using a polymerase chain reaction restriction fragment length polymorphism assay. By multiple logistic regression analysis, individuals carrying the Met/Met genotype of XRCC3 Thr241Met were at significantly increased risk of osteosarcoma when compared with the Thr/Thr (OR = 2.50, 95%CI = 1.13-5.66). The Thr/Met+Met/Met genotype of XRCC3 Thr241Met was furthermore found to be correlated with an elevated increased risk of osteosarcoma when compared with the Thr/Thr genotype (OR = 1.71, 95%CI = 1.03-2.87), and Met/Met genotype of XRCC3 Thr241Met was associated with an increased risk of osteosarcoma compared to the Thr/Thr (OR = 3.50, 95%CI = 1.51-8.79). In conclusion, our study firstly reports that XRCC3 Thr241Met gene polymorphism is associated with an elavated risk of osteosarcoma.

Effects of MK-801 concentration on cell proliferation in rats with focal cerebral ischemia-reperfusion.

We explored the relationship between MK-801 concentration and neural stem cell proliferation in rats with focal cerebral ischemia-reperfusion (FCIR). A total of 60 male Sprague Dawley rats were randomized into control (six rats), sham-operation (six rats), operation (12 rats), and MK-801 groups. The MK-801 group comprised 36 rats that were subjected to different doses of MK-801 (0.2, 0.4, 0.6, 0.8, 1.0, and 1.2 mg/kg). Suture occlusion was used to establish an ischemia reperfusion model of middle cerebral artery occlusion (MCAO); 30 min before establishing the FCIR model, the MK-801 group rats were intraperitoneally injected with different doses of MK-801, while the sham-operation and control groups were injected with normal saline. Seven days after model establishment, bromodeoxyuridine-positive cerebral cortex cells adjacent to the focus of infarction were labeled for immunohistochemistry. MK-801 at a concentration of 0.4 mg/kg prevented endogenous neural stem cell proliferation, and this inhibitory effect was strengthened with increasing MK-801 concentration, especially at concentrations greater than 0.8 mg/kg. MK-801 inhibits endogenous neural stem cell proliferation in rats with FCIR, and the inhibitory effect is strengthened with increasing MK-801 concentration.

Establishment and rapid detection of a heterozygous missense mutation in the CACNA1F gene by ARMS technique with double-base mismatched primers.

Retinitis pigmentosa (RP) is a retinal degenerative disorder that often causes complete blindness. Mutations of more than 50 genes have been identified as associated with RP, including the CACNA1F gene. In a recent study, by employing next-generation sequencing, we identified a novel mutation in the CACNA1F gene. In this study, we used the amplification refractory mutation system (ARMS) and identified a single nucleotide change c.1555C>T in exon 13 of the CACNA1F gene, leading to the substitution of arginine by tryptophan (p.R519W) in a Chinese individual affected by RP. This study actually confirms this novel mutation, and establishes the ARMS technique for the detection of mutations in RP.

Protective effects of bifidobacteria on intestines in newborn rats with necrotizing enterocolitis and its regulation on TLR2 and TLR4.

We established a necrotizing enterocolitis (NEC) rat model and explored the role of bifidobacteria in the intestines of the rats and its regulation on intestinal Toll-like receptors (TLRs). Seventy-five newborn Sprague-Dawley rats were randomly divided into 5 groups (15 rats/group): group A, artificial feeding group (formula-fed); group B, NEC model (LPS + formula-fed); group C, bifidobacterium (LPS + formula-fed + bifidobacterium microcapsules, intragastric administration); group D, artificial feeding + bifidobacterium (formula-fed + bifidobacterium microcapsules gavage); group E, rat breast-feeding group (rat breast-feeding). After 3 days of feeding, rats were placed in incubators, fasted for 12 h, and killed by decapitation. The ileocecal proximal segment ileum was fixed and sliced; pathological examination was conducted, and TLR2, TLR4, and nuclear factor-kB p65 protein expression in the intestinal tissue was detected by immunohistochemistry. There was a statistically significant difference in pathological scores between groups C and B (H = 21.789, P = 0.000), and the former was lower than the latter. TLR2, TLR4, and nuclear factor-kB p65 expression in intestinal tissue was determined in groups A-E. There were statistically significant differences between groups C and B (P = 0.001; P = 0.000; P = 0.000). Bifidobacteria had a protective effect on the intestines of newborn rats with NEC, which showed reduced NEC and intestinal damage severity. This observation may be related to the reduced levels of TLR2, TLR4, and nuclear factor-kB P65 observed during the inflammatory response.

Effect of flavonoid compounds extracted from Iris species in prevention of carbon tetrachloride-induced liver fibrosis in rats.

We investigated the effect of flavonoid compounds extracted from species of genus Iris L. on carbon tetrachloride (CCl4)-induced rat liver fibrosis. Thirty Sprague-Dawley rats were randomly divided into normal control group, liver fibrosis model group, and drug treatment group (N = 10 each). Next, 0.2 mL/100 g CCl4 was subcutaneously injected for 6 weeks in both model and treatment rats to generate the liver fibrosis model. In the control group, an equal volume of castor oil was injected subcutaneously. Rats in the treatment group also received 100 mg·kg(-1)·day(-1) flavonoid compounds via gastric tubes. After 6 weeks, rats were sacrificed, and their liver tissues were examined for pathological changes, including alanine aminotransferase, aspartate aminotransferase, total bilirubin, hyaluronic acid, laminin, and procollagen type-3. Liver tissues from control rats showed no significant pathological changes, while model animals showed significant liver fibrosis. In the treatment group, liver fibrosis significantly decreased compared to the model group (P < 0.05). Liver fibrotic indices, including hyaluronic acid, laminin, and procollagen type-3, in treatment rats were all significantly lower than those in the model group (P < 0.05), but not significantly different compared to the normal group (P > 0.05). Other liver function indices, including alanine aminotransferase, aspartate aminotransferase, and total bilirubin, in treatment rats were also significantly lower than those in model rats (P < 0.01) but higher than those in control animals (P < 0.05). Flavonoid compounds extracted from Iris plants showed significant inhibitory effects on CCl4-induced rat liver fibrosis.

Correlation between the decrease of cholesterol efflux from macrophages in patients with type II diabetes mellitus and down-regulated CYP7A1 expression.

The purpose of this study was to examine the changes of cellular cholesterol efflux from macrophages in patients with type II diabetes mellitus (DM), and to determine the expression of CYP7A1, ABCG5, and LXRß therein. We recruited 30 patients with type II DM (including 15 patients complicated with coronary heart disease and 15 patients with DM only) and 15 normal controls for this study. Peripheral blood monocytes were isolated for macrophage culture. The mRNA and protein expression levels of CYP7A1, ABCG5, and LXRß were determined using real-time polymerase chain reaction and western blot. The macrophage cholesterol efflux rate was determined with 10% autoserum and standard serum as receptors. We determined that the expression levels of macrophage CYP7A1 mRNA and protein in the type II DM group were significantly lower than those in the control group, but no differences were found in the ABCG5 and LXRß expression levels between the groups. The macrophage cholesterol efflux rate in the patients with type II DM was also significantly decreased compared with that of the normal control subjects (P < 0.01). Furthermore, CYP7A1 mRNA expression and macrophage cholesterol efflux rate were significantly positively correlated. In summary, this study demonstrated that the macrophage cholesterol efflux in patients with type II DM was significantly reduced, and that this reduction was associated with the down-regulation of CYP7A1 expression.

Characterization and effects of miR-21 expression in esophageal cancer.

The aim of this study was to investigate the expression of miR-21 in esophageal cancer and the impact of miR-21 on apoptosis, invasion, and the expression of target genes in esophageal cancer cells. Fluorescence quantitative polymerase chain reaction analysis was used to detect the expression of miR-21 in human esophageal tissues, adjacent tissues, and an esophageal cancer cell line (TE-13). The antisense miR-21 oligonucleotide was generated commercially using the solid-phase chemical synthesis method. Transient transfection was used to transfect esophageal cancer cells (TE-13 antisense and TE-13 control cells). Flow cytometry and Transwell cell assays were used to detect the apoptosis and invasion of esophageal cancer cells, respectively. The western blot method was used to detect the expression of PTEN, PDCD4, and K-ras proteins. These analyses determined that mir-21 expression significantly increased in esophageal cancer tissues and in TE-13 cells, and that this phenomenon was not associated with staging or lymph node metastasis. The apoptosis rate of TE-13 control cells was lower than that of antisense TE-13 cells indicating an enhanced invasive ability. In tissues adjacent to esophageal cancer and in TE-13 antisense cells, the expression of PTEN and PDCD4 was found to be higher than that in the control group, whereas the expression of K-ras showed the opposite pattern. Together, these results suggest that miR- 21 might be involved in the development and metastasis of esophageal cancer, through interaction with its PDCD4 and K-ras target genes.

Hypolipidemic effect of safflower yellow and primary mechanism analysis.

We examined the hypolipidemic effect of safflower yellow (SY) on hyperlipidemic mice and its influence on the biological synthesis of cholesterol in cells. Over 4 weeks, the levels of total cholesterol, triglyceride, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol in serum were detected using a kit; mouse liver samples were acquired for paraffin sections, and mouse liver cells were observed under light microscope. Chinese hamster ovary cells were cultured in vitro, and an amphotericin B-cell model was adopted to observe the inhibitory effect of SY on the biological synthesis of intracellular cholesterol. An enzyme-linked immunosorbent assay was used to detect the survival rate of Chinese hamster ovary cells. The middle and high doses of SY significantly reduced the levels of total cholesterol, triglycerides, and low-density lipoprotein cholesterol in the serum of hyperlipidemic mice and low-density lipoprotein cholesterol/high-density lipoprotein cholesterol ratio (P < 0.05), and the fatty liver of hyperlipidemic mice was significantly alleviated. SY had a protective effect on Chinese hamster ovary cells following amphotericin B injury (P < 0.01). SY exerts significant hypolipidemic effects and prevents fatty liver in a mechanism associated with inhibition of the biosynthesis of intracellular cholesterol.

Association of miR-21 with esophageal cancer prognosis: a meta-analysis.

The present study aimed to explore the relationship between miRNA expression and survival in patients with esophageal cancer (EC) using meta-analysis. We searched PubMed, EMBASE, CNKI, Wanfang, and ISI Web of Science databases without time restrictions, and extracted relevant data, such as the name of first author, publication year, age, gender, number of case, etc. from the studies included. We calculated the pooled hazard ratios (HRs) using the RevMan 5.2 software. A total of five studies involving 504 subjects were included in the meta-analysis, with the purpose of analyzing the association of miRNA-21 expression with EC prognosis. The pooled HR of elevated versus decreased miR-21 expression in EC was 1.87 [95% confidence interval (CI): 1.37-2.55, P < 0.001], with elevated miR-21 expression being associated with poorer prognosis for patients with EC. Our results support a prognostic role for miR-21 in EC.

Efficacy of Artemisia annua polysaccharides as an adjuvant to hepatitis C vaccination.

The traditional Chinese medicine Artemisia annua can prevent and treat hepatitis following an unclear mechanism. The aim of this study was to evaluate the effects of A. annua polysaccharides (AAP) on hepatitis C virus (HCV). A pcDNA3.1/NS3 expression vector was constructed. Ninety female BALB/c mice were randomly divided into six groups: high-dose AAP (1 mg/mL) + HCV/NS3 plasmid; middle-dose AAP (0.5 mg/mL) + HCV/NS3 plasmid; low-dose AAP (0.1 mg/mL) + HCV/NS3 plasmid; HCV/NS3 plasmid; high-dose AAP (1 mg/mL); normal saline control (N = 15). Except the control group and the high-dose AAP group, other groups were inoculated with 50 µg pcDNA3.1-HCV/NS3 plasmid. Serum antigenic-specific antibody was detected after the last immunization, and the levels of secreted IFN-γ and IL-4 were measured. pcDNA3.1/NS3 plasmid was successfully constructed, and the extracted product contained HCV/NS3 sequence. Compared with single inoculation with HCV/NS3 DNA vaccine, the specific antibody levels induced by middle-dose AAP plus HCV/NS3 DNA vaccine were significantly different in weeks 1, 3 and 5 (P < 0.05). However, there were no significant differences in the antibody levels induced by high-dose and low-dose AAP as adjuvant compared with those of single inoculation with DNA vaccine (P > 0.05). The level of serum IFN-γ secretion was significantly higher than that of IL-4 secretion. Compared with the single HCV/NS3 DNA vaccine group, AAP plus HCV/NS3 DNA vaccine groups had significant increased IFN-γ levels (P < 0.05), but the IL-4 levels were not significantly different among these groups (P > 0.05). AAP, as the adjuvant of HCV/NS3 DNA vaccine, can widely regulate the humoral immunity and cellular immune function of normal and cyclophosphamide-induced immunocompromised mice. AAP can promote IFN-γ secretion probably by inducing Th1-type cellular immune response.

Fluorescent quantitative PCR of Mycobacterium tuberculosis for differentiating intestinal tuberculosis from Crohn's disease.

Intestinal tuberculosis (ITB) and Crohn's disease (CD) are granulomatous disorders with similar clinical manifestations and pathological features that are often difficult to differentiate. This study evaluated the value of fluorescent quantitative polymerase chain reaction (FQ-PCR) for Mycobacterium tuberculosis (MTB) in fecal samples and biopsy specimens to differentiate ITB from CD. From June 2010 to March 2013, 86 consecutive patients (38 females and 48 males, median age 31.3 years) with provisional diagnoses of ITB and CD were recruited for the study. The patients' clinical, endoscopic, and histological features were monitored until the final definite diagnoses were made. DNA was extracted from 250 mg fecal samples and biopsy tissues from each patient. The extracted DNA was amplified using FQ-PCR for the specific MTB sequence. A total of 29 ITB cases and 36 CD cases were included in the analysis. Perianal disease and longitudinal ulcers were significantly more common in the CD patients (P<0.05), whereas night sweats, ascites, and circumferential ulcers were significantly more common in the ITB patients (P<0.05). Fecal FQ-PCR for MTB was positive in 24 (82.8%) ITB patients and 3 (8.3%) CD patients. Tissue PCR was positive for MTB in 16 (55.2%) ITB patients and 2 (5.6%) CD patients. Compared with tissue FQ-PCR, fecal FQ-PCR was more sensitive (X2=5.16, P=0.02). We conclude that FQ-PCR for MTB on fecal and tissue samples is a valuable assay for differentiating ITB from CD, and fecal FQ-PCR has greater sensitivity for ITB than tissue FQ-PCR.

Fluorescent quantitative PCR of Mycobacterium tuberculosis for differentiating intestinal tuberculosis from Crohn's disease

Intestinal tuberculosis (ITB) and Crohn's disease (CD) are granulomatous disorders with similar clinical manifestations and pathological features that are often difficult to differentiate. This study evaluated the value of fluorescent quantitative polymerase chain reaction (FQ-PCR) for Mycobacterium tuberculosis (MTB) in fecal samples and biopsy specimens to differentiate ITB from CD. From June 2010 to March 2013, 86 consecutive patients (38 females and 48 males, median age 31.3 years) with provisional diagnoses of ITB and CD were recruited for the study. The patients' clinical, endoscopic, and histological features were monitored until the final definite diagnoses were made. DNA was extracted from 250 mg fecal samples and biopsy tissues from each patient. The extracted DNA was amplified using FQ-PCR for the specific MTB sequence. A total of 29 ITB cases and 36 CD cases were included in the analysis. Perianal disease and longitudinal ulcers were significantly more common in the CD patients (P<0.05), whereas night sweats, ascites, and circumferential ulcers were significantly more common in the ITB patients (P<0.05). Fecal FQ-PCR for MTB was positive in 24 (82.8%) ITB patients and 3 (8.3%) CD patients. Tissue PCR was positive for MTB in 16 (55.2%) ITB patients and 2 (5.6%) CD patients. Compared with tissue FQ-PCR, fecal FQ-PCR was more sensitive (X2=5.16, P=0.02). We conclude that FQ-PCR for MTB on fecal and tissue samples is a valuable assay for differentiating ITB from CD, and fecal FQ-PCR has greater sensitivity for ITB than tissue FQ-PCR.