An easy-to-use site-directed mutagenesis method with a designed restriction site for convenient and reliable mutant screening

Site-directed mutagenesis (SDM) has been a very important method to probe the function-structure relationship of proteins. In this study, we introduced an easy-to-use, polymerase chain reaction (PCR)-based SDM method for double-stranded plasmid DNA, with a designed restriction site to ensure simple and efficient mutant screening. The DNA sequence to be mutated was first translated into amino acid sequence and then the amino acid sequence was reversely translated into DNA sequence with degenerate codons, resulting in a large number of sequences with silent mutations, which contained various restriction endonuclease (RE) sites. Certain mutated sequence with an appropriate RE site was selected as the target DNA sequence for designing a pair of mutation primers to amplify the full-length plasmid via inverse PCR. The amplified product was 5'-phosphorylated, circularized, and transformed into an Escherichia coli host. The transformants were screened by digesting with the designed RE. This protocol uses only one pair of primers and only one PCR is conducted, without the need for hybridization with hazardous isotope for mutant screening or subcloning step.     

Extraction of DNA suitable for PCR applications from mature leaves of Mangifera indica L.

Good quality deoxyribonucleic acid (DNA) is the pre-requisite for its downstream applications. The presence of high concentrations of polysaccharides, polyphenols, proteins, and other secondary me- tabolites in mango leaves poses problem in getting good quality DNA fit for polymerase chain reaction (PCR) applications. The problem is exacerbated when DNA is extracted from mature mango leaves. A reliable and modified protocol based on the cetyl- trimethylammonium bromide (CTAB) method for DNA extraction from mature mango leaves is described here. High concentrations of inert salt were used to remove polysaccharides; Polyvinylpyrrolidone (PVP) and β-mercaptoethanol were employed to manage phenolic compounds. Extended chloroform-isoamyl alcohol treatment followed by RNase treatment yielded 950?1050 μg of good quality DNA, free of protein and RNA. The problems of DNA degradation,contamination, and low yield due to irreversible binding of phenolic compounds and coprecipitation of polysaccharides with DNA were avoided by this method. The DNA isolated by the modified method showed good PCR amplification using simple se- quence repeat (SSR) primers. This modified protocol can also be used to extract DNA from other woody plants having similar problems.     

A study of the relationship between expression level of TRF1 protein and telomerase activity in human acute leukemia

INTRODUCTION Telomeres are distinctive DNA-protein struc-tures that cap the ends of linear chromosomes.It is very important to keep the chromosomes stabilization.Telomerase activity is closely linked to attainment of cellular immortality,a step in carcinogenesis,while lack of such activity contributes to cellular senes-cence.Telomerase is activated in more than85%ofmalignant tumors(Hiayma et al.,1997).Human te-lomeric repeat binding factor1(TRF1)is a telomere associated with proteins a…     

Learning Using Dynamic and Static Visualizations: Students’ Comprehension, Prior Knowledge and Conceptual Status of a Biotechnological Method

The importance of biotechnology education at the high-school level has been recognized in a number of international curriculum frameworks around the world. One of the most problematic issues in learning biotechnology has been found to be the biotechnological methods involved. Here, we examine the unique contribution of an animation of the polymerase chain reaction (PCR) in promoting conceptual learning of the biotechnological method among 12th-grade biology majors. All of the students learned about the PCR using still images (n = 83) or the animation (n = 90). A significant advantage to the animation treatment was identified following learning. Students’ prior content knowledge was found to be an important factor for students who learned PCR using still images, serving as an obstacle to learning the PCR method in the case of low prior knowledge. Through analysing students’ discourse, using the framework of the conceptual status analysis, we found that students who learned about PCR using still images faced difficulties in understanding some mechanistic aspects of the method. On the other hand, using the animation gave the students an advantage in understanding those aspects.     

Detection of plasmid-mediated IMP-1 metallo-β-lactamase and quinolone resistance determinants in an ertapenem-resistant Enterobacter cloacae isolate

Objective  To investigate the mechanism of carbapenem resistance and the occurrence of plasmid-mediated quinolone resistance determinants qnr and aac(6′)-Ib-cr in a clinical isolate of Enterobacter cloacae. Methods  An ertapenem-resistant E. cloacae ZY106, which was isolated from liquor puris of a female gastric cancer patient in a Chinese hospital, was investigated. Antibiotic susceptibilities were determined by agar dilution method. Conjugation experiments, isoelectric focusing, polymerase chain reaction (PCR), and DNA sequence analyses of plasmid-mediated carbapenemases and quinolone resistance determinants were preformed to confirm the genotype. Outer membrane proteins (OMPs) were examined by urea-sodium dodecyl sulfatepolyacrylamide gel electrophoresis (Urea-SDS-PAGE). Results  Minimum inhibitory concentrations (MICs) of imipenem, meropenem, and ertapenem for ZY106 were 2, 4, and 16 μg/ml, respectively. Conjugation studies with Escherichia coli resulted in the transfer of significantly reduced carbapenem susceptibility. ZY106 produced IMP-1 metallo-β-lactamase and CTX-M-3 extended-spectrum β-lactamase, and E. coli transconjugant produced IMP-1. Plasmid-mediated quinolone resistance determinant qnrS1 was detected in ZY106. Transfer of the qnrS1-encoding-plasmid into E. coli by conjugation resulted in intermediate resistance to ciprofloxacin in E. coli transconjugant. Urea-SDS-PAGE analysis of OMPs showed that ZY106 lacked an OMP of approximately 38 kDa. Conclusion  It is the first IMP-1-producing Enterobacteriaceae in China and the first report of a clinical isolate that harbors both blaIMP and qnrS genes as well. The blaIMP-1, blaCTX-M-3, and qnrS1 are encoded at three different plasmids. IMP-1 combined with the loss of an OMP possibly resulted in ertapenem resistance and reduced imipenem and meropenem susceptibility in E. cloacae.      

Agrobacterium tumefaciens-mediated genetic transformation of the phytopathogenic fungus Penicillium digitatum

Agrobacterium tumefaciens-mediated transformation (ATMT) system was assessed for conducting insertional mutagenesis in Penicillium digitatum, a major fungal pathogen infecting post-harvest citrus fruits. A transformation efficiency of up to 60 transformants per 106 conidia was achieved by this system. The integration of the hph gene into the fungal genome was verified by polymerase chain reaction (PCR) amplification and sequencing. These transformants tested were also shown to be mitotically stable. Southern blot analysis of 14 randomly selected transformants showed that the hph gene was randomly integrated as single copy into the fungal genome of P. digitatum. Thus, we conclude that ATMT of P. digitatum could be used as an alternatively practical genetic tool for conducting insertional mutagenesis in P. digitatum to study functional genomics.     

A system for screening agonists targeting β2-adrenoceptor from chinese medicinal herbs

In order to develop a model for screening the agonists of human β₂-adrenoceptor from Chinese medicinal herbs extracts, we used a cell-based functional assay based on a common G protein-coupled receptor (GPCR) regulation mechanism and destabilized enhanced green fluorescent protein (d₂EGFP) reporter gene technique. The positive cell clone was confirmed by real-time polymerase chain reaction (PCR) and imaging analysis. To assess the value of this model, we screened over 2000 high performance liquid chromatography (HPLC)-fractionated samples from the ethanol extracts of Chinese medicinal herbs. Six fractions (isolated from Panax japonicus, Veratrum nigrum, Phellodendron amurense, Fructus Aurantii Immaturus, Chaenomeles speciosa, and Dictamnus dasycarpus) showed significant effects on active reporter gene expression, three of which (isolated from Phellodendron amurense, Fructus Aurantii Immaturus, and Chaenomeles speciosa) were selected for further concentration response analysis and the half maximal effective concentration (EC_{1/2 max}) values were 4.2, 2.7, and 4.8 μg/ml, respectively. Therefore, this reporter gene assay was suitable for screening β₂-adrenoceptor agonists. The results suggest that the six herbal extracts are the possible agonists of β₂-adrenoceptor. Project (No. 30873103) supported by the National Natural Science Foundation of China     

Clock generator and OOK modulator for RFID application

The clock generator and OOK modulator for RFID (Radio Frequency Identification) presented in this paper consist of a current source and delay elements. The simple constant-gm structure is adopted in the current source design and the current consumption of the current source is only about 2 μA. The delay elements, the clock generator and OOK modulator are introduced in detail in the paper. The designed circuits are fabricated by 0.6 μm CMOS process. The area of the core circuit is only about 400 μmμ0 μm. The delay time of all three samples is in the range of 9 μs to 21 μs when the supply voltage varies from 2 V to 4 V. As the measured results satisfy the system requirements, these circuit structures are suitable for RFID application.     

Detection of bacterial DNA by PCR and reverse hybridization in the 16s rRNA gene

The clinical diagnosis of sepsis is difficult, particularly in neonates. To devise a rapid and reliable method for identifing bacteria in blood and cerebrospinal fluid (CSF), we developed a pair of primers according to the gene encoding 16 s rRNA, found in all bacteria. DNA fragments from different bacterial species and from clinical samples were detected with polymerase chain reaction (PCR), and with reverse hybridization using a universal bacterial probe, a gram-positive probe and a gram-negative probe. Our results showed that a 371 bp DNA fragment was amplified from 20 different bacterial species. No signal was observed when human DNA and viruses were used as templates. The sensitivity could be improved to 10⁻¹² g. All 26 culture-positive clinical samples (22 blood samples and 4 CSF samples), were positive with PCR. The gram-negative and gram-positive probe hybridized to clinical samples and to known bacterial controls, as predicted by Gram’s stain characteristics. Our results suggest that the method of PCR and reverse hybridization is rapid, sensitive and specific in detecting bacterial infections. This finding may be significant in the clinical diagnosis of sepsis in neonates. Project (396457) supported by the Zhejiang Provincal Natural Science Foundation.     

Construction and characterization of a cDNA library from human liver tissue with chronic hepatitis B

INTRODUCTION Chronic hepatitis B virus (HBV) infection is aserious clinical problem because of its wide distribu-tion and possible adverse consequences, such as he-patic decompensation, cirrhosis and/or primary livercancer (PLC). The natural course of chronic HBVinfection is characterized by a series of hepatitic flaresor exacerbations and remissions (Ganem and Prince,2004). The severity, extent, duration and frequency ofhepatic histopathological changes in hepatitic flaresare d…     

虎耳草ISSR反应体系的建立及优化

建立并优化虎耳草ISSR-PCR反应体系和扩增程序,为探讨虎耳草种质资源遗传多样性奠定基础.采用正交设计方法和单因子试验,研究TaqDNA聚合酶、dNTP、Mg2+、引物、模板DNA、延伸时间及循环次数对PCR扩增的影响.结果表明:虎耳草ISSR-PCR的最佳反应体系为:在25μL的反应体系中含模板DNA 35ng,Mg2+1.25mmo/lL、dNTP 380μmo/lL、引物1.2μmo/lL、Taq DNA聚合酶1.5U.反应程序为:95℃预变性5min;94℃变性1min,50℃(据不同引物的退火温度)退火70s,72℃延伸1.5min,40个循环;72℃延伸10min,4℃保存.经过11份虎耳草种质检验,证明该体系稳定可靠,可用于虎耳草种质资源遗传多样性分析及居群鉴别的研究.     

Evaluation of organ distribution of microcystins in the freshwater phytoplanktivorous fish <Emphasis Type="Italic">Hypophthalmichthys molitrix</Emphasis>

To evaluate the public health risk of exposure to microcystins in fish food in China, the distribution pattem of microcystin-LR and microcystin-RR in various organs （liver, intestine, kidney, muscle and lipid） of the dominant freshwater phytoplanktivorous fish Hypophthalmichthys molitrix in Hangzhou, China＇s Tiesha River was investigated with the method of HPLC-ESI-MS analysis. The distribution of microcystins was different in the fish organs and the major total microcystins （microcystin-LR and microcystin-RR） were present in the intestines （6.49 μg/g fresh weight）, followed by the livers （4.52 μg/g fresh weight） and the muscles （2.86 μg/g fresh weight）. Microcystins were detected in kidneys （1.35 μg/g fresh weight）, but not detected in lipid. The results suggested that the mean daily intake from fish was 0.03 μg/kg body weight which was very close to the recommended WHO tolerable daily intake （TDI） level of 0.04μg/kg body weight per day, and local people were wamed they may have health risk if they consumed fish from the river.     

Effects of different concentrations of antisense oligodeoxynucleotides (ASODN) on human pancreatic cancer cell line PaTu8988s

Objective: To study the effects of different concentrations of antisense oligodeoxynucleotides (ASODN) on human pancreatic cancer cell line PaTu8988s. Method: Human pancreatic cancer cell line PaTu8988s in exponential growth stage was used to study the effect of different drug concentrations on the cell line in the presence of different concentrations (0 μg/ml, 5 μg/ml, 25 μg/ml, 50 μg/ml, 10 μg/m, 200 μg/ml) of ASODN and sense oligodeoxynucleotides (SODN). Cell counts and 3-[4,5-dimethylthiazolzyl]-2,5-diphenyl tetrazolium bromide (MTT) assays were carried out. Results: The inhibitory rate on the cell line PaTu8988s was 98.73%, 95.76%, 69.49%, 33.05% and 0 for ASODM concentrations of 200 μg/ml, 100 μg/ml, 50 μg/ml, 25 μg/ml and 5 μg/ml at 48 hours. Conclusions: K-ras complementary ASODN can inhibit the growth of human pancreatic cancer cell line PaTu8988s by 30.05% to 98.73%. This is likely to contribute to the specificity of the K-ras mRNA complementary capped ASODN sequential codon. Non-specific effect and side effect of ASOND were observed for instance, the greater the concentration is, the earlier the peak of inhibitory rate is reached. In concentration, of 25 μg/ml to 100 μg/ml ASODN showed a dose-effect correlation.     

Rapid in vitro propagation of medicinally important Aquilaria agallocha

Aquilaria agallocha can produce fragrant agarwood used for incense, traditional medicine and other products. An efficient plant regeneration system was established via organogenesis from shoots developed from seedlings ofAquilaria agallocha. Shoots generated many buds on MS medium supplemented with 1.3 μmol/L BA (6-benzylaminopurine) in the first 7 weeks, and the buds elongated on MS medium with 1.3 μmol/L BA+0.5 μmol/L NAA (naphthaleneacetic acid) in another 7 weeks, 2.3 shoots 2 cm in length per explant were obtained within 14 weeks. Plantlets were rooted on 1/2 MS medium after being immersed in 5 μmol/L NAA for 48 h, 96.7% of the roots grew up two weeks later. All plantlets that survived acclimatization grew well in the pots. Project supported by the National Natural Science Foundation of China (No. 30070066) and the Science and Technology Project of Guangzhou City (No. 2003J1-C0241), China     

Evaluation and application of an efficient plant DNA extraction protocol for laboratory and field testing

Nucleic acids in plant tissue lysates can be captured quickly by a cellulose filter paper and prepared for amplification after a quick purification.In this study,a published filter paper strip method was modified by sticking the filter paper on a polyvinyl chloride resin(PVC)sheet.This modified method is named EZ-D,for EASY DNA extraction.Compared with the original cetyl trimethylammonium bromide(CTAB)method,DNA extracted by EZ-D is more efficient in polymerase chain reaction(PCR)amplification due to the more stable performance of the EZ-D stick.The EZ-D method is also faster,easier,and cheaper.PCR analyses showed that DNA extracted from several types of plant tissues by EZ-D was appropriate for specific identification of biological samples.A regular PCR reaction can detect the EZ-D-extracted DNA template at concentration as low as 0.1 ng/μL.Evaluation of the EZ-D showed that DNA extracts could be successfully amplified by PCR reaction for DNA fragments up to 3000 bp in length and up to 80%in GC content.EZ-D was successfully used for DNA extraction from a variety of plant species and plant tissues.Moreover,when EZ-D was combined with the loop-mediated isothermal amplification(LAMP)method,DNA identification of biological samples could be achieved without the need for specialized equipment.As an optimized DNA purification method,EZ-D shows great advantages in application and can be used widely in laboratories where equipment is limited and rapid results are required.     

Development and evaluation of immunoassay for zeranol in bovine urine

A high affinity polyclonal antibody-based enzyme linked immunosorbent assay （ELISA） was developed for the quantification of zeranol in bovine urine. On the basis of urine matrix studies, the optimized dilution factors producing insignificant matrix interference were selected as 1：5 in pretreatment. In the improved ELISA, the linear response range was between 0.02 and 1 μg/ml, and the detection limit was 0.02 μg/ml for the assay. The overall recoveries and the coefficients of variation （CVs） were in the range of 82%-127% and 3.5%-8.8%, respectively. Thirty-six bovine urine samples spiked with zeranol （ranging from 0.2 to 10 μg/ml） were detected by the ELISA and liquid chromatography （LC） method, and good correlations were obtained between the two methods （R^2=0.9643）. We conclude that this improved ELISA is suitable tool for a mass zeranol screening and can be an altemative for the conventional LC method for zeranol in bovine urine.     

Effect of high glucose levels on the calcification of vascular smooth muscle cells by inducing osteoblastic differentiation and intracellular calcium deposition via BMP-2/Cbfα-1 pathway

In this paper,we investigate the effect and the possible mechanism of high glucose levels on the calcification of human aortic smooth muscle cells (HASMCs).HASMCs were divided into four groups: normal glucose group (NG),osmolality control group (OC),high glucose group (HG,HASMCs culture medium containing 30 mmol/L glucose),and high glucose plus recombinant human Noggin protein (bone morphogenetic protein-2 (BMP-2) antagonist) group (HN).The mRNA levels and the protein expressions of BMP-2 and core binding factor alpha-1 (Cbfα-1) were measured by real-time quantitative polymerase chain reaction (PCR) and Western blot.After induced by 10 mmol/L β-glycerol phosphoric acid,cells were harvested for assessments of alkaline phosphatase (ALP) activities at Days 1,2,and 3,and intracellular calcium contents at Days 7 and 14,respectively.High glucose levels increased the mRNA levels and the protein expressions of BMP-2 and Cbfα-1 (P0.05).The expression of Cbfα-1 was partially blocked by Noggin protein (P0.05),while BMP-2 was not (P0.05).After being induced by β-glycerol phosphoric acid,high glucose levels increased the ALP activity [(48.63±1.03) vs.(41.42±2.28) U/mg protein,Day 3;P0.05] and the intracellular calcium content [(2.76±0.09) vs.(1.75±0.07) μmol/mg protein,Day 14;P0.05] in a time-dependent manner when compared with the NG group,while the ALP activity could not be blocked by Noggin protein [(48.63±1.03) vs.(47.37±0.97) U/mg protein,Day 3;P0.05].These results show that high glucose levels can evoke the calcification of HASMCs by inducing osteoblastic trans-differentiation and intracellular calcium deposition via the BMP-2/Cbfα-1 pathway,which can be partially blocked by Noggin protein.     

Development of an indirect competitive ELISA for simultaneous detection of enrofloxacin and ciprofloxacin

Modified 1-ethyl-3-(3-dimethylaminopropy) carbodiimide (EDC) method was employed to synthesize the artificial antigen of enrofloxacin (ENR), and New Zealand rabbits were used to produce anti-ENR polyclonal antibody (pAb). Based on the checkerboard titration, an indirect competitive enzyme-linked immunosorbent assay (ELISA) standard curve was established. This assay was sensitive and had a linear range from 0.6 to 148.0 μg/kg (R ²=0.9567), with the half maximal inhibitory concentration (IC₅₀) and limit of detection (LOD) values of 9.4 μg/kg and 0.2 μg/kg, respectively. Of all the competitive analogues, the produced pAb exhibited a high cross-reactivity to ciprofloxacin (CIP) (87%), the main metabolite of ENR in tissues. After optimization, the matrix effects can be ignored using a 10-fold dilution in beef and 20-fold dilution in pork. The overall recoveries and coefficients of variation (CVs) were in the ranges of 86%–109% and 6.8%–13.1%, respectively. It can be concluded that the established ELISA method is suitable for simultaneous detection of ENR and CIP in animal tissues.     

Production of conjugated linoleic acids by Lactobacillus plantarum strains isolated from naturally fermented Chinese pickles

Naturally fermented pickles harbour many lactic acid bacteria (LAB). Forty-three LAB strains with conjugated linoleic acid (CLA)-producing ability were isolated from three naturally fermented pickle brines. Of these isolates, lp15 identified as Lactobacillus plantarum by API 50 CHL system and full-length 16S rDNA sequence analysis exhibited the highest CLA-producing ability (26.1% conversion) at 48 h in de Man Rogosa Sharpe (MRS) broth in the presence of 100 μg/ml of linoleic acid (LA). Compared to other strains, L. plantarum strain lp15 showed the highest tolerance upon increased levels of LA in the medium, i.e., up to 600 μg/ml. This strain converted about 25% of LA into CLA isomers [predominantly cis-9, trans-11 CLA (9-CLA) and trans-10, cis-12 CLA (10-CLA)], of which 75% was 9-CLA. Interestingly, though the conversion rate of LA into CLA by lp15 remained stable between 100 to 600 μg/ml LA levels in the medium, it dropped sharply at 1000 μg/ml. Taken together, the lp15 strain displayed relatively high LA tolerance with higher conversion rate, which implies that this strain is a valuable candidate for enhancing the CLA content in food-sources like pickles.