OBJECTIVE: To investigate the interaction between polymorphism of Toll-like receptor 4 (TLR4) gene G11367C in 3' untranslated region (UTR) and inhibitor of nuclear factor kappaB (IκB)-α 
Hae III in acute pancreatitis (AP) and the degree of severity.
 METHODS: A total of 450 patients with confirmed AP (AP group), who came from the First Affiliated Hospital of Xinxiang Medical College from May 2013 to June 2015, were divided into a mild AP subgroup (MAP subgroup), a moderately severe AP (MSAP subgroup), and a severe acute AP (SAP subgroup) (n=150 in each group). One hundred fifty healthy persons were served as a control group. There was no significant difference in age, gender, ethnicity and birthplace among all groups. The genetic polymorphisms of TLR4 gene G11367C in 3' untranslated region and IκB-α Hae III were analyzed by polymerase chain reaction (PCR). Eligible participants were personally interviewed by a questionnaire. Unconditional logistic regression model and single factor analysis were performed to calculate the adjusted odds ratios (OR) and 95% confidence intervals (95% CI) of G11367C and IκB-α Hae III polymorphisms, respectively. The interaction of nucleotide polymorphisms was analyzed.
 RESULTS: The frequencies of G11367C (GC), IκB-α Hae III (AG) and IκB-α Hae III (GG) were 69.56%, 33.78% and 36.22% in the AP group; 49.33%, 24.67% and 26.00% in the MAP subgroup; 70.67%, 34.67% and 36.67% in the MSAP subgroup; 88.67%, 42.00% and 46.00% in the SAP subgroup and 26.67%, 14.00% and 14.67% in the control group, respectively. There was significant difference in the frequencies betweenc the AP group and the control group, or among each AP subgroup (all P<0.01). The risk of AP was significantly increased in the subjects with G11367C (GC) genotype (ORAP=6.2828, ORMAP=2.6776, ORMSAP=6.6250, ORSAP=21.5147), which was also increased in those with IκB-α Hae III (AG) genotype (ORAP=5.7369, ORMAP=2.5277, ORMSAP=6.1824, ORSAP=17.8572) and in those with IκB-α Hae III (GG) genotype (ORAP=5.8724, ORMAP=2.5902, ORMSAP=6.4027, ORSAP=18.9022). The combined analysis of the polymorphisms showed that the percentage of G11367C (GC)/ IκB-α Hae III (GG) in the AP group, the MAP subgroup, the MSAP subgroup, the SAP subgroup and the control groups was 26.44%, 12.67%, 26.00%, 40.67% and 4.00%, respectively, with significant difference in the frequency among all groups (all P<0.01). The people who carried with Pro12Ala (AA)/Pro198Leu (LL) had a high risk of AP (ORAP=30.1314, ORMAP=6.7612, ORMSAP=39.5000, ORSAP=401.5833), and the statistical analysis suggested a positive interaction between Pro12Ala (AA) and Pro198Leu (LL) in increasing the risk of AP (All γ>1). Similarly, there were also positive interactions in the pathogenesis of AP between G11367C (GC) and IκB-α Hae III (AG) (All γ>1). 
 CONCLUSION These carriers of G11367C(GC), IκB-α Hae III(AG) and IκB-α Hae III (GG) genotypes may have a high risk of AP occurency, and there are significant interactions between genetic polymorphisms of G11367C and IκB-α Hae III, which increaes the risk of the occurrence and development of AP.
3' Untranslated Regions ; Acute Disease ; Deoxyribonucleases, Type II Site-Specific ; Ethnic Groups ; Genetic Predisposition to Disease ; Genotype ; Humans ; I-kappa B Kinase ; Logistic Models ; NF-KappaB Inhibitor alpha ; Odds Ratio ; Pancreatitis ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Promoter Regions, Genetic ; Toll-Like Receptor 4

OBJECTIVETo assess the association of vitamin D receptor gene (VDR) Apa I, Bsm I genotypes and allele frequencies and mild cognitive impairment (MCI) among elderly ethnic Uygurs from Xinjiang, China.

METHODSThe polymorphisms of the VDR genotypes (Apa I and Bsm I) were analyzed by the SNaPshot method in 124 MCI patients and 124 controls.

RESULTSFactors which can increase the risk for MCI have included the A allele of the Apa I polymorphism [OR=1.62, 95%CI(1.13-2.31)] and the AA genotype [OR=3.49, 95% CI(1.57-7.74)], the T allele of the Bsm I polymorphism [OR=1.94, 95%CI(1.24-3.05)], higher triglyceride and systolic blood pressure levels.

CONCLUSIONPolymorphisms of the VDR gene including the A allele and AA genotype of Apa I, and the T allele of Bsm I are probably associated with MCI among elderly ethnic Uygurs, and so are higher levels of triglyceride and systolic blood pressure.

Aged ; Alleles ; Asian Continental Ancestry Group ; genetics ; Binding Sites ; genetics ; Blood Pressure ; China ; Cognitive Dysfunction ; ethnology ; genetics ; psychology ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Diagnostic and Statistical Manual of Mental Disorders ; Ethnic Groups ; genetics ; Female ; Gene Frequency ; Genetic Predisposition to Disease ; ethnology ; genetics ; Genotype ; Humans ; Logistic Models ; Male ; Middle Aged ; Multivariate Analysis ; Polymorphism, Single Nucleotide ; Receptors, Calcitriol ; genetics ; Triglycerides ; blood

OBJECTIVETo investigate the single nucleotide polymorphisms (SNPs) at interleukin 6 (IL-6)-174 and TNF-β NcoI in Chinese Han children in Guangzhou, China and to provide basic information for study on the association between IL-6-174 and TNF-β NcoI polymorphisms and systemic inflammatory response syndrome (SIRS).

METHODSAllele-specific polymerase chain reaction and polymerase chain reaction-restriction fragment length polymorphism were used to determine the SNPs at IL-6-174 and TNF-β NcoI in 481 children selected from the Han population in Guangzhou in 2012. Genotype analysis and comparison with other populations were made with reference to relevant literature.

RESULTSChinese Han children in Guangzhou had only GG genotype at IL-6-174, and the SNP at this locus was rare or not seen in the Han population in Guangzhou. At TNF-β NcoI, the frequencies of TNF-β 1*1, TNF-β 1*2, and TNF-β 2*2 genotypes were 24.7%, 49.7%, and 25.6%, respectively. The sample distribution was in accordance with Hardy-Weinberg equilibrium. The TNF-β 1 allele frequency was significantly higher in Guangzhou Han population than in European and American white population (P<0.05).

CONCLUSIONSTNF-β NcoI SNP is prevalent in the Han population in Guangzhou, and the distribution of alleles is significantly different from that in the white population. The sample from an Hardy-Weinberg equilibrium population can be further used for study on the association between TNF-β NcoI SNP and SIRS in Chinese Han children in Guangzhou. IL-6-174 SNP is rare or not seen in the Han population in Guangzhou, so SNP at this locus cannot be selected for disease association analysis.

Asian Continental Ancestry Group ; genetics ; Child, Preschool ; China ; ethnology ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Female ; Gene Frequency ; Humans ; Interleukin-6 ; genetics ; Lymphotoxin-alpha ; genetics ; Male ; Polymorphism, Single Nucleotide ; Systemic Inflammatory Response Syndrome ; genetics

To reveal the effect of rotation cropping and bacterial manure on the growth of Chrysanthemum morifolium and screen the beneficial endophytic, the diversity of endophytic and dominant genera of different treatment groups were analyzed. Four different treatments were continuous cropping, rotation, self-made organic fertilizer and commercially available fertilizer, respectively. Endophytic bacterial diversity and dominant genera in different organs were examined using Terminal Restriction Fragment Length Polymorphism (T-RFLP). The results showed that enzyme Hae III was more appropriate than enzyme Hinfl because the number of TRFs digested by enzyme Hae III was more than that of enzyme Hinfl. In comparison of diversity, the endophytic bacterial communities' diversity index in group of cropping rotation and fertilizer was higher than that of continuous cropping which indicated that the addition of exogenous microorganism in soil could increase the diversity of plant endophyte. 18 dominant species were selected, including 3 kinds of Firmicutes, 4 kinds of Actinomycetes and 11 kinds of Proteobacteria. The results of dominant species comparison showed that the number of dominant species in continuous cropping of Ch. morifolium was significantly less than that of the rotation group. Some dominant bacteria in rotation group and fertilizer group such as Arthrobacter, Streptomyces, Streptomyces, Flavobacterium and Mycobacterium were not found in the continuous cropping of Ch. mortfolium group. Dominant species of fertilizer treatment group was similar with the rotation group, and the continuous cropping group's dominant species was more abundant. It indicates that these bacteria may be able to mitigate hindrance in continuous cropping, especially the Flavobacterium which can decompose the pathogenic fungi is worthy of further attention. Compared with leaves, there are more dominant species in roots and stems. The diversity of edophytic bacterial communities in continuous cropping of Ch. morifolium stays below than that in the rotation of Ch. morifolium, and fertilizer treatment can increase the diversity of continuous cropping so that it could mitigate hindrance in continuous cropping.
Actinobacteria ; physiology ; Agriculture ; Biodiversity ; Chrysanthemum ; growth & development ; microbiology ; Deoxyribonucleases, Type II Site-Specific ; Endophytes ; Fertilizers ; Gram-Positive Bacteria ; physiology ; Phylogeny ; Plant Leaves ; Plant Roots ; microbiology ; Polymorphism, Restriction Fragment Length ; Proteobacteria ; physiology ; RNA, Ribosomal, 16S ; chemistry ; genetics ; Soil ; Soil Microbiology

DraIII is a type IIP restriction endonucleases (REases) that recognizes and creates a double strand break within the gapped palindromic sequence CAC↑NNN↓GTG of double-stranded DNA (↑ indicates nicking on the bottom strand; ↓ indicates nicking on the top strand). However, wild type DraIII shows significant star activity. In this study, it was found that the prominent star site is CAT↑GTT↓GTG, consisting of a star 5' half (CAT) and a canonical 3' half (GTG). DraIII nicks the 3' canonical half site at a faster rate than the 5' star half site, in contrast to the similar rate with the canonical full site. The crystal structure of the DraIII protein was solved. It indicated, as supported by mutagenesis, that DraIII possesses a ββα-metal HNH active site. The structure revealed extensive intra-molecular interactions between the N-terminal domain and the C-terminal domain containing the HNH active site. Disruptions of these interactions through site-directed mutagenesis drastically increased cleavage fidelity. The understanding of fidelity mechanisms will enable generation of high fidelity REases.
Amino Acid Sequence ; Base Sequence ; Calorimetry, Differential Scanning ; Catalytic Domain ; Crystallography, X-Ray ; DNA ; metabolism ; DNA Cleavage ; Deoxyribonucleases, Type II Site-Specific ; chemistry ; genetics ; metabolism ; Escherichia coli ; metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Recombinant Proteins ; chemistry ; genetics ; metabolism ; Sequence Alignment ; Substrate Specificity

OBJECTIVETo explore the diagnostic value of serum levels of BamHI-W fragment, latent membrane protein-1 (LMP-1), BZLF1 and ZEBRA protein in patients with natural killer (NK)/T-cell lymphomas (NKTCLs), and to evaluate their relationship with clinical features.

METHODSA total of 144 cases were analyzed in this study, including 48 NKTCLs patients, 48 other types of non-Hodgkin's lymphomas (NHL) patients and 48 healthy individuals as controls. Fluorescent quantitative real-time polymerase chain reaction (RQ-PCR) was used to measure the copy number of BamHI-W, LMP-1 and BZLF1 in serum. Enzyme linked immunosorbent assay (ELISA) was applied to measure the serum levels of ZEBRA protein. The relative operating characteristic (ROC) curve was applied in the evaluation of the tested markers in diagnosis of NKTCL patients, and the correlations among the tested markers and clinical feature were analyzed.

RESULTSCompared with the controls, NKTCL group showed significantly higher levels of all the tested markers (P < 0.01). The median values of serum BamHI-W, LMP-1 and BZLF1 DNAs level were 1870, 394 and 499 copies/ml, respectively. And the median value of ZEBRA protein level was 73.3 µg/L. Furthermore, the ROC curves analysis revealed that all the area under curve (AUC) of LMP-1, BZLF1 and ZEBRA were more than 0.70, which were probably helpful in the diagnosis of NKTCL. To predict the presence of NKTCL, BamHI-W showed a high sensitivity of 81.3%, while BZLF1 showed a high specificity of 81.2%. Untreated patients seemed to have a significantly higher level of serum LMP1 DNA than that of treated patients (median value 898 copies/ml vs 0 copies/ml, P = 0.050). Correlation analysis showed that serum BamHI-W DNA level was correlated with the presence of B symptoms. All the three genes expressed in 94.4% of the untreated cases. On the other hand, none of them expressed in treated cases.

CONCLUSIONSIt suggested that combined measurements of BamHI W, LMP1 and BZLF1 DNA levels might be helpful to the diagnosis and therapeutic monitor of NKTCL.

Adolescent ; Adult ; Aged ; Aged, 80 and over ; Case-Control Studies ; Deoxyribonuclease BamHI ; blood ; Female ; Herpesvirus 4, Human ; Humans ; Lymphoma, T-Cell ; blood ; diagnosis ; Male ; Middle Aged ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; Trans-Activators ; blood ; Viral Matrix Proteins ; blood ; Young Adult

OBJECTIVETo optimize the performance of Pulsed-Field Gel Electrophoresis (PFGE) for the comparison of inter-laboratory results and information exchange of Borrelia burgdorferi subtyping.

METHODSA panel of 34 strains of B. burgdorferi were used to optimize PFGE for subtyping. In order to optimize the electrophoretic parameters (EPs), all 34 strains of B. burgdorferi were analyzed using four EPs, yielding different Simpson diversity index (D) values and the epidemiological concordance was also evaluated.

RESULTSThe EP of a switch time of 1 s to 25 s for 13 h and 1 s to 10 s for 6 h produced the highest D value and was declared to be optimal for MluI and SmaI PFGE of B. burgdorferi. MluI and SmaI were selected as the first and second restriction enzymes for PFGE subtyping of B. burgdorferi according to discrimination and consistency with epidemiological data.

CONCLUSIONPFGE can be used as a valuable test for routine genospecies identification of B. burgdorferi.

Animals ; Bacterial Proteins ; metabolism ; Bacterial Typing Techniques ; Borrelia burgdorferi ; classification ; genetics ; isolation & purification ; DNA, Bacterial ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Electrophoresis, Gel, Pulsed-Field ; Humans ; Ixodes ; Rats

BACKGROUNDUntreated human cytomegalovirus (CMV) disease (CMVD) is an identified risk factor for reduced rates of patient (and graft) survival, death or retransplantation in kidney transplant recipients due to increased immunological tolerance after transplant. Vitamin D receptor (VDR) gene polymorphisms have an obvious relationship with autoimmune diseases but the relationship between VDR gene polymorphisms and CMVD are not well understood. This study investigated the relationship between VDR FokI and ApaI gene polymorphisms and CMVD, and their value for predicting risk of CMVD.

METHODSNinety-eight kidney transplantation recipients were randomly chosen for which peripheral blood samples and case histories for the first three months after kidney transplantation were obtained. Using polymerase chain reaction-restriction fragment length polymorphisms, 30 recipients were found to be homozygous for the FokI gene (FF), 47 heterozygous (Ff), and 21 were homozygous (ff). Likewise, similar analyses determined that 12 recipients were homozygous for the ApaI gene (AA), 36 heterozygous (Aa), and 50 homozygous (aa). Factors affecting the prognosis of the kidney transplantation were compared for all genotypes by statistical analysis before operation. Infection by CMV for all recipients was detected by immunofluorescence assay to diagnose CMVD.

RESULTSNo statistical significance was observed for the factors affecting the prognosis of the kidney transplantation between both genotypes; however, statistical differences in CMVD among the FokI genotypes were identified. It was determined that the risk of CMVD was significantly increased for recipients of the ff genotype than for other genotypes. There was no statistical significance observed for CMVD among ApaI genotypes.

CONCLUSIONSThe recessive f allelic gene of VDR can be regarded as a risk factor of CMVD while FF recipients have lower incidence of CMVD after kidney transplantation. ApaI genotypes showed no relationship with predisposition to CMVD.

Adolescent ; Adult ; Alleles ; Cytomegalovirus Infections ; genetics ; Deoxyribonucleases, Type II Site-Specific ; genetics ; Female ; Genotype ; Homozygote ; Humans ; Kidney Transplantation ; adverse effects ; Male ; Polymorphism, Genetic ; genetics ; Polymorphism, Restriction Fragment Length ; genetics ; Receptors, Calcitriol ; genetics ; Site-Specific DNA-Methyltransferase (Adenine-Specific) ; genetics ; Young Adult

OBJECTIVE: To quantitatively investigate the association between the polymorphism of FokI of the VDR gene and the susceptibility of prostatic cancer. METHODS: Databases of Pubmed, EMBase, CBM, CNKI, VIP, and Wanfang Data were retrieved from the date they formed till May 2011. All randomized controlled clinical trials which matched both the inclusive criteria and exclusive criteria were subjected to meta-analysis, conducted on Revman 5.0.0 software. Stata 11.0 software was employed to process Begg's test. RESULTS: Ten studies were included. Total sample cases were 8360, with 3749 cases in the patient group and 4611 cases in the control group, respectively. The quantitative analysis showed there were no significantly differences between the polymorphism of VDR FokI alleles and the susceptibility of prostatic cancer (allele F to f: OR=1.00, 95% CI=0.94-1.06, P=0.96; genotypes FF/Ff to ff: OR=1.04, 95% CI=0.93-1.51, P=0.48; genotypes FF to Ff/ff: OR=0.97, 95% CI=0.89-1.06, P=0.53). Though one research on Indian people indicated that allele F was a risk factor for prostatic cancer, in Begg's test we observed relatively high publication bias. The subgroup analysis showed there were no significantly differences between the polymorphism of VDR FokI alleles and the susceptibility of prostatic cancer (allele F to f, white race: OR=0.91, 95% CI=0.88-1.02, P=0.17; yellow race: OR=1.09, 95% CI=0.95-1.24, P=0.22; Indian: OR=1.91, 95% CI=1.30-2.81, P=0.0009). CONCLUSION VDR FokI allele F might be a protective factor for European and American Caucasians.
Alleles ; Deoxyribonucleases, Type II Site-Specific ; genetics ; Genetic Predisposition to Disease ; Humans ; Male ; Polymorphism, Single Nucleotide ; Prostatic Neoplasms ; genetics ; Receptors, Calcitriol ; genetics

Adrenal Hyperplasia, Congenital ; genetics ; Chromatography, High Pressure Liquid ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Female ; Humans ; Point Mutation ; genetics ; Polymerase Chain Reaction ; methods ; Pregnancy