Multiobjective H2/H∞ synthetic gene network design based on promoter libraries

Some current promoter libraries have been developed for synthetic gene networks. But an efficient method to engineer a synthetic gene network with some desired behaviors by selecting adequate promoters from these promoter libraries has not been presented. Thus developing a systematic method to efficiently employ promoter libraries to improve the engineering of synthetic gene networks with desired behaviors is appealing for synthetic biologists.In this study, a synthetic gene network with intrinsic parameter fluctuations and environmental disturbances in vivo is modeled by a nonlinear stochastic system. In order to engineer a synthetic gene network with a desired behavior despite intrinsic parameter fluctuations and environmental disturbances in vivo, a multiobjective H₂/H_∞ reference tracking (H₂ optimal tracking and H_∞ noise filtering) design is introduced. The H₂ optimal tracking can make the tracking errors between the behaviors of a synthetic gene network and the desired behaviors as small as possible from the minimum mean square error point of view, and the H_∞ noise filtering can attenuate all possible noises, from the worst-case noise effect point of view, to achieve a desired noise filtering ability. If the multiobjective H₂/H_∞ reference tracking design is satisfied, the synthetic gene network can robustly and optimally track the desired behaviors, simultaneously.First, based on the dynamic gene regulation, the existing promoter libraries are redefined by their promoter activities so that they can be efficiently selected in the design procedure. Then a systematic method is developed to select an adequate promoter set from the redefined promoter libraries to synthesize a gene network satisfying these two design objectives. But the multiobjective H₂/H_∞ reference tracking design problem needs to solve a difficult Hamilton–Jacobi Inequality (HJI)-constrained optimization problem. Therefore, the fuzzy approximation method is employed to simplify the HJI-constrained optimization problem to an equivalent linear matrix inequality (LMI)-constrained optimization problem, which can be easily solved by selecting an adequate promoter set from the redefined promoter libraries using the LMI toolbox in Matlab.Based on the confirmation of in silico design examples, we can select an adequate promoter set from the redefined promoter libraries to achieve the multiobjective H₂/H_∞ reference tracking design. The proposed method can reduce the number of trial-and-error experiments in selecting an adequate promoter set for a synthetic gene network with desired behaviors. With the rapid increase of promoter libraries, this systematic method will accelerate progress of synthetic biology design.     

Marker-aided genetic divergence analysis inBrassica

Genetic divergence was evaluated in 31 breeding lines from fourBrassica species using Mahalanobis'D ² . A new method of grouping usingD ² values was used to group the 31 lines, based on diagnostic morphological traits (called morphoqts). Isozyme variation of the individual enzymes esterase and glutamate oxaloacetate was quantified by five parameters (called isoqts) developed earlier. Grouping by the same method was also done based on the isoqts, and the grouping by isozymes was compared with that by morphoqts. Overall, there was an agreement of 73% suggesting that isoqts can be used in the choice of parents and also first stage selection of segregants in the laboratory. It was suggested that such an exercise would help to take care of season-bound and field-related problems of breeding. The new isozyme QTs, within lane variance of relative mobility and relative absorption, accounted for about 50% of the total divergence. The utility of the new method and isoqts in cost-effective breeding were highlighted.     

Screening of <Emphasis Type="Italic">cry2</Emphasis> genes in <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> isolates from Argentina

A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for identification of cry2 genes from Bacillus thuringiensis (Bt) was established. Strains from different sources of Argentina were analyzed to study the distribution of cry2 genes. The results showed that cry2Aa/cry2Ab profile was the most abundant irrespective of source and represented 56 of 59 Bt isolates (94.9%). Three different cry2 profiles were found in this collection, one of which was novel.     

Filtering and feeding rates of cyclopoid copepods feeding on phytoplankton

The algal biomass ingested by omnivorous cyclopoid copepods (Cyclops kolensis and C. vicinus) was measured by two methods in the hypertrophic Heiligensee in Berlin (West Germany). The clearance and ingestion rates inferred from measurements of natural populations of ¹⁴C labelled phytoplankton were compared with those obtained from chlorophyll a determinations using the presence/absence method (observed chlorophyll a content of natural lake phytoplankton with and without addition of cyclopoids). Both methods gave similar results. Nevertheless, the radio tracer method is preferred, mainly because the short feeding duration excludes high variations in both the food composition and food concentration that limit the presence/absence method.     

Isolation of several anti-stress genes from the halotolerant green alga Chlamydomonas by simple functional expression screening with Escherichia coli

To isolate anti-stress genes from a halotolerant marine green alga, a simple screening method based on the bacterial expression system was examined. The method consisted of three steps: (i) directional cDNA library construction in a ZAPII vector, (ii) in vivo mass excision of a ZAPII library into phagemid DNA, and (iii) screening for anti-salt-stress and anti-oxidative-stress genes by culturing bacterial cells carrying the in vivo excised phagemid on selection agar plates with a high concentration of NaCl and/or methyl viologen (MV), and by isolating stress-tolerant bacterial colonies. By this method, we screened the cDNA library of halotolerant Chlamydomonas sp. strain W-80, and isolated several stress-related gene homologs, such as glutathione peroxidase, ascorbate peroxidase, bbc1 (breast basic conserved; a low temperature induced gene in Brassica napus), and cyanide-resistant alternative oxidase.     

Detection of streptomycin resistance in Mycobacterium tuberculosis clinical isolates from China as determined by denaturing HPLC analysis and DNA sequencing

China is regarded by the World Health Organization as a major hot-spot region for Mycobacterium tuberculosis infection. Streptomycin has been deployed in China for over 50 years and is still widely used for tuberculosis treatment. We have developed a denaturing HPLC (DHPLC) method for detecting various gene mutations conferring drug resistance in M. tuberculosis. The present study focused on rpsL and rrs mutation analysis. Two hundred and fifteen M. tuberculosis clinical isolates (115 proved to be streptomycin-resistant and 100 susceptible by a routine proportional method) from China were tested to determine the streptomycin minimal inhibitory concentration (MIC), and subjected to DHPLC and concurrent DNA sequencing to determine rpsL and rrs mutations. The results showed that 85.2% (98/115) of streptomycin-resistant isolates harbored rpsL or rrs mutation, while rpsL mutation (76.5%, 88/115) dominated. MIC of 98 mutated isolates revealed no close correlation between mutation types and levels of streptomycin resistance. No mutation was found in any of the susceptible isolates. The DHPLC results were completely consistent with those of sequencing. The DHPLC method devised in this study can be regarded as a useful and powerful tool for detection of streptomycin resistance. This is the first report to describe DHPLC analysis of mutations in the rpsL and rrs genes of M. tuberculosis in a large number of clinical isolates.     

Biomolecular structure refinement based on adaptive restraints using local-elevation simulation

Introducing experimental values as restraints into molecular dynamics (MD) simulation to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, dipolar couplings, ³ J-coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement method. Because multiple torsion angle values ϕ correspond to the same ³ J-coupling constant and high-energy barriers are separating those, restraining ³ J-coupling constants remains difficult. A method to adaptively enforce restraints using a local elevation (LE) potential energy function is presented and applied to ³ J-coupling constant restraining in an MD simulation of hen egg-white lysozyme (HEWL). The method succesfully enhances sampling of the restrained torsion angles until the 37 experimental ³ J-coupling constant values are reached, thereby also improving the agreement with the 1,630 experimental NOE atom–atom distance upper bounds. Afterwards the torsional angles ϕ are kept restrained by the built-up local-elevation potential energies.     

The chloroplast cytochrome b 6 f complex can exist in monomeric and dimeric states

The cytochrome b ₆ f complex isolated from spinach chloroplast membranes can be resolved into two forms, a monomeric and a dimeric form, by centrifugation on sucrose gradients. The conversion of the dimeric form of the complex into the monomeric form could be prevented by cross-linking with the homobifunctional reagent, dithiobis(succinimidylpropionate) but not by cross-linking with disuccinimidyltartrate or glutaraldehyde. SDS-PAGE analyses of the monomeric and dimeric forms of the cytochrome complex showed the presence of specific cross-linked products in each respective form of the complex. For example, the monomeric form contained a cross-linked product of cytochrome f, cytochrome b ₆ f and subunit IV while the dimeric form contained a cross-linked dimer of cytochrome b ₆ f. The presence of the former in the isolated cytochrome b ₆ f complex prepared by the method of Hurt and Hauska (Eur J Biochem 117: 591–599, 1981) indicates the presence of the monomer in his preparation.Abbreviations DBMIB 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone - DSP dithiobis(succinimidylpropionate) - DST disuccinimidyltartrate     

A single-base deletion mutation in <Emphasis Type="Italic">SlIAA9</Emphasis> gene causes tomato (<Emphasis Type="Italic">Solanum lycopersicum</Emphasis>) <Emphasis Type="Italic">entire</Emphasis> mutant

The entire (e) locus of tomato (Solanum lycopersicum L.) controls leaf morphology. Dominant E and recessive e allele of the locus produce pinnate compound and complex reduced leaves. Previous research had indicated that SlIAA9, an Aux/IAA gene, was involved in tomato leaf morphology. Down-regulation of SlIAA9 gene by antisense transgenic method decreased the leaf complex of tomato and converted tomato compound leaves to simple leaves. The leaf morphology of these transgenic lines was similar with leaf morphology of tomato entire mutant. In this paper, we report that a single-base deletion mutation in the coding region of SlIAA9 gene results in tomato entire mutant phenotypes.     

Assessing Methods for Developing Phosphorus Desorption Isotherms from Soils using Anion Exchange Membranes

Developing desorption isotherms for inorganic phosphorus (P) is a time-consuming and non-standardized procedure. Anion exchange membranes (AEMs) have been successfully used in studies of P desorption kinetics and total membrane-desorbable P, but rarely have they been used for developing P desorption isotherms. Our study had two objectives: (1) to evaluate the suitability of using multiple strips of AEMs (termed the Multiple AEM Method) to develop P desorption isotherms; and (2) to compare the Multiple AEM Method with a sequential-extraction approach using AEMs (termed the Sequential AEM Method) to determine if the manner in which AEMs were used would influence the slope of the desorption isotherm, i.e. the partition coefficient. Both methods yielded well-defined, but numerically different desorption isotherms for all levels of sorbed P. However, estimated K _d values among methods were equivalent in the low and medium levels of P sorbed. The Multiple AEM method was quicker than the Sequential AEM method, but both gave similar K _d values in an agriculturally significant range of soil solution concentrations. These methods should be tested on a range of soil type to determine their suitability in developing P desorption isotherms and to move toward method standardization for desorption isotherms.     

Automated multiple development method for determination of glycerol produced by wine yeasts

A rapid and efficient analytical method for the determination of glycerol in wines is described. This method utilizes high-performance thin layer chromatography (HPTLC) plates coupled with an automated multiple development system with an elution gradient based on acetonitrile–acetone–hexane on silica gel layers. The absence of clean-up procedures, sometimes only centrifugation, makes this method suitable also for the large-scale control of alcoholic beverages. In particular the capacity of different wine yeast species (Saccharomyces cerevisiae, Zygosaccharomyces bailii, Kloeckera apiculata and Saccharomycodes ludwigii) to produce glycerol was determined. Generally, the strains of S. cerevisiae produced elevated amounts of glycerol together with Z. bailii, whereas K. apiculata strains formed the lowest amounts of glycerol, exhibiting also a great strain variability.     

Identification of five Orius species in Japan by multiplex polymerase chain reaction

We developed multiplex polymerase chain reaction methods to identify five Orius (Heteroptera: Anthocoridae) species that occur commonly in Japan: Orius sauteri, Orius minutus, Orius strigicollis, Orius nagaii, and Orius tantillus. The method amplified internal transcribed spacer 1 of the nuclear ribosomal DNA by using five primers simultaneously and produced species-specific banding patterns upon agarose gel electrophoresis. Reliability of the method was tested for 350 individuals of 23 strains, and consistent results were obtained. Dichotomous keys are also provided for easy and quick species identification.     

None of polymorphism of ovine fecundity major genes FecB and FecX was tested in goat

The polymorphism of mutation Q249R in BMPR-IB gene (FecB) and loci FecX^I, FecX^H, FecX^G, FecX^B in BMP15 gene was analyzed by forced PCR-RFLP method in 550 individuals from 6 flocks or breeds of goats with litter size varied from 1.4 to 2.7 including Boer (209), Haimen (128), second generation of Boer goat crossed with Huanghuai goat (82), Huanghuai (71), Nubi (37) and Matou (23) goat. None of mutations was detected in these goat breeds and their crossbreed. These results suggest that fecundity of goat is not linked to the same loci in BMPR-IB and BMP15 as sheep. Therefore, it is necessary to seek for other genes or loci in order to develop marker assistance selection techniques and study the prolific mechanism of the goat.     

Hydrogen peroxide-induced chlorophyll a bleaching in the cytochrome b 6 f complex: a simple and effective assay for stability of the complex in detergent solutions

The instability of cytochrome b ₆ f complex in detergent solutions is a well-known problem that has been studied extensively, but without finding a satisfactory solution. One of the important reasons can be short of the useful method to verify whether the complex suspended in different detergent is in an intact state or not. In this article, a simple and effective assay for stability of the complex was proposed based on the investigation on the different effects of the two detergents, n-octyl-β-d-glucopyranoside (OG) and dodecyl-β-d-maltoside (DDM), on the properties of the complex. DDM stabilizes the complex preparation more effectively whereas OG denatures the interactions of the heme groups and pigment molecules with the protein environment, leading to the bleaching of chlorophyll a induced by addition of hydrogen peroxide. The assay of the use of hydrogen peroxide to characterize the complex by studying the bleaching of chlorophyll induced by hydrogen peroxide and the peroxidase activity of the complex was discussed. This simple method will probably be useful to study the stability of the complex. Xiao-Bo Chen and Xiao-Hui Zhao contributed equally to this work.     

Isolation and PCR detection of <Emphasis Type="Italic">Enterobacter sakazakii</Emphasis> in South African food products,specifically infant formula milks

Enterobacter sakazakii has recently been identified as an opportunistic pathogen. The current culture-dependent detection methods for these bacteria are time-consuming and in this study a PCR method for the detection of E. sakazakii in South African food products, including an internal amplification control (IAC) was developed. DNA was isolated and amplified from the products and they were plated on selective growth media after pre-enrichment and enrichment in Enterobacteriaceae enrichment broth. Four of the 22 products tested positive for the presence of E. sakazakii, confirmed by PCR detection and growth on selective media. The PCR method proved effective in detecting E. sakazakii in South African products after three days and could serve as an alternative for traditional microbiological techniques.     

Determination of root biomasses of three species grown in a mixture using stable isotopes of carbon and nitrogen

A method is evaluated that employs variation in stable C and N isotopes from fractionations in C and N acquisition and growth to predict root biomasses of three plant species in mixtures. Celtis laevigata Willd. (C₃), Prosopis glandulosa Torr. (C₃, legume) and Schizachyrium scoparium (Michx.) Nash (C₄), or Gossypium hirsutum L. (C₃), Glycine max (L.) Merr. (C₃ legume), and Sorghum bicolor (L.) Moench (C₄) were grown together in separate, three-species combinations. Surface roots (0–10 cm depth) of each species from each of the two combinations were mixed in various proportions, and the relative abundances of ¹⁵N and ¹⁴N and ¹³C and ¹²C in prepared mixtures, surface roots of single species, and roots extracted from the 80-cm soil profile in which each species combination was grown were analyzed by mass spectrometry. An algebraic determination which employed the δ ¹³C, % ¹⁵N, and C and N concentrations of root subsamples of individual species accounted for more than 95% of the variance in biomass of each species in prepared mixtures with G. max, G. hirsutum, and S. bicolor. A similar analysis demonstrated species-specific differences in rooting patterns. Root biomasses of the C₄ monocots in each combination, S. scoparium and S. bicolor, were concentrated in the upper 20 cm of soil, while those of G. hirsutum and the woody P. glandulosa were largest in lower soil strata. Analyses of stable C and N isotopes can effectively be used to distinguish roots of species which differ in ratios of ¹⁵N to ¹⁴N and ¹³C to ¹²C and thus to study belowground competition between or rooting patterns of associated species with different C and N isotope signatures. The method evaluated can be extended to quantify aboveground and belowground biomasses of component species in mixtures with isotopes of other elements or element concentrations that differ consistently among plants of interest.     

旱麦草EtAP2基因的克隆及其对干旱胁迫的响应表达

以旱麦草(Eremopyrum triticeum)为实验材料,利用RT-PCR技术从旱麦草叶片中克隆了1个AP2/ERF家族基因,命名为EtAP2(GenBank登录号KX622583)。EtAP2基因含有1 128bp开放阅读框,编码375个氨基酸,相对分子质量40.87kD,等电点为5.36。多序列比对和进化树分析表明,该基因编码蛋白具有2个AP2保守结构域,与小麦AP2/ERF家族蛋白具有较近的亲缘关系。实时荧光定量PCR分析表明,15%PEG 6000模拟干旱胁迫可诱导EtAP2基因在根和叶中表达,且在根中对干旱胁迫的响应大于叶片。研究表明,EtAP2可能参与旱麦草对干旱逆境胁迫应答的调节。     

中国的被孢霉种类

被孢霉属(Mortierella Coemans)是接合菌纲(Zygomycetes)、毛霉目(Mucorales)、被孢霉科(Mortierellaceae)中的一个大属,目前已知约有90种;主要存在于土壤、植物残体、动物粪便等基物中。我国过去对被孢霉的研究不多,在《中国真菌总汇》(1979)中记录了8个种。本研究从全国22个省、市、自治区采集的2000多号样品中,分离到约220个被孢霉菌株。本研究主要采用Gams (1970, 1977)的分类系统进行分类鉴定,并对该系统进行了修改。在属下分3个亚属(Micromucor, Mortierella和Gamsiella), 8个组(Actinomortierella, Alpina,Hygrophila, Mortierella, Schmuckii, Simplex, Spinosa和Stylospora),单囊霉(Haplosporangium)被承认为独立的一个属。本研究鉴定出22个种和3个变种,包括一个新种(武夷山被孢霉Mortierella wuyishanensis sp. nov.)和一个新变种(极细无色被孢霉Mortierella hyalina(Harz) W. Gams var. subtilissima var. nov.), 14个中国新纪录。这14个新纪录为:产芽胞被孢霉(Mortierella. gemmifera M. Ellis)、园圃被孢霉(M. horticola Linnem.)、矮小被孢霉(M. humilis Linnem.)、无色被孢霉(M. hyalina(Harz) W. Gams)、印度被孢霉(M. indica B.S. Mehrotra)、英杜被孢霉(M. indohii C.Y. Chien),詹金氏被孢霉(M. jenkinii (A.L. Sm.) Naumov)、可疑极小被孢霉(M. minutissima Tiegh. var. dubia Linnem.)、易变被孢霉(M. mutabilis Linnem.)、微孢被孢霉(M. parvispora Linnem.)、角胞拉曼被孢霉(M. ramanniana(Moller) Linnem. var. angulispora (Naumov) Linnem.)、网孢被孢霉(M. reticulata Tiegh.& G. Le Monn.)、多疣被孢霉(M. verrucosa Linnem.)、轮枝被孢霉(M. verticillata Linnem.)。文中讨论和评价了一些分类性状,还列出分亚属、分组、分种和变种的检索表.每个分类单元都有描述和讨论以及线条图、并列出分布地区。     

Simplified amplified-fragment length polymorphism method for genotyping Mycobacterium tuberculosis isolates

A simplified amplified-fragment length polymorphism (AFLP) method was developed and applied to genotype 52 Mycobacterium tuberculosis isolates. This method can be carried out using only one restriction enzyme (XhoI), one double strand adapter, and one PCR primer. The amounts of DNA and DNA polymerase, and the concentrations of primer and Mg²⁺ in the PCR step were optimized using the Basic Sequential Simplex method. AFLP analysis of the isolates generated a total of 24 differently sized bands ranging from 1537 to 121 bp, and 52 different band patterns, with a minimum of 2 and a maximum of 13 bands. The results were compared with the well-established IS6110 restriction fragment length polymorphism (IS6110-RFLP) typing method, which rendered a total of 32 differently sized bands from 1 to 12 kbp, and 52 different band patterns, with a minimum of 3 and a maximum of 15 bands. Therefore, both genotyping methods showed a discriminatory power of samples of 100%. Nevertheless, pairwise comparisons of the 1326 similarity indexes calculated for both typing methods showed a total absence of correlation between the similarity indexes of the two methods. The simplified AFLP method is expected to be more useful for genotyping M. tuberculosis isolates compared to the IS6110-RFLP method, since the former evaluates genetic variations throughout the M. tuberculosis genome. Furthermore, the relatively rapid and low-cost simplified AFLP method compares favorably to the IS6110-RFLP or conventional AFLP methods, and shows great promise for genotyping M. tuberculosis isolates, especially in developing countries or for preliminary screening.     

Genetic polymorphisms of GSTO2, GSTM1, and GSTT1 and risk of gastric cancer

Objective The glutathione S-transferases (GSTs) are a superfamily of proteins that participates in detoxification. The GSTs were dividing into several classes including omega (GSTO), mu (GSTM) and theta (GSTT) classes. In human GSTO2, GSTM1, and GSTT1 are polymorphic. In order to study whether GSTO2, GSTM1, and GSTT1 polymorphisms are associated with increased gastric cancer risk in Iranian patients, the present case–control study was done. Methods Genomic DNA was extracted from peripheral blood of 67 gastric cancer patients and 134 control subjects. The genotyping was performed using PCR-based method. The possible association of gastric cancer with the GSTO2 N142D polymorphism was estimated with assuming additive, dominant, and recessive effect of the variant 142D allele. To investigate whether profiles of GST genotypes are associated with the risk of gastric cancer, we used unconditional logistic regression analysis. Results The GSTO2 142D allele in additive, dominant and recessive models was not associated with the risk. Because GSTM1, GSTT1, and GSTO2 genes belong to low-penetrance genes which might be involved in the carcinogenesis, patients and controls without family of cancer in first-degree relatives were also analyzes separately. To investigate whether profiles of GST genotypes are associated with the risk of gastric cancer, we used unconditional logistic regression analysis with GSTM1, GSTT1, and GSTO2 genotypes as predictor factors. The GSTO2 DD genotype was associated with decreased risk as compared to GSTO2 NN genotype (OR = 0.21, 95% CI: 0.05–0.92, P = 0.038). Conclusions Present findings show that GSTO2 DD genotype decreases the risk of gastric cancer in individuals without history of cancer in their first-degree relatives.