In vitro selection of a DNA aptamer targeted against Shigella dysenteriae

To identify DNA aptamers demonstrating binding specificity for Shigella dysenteriae, a whole-bacterium Systemic Evolution of Ligands by Exponential enrichment (SELEX) method was applied to a combinatorial library of single-stranded DNA (ssDNA) molecules. After several rounds of selection using S. dysenteriae as the target, the highly enriched oligonucleotide pool was sequenced and then grouped into different families based on primary sequence homologies and similarities in the secondary structures. Aptamer S 1, which showed particularly high binding affinity in preliminary studies, was chosen for further characterisation. This aptamer displayed a dissociation constant (K_d value) of 23.47 ± 2.48 nM. Binding assays to assess the specificity of aptamer S 1 showed high binding affinity for S. dysenteriae and low apparent binding affinity for other bacteria. The ssDNA aptamers generated may serve as a new type of molecular probe for microbial pathogens, as it has the potential to overcome the tedious isolation and purification requirements for complex targets.     

铁基纳米酶对鼠伤寒沙门菌生物被膜的影响

运用结晶紫染色定量法、生物被膜形态观察、生物被膜干重称量法、活菌定量计数法和细菌内活性氧检测法,评估氧化铁纳米酶和硫化铁纳米酶对鼠伤寒沙门菌生物被膜的影响及其机制.结果显示:鼠伤寒沙门菌S025株与这两类铁基纳米酶共孵育48h后,其生物被膜结晶紫染色吸光度值(A)、生物被膜厚度、生物被膜干重和活菌数量与未处理组相比均显著下降,活性氧水平显著上升,其中硫化铁纳米酶效果优于四氧化三铁纳米酶;在生物被膜形成后,加入铁基纳米酶处理0.5h、2h和12h,生物被膜结晶紫染色A值、生物被膜厚度、生物被膜干重和活菌数量与未处理组相比均显著下降,活性氧水平显著上升,硫化铁纳米酶效果同样优于四氧化三铁纳米酶.以上结果表明,铁基纳米酶通过调控鼠伤寒沙门菌胞内活性氧水平,不仅可以预防该菌的生物被膜形成,而且可以破坏已形成的生物被膜,本研究将有助于预防和治疗鼠伤寒沙门菌生物被膜引起的相关疾病.     

一种来源于Phialophora attae的玉米赤霉烯酮内酯水解酶ZHD11F的酶学表征和结构特点

玉米赤霉烯酮(zearalenone,ZEN)是一种雌激素类真菌毒素,可以与动物的雌激素受体竞争性结合,导致动物生殖系统内的激素紊乱。ZEN内酯水解酶(ZEN lactone hydrolase,ZHD)可以水解ZEN中的内酯键,进而使其转化为无雌激素毒性的产物。【目的】利用生物信息学分析以及酶学性质探索,鉴定出一个具有新特性的ZEN内酯水解酶。【方法】构建pET28a-zhd11f表达载体,在大肠杆菌BL21(DE3)中诱导表达ZHD11F,利用Ni-NTA纯化得到ZHD11F,对其酶学性质进行分析,并通过结构模拟和分子动力学分析阐明ZHD11F低温活性的机制。【结果】ZHD11F以ZEN为底物,比酶活为40.04 U/mg,最适反应温度与pH值分别为35 °C和8.0,在pH 6.0–9.5的范围内具有超过60%的酶活力,在35 °C以下具有较好的热稳定性,能够耐受多种金属离子。ZHD11F在10 °C和20 °C时,其活性分别保持20%和40%。更多的loop区增加了结构的柔韧性是该酶稳定性较差、在低温活性比较高的主要原因。【结论】Phialophora attae是瓶霉属的一种真菌,目前此真菌来源的酶极少被鉴定。关于本研究将Phialophora attae来源的ZEN内酯水解酶ZHD11F,在大肠杆菌中成功可溶性表达并得到纯酶,表征分析显示该酶是目前报道的第一个低温ZEN内酯水解酶,为研究此类酶的耐冷机制、广温度范围提供了候选,同时拓展了Phialophora attae来源酶的功能研究。     

Application of next-generation sequencing to screen for pathogenic mutations in 123 unrelated Chinese patients with Marfan syndrome or a related disease

Marfan syndrome(MFS) is a systemic connective tissue disease principally affecting the ocular, skeletal and cardiovascular systems. This autosomal dominant disorder carries a prevalence of 1:3,000 to 1:5,000. This study aims to define the mutational spectrum of MFS related genes in Chinese patients and to establish genotype-phenotype correlations in MFS. Panel-based targeted next-generation sequencing was used to analyze the FBN1, TGFBR1 and TGFBR2 genes in 123 unrelated Chinese individuals with MFS or a related disease. Genotype-phenotype correlation analyses were performed in mutation-positive patients. The results showed that 97 cases/families(78.9%; 97/123) harbor at least one(likely) pathogenic mutation, most of which were in FBN1; four patients had TGFBR1/2 mutations; and one patient harbored a SMAD3 mutation. Three patients had two FBN1 mutations, and all patients showed classical MFS phenotypes. Patients with a dominant negative-FBN1 mutation had a higher prevalence of ectopia lentis(EL). Patients carrying a haploinsufficiency-FBN1 mutation tended to have aortic dissection without EL. This study extends the spectrum of genetic backgrounds of MFS and enriches our knowledge of genotype-phenotype correlations.     

Upconversion luminescence resonance energy transfer-based aptasensor for the sensitive detection of oxytetracycline

In this work, a biosensor based on luminescence resonance energy transfer (LRET) from NaYF₄:Yb,Tm upconversion nanoparticles (UCNPs) to SYBR Green I has been developed. The aptamers are covalently linked to UCNPs and hybridized with their complementary strands. The subsequent addition of SYBR Green allows SYBR Green I to insert into the formed double-stranded DNA (dsDNA) duplex and brings the energy donor and acceptor into close proximity, leading to the fluorescence of UCNPs transferred to SYBR Green I. When excited at 980 nm, the UCNPs emit luminescence at 477 nm, and this energy is transferred to SYBR Green I, which emits luminescence at 530 nm. In the presence of oxytetracycline (OTC), the aptamers prefer to bind to its corresponding analyte and dehybridize with the complementary DNA. This dehybridization leads to the liberation of SYBR Green I, which distances SYBR Green I from the UCNPs and recovers the UCNPs' luminescence. Under optimal conditions, a linear calibration is obtained between the ratio of I₅₃₀ to I₄₇₇ nm (I₅₃₀/I₄₇₇) and the OTC concentration, which ranges from 0.1 to 10 ng/ml with a limit of detection (LOD) of 0.054 ng/ml.     

Expression and purification of an FGF9 fusion protein in E. coli,and the effects of the FGF9 subfamily on human hepatocellular carcinoma cell proliferation and migration

Fibroblast growth factor (FGF) 9 has oncogenic activity and plays an important role in the development of ovarian, lung, prostate, and gastric cancers. In the present study, with the aim of reducing the cost of utilizing growth factors in cancer research, a simple and efficient method for the preparation of recombinant human (rh)FGF9 in Escherichia coli was established. The rhFGF9 fusion protein (6 × His-TEV-rhFGF9) and the native protein released by tobacco etch virus (TEV) protease were obtained using a Ni-NTA system, with > 95% purity. Both purified forms of rhFGF9, with and without fusion tags, significantly stimulated the proliferation of NIH3T3 cells. The FGF9 subfamily, including FGF9, FGF16, and FGF20, in addition to rhFGF16, rhFGF9, and rhFGF20, were shown to stimulate the proliferation and migration of HuH7 human hepatocellular carcinoma (HCC) cells. Mechanistic studies revealed that the stimulation of HuH7 cell proliferation and migration with rhFGF9 and rhFGF20 were associated with the activation of the extracellular signal-regulated kinase (ERK) and nuclear factor κB (NF-κB) pathways and matrix metalloproteinase-26 (MMP26). Inhibition of the ERK and NF-κB pathways blocked cell migration, and NF-κB was demonstrated to be regulated by ERK. Therefore, the present study demonstrates a simple method for the preparation of biologically active rhFGF9 protein. Furthermore, the results indicate that exogenous rhFGF9- and rhFGF20-activated ERK/NF-κB signal transduction pathways play important roles in the regulation of HCC cell proliferation and migration, and this discovery helps to find the potential for new solutions of the treatment of liver cancer.

     

Global transcriptional analysis of stress-response strategies in Acidithiobacillus ferrooxidans ATCC 23270 exposed to organic extractant—Lix984n

Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed.     

Vector-based RNAi,a novel tool for isoform-specific knock-down of VEGF and anti-angiogenesis gene therapy of cancer

Vascular endothelial growth factor (VEGF) carries out multifaceted functions in tumor development, and it exists as at least five isoforms with distinct biologic activities and clinical implications. Several strategies have been developed to block VEGF for cancer therapy; however, the approach to target-specific VEGF isoform(s) has not been explored to date. In the present study, we show that DNA vector-based RNA interference (RNAi), in which RNAi sequences targeting murine VEGF isoforms are inserted downstream of an RNA polymerase III promoter, has potential applications in isoform-specific "knock-down" of VEGF. Large molecular weight VEGF isoforms were specifically reduced in vitro in the presence of isoform-specific RNAi constructs. Additionally, H1 promoter may be superior to U6 promoter when used for vector-based RNAi of VEGF isoforms. This strategy provides a novel tool to study the function of various VEGF isoforms and may contribute to VEGF isoform-specific treatment in cancer.     

龙葵抗阿特拉津生物型叶绿体基因文库的建立

用对阿特拉津(Atrazine)除草剂抗性的龙葵生物型B_(12)株系作材料,制备叶绿体DNA。B_(12)株ctDNA(叶绿体DNA)经BamHI酶解,在0.7％琼脂糖凝胶电泳上呈现24条带,其中最大的片段为18.6kb,最小的片段为1kb。用pBR322作为载体,构建B_(12)株ctDNA BamHI片段文库。通过与探针的分子杂交,从中筛选出含有编码叶绿体32kd蛋白质的阿特拉津抗性基因的克隆pSB135和含有ATP合酶α亚单位基因的克隆pSB132。