β-六六六对多刺裸腹溞生命表统计学参数的影响

应用生命表统计学方法研究了不同浓度(0.001、0.01、0.1、1、10、100和1000μg/L)的β-六六六对多刺裸腹溞(Moina macrocopa)种群统计学参数的影响。结果表明,与对照组相比,浓度为1000μg/L的β-六六六显著降低了多刺裸腹溞出生时的生命期望和净生殖率,100和1000μg/L的β-六六六显著降低了多刺裸腹溞的世代时间,0.1和1μg/L的β-六六六显著提高了多刺裸腹溞的种群内禀增长率。     

Meta-analysis of TYK2 gene polymorphisms association with susceptibility to autoimmune and inflammatory diseases

The aim of our meta-analysis was to quantitatively summarize the association of TYK2 gene polymorphisms with autoimmune and inflammatory diseases. 11 studies that included data from 21497 cases and 22647 controls were identified. OR was used as a measure of the effect of the association in a fixed/random effect model. Meta-analysis was performed for six TYK2 gene polymorphisms (rs34536443, rs2304256, rs280523, rs280519, rs12720270 and rs12720356). Significant association was found in rs34536443 (C versus G: OR = 0.76, 95% CI = 0.69–0.84, P < 0.00001; GC + CC versus GG: OR = 0.78, 95% CI = 0.68–0.90, P = 0.0005; CC versus GG + GC: OR = 0.76, 95% CI = 0.28–2.05, P = 0.58; CC versus GG: OR = 0.74, 95% CI = 0.27–2.02, P = 0.56; GC versus GG: OR = 0.78, 95% CI = 0.68–0.90, P = 0.0006) and rs2304256 (A versus C: OR = 0.78, 95% CI = 0.70–0.87, P < 0.0001; CA + AA versus CC: OR = 0.69, 95% CI = 0.59–0.81, P < 0.0001; AA versus CC + CA: OR = 0.75, 95% CI = 0.66–1.00, P = 0.05; AA versus CC: OR = 0.64, 95% CI = 0.47–0.86, P = 0.003; CA versus CC: OR = 0.70, 95% CI = 0.60–0.83, P < 0.0001) in TYK2 gene, but not for the other polymorphisms (rs280523, rs280519, rs12720270, and rs12720356). This meta-analysis demonstrates that autoimmune and inflammatory diseases is associated with TYK2 gene rs34536443 and rs2304256 polymorphisms, but not rs280523, rs280519, rs12720270 and rs12720356.     

Association of interleukin 23 receptor gene polymorphisms (rs10489629, rs7517847) with rheumatoid arthritis in European population: a meta-analysis

The interleukin 23 receptor (IL-23R) polymorphisms have been already discussed in rheumatoid arthritis (RA) repeatedly, but the results are conflict. The purpose of this meta-analysis was to assess whether IL-23R gene polymorphisms are associated with RA. We retrieved the available data from Pubmed, Medline, CNKI and CBM. Our study evaluated the effects of two polymorphisms (rs10489629, rs7517847) in European population. Pooling all the subjects, we found significant associations between the two polymorphisms and RA. For rs10489629, the pooled ORs (95 % CI) of C versus T, C/C+C/T versus T/T and C/C versus C/T+T/T were 1.092 (1.038-1.149), 1.146 (1.059-1.240) and 1.099 (1.008-1.199), respectively. For rs7517847, the combined ORs (95 % CI) of G versus T, G/G+G/T versus T/T and G/G versus G/T+T/T were 1.121 (1.063-1.183), 1.184 (1.092-1.283) and 1.133 (1.030-1.246), respectively. In conclusion, this meta-analysis demonstrates that the polymorphisms rs10489629 and rs7517847 of the IL-23R gene may be considered as risk factors for developing RA in European population.     

Overexpression of a TFIIIA-type zinc finger protein gene ZFP252 enhances drought and salt tolerance in rice (Oryza sativa L.)

We previously identified a salt and drought stress-responsive TFIIIA-type zinc finger protein gene ZFP252 from rice. Here we report the functional analysis of ZFP252 using gain- and loss-of-function strategies. We found that overexpression of ZFP252 in rice increased the amount of free proline and soluble sugars, elevated the expression of stress defense genes and enhanced rice tolerance to salt and drought stresses, as compared with ZFP252 antisense and non-transgenic plants. Our findings suggest that ZFP252 plays an important role in rice response to salt and drought stresses and is useful in engineering crop plants with enhanced tolerance to salt and drought stresses.     

An accurate feature-based method for identifying DNA-binding residues on protein surfaces

Proteins that interact with DNA play vital roles in all mechanisms of gene expression and regulation. In order to understand these activities, it is crucial to analyze and identify DNA-binding residues on DNA-binding protein surfaces. Here, we proposed two novel features B-factor and packing density in combination with several conventional features to characterize the DNA-binding residues in a well-constructed representative dataset of 119 protein-DNA complexes from the Protein Data Bank (PDB). Based on the selected features, a prediction model for DNA-binding residues was constructed using support vector machine (SVM). The predictor was evaluated using a 5-fold cross validation on above dataset of 123 DNA-binding proteins. Moreover, two independent datasets of 83 DNA-bound protein structures and their corresponding DNA-free forms were compiled. The B-factor and packing density features were statistically analyzed on these 83 pairs of holo-apo proteins structures. Finally, we developed the SVM model to accurately predict DNA-binding residues on protein surface, given the DNA-free structure of a protein. Results showed here indicate that our method represents a significant improvement of previously existing approaches such as DISPLAR. The observation suggests that our method will be useful in studying protein-DNA interactions to guide consequent works such as site-directed mutagenesis and protein-DNA docking.     

SCYPPred: a web-based predictor of SNPs for human cytochrome P450

Human cytochrome P450(CYP 450) enzymes mediate over 60% of the phase I-dependent metabolism of clinical drugs. They are also known for the polymorphism functions that have significant impacts on the enzyme activities. In this study, a web-server called SCYPPred was developed for predicting human cytochrome P450 SNPs (Single Nucleotide Polymorphisms) based on the SVM flanking sequence method; SCYPPred can rapidly yield the desired results by using the amino acid sequences information alone. The web-server is accessible to the public at http://snppred.sjtu.edu.cn. Hopefully SCYPPred could be a useful bioinformatics tool for elucidating the mutation probability of a specific CYP450 enzyme.     

Fas expression on peripheral blood lymphocytes in systemic lupus erythematosus: relation to the organ damage and lymphocytes apoptosis

Systemic lupus erythematosus (SLE) is a common autoimmune disease with complex etiology. Recently, a possible role of apoptotic cells in its pathogenesis has been suggested. This study is to evaluate the expression of Fas antigen on peripheral blood lymphocytes (PBLs) in SLE, to determine whether membrane Fas (mFas) has a role in the organ damage in SLE and to explore its relationship with the early apoptosis of the PBLs in SLE. Flow cytometry was used to evaluate the expression of mFas on PBLs in 68 Chinese SLE patients and 37 healthy controls. Systemic lupus international collaborative clinics/american colleges of rheumatology damage index (SDI) scores were calculated to further estimate the relationship of the expression of mFas with disease severity. Results showed that mFas expression levels were significantly higher (P < 0.01) among SLE patients than those in healthy controls. Higher (P = 0.01) expressions of mFas were found in patients with SDI scores ≥ as compared to those with SDI scores <3. Patients with neuropsychiatric or renal disease had a higher expression of mFas than those without neuropsychiatric (P = 0.03) or renal disease (P = 0.01). In addition, the expression levels had a positive (r = 0.381, P < 0.01) correlation with the early apoptosis rate of PBLs in SLE patients. Taken together, our study showed that Fas-expressing PBLs were increased in SLE patients, especially in patients with higher SDI score, and the expression levels of mFas were correlated to the organ damage and lymphocytes apoptosis.     

UreB蛋白B细胞抗原表位快速筛选与鉴定

以幽门螺旋杆菌(Helicobacterpylori,Hp)主要抗原蛋白尿素酶B(ureaseB,UreB)为靶蛋白,建立一种新的B细胞抗原表位筛选与鉴定方法.运用Fmoc固相肽合成法合成11条HpUreB蛋白的单表位抗原肽片段,在其氨基端标记FITC荧光素,应用荧光偏振方法(fluorescencepolarization,FP)快速鉴定这些肽片段的抗原性,并通过FP法在大规模样品中快速筛选相应抗体滴度高、分布人群广的优势抗原表位肽.结果表明,合成的11条UreB蛋白线性抗原肽中,10条具有较强的抗原性,其中No.2、No.5和No.11抗原肽相应的特异性抗体在感染Hp的人群中分布较广,抗体滴度较高,为UreB的优势抗原表位肽.对抗原表位进行多参数综合分析与设计,通过FP技术快速鉴定抗原肽,并筛选优势抗原表位肽,对于疾病的抗原表位谱研究具有重要的意义,同时在疾病的诊断、分型及治疗中具有重要的应用前景.     

SARS-CoV-2 nucleocapsid and Nsp3 binding: an in silico study

Archives of Microbiology - Severe acute respiratory syndrome virus 2 (SARS-CoV-2) belongs to the single-stranded positive-sense RNA family. The virus contains a large genome that encodes four...