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A temperate phage, phiSTEC1575-Stx2k, was induced by mitomycin C treatment from a clinical Escherichia coli isolate producing a recently identified Shiga toxin 2k subtype. Transmission electron microscopy revealed that phiSTEC1575-Stx2k belongs to the family Siphoviridae. The complete genome of the phage contained 46,647 bp of circular double-stranded DNA with an average G+C content of 51%. Eighty putative open reading frames were predicted, 44 of which encode proteins involved in phage integration, DNA packaging and replication, regulation, toxicity, bacterial lysis, and morphogenesis. The phage was determined to be inserted into the dusA of lysogenic host chromosome by comparative genomic analysis. These results expand our knowledge on the genomic characteristics of Stx phages.

Previous observational studies focused on the association of serum magnesium (SMg) and chronic kidney disease (CKD), but the conclusion was inconsistent. To investigate the causal relationship of SMg and CKD, we performed a two-sample mendelian randomization (TSMR) analysis using publicly datasets.In mendelian randomization (MR) analysis, we used single nucleotide polymorphisms (SNPs) which had genetic statistical significance with SMg but not associated with kidney function and confounding factors as instrumental variable (IV). To select SNPs, we used publicly database of Genome Wide Association Study (GWAS) and Chronic Kidney Disease Genetics (CKDGen) Confirms. We used inverse-variance weighted (IVW), weighted median, MR-Egger regression, weighted mode, and simple mode approaches in TSMR analysis.We selected 4 SNPs (rs4072037, rs7965584, rs11144134 and rs448378) as IV. In IVW approach, the result of MR analysis for CKD was OR = 0.55, 95% CI: 0.06, 4.75, P = 0.58; for estimated glomerular filtration rate from creatinine (eGFR)crea was β = -0.06, 95% CI: -1.08, 0.07, P = 0.39; for estimated glomerular filtration rate from cystatin C (eGFR)cys was β = -0.03, 95% CI: -0.43, 0.36, P = 0.86, respectively per SD increase in SMg. When subgroup by diabetes mellitus (DM), the results for DM-eGFRcrea was β = -0.33, 95% CI: -0.85, 0.19, P = 0.21; and for non-DM-eGFRcrea was β = -0.03, 95% CI: -0.16, 0.11, P = 0.71. The results of other four MR approaches were consistent with IVW approach (all P 0.05).Our TSMR analysis showed that SMg had no causal effect on kidney function and progress CKD in European descent. As for the results about overall population, the verified study is needed in future study.

Background: Rheumatoid arthritis (RA) is a systematic autoimmune disease with evidence of genetic predisposition. The IKZF1 (IKAROS family zinc finger 1 (Ikaros)) gene is located at chromosome 7, encodes a transcription factor related tochromatin remodeling, regulates lymphocyte differentiation, and is associated with some autoimmune diseases. However, there were few studies reported the association between IKZF1 and the risk of RA in China. For this, we determined to investigate the possibility of association between the IKZF1 locus and RA. Methods: we selected one single nucleotide polymorphisms (SNP) in the IKZF1 locus, rs1456893, based on a detailed analysis of genome-wide association study (GWAS) data and performed genotyping in 410 RA patients and 421 healthy controls in Han Chinese. We studied the systematic genome-wide interrogation of DNA methylation between RA group and control group and we also studied the association between CpGs and RA. Results: The results showed that the rs1456893 locus was correlated with RA in different models(P＜0.05). Through comparison with methylation levels determined in their equivalent healthy counterparts we have identified and validated a restricted set of CpGs that show distinct methylation differences between patients with RA and control group. The Multiple logistic regression results showed CpG_3 (OR=3.17,95%CI=1.05-9.60,P=0.041) and CpG_13.14(OR=4.96,95%CI=1.77-13.86,P=0.002)were associated with RA. Conclusion: IKZF1 can be used as a marker for the diagnosis of RA. Higher CpG_3 and CpG_13.14 methylation levels would increase the risk of RA.

Background One of most important concerns of postmenopausal women is obesity. The relationships between menstruation status and obesity phenotypes are unclear. This study aimed to assess the associations between menstrual status and different obesity phenotypes in women. Methods In total, 5373 women aged ≥40 years were recruited from the Jidong and Kailuan communities. Basic information was collected via clinical examination, laboratory testing and standardized questionnaires. The women were stratified into the following three groups: menstrual period, menopausal transition period and postmenopausal period. General obesity was defined as a body mass index (BMI) of ≥28 kg/m2. Central obesity was defined as a waist-to-hip ratio (WHR) of > 0.85. Visceral obesity was defined as the presence of nonalcoholic fatty liver disease (NAFLD) and increased pericardial fat volume (PFV). Results The numbers of women in the menstrual, menopausal transition, and postmenopausal periods were 2807 (52.2%), 675 (12.6%) and 1891 (35.2%), respectively. The adjusted odds ratio (OR) and 95% confidence interval (CI) for central obesity among women in the menopausal transition and postmenopausal periods compared with women in the menstrual period were 0.99 (0.82–1.19) and 1.52 (1.26–1.84), respectively. The OR for NAFLD among postmenopausal women was 1.78 (1.44–2.20). The adjusted β-coefficient (standard error, SE) for PFV among postmenopausal women was 41.25 (7.49). The adjusted OR for general obesity among postmenopausal women was 1.01 (0.77–1.34). Conclusions This study demonstrated that menopause is an independent risk factor for central and visceral obesity but not general obesity.

Trehalose 6-phosphate phosphatase (TPP) dephosphorylates trehalose 6-phosphate to trehalose, an important growth regulator, and is involved in starch accumulation and grain yield. In this study, wheat TPP homologs were isolated from chromosomes 6AL, 6BL, and 6DL, designated as TaTPP-6AL1, TaTPP-6BL1, and TaTPP-6DL1, respectively. Sequence alignment showed a single-nucleotide polymorphism (SNP) at TaTPP-6AL1 locus between cultivars with contrasting thousand grain weight (TGW), forming alleles TaTPP-6AL1a and TaTPP-6AL1b, respectively. A cleaved amplified polymorphic sequence (CAPS) marker, TaTPP-6AL1-CAPS, was developed to differentiate the two alleles. TaTPP-6AL1 was mapped within the interval of IWB65749 and IWB60449 in a recombinant inbred line (RIL) population derived from Zhou8425B/Chinese Spring using the wheat 90K SNP assay. A QTL for TGW identified in the interval explained 12.1–19.1% of the phenotypic variance across five environments. Association analysis on 141 Chinese wheat cultivars also indicated a significant correlation of TaTPP-6AL1 with TGW. In conclusion, TaTPP-6AL1 and its functional marker are valuable to improve grain yield in wheat breeding.

Cultivated barley ( Hordeum vulgare L.) is considered as a non-host or inappropriate host species for wheat stripe rust caused by Puccinia striiformis f. sp. tritici . Most barley cultivars show a broad-spectrum resistance to wheat stripe rust. To determine the genes for resistance to wheat stripe rust in barley, a cross was made between a resistant barley line Y12 and a susceptible line Y16. The two parents, F 1 and 147 BC 1 plants were tested at seedling stage with Chinese prevalent race CYR32 of Puccinia striiformis f. sp. tritici by artifi cial inoculation in greenhouse. The results indicated that Y12 possessed one dominant resistance gene to wheat stripe rust, designated YrpstY1 provisionally. A total of 388 simple sequence repeat (SSR) markers were used to map the resistance gene in Y12 using bulked segregant analysis. A linkage map, including nine SSR loci on chromosome 7H and YrpstY1 , was constructed using the BC 1 population, indicating that the resistance gene YrpstY1 is located on chromosome 7H. It is potential to transfer the resistance gene into common wheat for stripe rust resistance.

Cultivated barley (Hordeum vulgare L.) is considered as a non-host or inappropriate host species for wheat stripe rust caused by Puccinia striiformis f. sp. tritici. Most barley cultivars show a broad-spectrum resistance to wheat stripe rust. To determine the genes for resistance to wheat stripe rust in barley, a cross was made between a resistant barley line Y12 and a susceptible line Y16. The two parents, F(1) and 147 BC(1) plants were tested at seedling stage with Chinese prevalent race CYR32 of Puccinia striiformis f. sp. tritici by artificial inoculation in greenhouse. The results indicated that Y12 possessed one dominant resistance gene to wheat stripe rust, designated YrpstY1 provisionally. A total of 388 simple sequence repeat (SSR) markers were used to map the resistance gene in Y12 using bulked segregant analysis. A linkage map, including nine SSR loci on chromosome 7H and YrpstY1, was constructed using the BC(1) population, indicating that the resistance gene YrpstY1 is located on chromosome 7H. It is potential to transfer the resistance gene into common wheat for stripe rust resistance.

Low-molecular-weight glutenin subunits (LMW-GS) have significant effects on the processing quality of end-use products of common wheat. It is more efficient to discriminate LMW-GS alleles with PCR-based molecular markers than with SDS-PAGE. In the present study, we developed an allele-specific PCR marker, designated Glu-B3abefg, which can be used to discriminate protein alleles Glu-B3a, b, e, f, and g simultaneously. Based on ten previously developed allele-specific STS markers, three multiplex PCRs, viz. Glu-B3c + Glu-B3d, Glu-B3b + Glu-B3g, and Glu-B3h + Glu-B3i, were established. Six Glu-B3 alleles (b, c, d, g, h, and i) could be discriminated using the three multiplex PCRs. Results of tests on 158 wheat varieties and lines using Glu-B3abefg and the three multiplex PCRs were consistent with those using the ten STS markers separately. The new allele-specific marker and three multiplex PCRs represent an efficient way to undertake marker-assisted selection of Glu-B3 alleles.