构建噬菌体展示抗体库过程中电穿孔法的条件优化

目的：确定稳定且高效的电转化实验方案以达到构建高库容噬菌体展示抗体库的目的。方法：探索电压、脉冲时间、噬菌粒DNA质量与浓度、TG1大肠杆菌的生长周期、重悬洗涤缓冲液及培养基优化等方面对TG1大肠杆菌电转化效率的影响。结果：当电转杯电极间距为2mm时,设定电转仪参数为3kV、25μF、5ms、200Ω;外源DNA经纯化后加入感受态菌液中使终浓度为1ng/μl;培养基中加入20mmol/L的MgCl₂,并将TG1的生长阶段调控在OD₆₀₀=0.8,用无菌超纯水重悬及洗涤细胞,将感受态细胞浓度调整为4×10¹⁰个/ml。在上述条件下,电转化效率可达到4.9×10⁹CFU/μg DNA。结论：通过多种条件优化,提高了电转化效率,为构建高库容噬菌体展示抗体库建立了基础。     

环境水体中肠道感染菌群与几种典型致病菌的QPCR检测及相关性分析

利用定量PCR(QPCR)方法,对环境水体中的肠道感染菌群及几种致病菌进行4个月的连续检测。结果表明:在污染严重的水体中,埃希氏大肠菌(E.coli)是水中肠道感染菌群的主体,其强度接近于用通用引物检测出的肠道感染菌群强度。当肠道感染菌群拷贝数超过10⁴copies·100 mL^-1时,沙门氏菌(S.typhrmurium)和志贺氏痢疾杆菌(Shigella flexneri)也持续被检出,可以认为是水体病原污染的标志之一;在轻度污染和清洁水体中,当肠道感染菌群拷贝数低于10⁴copies·100 mL^-1时,通过通用引物检测到的肠道感染菌群主要是上述3种病原细菌以外的细菌,且3种病原细菌的出现频度和强度与肠道感染菌群之间没有明显的相关性。     

Evaluation of 5'-nuclease and hybridization probe assays for the detection of shiga toxin-producing Escherichia coli in human stools

5′-Nuclease and a hybridization probe assays for the detection of shiga toxin-producing Escherichia coli were validated with regard to selectivity, analytical sensitivity, reproducibility and clinical performance. Both assays were capable of detecting the classical stx₁ and stx₂ genes when challenged with reference strains of E. coli (n = 40), although 1 to 4 minority sequence variants, whose clinical relevance is limited (stx_1c, stx_1d, and stx_2f), were detected less efficiently or not at all by one or both assays. No cross reaction was observed for both assays with 37 strains representing other gastrointestinal pathogens, or normal gastrointestinal flora. Analytical sensitivity ranged from 3.07 to 3.52 log₁₀ and 3.42 to 4.63 log₁₀ CFU/g of stool for 5′-nuclease and hybridization probe assay, respectively. Reproducibility was high with coefficients of variation of ≤ 5% for both inter- and intra-assay variation. Clinical performance was identical with a panel of archived positive specimens (n = 19) and a prospective panel of stools associated with bloody diarrhea (n = 115). In conclusion, both assays proved to be sensitive and reproducible.     

Bacterial cell surface display of lipase and its randomly mutated library facilitates high-throughput screening of mutants showing higher specific activities

The thermostable lipase (TliA) from Pseuodmonas fluorescens was functionally displayed on the surface of Escherichia coli using the ice-nucleation protein (INP) as an anchor. The INP–TliA fusion proteins were correctly synthesized and localized on the surface, confirmed by flow cytometer and halo forming activity on tributyrin emulsion agar plate. Lipase-displaying cells were used as an alternative immobilized biocatalyst to hydrolyze olive oil in aqueous–organic solvent two phases reaction. Furthermore, the randomly generated library of TliA was also displayed on E. coli. In order to be able to screen mutants showing increased specific activities, we optimized culture conditions, induction condition and host cell types. From more than 10⁵ members of library, top four mutants were selected. Selected clones of T48, T54, T61, and T68 showed 29-, 24-, 2-, and 19-fold increases, respectively, in whole-cell activities compared to wild-type enzyme. The DNA sequencing showed that one or three amino acids were exchanged and positions critical for increased activities were random. These results demonstrate that surface display provide a useful technology for directed evolution of industrially important lipases.     

The cryoprotectant trehalose destabilises the bilayer organisation of Escherichia coli-derived membrane systems at elevated temperatures as determined by H and P-NMR

In this study, ²H and ³¹P-NMR techniques were used to study the effects of trehalose and glycerol on phase transitions and lipid acyl chain order of membrane systems derived from cells of E. coli unsaturated fatty acid auxotroph strain K1059, which was grown in the presence of [11,11-²H₂]-oleic acid or [11,11-²H₂]-elaidic acid. From an analysis of the temperature dependence of the quadrupolar splitting it could be concluded that neither 1 M trehalose or glycerol generally had any significant effect on the temperature of the lamellar gel to liquid-crystalline phase transition. In the case of the oleate-containing hydrated total lipid extract, glycerol but not trehalose caused a 5°C increase of this transition temperature. In general, both cryoprotectants induced an ordering of the acyl chains in the liquid-crystalline state. Trehalose and glycerol both decrease the bilayer to non-bilayer transition temperature of the hydrated lipid extract of oleate-grown cells by about 5°C, but only trehalose in addition induces an isotropic to hexagonal (H_II) phase transition. In the biological membranes, trehalose and not glycerol destabilised the lipid bilayer, and in the case of the E. coli spheroplasts, part of the induced non-bilayer structures is ascribed to a hexagonal (H_II) phase in analogy with the total lipids. Interestingly, 1 mM Mg²⁺ was a prerequisite for the destabilisation of the lipid bilayer. In the hydrated total lipid extract of E. coli grown on the more ordered elaidic acid, both transition temperatures were shifted about 20°C upwards compared with the oleate-containing lipid, but the effect of trehalose on the lipid phase behaviour was similar. The bilayer destabilising ability of trehalose might have implications for the possible protection of biological systems by (cryo-)protectants during dehydration, in that protection is unlikely to be caused by preventing the occurrence of polymorphic phase transitions.     

Characterization of Growth and Conidia Production of Exserohilum monoceras on Different Substrates

On agar media the maximum conidia production of Exserohilum monoceras occurred on V-8 juice agar (VA) or centrifuged V-8 juice agar, whereas the optimal radial mycelial growth occurred on Czapek-Dox agar. The optimal temperatures for radial mycelial growth and conidia production were 28 and 27°C respectively. Light prohibited E. monoceras conidia production. The best sporulation occurred under continuous dark conditions. Echinochloa leaf decoction significantly increased conidia production on potato dextrose agar (PDA) and VA, and significantly increased germ tube length on PDA, lima bean agar and VA, but did not affect conidia germination. No conidia were produced in liquid media. Of 22 agricultural-based products evaluated as solid substrates, the most abundant sporulation (1.8 × 10⁶ conidia g^-1 of dry weight) occurred on corn leaves. The conidia production of E. monoceras on corn leaves was affected by incubation period, moisture content and substrate quantity. There were no differences in germination rate, germ tube length and virulence of conidia produced on agar media or corn leaves.     

Microbial characterization during composting of municipal solid waste

This study investigates the prevailing physico-chemical conditions and microbial community; mesophilic bacteria, yeasts and filamentous fungi, bacterial spores, Salmonella and Shigella as well as faecal indicator bacteria: total coliforms, faecal coliforms and faecal Streptococci, present in a compost of municipal solid waste. Investigations were conducted in a semi-industrial pilot plant using a moderate aeration during the composting process. Our results showed that: (i) auto-sterilization induced by relatively high temperatures (60–55°C) caused a significant change in bacterial communities. For instance, Escherichia coli and faecal Streptococci populations decreased, respectively, from 2×10⁷ to 3.1×10³ and 10⁷ to 1.5×10³ cells/g waste dry weight (WDW); yeasts and filamentous fungi decreased from 4.5×10⁶ to 2.6×10³ cells/g WDW and mesophilic bacteria were reduced from 5.8×10⁹ to 1.8×10⁷ bacteria/g WDW. On the other hand, the number of bacterial spores increased at the beginning of the composting process, but after the third week their number decreased notably; (ii) Salmonella disappeared completely from compost by the 25th day as soon as the temperature reached 60°C; and (iii) the bacterial population increased gradually during the cooling phase. While Staphylococci seemed to be the dominant bacteria during the mesophilic phase and at the beginning of the thermophilic phase, bacilli predominated during the remainder of the composting cycle. The appearance of gram-negative rods (opportunistic pathogens) during the cooling phase may represent a serious risk for the sanitary quality of the finished product intended for agronomic reuse. Compost sonication for about 3 min induced the inactivation of delicate bacteria, in particular gram-negatives. By contrast, gram-positive bacteria, especially micrococcus, spores of bacilli, and fungal propagules survived, and reached high concentrations in the compost.     

DNA buoyant density shifts during 15N-DNA stable isotope probing

DNA-based stable isotope probing (SIP) is a novel technique for the identification of organisms actively assimilating isotopically labeled compounds. Herein, we define the limitations to using ¹⁵N-labeled substrates for SIP and propose modifications to compensate for these shortcomings. Changes in DNA buoyant density (BD) resulting from ¹⁵N incorporation were determined using cultures of disparate GC content (Escherichia coli and Micrococcus luteus). Incorporation of ¹⁵N into DNA increased BD by 0.015±0.002 g mL⁻¹ for E. coli and 0.013±0.002 g mL⁻¹ for M. luteus. The DNA BD shift was greatly increased (0.045 g mL⁻¹) when dual isotope (¹³C plus ¹⁵N) labeling was employed. Despite the limited DNA BD shift following ¹⁵N enrichment, we found the use of gradient fractionation, followed by a comparison of T-RFLP profiles from fractions of labeled and control treatments, facilitated detection of enrichment in DNA samples from either cultures or soil.     

The cyclization of linear DNA in Escherichia coli by site-specific recombination

The efficiency with which linearized plasmid DNA can transform competent Escherichia coli can be significantly increased by use of the Cre-lox site-specific recombination system of phage P1. Linear plasmid molecules containing directly repeated loxP sites (lox² plasmids) are cyclized in Cre⁺ E. coli strains after introduction either by transformation or by mini-Mu transduction, Exonuclease V activity of the RecBC enzyme inhibits efficient cyclization of linearized lox² plasmids after transformation. By use of E. coli mutants which lack exonuclease V activity, Cre-mediated cyclization results in transformation efficiencies for linearized lox² plasmids identical to those obtained with covalently closed circular plasmid DNA. Moreover, Cre⁺ E. coli recBC strains allow the efficient recovery of lox² plasmids integrated within large linear DNA molecules such as the 150-kb genome of pseudorabies virus.     

The solution molecular weight and shape of the bacterial exopolysaccharides amylovoran and stewartan

Amylovoran, the acidic exopolysaccharide (EPS) of Erwinia amylovora, and stewartan, the capsular EPS of E. stewartii, were characterized by analytical ultracentrifugation and by size exclusion chromatography connected to dual detection of light scattering and mass. The average molecular weights of amylovoran and stewartan were determined as 1.0×10⁶ and 1.7×10⁶ Da, with polydispersity values (M_w/M_n) of 1.5 and 1.4, respectively. Based on the sugar composition and their molecular weight, both exopolysaccharides consist of approximately 1000 repeating units per molecule, this suggests a similar mechanism for chain length determination during biosynthesis of EPS in both organisms.     

MINIATURIZED TWO-FOLD DILUTION METHOD FOR ENUMERATING TOTAL MICROBIAL LOAD AND COLIFORMS IN RAW MILK

A rapid and simple method for enumerating total aerobic plate counts (APC) and coliforms in raw milk was developed and compared with conventional plating method. Following two-fold serial dilution of samples in a 96 well microtiter plate, double strength of two different modified media for APC or coliforms was added to each well. The final positive well (purple to yellow color) was determined and converted to dilution factors. The dilution factor of each sample was converted to Log₁₀ DF (Dilution factors) and compared to actual microbial numbers Log₁₀ CFU/mL. The results of 2-fold dilution method (Log₁₀ DF) were strongly correlated to conventional plating method (Log₁₀ CFU/mL) (P < 0.05). The correlation of the scatterplot of spread plating and 2-fold dilution method indicated a high level of agreement between two methods (R²= 0.921 for total counts and R²= 0.916 for forms from raw milk). This 2-fold dilution method is an easy, rapid, and economical method for enumeration of total microbial loads and coliforms in raw milk.     

[I]Iodonaphtylazide labeling selectively a cysteine residue in the F0 of the ATP-synthase from E. coli is unsuitable for topographic studies of membrane proteins

The ATP synthase from E. coli was reacted with the hydrophobic photolabel [¹²⁵I]iodonaphtylazide. Subunit b in the F₀-part was selectively labelled. Label was traced back to the single cysteine₂₁ in subunit b. Thus the reactive intermediate of INA generated by photolysis had a high preference for nucleophiles. Due to this high selectivity the detection of membrane spanning peptide segments by labelling with INA is not reliable.     

副溶血弧菌外膜铁蛋白受体pvuA基因的原核表达及产物的诱导条件优化

为构建弧菌铁蛋白受体pvuA重组质粒,提高其在大肠杆菌BL21中的表达产量,优化表达条件,并为其免疫原性研究奠定基础,从副溶血弧菌基因组DNA扩增了弧菌铁蛋白受体pvuA基因,构建了重组质粒pET-28a(+)-ferric vibrioferrin receptor,转入大肠杆菌BL21并经异丙基硫代半乳糖苷（isopropyl β-D-thiogalactoside,IPTG）诱导表达蛋白。在单因素试验的基础上,以菌体初始浓度、诱导时间、诱导温度、诱导剂浓度为自变量,菌体蛋白浓度为响应值,根据响应面法的Box-Benhnken中心设计原理,研究自变量及其交互作用对弧菌铁蛋白产量的影响,利用Design-Expert和响应面分析相结合的方法对诱导条件进行优化。IPTG诱导获得的重组蛋白以包涵体的形式存在,优化后最终确定重组弧菌铁蛋白受体pvuA最佳表达条件为菌体初始浓度OD600=0.6,诱导时间10 h,诱导温度37℃,IPTG浓度为1.0 mmol·L-1,此时包涵体沉淀中蛋白含量最高,为11.00 mg·mL-1。构建了弧菌铁蛋白受体pvuA的大肠杆菌重组表达质粒,通过优化表达...     

塔克拉玛干沙漠不同区域柽柳沙包土壤盐分分布特征及其影响因素

柽柳(Tamarix chinensis)沙包是塔克拉玛干沙漠特殊的生物地貌景观, 对维持区域生态环境的稳定具有极其重要的作用。该研究采用野外调查与室内分析相结合的方法, 选取且末、阿拉尔、策勒、塔中4个典型区域的柽柳沙包为研究对象, 对柽柳沙包0-500 cm土壤垂直剖面进行采样, 测定土壤pH值、枯落物含量、电导率及HCO₃ ^-、Cl ^-、SO₄ ^2-、Ca ²⁺、Mg ²⁺、K ⁺、Na ⁺含量, 分析柽柳沙包中土壤盐分的空间变化规律及其影响因素。结果表明: 1)从且末、阿拉尔、策勒到塔中, 土壤pH值总体呈升高趋势, 土壤电导率及Na ⁺、Ca ²⁺、Mg ²⁺、SO₄ ^2-含量总体呈降低趋势, K ⁺、Cl ^-、HCO₃ ^-含量没有明显的变化规律。2)盐分在4个样区的垂直分布主要表现为: 且末和策勒样区柽柳沙包的土壤盐分呈表层聚集现象; 阿拉尔和塔中样区柽柳沙包的土壤盐分呈深层聚集现象。随着土层深度的增加, 土壤pH值总体呈升高的趋势, 土壤枯落物含量总体呈降低趋势; 土壤电导率在且末和策勒样区总体呈降低趋势, 阿拉尔样区呈先降低后升高再降低的变化趋势, 而塔中样区呈先升高后降低再升高的变化趋势。3)根据相关性分析和主成分分析, 且末样区土壤枯落物含量、SO₄ ^2-、Na ⁺、K ⁺为影响土壤盐分含量的主要因子, 且土壤盐分以硫酸盐为主; 阿拉尔样区影响土壤盐分组成的主要因子为Cl ^-、Na ⁺; 策勒样区为Cl ^-、K ⁺、Na ⁺; 塔中样区为Cl ^-、Na ⁺、Ca ²⁺、SO₄ ^2-, 且土壤盐分均以氯化物为主。综合分析表明, 不同区域柽柳沙包中土壤盐分存在空间变异性, 柽柳沙包土壤盐分的变化与干旱沙漠地区强烈的蒸发作用、地表风蚀强度、地下水埋深、土壤中枯落物及柽柳的生物积盐效应等因素密切相关, 是影响不同区域土壤盐分分布的关键因子。     

Differential inactivation of glucose- and glutamate dependent acid resistance of Escherichia coli TMW 2.497 by high-pressure treatments

The inactivation by 200–400 MPa and post-pressure survival at acid conditions of E. coli TMW 2.497 was characterized by the measurement of intracellular pH (pH_in), viable cell counts, glutamate (Glu) and arginine (Arg) consumption, and the influence of mild adaptation to mild acid stress prior to pressure treatment. Glutamate and arginine did not affect viable cell counts or the pH_in during pressure application but improved the ability to maintain a high pH_in after pressure treatment. In pH 4.0 buffer without arg and glu, a 3 log reduction of cell counts occurred after 24 h of incubation, whereas little or no loss of viability was observed after 24 h incubation in the presence of glu and arg. During post-pressure incubation at pH 4.0, 10 mM glutamate were metabolized but only 2 mM arginine were used, indicating that glutamate rather than arginine was responsible for the protective effect on pH_in and survival. In conclusion, the pressure induced, irreversible loss of the transmembrane ΔpH correlates to cell death and glu stabilizes the pH_in of E. coli during post-pressure incubation.     

An over expression and high efficient mutation system of a cobalt-containing nitrile hydratase

A superior novel recombinant strain, E. coli BL21(DE3)/pETNH^M, containing the start codon mutation of the subunit, was constructed and selected as an overexpression and high efficient mutation platform for the genetic manipulation of the nitrile hydratase (NHase). Under optimal conditions, the specific activity of the recombinant strain reached as high as 452 U/mg dry cell. Enzymatic characteristics studies showed that the reaction activation energy of the recombinant NHase^M was 24.4 ± 0.5 kJ/mol, the suited pH range for catalysis was 5.5–7.5, and the K_m value was 4.34 g/L (82 mM). To assess the feasibility of the NHase improvement by protein rational design using this E. coli, site-directed mutagenesis of S122A, S122C, S122D and βW47E of the NHase^M were carried out. The NHase^M (S122A) and NHase^M (S122D) mutants were entirely inactive due to the charge change of the side-chain group. The product tolerance of the NHase^M (S122C) mutant was enhanced while its activity decreased by 30%. The thermo-stability of the NHase^M (βW47E) mutant was significantly strengthened, while its activity reduced by nearly 50%. These results confirmed that the specific activity of the mutant NHase expressed by the recombinant E. coli BL21(DE3)/pETNH^M can reasonably change with and without mutations. Therefore, this recombinant E. coli can be efficiently and confidently used for the further rational/random evolution of the NHase to simultaneously improve the activity, thermo-stability and product tolerance of the target NHase.     

Lysozyme for capture of microorganisms on protein biochips

Lysozyme placed on the SiO₂ surfaces that have previously been derivatized with C₁₈ coating will capture both Escherichia coli and Listeria monocytogenes cells from PBS buffer at pH 7.2. This phenomenon is of significance for the design and fabrication of protein biochips that are designed to capture bacteria from buffer or water so that these can be further interrogated with respect to possible pathogenicity. Fluorescent microscopy shows that two types of bacteria (gram-negative E. coli and gram-positive Listeria spp.) will be adsorbed by lysozyme placed on the surface of the biochip but that strong adsorption of the bacteria is reduced but not eliminated when Tween 20 is present (at 0.5%) in the PBS buffer in which the cells are suspended. In comparison, Tween 20 and Bovine Serum Albumin (BSA) almost completely block adsorption of these bacteria on C₁₈ coated surfaces. The combination of a lysozyme surface with Tween 20 gives a greater degree of adsorption of L. monocytogenes than E. coli, and hence suggests selectivity for the more hydrophobic E. coli may be reduced by the Tween 20. This paper presents protocols for preparing protein-coated, SiO₂ surfaces and the effect of buffer containing Tween 20 on adsorption of bacteria by SiO₂ surfaces coated with C₁₈ to which BSA, lysozyme or C11E9 antibody is immobilized at pH 7.2 and ambient temperature.     

Development of a cleaning in place protocol and repetitive application of Escherichia coli homogenate on STREAMLINE™ Q XL

An optimization of a cleaning in place (CIP) protocol has been performed for STREAMLINE™ Q XL separation medium using homogenised Escherichia coli as sample. The effectiveness of the different cleaning protocols was tested by analysing the content of fatty acids, phosphorus compounds and amino acids in STREAMLINE™ Q XL. Additionally, RAMAN and FT-IR measurements were used to verify the degree of contamination of separation medium. From the results of the optimization experiments, a cleaning procedure was suggested and subsequently tested with 50 repetitive applications. The study shows that of the different agents tested, 1 M NaOH is the most efficient cleaning solution and that long contact time (8 h) with 1 M NaOH is important. An additional cleaning step with 30% 2-propanol (v/v) is also recommended for E. coli samples.