Association of the IRF5 SNP rs2004640 with systemic sclerosis in Han Chinese

Systemic sclerosis (SSc) is a complex disease involving multiple genetic factors. An association of the IRF5 polymorphism with SSc was reported in Caucasian populations of Europe and North America, as well as in Japanese populations. The present study aimed to examine whether the SSc-associated SNP rs2004640 of IRF5 gene confer susceptibility to SSc and clinical features of SSc in a Han Chinese population. A Han Chinese cohort consisting of 424 SSc patients and 502 healthy controls were examined in the study. TaqMan assays were carried out to examine the SNP. Exact p-values were obtained (Fisher’s test) from 2x2 tables of allele counts and disease status. SSc patients of Han Chinese showed increased homozygous TT genotype of the rs2004640 (p = 0.027, odds ratio (OR) = 1.4, CI =1.03-1.93), which was significantly associated with pulmonary fibrosis of SSc and ATA-positive SSc of Han Chinese. The lcSSc and ACA-positive SSc of Han Chinese appeared also in association with the increased T allele frequency. However, the Chinese dcSSc did not show any association with the rs2004640. The results were consistent with previous reports in other ethnic populations in supporting the notion that polymorphisms of IRF5 may play an important role in susceptibility to SSc.

MicroRNA-25 promotes gastric cancer migration, invasion and proliferation by directly targeting transducer of ERBB2, 1 and correlates with poor survival

Gastric cancer (GC) is one of the most common tumors and the molecular mechanism underlying its metastasis is still largely unclear. Here, we show that miR-25 was overexpressed in plasma and primary tumor tissues of GC patients with tumor node metastasis stage (III or IV) or lymph node metastasis. MiR-25 inhibition significantly decreased the metastasis, invasion and proliferation of GC cells in vitro, and reduced their capacity to develop distal pulmonary metastases and peritoneal dissemination in vivo. Furthermore, miR-25 repressed transducer of ERBB2, 1 (TOB1) expression by directly binding to TOB1-3'-UTR, and the inverse correlation was observed between the expressions of miR-25 and TOB1 mRNA in primary GC tissues. Moreover, the loss of TOB1 increased the metastasis, invasion and proliferation of GC cells, and the restoration of TOB1 led to suppressed metastasis, invasion and proliferation. The receiver operating characteristics analysis yielded an area under the curve value of 0.7325 in distinguishing the GC patients with death from those with survival. The analysis of optimal cutoff value revealed poor survival in GC patients with high plasma concentrations of miR-25 (>0.2333 amol/μl). Taken together, miR-25 promotes GC progression by directly downregulating TOB1 expression, and may be a noninvasive biomarker for the prognosis of GC patients.

Meta-analysis of the association of dermatomyositis and polymyositis with cancer

BACKGROUND

Although some features of dermatomyositis (DM) and polymyositis (PM) have been reported as possible prognostic indicators for cancer development, previous studies were small in size and were unable to establish a definitive relationship between neoplasms and DM and PM.

OBJECTIVES

To evaluate risk factors for developing malignancies in patients with DM and PM.

METHODS

Meta-analysis of the studies reported in the literature was performed to unveil risk factors for developing cancer among patients with DM and PM. The included studies were either cohort or retrospective case-control studies with information on cancer status. Risk for malignancy was determined as the odds ratio (OR) or weighted mean difference (WMD) with a 95% confidence interval (CI), determined by fixed and random effects models. Stata 10.0 software was used to identify possible publication bias.

RESULTS

Twenty studies with 380 patients and 1575 controls were included in the analysis. The factors that may increase the risk of cancer in patients with DM and PM were older age (WMD 11·41, 95% CI 9·84-12·98), male sex (OR 1·92, 95% CI 1·49-2·48), cutaneous necrosis (OR 5·52, 95% CI 3·49-8·74) and dysphagia (OR 2·41, 95% CI 1·50-3·86), whereas those that may provide protection against cancer included arthritis (OR 0·38, 95% CI 0·24-0·61) and interstitial lung disease (OR 0·32, 95% CI 0·20-0·51).

CONCLUSIONS

Our data suggest that age, sex, cutaneous necrosis, dysphagia, arthritis and lung complications may influence susceptibility to cancer in patients with DM and PM.

Antimicrobial resistance and toxin gene profiles of Staphylococcus aureus strains from Holstein milk

Isolation of Staphylococcus aureus (Staph. aureus) from Holstein milk samples with mastitis and nonmastitis was conducted to estimate its prevalence, antimicrobial resistance and toxin genes. A total of 353 milk samples were collected from three Chinese Holstein herds. Fifty-three Staph. aureus isolates collected from 29 Staph. aureus-positive samples were characterized via antimicrobial susceptibility, toxin genes and Pulsed-field Gel Electrophoresis (PFGE) profiles. The prevalence of Staph. aureus was 4·0-9·5% in mastitic and 7·3-11·5% in nonmastitic samples in the analysed herds. Approximately 61·0% of Staph. aureus strains isolated from mastitis cows were resistant to ≥10 antimicrobials compared with 0% of isolates with nonmastitis. The most frequently observed super antigenic toxin gene was pvl (41·5%) followed by seh + pvl (13·2%). We did not find mecA-positive methicillin-resistant Staph. aureus (MRSA) strains, while mecA-negative MRSA strains were identified in the three herds. PFGE results suggested potential transmission of Staph. aureus strains in different farms. These results open new insights into Staph. aureus transmission and antimicrobial resistance of Holstein dairy cows and into developing strategies for udder health improvement of dairy cattle.

SIGNIFICANCE AND IMPACT OF THE STUDY

Significantly higher levels of antibiotic resistance of Staphylococcus aureus strains were detected in the lactating Holstein milk with clinical mastitis compared with that without clinical mastitis. PFGE results suggest potential transmission of Staph. aureus strains in different dairy farms. The results imply that the dairy farms need to select effective antibiotics in the treatment of Staph. aureus-infected cows and prevent the transmission of Staph. aureus strains from one herd to another.

Quantum state tomography via linear regression estimation

A simple yet efficient state reconstruction algorithm of linear regression estimation (LRE) is presented for quantum state tomography. In this method, quantum state reconstruction is converted into a parameter estimation problem of a linear regression model and the least-squares method is employed to estimate the unknown parameters. An asymptotic mean squared error (MSE) upper bound for all possible states to be estimated is given analytically, which depends explicitly upon the involved measurement bases. This analytical MSE upper bound can guide one to choose optimal measurement sets. The computational complexity of LRE is O(d⁴) where d is the dimension of the quantum state. Numerical examples show that LRE is much faster than maximum-likelihood estimation for quantum state tomography.

STAT4 is a genetic risk factor for systemic sclerosis in a Chinese population

Systemic sclerosis (SSc) is an immune-mediated and complex genetic disease. An association of single-nucleotide polymorphisms (SNPs) in the STAT4 gene with SSc has been reported in European Caucasians, North Americans and Japanese. We undertook the current study to examine whether the STAT4 SNPs are also associated with susceptibility to SSc and SSc subsets in a Han Chinese population. A total of 453 Han Chinese patients with SSc and 534 healthy controls were examined in the study. The SNPs rs7574865, rs10168266 and rs3821236 of the STAT4 gene were examined with SNP TaqMan assays. The T-allele carriers of rs7574865 and rs10168266 were strongly associated with the presence of anti-topoisomerase I (ATA) and pulmonary fibrosis in SSc patients, as well as with diffuse cutaneous SSc (dcSSc). The presence of anti-centromere (ACA) and limited cutaneous SSc (lcSSc) did not show significant association with any of the examined SNPs. The results were consistent with previous reports in other ethnic populations in supporting the notion that polymorphisms of STAT4 may play an important role in susceptibility to SSc. It also revealed different genetic aspects of SSc subsets in a Han Chinese population.

Effect of methylprednisolone and edaravone administration on spinal cord injury

BACKGROUND

Spinal cord injury (SCI) is one of the most devastating traumatic conditions that primarily affects young males with an annual incidence of 15-40 cases per million.

AIM

To explore the superior neuroprotective effect of edaravone (ED) on spinal cord injury during maintenance therapy compared with methylprednisolone (MP).

MATERIALS AND METHODS

Sprague-Dawley rat model of spinal cord injury was established by modified Allen's method. Total 114 rats were divided into two groups and then six subgroups individually: A1 (control group, normal saline injection within 8 h), B1 (MP group, MP injection within 8 h), C1(ED group, ED injection within 8 h), A2 (control group, normal saline injection after 8 h), B1 (MP group, MP injection after 8 h), C1 (ED group, ED injection after 8 h). Further, we investigated the changes of histopathology, caspase-3 and Bcl-xL positive cell.

RESULTS

Haemorrhage, swelling, hyperaemia, gliocytes hyperplasia, inflammatory cells infiltration, vacuolar denaturation, and nucleus concentration could be observed, especially in control group. Caspase-3 positive cell was significantly decreased in MP and ED group within 8 h administration, but caspase-3 positive cell was only significantly decreased in ED group after 8 h administration. And B-cell lymphoma extra large (Bcl-xL) was significantly increased in ED group than MP group no matter within 8 h or after 8 h administration.

CONCLUSIONS

More attention should be paid on the time point of MP administration, and ED administration seem to be more effective for maintenance therapy.

Antibiotic resistance of lactic acid bacteria isolated from Chinese yogurts

The aim of this study was to evaluate the susceptibility of 43 strains of lactic acid bacteria, isolated from Chinese yogurts made in different geographical areas, to 11 antibiotics (ampicillin, penicillin G, roxithromycin, chloramphenicol, tetracycline, chlortetracycline, lincomycin, kanamycin, streptomycin, neomycin, and gentamycin). The 43 isolates (18 Lactobacillus bulgaricus and 25 Streptococcus thermophilus) were identified at species level and were typed by random amplified polymorphic DNA analysis. Thirty-five genotypically different strains were detected and their antimicrobial resistance to 11 antibiotics was determined using the agar dilution method. Widespread resistance to ampicillin, chloramphenicol, chlortetracycline, tetracyclines, lincomycin, streptomycin, neomycin, and gentamycin was found among the 35 strains tested. All of the Strep. thermophilus strains tested were susceptible to penicillin G and roxithromycin, whereas 23.5 and 64.7% of Lb. bulgaricus strains, respectively, were resistant. All of the Strep. thermophilus and Lb. bulgaricus strains were found to be resistant to kanamycin. The presence of the corresponding resistance genes in the resistant isolates was investigated through PCR, with the following genes detected: tet(M) in 1 Lb. bulgaricus and 2 Strep. thermophilus isolates, ant(6) in 2 Lb. bulgaricus and 2 Strep. thermophilus isolates, and aph(3')-IIIa in 5 Lb. bulgaricus and 2 Strep. thermophilus isolates. The main threat associated with these bacteria is that they may transfer resistance genes to pathogenic bacteria, which has been a major cause of concern to human and animal health. To our knowledge, the aph(3')-IIIa and ant(6) genes were found in Lb. bulgaricus and Strep. thermophilus for the first time. Further investigations are required to analyze whether the genes identified in Lb. bulgaricus and Strep. thermophilus isolates might be horizontally transferred to other species.

BOLDMirror: a global mirror system of DNA barcode data

DNA barcoding is a novel concept for taxonomic identification using short, specific genetic markers and has been applied to study a large number of eukaryotes. The huge amount of data output generated by DNA barcoding requires well-organized information systems. Besides the Barcode of Life Data system (BOLD) established in Canada, the mirror system is also important for the international barcode of life project (iBOL). For this purpose, we developed the BOLDMirror, a global mirror system of DNA barcode data. It is open-sourced and can run on the LAMP (Linux + Apache + MySQL + PHP) environment. BOLDMirror has data synchronization, data representation and statistics modules, and also provides spaces to store user operation history. BOLDMirror can be accessed at http://www.boldmirror.net and several countries have used it to setup their site of DNA barcoding.

Accuracy of noninvasive quantification of brain NAA concentrations using PRESS sequence: verification in a swine model with external standard

The metabolite ratios had been employed in the field of MR spectroscopy (MRS) for a long period. The main drawback of metabolite ratio is that ratio results are not comparable with absolute metabolite concentration in vivo. The purpose of this study was to examine the accuracy of noninvasive quantification of brain N-acetylaspartate (NAA) concentrations using previously reported MR external standard method. Eight swine were scanned on a GE 1.5 T scanner with a standard head coil. The external standard method was utilized with a sphere filled with NAA, GABA, glutamine, glutamate, creatine, choline chloride, and myo-inositol. The position resolved spectroscopy (PRESS) sequence was used with TE=135 msec, TR=1500 msec, and 128 scan averages. The analysis of MRS was done with SAGE/IDL program. In vivo NAA concentration was obtained using the equation S=N * e(-TE/T₂) * [1-e(-TR/T₁). In vitro NAA concentration was measured by high performance liquid chromatography (HPLC). In the MRS group, the mean concentration of NAA was 10.03 plusmn 0.74 mmol/kg. In the HPLC group, the mean concentration of NAA was 9.22 plusmn 0.55 mmol/kg. There was no significant difference between the two groups (p = 0.46). However, slightly higher value was observed in the MRS group (7/8 swine), compared with HPLC group. The range of differences was between 0.02~2.05 mmol/kg. MRS external reference method could be more accurate than internal reference method. ¹H MRS does not distinguish between N-acetyl resonance frequencies and other N-acetylated amino acids.

Genetic effects of stearoyl-coenzyme A desaturase (SCD) polymorphism on milk production traits in the Chinese dairy population

Stearoyl-CoA desaturase (SCD) is a multifunctional complex enzyme important in the cellular biosynthesis of fatty acids. The present study was to investigate the association of the SCD gene with milk production traits in dairy cattle. Two single nucleotide polymorphisms (SNPs) (g.6926A>G and g.8646A>G) in introns 3 and 4, and three SNPs (g.10153A>G, g.10213T>C and g.10329C>T) in exon 5 were identified with pooled DNA sequencing and genotyped using matrix-assisted laser desorption/ionization time of flight mass spectrometry assay in 752 Chinese Holstein cows. Polymorphism g.10329C>T was predicted to result in an amino acid replacement from alanine to valine in the SCD protein. With a mixed animal model, the significant associations of the five SNPs with 305-day milk, fat and protein yields and protein percentage were determined. We further demonstrated cows with heterozygous genotypes (A/G or C/T) had highest 305 day milk yield, fat yield, protein yield and lowest protein percentage. Heterozygous cows with genotype AG at the g.6926A>G locus showed the greatest milk yield (P < 0.0001), fat yield (P < 0.0001) and protein yield (P < 0.0001) among other heterozygous genotypes at any of the loci. Dominance effects of all identified SNPs on milk, fat and protein yields and protein percentage were significant. Moreover, significant allele substitution effects at g.6926A>G locus on milk yield and at g.10213T>C on protein yield were observed. Five-locus haplotypes and strong linkage disequilibrium (D' > 0.9) between the five SNPs were also observed. The results suggest that identified polymorphisms could be potential genetic markers to improve the production performance of Chinese Holstein.

Comparative proteomic analysis of grain development in two spring wheat varieties under drought stress

Two spring wheat varieties Ningchun 4 and Chinese Spring with good and poor resistance to abiotic stress, respectively, were used to investigate proteomic changes in the developing grains under drought stress by a comparative proteomics approach. A total of 152 protein spots showed at least twofold differences in abundance on two-dimensional electrophoresis (2-DE) maps, of which 28 and 68 protein spots were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry, respectively. Of the 96 identified protein spots, six different expression patterns were found and they were involved in stress/defense/detoxification, carbohydrate metabolism, photosynthesis, nitrogen metabolism, storage proteins and some other important functions. Comparative proteomic analysis revealed that under the drought conditions the decreased degree of ascorbate peroxidases was more significant in Chinese Spring than in Ningchun 4 during grain development whereas translationally controlled tumor protein, which was significantly upregulated at 14 DAF, was present in Ningchun 4 and absent in Chinese Spring. The Rubisco large subunit displayed an upregulated expression pattern in Ningchun 4. In addition, two drought-tolerant proteins, triosephosphate isomerase and oxygen-evolving complex showed B and F type expression patterns in Chinese Spring, but D and B types in Ningchun 4, respectively. These differentially expressed proteins might be responsible for the stronger drought resistance of Ningchun 4 compared to Chinese Spring.

Proteome analysis of wheat leaf under salt stress by two-dimensional difference gel electrophoresis (2D-DIGE)

Salt stress is a major abiotic stress that limits agricultural productivity in many regions of the world. To understand the molecular basis of the salt stress response in wheat (Triticum aestivum L.), a proteomic approach was used to identify the salt stress-responsive proteins in an elite Chinese wheat cultivar, Zhengmai 9023, which exhibits a high yield, superior gluten quality and better biotic resistance. Three-week-old seedlings were treated with NaCl of four different concentrations (1.0%, 1.5%, 2.0%, and 2.5%). The total proteins from the leaves of untreated and NaCl-treated plants were extracted and separated by two-dimensional difference gel electrophoresis (2D-DIGE). A total of 2358 protein spots were detected on the gels, among which 125 spots showed a significant change in protein abundance, and 83 differentially expressed spots were localised on preparative gels. Using Q-TOF mass spectrometry, 52 salt-responsive spots were identified, which were classified into six functional categories that included transport-associated proteins, detoxifying enzymes, ATP synthase, carbon metabolism, protein folding, and proteins with unknown biological functions. Of the 52 differentially expressed proteins, 26 were up-regulated, 21 were down-regulated, and five spots showed multi-expression patterns. In particular, some important proteins for salt tolerance were found to be up-regulated in Zhengmai 9023 under salt stress, such as H(+)-ATPases, glutathione S-transferase, ferritin and triosephosphate isomerase.

Comparison between genomic predictions using daughter yield deviation and conventional estimated breeding value as response variables

This study compared genomic predictions using conventional estimated breeding values (EBV) and daughter yield deviations (DYD) as response variables based on simulated data. Eight scenarios were simulated in regard to heritability (0.05 and 0.30), number of daughters per sire (30, 100, and unequal numbers with an average of 100 per sire) and numbers of genotyped sires (all or half of sires were genotyped). The simulated genome had a length of 1200 cM with 15,000 equally spaced Single-nucleotide polymorphism (SNP) markers and 500 randomly distributed Quantitative trait locus (QTL). In the simulated scenarios, the EBV approach was as effective as or slightly better than the DYD approach at predicting breeding value, dependent on simulated scenarios and statistical models. Applying a Bayesian common prior model (the same prior distribution of marker effect variance) and a linear mixed model (GBLUP), the EBV and DYD approaches provided similar genomic estimated breeding value (GEBV) reliabilities, except for scenarios with unequal numbers of daughters and half of sires without genotype, for which the EBV approach was superior to the DYD approach (by 1.2 and 2.4%). Using a Bayesian mixture prior model (mixture prior distribution of marker effect variance), the EBV approach resulted in slightly higher reliabilities of GEBV than the DYD approach (by 0.3-3.6% with an average of 1.9%), and more obvious in scenarios with low heritability, small or unequal numbers of daughters, and half of sires without genotype. Moreover, the results showed that the correlation between GEBV and conventional parent average (PA) was lower (corresponding to a relatively larger gain by including PA) when using the DYD approach than when using the EBV approach. Consequently, the two approaches led to similar reliability of an index combining GEBV and PA in most scenarios. These results indicate that EBV can be used as an alternative response variable for genomic prediction.