An efficient field screening procedure for identifying transposants for constructing an Ac/Ds-based insertional-mutant library of rice.

An efficient system was developed, and several variables tested, for generating a large-scale insertional-mutagenesis population of rice. The most important feature in this improved Ac/Ds tagging system is that one can conveniently carry out large-scale screening in the field and select transposants at the seedling stage. Rice was transformed with a plasmid that includes a Basta-resistance gene (bar). After the Ds element is excised during transposition, bar becomes adjacent to the ubiquitin promoter, and the rice plant becomes resistant to the herbicide Basta. In principle, one can plant up to one million plants in the field and select those plants that survive after spraying with Basta. To test the utility of this system, 4 Ds starter lines were crossed with 14 different Ac plants, and many transposants were successfully identified after planting 134,285 F2 plants in the field. Over 2,800 of these transposants were randomly chosen for PCR analysis, and the results fully confirmed the reliability of the field screening procedure.     

An indexed genomic library for Paramecium complementation cloning

Recent pioneering work opened the way for cloning genes in Paramecium by functional complementation of mutants. We present here the construction and pilot utilization of a new indexed library of Paramecium macronuclear DNA. The library is made of 61,440 clones containing inserts mostly between 6 and 12 kilobases. It has already allowed the complementation cloning of four new genes, and this library has proven to be very useful for rapid hybridization cloning.     

An efficient method for mutant library creation in Pichia pastoris useful in directed evolution

Abstract

The yeast Pichia pastoris is being increasingly used as a host for expressing enzymes on a large scale, but application in directed evolution requiring efficient expression of libraries of mutants is hampered due to the time-consuming multistep procedure which includes an intermediate bacterial host (Escherichia coli). Here we introduce a fast and highly simplified method to produce gene libraries in P. pastoris expression vectors. For the purpose of illustration, Galactomyces geotrichum lipase 1 (GGL1) was used as the catalyst in the enantioselective hydrolytic kinetic resolution of 2-methyldecanoic acid p-nitrophenyl ester, the gene mutagenesis method being saturation mutagenesis. The phosphorylated linear plasmid which is integrated in the yeast genome was obtained by combination of partially overlapped fragments using overlap-extension PCR. An intermediate bacterial host is not necessary, neither are restriction enzymes. This method is also applicable when using error-prone PCR for library creation in directed evolution.     

An efficient method for producing alpha(1,3)-galactosyltransferase gene knockout pigs

We have reported relatively efficient methods for somatic cell nuclear transfer and for knocking out the alpha(1,3)-galactosyltransferase (alpha1,3-GT) gene in porcine fetal fibroblasts using a nonisogenic promoterless construct approach. Here we report the production of alpha1,3-GT gene knockout pigs using these procedures. Seven alpha1,3-GT gene knockout cell clones were identified by long-range PCR from 108 neomycin resistant (neo(R)) colonies, giving a 6.5% targeting efficiency. Three cell clones were used for nuclear transfer. Nuclear transfer was performed using a fusion before activation protocol using in vitro-matured adult oocytes. Between 51 and 110 fused couplets were transferred to 10 recipients synchronized 1 day behind the embryos. Parturition was induced on day 115, and piglets were delivered by caesarean section. Four recipients gave birth to a total of 18 live piglets. All pigs were female, and all three clones resulted in the birth of live pigs. alpha1,3-GT gene knockout pigs were identified by long-range PCR and confirmed by Southern blot analysis. The efficiency (embryos transferred/piglets born) of our cloning protocol was 1.9% for all transfers and 4.6% for animals that gave birth.     

Combinatorial synthesis and antibacterial evaluation of an indexed chalcone library

A 120-membered chalcone library has been designed and prepared from six differently substituted acetophenones (A1-A6) and 20 benzaldehydes (B1-B20). The library was subjected to biological studies targeted against six bacterial strains. For the identification of the most-active member(s) of the library, the so-called indexed or positional-scanning method was applied. Six out of 26 sub-libraries, i.e., AL1-AL6, were synthesized by keeping the acetophenone moiety A fixed and using equimolar quantities of the 20 different benzaldehydes. The remaining 20 sub-libraries BL1-BL20 were prepared by keeping the benzaldehyde B component fixed and varying the six acetophenones (Table 1). The bactericidal activities of the resulting sub-libraries were tested and used as indices to the rows or columns of a two-dimensional matrix. Finally, parallel synthesis of 24 specific members with the highest-expected antibacterial activities, present in two sub-libraries, was carried out. These chalcones were screened again, and the results were exploited for establishing the structure-activity relationship (SAR) and the identification of the lead compound, which turned out to be 1,3-bis(2-hydroxyphenyl)prop-2-en-1-one (A2B2) in terms of activity towards Staphylococcus aureus and Bacillus subtilis (Tables 5-7).     

An efficient and information-rich biochemical method design for fragment library screening on ion channels

Drug discovery requires a simple, rapid, and cost-effective method for the early identification of novel leads and elimination of poor candidates. Here we present an experimental design that fulfils these criteria, using a ligand-gated ion channel expressed in a mammalian cell line, whose function can be probed using a voltage-sensitive dye. The experimental design is novel, as it uses the same screen to identify hit fragments and to characterize them as agonists or antagonists. The results were independently validated using radioligand binding, although the new technique has several advantages over radioligand methods. A number of novel high-affinity ligands were found. The method is broadly applicable to a wide range of receptor types including ligand-gated ion channels (LGICs), voltage-gated ion channels (VGICs), and G protein-coupled receptors (GPCRs), all of which are important drug targets.     

A simple, efficient method to create a cDNA library.

The simplified "All In One Tube" protocol for constructing a cDNA library combines the advantages of the "Classic method" and the Okayama-Berg method while overcoming some of their drawbacks. In this method, adding adapters, linkers or enzyme digestion steps are no longer necessary after cDNA synthesis, thus making it quicker and especially useful when dealing with small samples of mRNA.     

Studies on locus expansion, library representation, and chromosome walking using an efficient method to screen cosmid libraries

We have developed an efficient screening method to search for clones in cosmid libraries prepared from human genomic DNA. Genomic, cDNA, and cosmid probes have been used to isolate homologous cosmids from human chromosomes 7, 10, 16, 17 and X as part of a search for polymorphic nucleotide sequences. This method has been successfully applied to chromosome walking experiments at the interstitial retinol-binding protein locus on chromosome 10, and may be a useful tool for investigating representation of cloned sequences in cosmid libraries. Our library was prepared in the vector c2RB (Bates and Swift, 1983), but the method is applicable to any cosmid cloning system in which the inserted DNA can be separated from the vector by restriction enzyme digestion. A cosmid library containing five human genome equivalents can be rapidly screened using three to four Southern hybridization filters. This results in substantial labor saving, particularly when screening genomes of high complexity with many different probes. Another advantage of the system is that it allows for the long-term storage of the cosmids so that they can be screened whenever necessary. As a consequence, cosmid screening can be made a routine laboratory procedure.     

Gene isolation through genomic complementation using an indexed library of Chlamydomonas reinhardtii DNA

Hundreds of mutants with defects in a variety of physiologically important functions, such as photosynthesis, respiration, flagellar motility, phototaxis, circadian rhythms and the cell cycle, have been isolated from cultures of Chlamydomonas reinhardtii. In only a few cases have the genes responsible for these mutations been cloned and sequenced. The development of efficient methods for transformation with nuclear genes [7] has allowed the recent demonstration of gene isolation through genomic complementation with a pooled library of C. reinhardtii DNA [9]. To improve the efficiency with which genes complementing a particular mutation can be isolated, we have established an indexed (ordered) cosmid library of 11,280 individual clones contained in the separate wells of 120 microtiter plates. The average insert size is ca. 38 kb. PCR analysis of five sequenced nuclear genes present in the Chlamydomonas library revealed a range from two copies for the ₂ and ₂ tubulin genes to at least seven copies for the agininosuccinate lyase gene. Overall, these five clones were represented an average of >-3.4 times in the library. Thus, the probability that any one particular nuclear gene of < 1000 bp will be found in the library is >-97%, and the probability that a gene of ca. 10 000 bp will be found in the library is ca. 92%. Rapid screening methods with cosmid DNAs pooled from individual microtiter dishes have been applied successfully. Bacteria containing clones of the argininosuccinate lyase gene have been identified through genomic complementation of a Chlamydomonas mutant bearing an inactive arginnosuccinate lyase gene.We are using the nomenclature of indexed library versus ordered library to avoid confusion of this library with a library of ordered contigs.     

2-Steps KOH activation of rice straw: An efficient method for preparing high-performance activated carbons

Effects of both pre-treatment and number of steps in KOH activation of raw rice straw (RS) on textural and adsorption properties of RS-derived activated carbons (ACs) were investigated. Three pre-treatment protocols were tested: mechanical, chemical by NaOH pulping, and a combination of both. Activation of RS-based materials was investigated, at a constant temperature of 800 °C, according to two ways: a 1-step simultaneous carbonisation–activation with KOH, and a 2-steps process: carbonisation followed by activation by KOH.     

A fibroin secretion-deficient silkworm mutant, Nd-sD, provides an efficient system for producing recombinant proteins

The silkworm Nd-s(D) mutant is silk fibroin-secretion deficient. In the mutant, a disulfide linkage between the heavy (H) and light (L) chains, which is essential for the intracellular transport and secretion of fibroin, is not formed because of a partial deletion of the L-chain gene. To utilize the inactivity of the mutant L-chain, we investigated the possibility of using the Nd-s(D) mutant for the efficient production of recombinant proteins in the silkworm. A germ line transformation of the mutant with a normal L-chain-GFP fusion gene was performed. In the transgenic mutant, normal development of the posterior silk gland (PSG) was restored and it formed a normal cocoon. The biochemical analysis showed that the transgenic silkworms expressed the introduced gene in PSG cells, produced a large amount of the recombinant protein, secreted it into the PSG lumen, and used it to construct the cocoon. The molar ratio of silk proteins, H-chain:L-chain-GFP:fibrohexamerin, in the lumen and cocoon in the transgenic silkworm was 6:6:1, and the final product of the fusion gene formed about 10% of the cocoon silk. This indicates that the transgenic mutant silkworm possesses the capacity to produce and secrete the recombinant proteins in a molar ratio equal to that of the fibroin H-chain, contributing around half molecules of the total PSG silk proteins.     

An efficient mutational method for photosynthetic bacteria

The pigment and auxotrophic mutants of Rhodobacter sphaeroides Y6 were obtained by treatment with ethyl methanesulfonate (EMS) followed by lithium chloride (LiCl). Treatment with 0.081 MEMS and subsequent treatment with 0.071 M LiCl resulted in 12% higher frequency og than that by 0.081 mol/L EMS alone, and the same frequency of pigment mutations than application of 0.081 M EMS alone; the frequency of auxotrophic mutations increased 2.5-fold when treatment with lithium chloride was applied. A blue shift by 10 nm was recorded in the absorption spectrum of carotenoids form YM5-3 green mutant; considerable accumulation of neurosporine was revealed by HPLC and mass spectrometry. The method is efficient for isolating the mutants of photosynthetic bacteria. Published in Russian in Mikrobiologiya, 2006, Vol. 75, No. 6, pp. 758–764. The text was submitted by the authors in English.     

An efficient method for multi-locus molecular haplotyping

Many methods exist for genotyping—revealing which alleles an individual carries at different genetic loci. A harder problem is haplotyping—determining which alleles lie on each of the two homologous chromosomes in a diploid individual. Conventional approaches to haplotyping require the use of several generations to reconstruct haplotypes within a pedigree, or use statistical methods to estimate the prevalence of different haplotypes in a population. Several molecular haplotyping methods have been proposed, but have been limited to small numbers of loci, usually over short distances. Here we demonstrate a method which allows rapid molecular haplotyping of many loci over long distances. The method requires no more genotypings than pedigree methods, but requires no family material. It relies on a procedure to identify and genotype single DNA molecules, and reconstruction of long haplotypes by a ‘tiling’ approach. We demonstrate this by resolving haplotypes in two regions of the human genome, harbouring 20 and 105 single-nucleotide polymorphisms, respectively. The method can be extended to reconstruct haplotypes of arbitrary complexity and length, and can make use of a variety of genotyping platforms. We also argue that this method is applicable in situations which are intractable to conventional approaches.     

An efficient mutational method for photosynthetic bacteria

The pigment and auxotrophic mutants of Rhodobacter sphaeroides Y6 were obtained by treatment with ethyl methanesulfonate (EMS) followed by lithium chloride (LiCI). Treatment with 0.081 M EPS and subsequent treatment with 0.071 M LiCI resulted in 12% higher frequency of pigment mutations than application of 0.081 M EMS alone; the frequency of auxotrophic mutations increased 2.5-fold when treatment with lithium chloride was applied. A blue shift 10 nm was recorded in the absorption spectrum of carotenoids form YM5-3 green mutant; considerable accumulation of neurosporine was revealed by HPLC and mass spectrometry. The method is efficient for isolating mutants of photosynthetic bacteria.     

An efficient method for in vitro fertilization in rabbits

Abstract

This experiment was carried out to study a simple and efficient method for in vitro production of rabbit embryos. Newly ejaculated rabbit spermatozoa were used to fertilize superovulated oocytes after capacitation in vitro with four different media: (A) isotonic defined medium (DM)+heparin, (B) DM only,(C) DM+ high ionic strength defined medium (HIS), and (D) DM supplemented with 10mM NaHCO₃ (mDM) +HIS supplemented with 10mM NaHCO₃ (mHIS). The presumptive zygotes were cultured in M199 supplemented with 10% FCS, 1.25mM Na Pyruvate and 0.1mM EDTA (mM199). The cleavage rates after 24h of incubation were 29.3%, 32.1%, 64.9%, and 91.6% respectively, and the rates of blastocyst formation after 72h were 0, 27.3%, 58.4% and 85.2%, respectively. The results in the (D) treatment were significantly better than the other three treatments (p<0.01). Developmental potential of in vivo and in vitro derived zygotes was also compared using the mM199. The percentages of blastocyst and hatching blastocyst in the two groups were 92.5% and 87.2% after 84h, and 84.9% and 83.7% after 108h, respectively, and the two groups were not significantly different (p>0.05). The developmental progress of the two groups was nearly synchronous towards the end of culture. When IVF embryos from 2‐ to 4‐cell stage were transferred into recipients, the pregnancy rate did not differ from in vivo fertilization, but the rate of live young from IVF was significantly lower than from in vivo. The results of this experiment showed that ejaculated rabbit sperm could be capacitated efficiently after treatment of mDM and mHIS, and rabbit IVF embryos achieved great development in mM199 in vitro.     

An efficient method for in vitro fertilization in rabbits

This experiment was carried out to study a simple and efficient method for in vitro production of rabbit embryos. Newly ejaculated rabbit spermatozoa were used to fertilize superovulated oocytes after capacitation in vitro with four different media: (A) isotonic defined medium (DM)+heparin, (B) DM only,(C) DM+ high ionic strength defined medium (HIS), and (D) DM supplemented with 10mM NaHCO3 (mDM) +HIS supplemented with 10mM NaHCO3 (mHIS). The presumptive zygotes were cultured in M199 supplemented with 10% FCS, 1.25mM Na Pyruvate and 0.1mM EDTA (mM199). The cleavage rates after 24h of incubation were 29.3%, 32.1%, 64.9%, and 91.6% respectively, and the rates of blastocyst formation after 72h were 0, 27.3%, 58.4% and 85.2%, respectively. The results in the (D) treatment were significantly better than the other three treatments (p<0.01). Developmental potential of in vivo and in vitro derived zygotes was also compared using the mM199. The percentages of blastocyst and hatching blastocyst in the two groups were 92.5% and 87.2% after 84h, and 84.9% and 83.7% after 108h, respectively, and the two groups were not significantly different (p>0.05). The developmental progress of the two groups was nearly synchronous towards the end of culture. When IVF embryos from 2- to 4-cell stage were transferred into recipients, the pregnancy rate did not differ from in vivo fertilization, but the rate of live young from IVF was significantly lower than from in vivo. The results of this experiment showed that ejaculated rabbit sperm could be capacitated efficiently after treatment of mDM and mHIS, and rabbit IVF embryos achieved great development in mM199 in vitro.     

An efficient method for extraction of RNA from rice leaves at different ages using benzyl chloride.

With a conventional method of RNA extraction using an acid guanidinium thiocyanate-water-saturated phenol-chloroform mixture, extraction efficiency of extractable RNA to total RNA (extractable RNA+ residual RNA) in rice leaves at various ages was 54-69%. With a new method, an improvement of the above, using benzyl chloride instead of water-saturated phenol together with further maceration with a small amount of quartz sand, the efficiency was increased to 81-95%. When RNA fractions obtained with the improved method were subjected to agarose gel electrophoresis, intact bands of 25 S and 17 S rRNAs were detected. With a DNA probe for rice rbcS, only a single band was observed on the blotted membrane. These results indicate that the improved extraction method of RNA with benzyl chloride is useful for quantitative and qualitative analysis of RNA in plant tissues such as stiff leaves of rice.     

An efficient method for gene disruption in Neurospora crassa

The frequency with which transforming DNA undergoes homologous recombination at a chromosomal site can be quite low in some fungal systems. In such cases, strategies for gene disruption or gene replacement must either select against ectopic integration events or provide easy screening to identify homologous site, double-crossover insertion events. A protocol is presented for efficient isolation of Neurospora crassa strains carrying a definitive null allele in a target gene. The protocol relies on the presence of a selectable marker flanking a disrupted plasmid-borne copy of the gene, and in the case presented led to a seven-fold enrichment for putative homologous site replacement events. In addition, a polymerase chain reaction assay is utilized for rapid identification of homologous recombinants among the remaining candidates. This protocol was used to identify 3 isolates, out of 129 primary transformants, which have a disruption in the Neurospora ccg-1 gene. The method should be applicable to a variety of fungal systems in which two selectable markers can be expressed, including those in which homologous recombination rates are too low to allow easy identification of homologous site insertions by the more traditional molecular method of Southern analysis. In addition to disrupting target genes for the purpose of generating null mutations, this method is useful for the targeting of reporter gene fusions to a native chromosomal site for the purpose of studying gene regulation.