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Marinković P, Godinho L, Misgeld T. Generation of Thy1 Constructs for Pronuclear Injection. Cold Spring Harb Protoc 2015; 2015:937-940. [PMID: 26430258 DOI: 10.1101/pdb.prot087676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
With easy access to core facilities or commercial providers of pronuclear injections, generating simple Thy1-XFP transgenic mice (where XFP stands for any fluorescent protein) is now a possibility even for small laboratories. The generation of new Thy1 transgenic lines generally consists of five steps: (1) engineering and characterization of the desired fluorescent reporter protein, (2) cloning of the reporter protein into the Thy1 vector, (3) linearization and purification of the new Thy1 construct, (4) pronuclear injection to generate founders, and (5) screening of founder progeny to establish transgenic lines. Here, we provide a protocol for Steps 2 and 3. The sequence for a desired fluorescent reporter protein is cloned into the XhoI restriction site of the Thy1 vector. This usually involves blunt-end cloning because the traditional Thy1 vector does not carry an intact multiple cloning site. Following successful cloning, the DNA is prepared for pronuclear injection by linearizing it using EcoRI and PvuI restriction enzymes. The purified linearized DNA must then be sent to a facility specializing in pronuclear injection to generate transgenic founder mice.
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2
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Abstract
Baculovirus expression vector system (BEVS) is well known as a feasible and safe technology to produce recombinant (re-)proteins in a eukaryotic milieu of insect cells. However, its proven power in gene delivery and gene therapy is still poorly recognized. The basis of BEVS lies in large enveloped DNA viruses derived from insects, the prototype virus being Autographa californica multiple nucleopolyhedrovirus (AcMNPV). Infection of insect cell culture with a virus encoding a desired transgene under powerful baculovirus promoter leads to re-protein production in high quantities. Although the replication of AcMNPV is highly insect specific in nature, it can penetrate and transduce a wide range of cells of other origin. Efficient transduction requires only virus arming with an expression cassette active in the cells under investigation. The inherent safety, ease and speed of virus generation in high quantities, low cytotoxicity and extreme transgene capacity and tropism provides many advantages for gene delivery over the other viral vectors typically derived from human pathogens.
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Affiliation(s)
- Kari J Airenne
- Department of Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland.
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3
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O'Grady M, Batchelor RH, Scheyhing K, Kemp CW, Hanson GT, Lakshmipathy U. BacMam-mediated gene delivery into multipotent mesenchymal stromal cells. Methods Mol Biol 2011; 698:485-504. [PMID: 21431539 DOI: 10.1007/978-1-60761-999-4_34] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Baculoviruses have been used over the last several decades for high-level protein production in insect cells. Recently, modified baculovirus containing a mammalian promoter, known as BacMam virus, has been shown to give high transduction efficiencies across several cell types with minimal cytopathic effects. Cell types amenable to BacMam transduction include primary and adult stem cells. The shuttle vectors used in the construction of BacMam viruses can hold gene fragments up to 38 kb in size, and multiple BacMam viruses can be used in a single transduction for the delivery of more than one gene. BacMam technology has been used in the delivery and expression of targeted fluorescent protein cellular markers, small interfering RNAi, and extensively in the development of cell-based assays. BacMam offers an ideal method for the delivery and expression of large genes in hard-to-transfect cells such as primary and adult stem cells. In this chapter, we describe methods of generating high titer stocks of BacMam for transducing MSC and their derivatives.
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Affiliation(s)
- Michael O'Grady
- Primary and Stem Cell Systems, Life Technologies, Carlsbad, CA, USA
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4
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Abstract
We have isolated and sequenced a beta crystallin cDNA clone derived from the mRNA of cow lenses. Comparisons of the deduced amino acid sequence with the amino acid sequences of the principal beta crystallins of the cow, Beta Bp (1) and the mouse (2,3), confirm the general homology within the beta crystallin family and with the gamma crystallins. This beta crystallin cDNA, designated pBeta25/23, has 96% amino acid homology with the murine beta23 and only 43% amino acid homology with the cow beta Bp. The N-terminal 14 amino acids of the murine beta23, which are composed of a high percentage of hydrophobic amino acid residues, bear no similarity to the predicted amino acid sequence of the cow beta crystallin cDNA clone which we have isolated. The remaining amino acid sequences show greater homology between the mouse and cow beta crystallins than the corresponding alpha and beta globins between the two species. The degree of homology is comparable to that of the alpha crystallins for the cow and mouse. The pBeta25/23 cDNA is interesting for the presence of two potential translation initiation sites which are in phase and, if both are used, would code for two polypeptides of MW 25,100 and 23,200. These correspond to the 25,000 and 23,000 dalton beta crystallins that have been partially sequenced by Berbers et al. (4). This raises the possibility that the beta 25 and the beta23 synthesized in the cow lens are not encoded by two separate genes but may be derived from single mRNA using two translation initiation sites or by post-translational processing of the larger peptide. It is possible also that the two proteins are from two mRNA's derived from a single hnRNA by differential splicing of a intervening sequence at the 5' end of the gene.
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5
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Abstract
Efficient methods to characterize transgenic plants are important to quickly understand the state of the transformant. Determining transgene copy number is an important step in transformant characterization and can differentiate between complex and simple transformation events. This knowledge can be extremely useful when determining what future experiments and uses the transgenic lines can be utilized for. The method described here uses real-time quantitative PCR to determine the transgene copy number present in the genome of the transformant. Specifically, this method measures the relative transgene copy number by comparing it with an endogenous gene with a known copy number. This method is a quick alternative to the Southern blot, a method that is commonly used to determine gene copy number, and is effective when screening large numbers of transformants.
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Abstract
Sensitive and reproducible genotyping tools are fundamental in interpreting and substantiating genetic data. In cases where alternative assays like PCR are not applicable, a sensitive genomic Southern protocol is needed. Our maize gene discovery work using the RescueMu transgenic lines was such a task. The direct proof of each new germinal insertion event can be assessed only on a genomic DNA hybridization analysis, and therefore we developed the following protocol to screen efficiently through hundreds up to thousands of samples in a relatively short time. The DNA extraction protocol was scaled to accommodate samples processed in a microcentrifuge with consistent yield of approximately 50 microg of high molecular weight DNA. A trained person can easily process several hundred samples in a few days. Once the DNA is extracted, final results can be obtained routinely within a week on approximately 100 or more samples, depending on the capacity of the electrophoresis and hybridization apparatus available. Under our optimized conditions, the method described below generates blots with high sensitivity and low background even after repeated stripping and reprobing. Single to low-copy transgenes as well as maize genomic sequences can be detected consistently. The nonradioactive DNA probes employed are not only safer, compared to the conventional radioactive probes, but also greatly shorten the exposure time. Confident estimation of copy number - as good as quantitative PCR - and visualization of transgene complexity are just a few more advantages of this protocol.
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Affiliation(s)
- Guo-Ling Nan
- Biological Sciences/Walbot Lab, Stanford University, 385 Serra Mall, Stanford, CA 94305-5020, USA.
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7
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Li MN, Zheng GH, Wang L, Xiao W, Fu XH, Le YQ, Ren DM. Evaluation of the effectiveness and safety of the thermo-treatment process to dispose of recombinant DNA waste from biological research laboratories. Sci Total Environ 2009; 407:791-797. [PMID: 18849060 DOI: 10.1016/j.scitotenv.2008.08.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 07/18/2008] [Accepted: 08/06/2008] [Indexed: 05/26/2023]
Abstract
The discharge of recombinant DNA waste from biological laboratories into the eco-system may be one of the pathways resulting in horizontal gene transfer or "gene pollution". Heating at 100 degrees C for 5-10 min is a common method for treating recombinant DNA waste in biological research laboratories in China. In this study, we evaluated the effectiveness and the safety of the thermo-treatment method in the disposal of recombinant DNA waste. Quantitative PCR, plasmid transformation and electrophoresis technology were used to evaluate the decay/denaturation efficiency during the thermo-treatment process of recombinant plasmid, pET-28b. Results showed that prolonging thermo-treatment time could improve decay efficiency of the plasmid, and its decay half-life was 2.7-4.0 min during the thermo-treatment at 100 degrees C. However, after 30 min of thermo-treatment some transforming activity remained. Higher ionic strength could protect recombinant plasmid from decay during the treatment process. These results indicate that thermo-treatment at 100 degrees C cannot decay and inactivate pET-28b completely. In addition, preliminary results showed that thermo-treated recombinant plasmids were not degraded completely in a short period when they were discharged into an aquatic environment. This implies that when thermo-treated recombinant DNAs are discharged into the eco-system, they may have enough time to re-nature and transform, thus resulting in gene diffusion.
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Affiliation(s)
- Meng-Nan Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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8
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Gemmill RM, Bolin R, Strauss WM, Pavan W. Purification and characterization of YACs containing large inserts. Curr Protoc Hum Genet 2008; Chapter 5:Unit 5.7. [PMID: 18428294 DOI: 10.1002/0471142905.hg0507s00] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This unit provides protocols for characterizing DNA segments cloned in YACs and for purifying YACs from yeast chromosomes. The first basic protocol describes Southern blotting and partial-digest restriction analysis of YACs. These methods are useful for determining the size and complexity of the cloned insert DNA, the presence and location of particular restriction sites or sequences, and even the species of origin of the insert DNA (indicated by hybridization to species-specific repetitive elements such as Alu repeats). The second basic protocol describes gel purification of YACs for use in procedures requiring pure YAC DNA, such as mammalian-cell transformation and subcloning into smaller insert vectors. The third basic protocol details characterizing and analyzing YACs: in vivo fragmentation via homologous recombination with specialized fragmentation vectors containing specific probe sequences or repetitive elements, followed by Southern blotting with YAC- and human-derived probes.
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Affiliation(s)
- R M Gemmill
- Eleanor Roosevelt Institute for Cancer Research, Denver, Colorado, USA
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9
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Sakurai T, Kamiyoshi A, Watanabe S, Sato M, Shindo T. Rapid zygosity determination in mice by SYBR Green real-time genomic PCR of a crude DNA solution. Transgenic Res 2007; 17:149-55. [PMID: 17851772 DOI: 10.1007/s11248-007-9134-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Accepted: 08/14/2007] [Indexed: 10/22/2022]
Abstract
We examined whether crude DNA extracts prepared from gene-engineered mouse tissues are suitable as a template for zygosity determination by SYBR Green real-time genomic PCR. A crude DNA solution was prepared by brief incubation with lysis buffer containing ear, tail, or fetus of ROSA26 mouse, a gene-trapped strain carrying the beta-galactosidase (beta-gal) gene. Five serially diluted crude DNA samples (original, 2-, 4-, 8-, 16-diluted) were next prepared and then subjected to three-step (95 degrees C, 60 degrees C and 72 degrees C) reactions of real-time PCR to detect the beta-gal gene and the receptor-activity-modifying protein 3 (ramp3) gene (as an internal reference gene). The slopes of standard curves obtained from the real-time PCR indicated that amplification efficiency was approximately 99%, and the efficiencies of target and reference were almost equal. With this system, we next determined the zygosity of mice derived from mating heterozygous ROSA26 females and males, and found a sharp distinction in zygosity, wild-type, heterozygous and homozygous. Assessment of crude DNA samples from other gene-engineered mice including B6ZP3Cre-Tg, B6rAM-Tg, and Ramp2-gene-targeted strains revealed that our method was effective for determination of zygosity. The present method is more convenient and rapid than formerly published methods employing purified genomic DNA as a template. Our method will be particularly useful for experiments requiring rapid and accurate genotyping of gene-modified animals/fetuses.
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Affiliation(s)
- Takayuki Sakurai
- Department of Organ Regeneration, Graduate school of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.
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10
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Gao Q, Sun M, Wang X, Geller AI. Isolation of an enhancer from the rat tyrosine hydroxylase promoter that supports long-term, neuronal-specific expression from a neurofilament promoter, in a helper virus-free HSV-1 vector system. Brain Res 2007; 1130:1-16. [PMID: 17169349 PMCID: PMC2694737 DOI: 10.1016/j.brainres.2006.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 09/27/2006] [Accepted: 10/03/2006] [Indexed: 12/13/2022]
Abstract
Direct gene transfer into neurons, using a virus vector, has been used to study neuronal physiology and learning, and has potential for supporting gene therapy treatments for specific neurological diseases. Many of these applications require high-level, long-term recombinant gene expression, in forebrain neurons. We previously showed that addition of upstream sequences from the rat tyrosine hydroxylase (TH) promoter to a neurofilament heavy gene (NF-H) promoter supports long-term expression in forebrain neurons, from helper virus-free Herpes Simplex Virus (HSV-1) vectors. This element in the TH promoter satisfied the definition of an enhancer; it displayed activity at a distance from the basal promoter, and in both orientations. This enhancer supported physiological studies that required long-term expression; a modified neurofilament promoter, containing an insulator upstream of the TH-NFH promoter, supported expression in approximately 11,400 striatal neurons at 6 months after gene transfer, and expression for 7, 8, or 14 months, the longest times tested. In contrast, the NF-H promoter alone does not support long-term expression, indicating that the critical sequences are in the 6.3 kb fragment of the TH promoter. In this study, we performed a deletion analysis to identify the critical sequences in the TH promoter that support long-term expression. We localized these critical sequences to an approximately 320 bp fragment, and two subfragments of approximately 100 bp each. Vectors that contained each of these small fragments supported levels of long-term, neuronal-specific expression that were similar to the levels supported by a vector that contained the initial 6.3 kb fragment of the TH promoter. These small fragments of the TH promoter may benefit construction of vectors for physiological studies, and may support studies on the mechanism by which this enhancer supports long-term expression.
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Affiliation(s)
- Qingshen Gao
- Department of Neurology, West Roxbury VA Hospital/Harvard Medical School, W. Roxbury, MA, 02132
| | - Mei Sun
- Department of Neurology, West Roxbury VA Hospital/Harvard Medical School, W. Roxbury, MA, 02132
| | - Xiaodan Wang
- Department of Neurology, West Roxbury VA Hospital/Harvard Medical School, W. Roxbury, MA, 02132
| | - Alfred I. Geller
- Department of Neurology, West Roxbury VA Hospital/Harvard Medical School, W. Roxbury, MA, 02132
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11
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Begg GS, Cullen DW, Iannetta PPM, Squire GR. Sources of uncertainty in the quantification of genetically modified oilseed rape contamination in seed lots. Transgenic Res 2006; 16:51-63. [PMID: 17106767 DOI: 10.1007/s11248-006-9029-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 07/20/2006] [Indexed: 10/23/2022]
Abstract
Testing of seed and grain lots is essential in the enforcement of GM labelling legislation and needs reliable procedures for which associated errors have been identified and minimised. In this paper we consider the testing of oilseed rape seed lots obtained from the harvest of a non-GM crop known to be contaminated by volunteer plants from a GM herbicide tolerant variety. The objective was to identify and quantify the error associated with the testing of these lots from the initial sampling to completion of the real-time PCR assay with which the level of GM contamination was quantified. The results showed that, under the controlled conditions of a single laboratory, the error associated with the real-time PCR assay to be negligible in comparison with sampling error, which was exacerbated by heterogeneity in the distribution of GM seeds, most notably at a small scale, i.e. 25 cm3. Sampling error was reduced by one to two thirds on the application of appropriate homogenisation procedures.
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Affiliation(s)
- Graham S Begg
- Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK.
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12
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Abstract
In recent years, recombinant adenoviral and adeno-associated viral (AAV) vectors have been exploited in a number of gene delivery approaches. The use of these vectors in clinical gene transfer has increased the demand for their characterization, production and purification. Although the classical method of adenovirus or AAV purification by density gradient centrifugation is effective on a small scale, chromatographic separation is the most versatile and powerful method for large-scale production of recombinant adenovirus or AAV. This review describes different chromatographic modes for adenovirus or AAV purification and process development, as well as the utility of different purification steps for virus production. Advances in the development of viral vectors for gene therapy, such as the discovery of new AAV serotypes, adenoviral and AAV retargeting and improved production of helper-dependent adenoviral vectors, require further development of efficient purification methods.
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Affiliation(s)
- E Burova
- Regeneron Parmaceuticals Inc., Tarrytown, NY, USA
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13
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Abstract
Adeno-associated virus (AAV) is currently one of the most promising systems for human gene therapy. Numerous preclinical studies have documented the excellent safety profile of these vectors along with their impressive performances in their favored target, consisting of highly differentiated postmitotic tissues such as muscle, central nervous system and liver. Clinical trials have been conducted confirming these data, but also emphasizing the requirement of further high-tech developments of the production and purification procedures that would allow both scaling-up and improvement of vector batch quality, necessary to human application. The scope of this review will be the state of the art in the various production methods of recombinant AAV (rAAV), delimiting their respective perimeter of application and also their main advantages and drawbacks, and thereby shedding light on the main challenges to take in the near future to bring AAV vectors more widely into the clinics.
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Affiliation(s)
- O-W Merten
- Genethon, 1 bis, rue de l'Internationale, Evry, France
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14
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Mazza R, Soave M, Morlacchini M, Piva G, Marocco A. Assessing the Transfer of Genetically Modified DNA from Feed to Animal Tissues. Transgenic Res 2005; 14:775-84. [PMID: 16245168 DOI: 10.1007/s11248-005-0009-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Accepted: 06/17/2005] [Indexed: 10/25/2022]
Abstract
In Europe, public and scientific concerns about the environmental and food safety of GM (Genetically Modified) crops overshadow the potential benefits offered by crop biotechnology to improve food quality. One of the concerns regarding the use of GM food in human and animal nutrition is the effect that newly introduced sequences may have on the organism. In this paper, we assess the potential transfer of diet-derived DNA to animal tissues after consumption of GM plants. Blood, spleen, liver, kidney and muscle tissues from piglets fed for 35 days with diets containing either GM (MON810) or a conventional maize were investigated for the presence of plant DNA. Only fragments of specific maize genes (Zein, Sh-2) could be detected with different frequencies in all the examined tissues except muscle. A small fragment of the Cry1A(b) transgene was detected in blood, liver, spleen and kidney of the animals raised with the transgenic feed. The intact Cry1A(b) gene or its minimal functional unit were never detected. Statistical analysis of the results showed no difference in recovery of positives for the presence of plant DNA between animals raised with the transgenic feed and animals raised with the conventional feed, indicating that DNA transfer may occur independently from the source and the type of the gene. From the data obtained, we consider it unlikely that the occurrence of genetic transfer associated with GM plants is higher than that from conventional plants.
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Affiliation(s)
- Raffaele Mazza
- Instituto di Agronomia generale e Coltivazioni erbacee, Università Cattolica S. Cuore, Via E. Parmense, 84, Piacenza 29100, Italy.
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15
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Ortiz-García S, Ezcurra E, Schoel B, Acevedo F, Soberón J, Snow AA. Absence of detectable transgenes in local landraces of maize in Oaxaca, Mexico (2003-2004). Proc Natl Acad Sci U S A 2005; 102:12338-43. [PMID: 16093316 PMCID: PMC1184035 DOI: 10.1073/pnas.0503356102] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 2000, transgenes were detected in local maize varieties (landraces) in the mountains of Oaxaca, Mexico [Quist, D. & Chapela, I. H. (2001) Nature 414, 541-543]. This region is part of the Mesoamerican center of origin for maize (Zea mays L.), and the genetic diversity that is maintained in open-pollinated landraces is recognized as an important genetic resource of great cultural value. The presence of transgenes in landraces was significant because transgenic maize has never been approved for cultivation in Mexico. Here we provide a systematic survey of the frequency of transgenes in currently grown landraces. We sampled maize seeds from 870 plants in 125 fields and 18 localities in the state of Oaxaca during 2003 and 2004. We then screened 153,746 sampled seeds for the presence of two transgene elements from the 35S promoter of the cauliflower mosaic virus and the nopaline synthase gene (nopaline synthase terminator) from Agrobacterium tumefaciens. One or both of these transgene elements are present in all transgenic commercial varieties of maize. No transgenic sequences were detected with highly sensitive PCR-based markers, appropriate positive and negative controls, and duplicate samples for DNA extraction. We conclude that transgenic maize seeds were absent or extremely rare in the sampled fields. This study provides a much-needed preliminary baseline for understanding the biological, socioeconomic, and ethical implications of the inadvertent dispersal of transgenes from the United States and elsewhere to local landraces of maize in Mexico.
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Affiliation(s)
- S Ortiz-García
- Instituto Nacional de Ecología, Secretaría del Medio Ambiente y Recursos Naturales, Colonia Insurgentes Cuicuilco, Delegación Coyoacán, 04530 México D.F., Mexico
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16
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Watanabe T, Kuribara H, Mishima T, Kikuchi H, Kodama T, Futo S, Kasama K, Toyota A, Nouno M, Saita A, Takahashi K, Hino A, Akiyama H, Maitani T, Kubo M. New qualitative detection methods of genetically modified potatoes. Biol Pharm Bull 2005; 27:1333-9. [PMID: 15340215 DOI: 10.1248/bpb.27.1333] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Japan, 8 lines of genetically modified (GM) potato (2 lines of NewLeaf potato; NL, 3 lines of NewLeaf Plus potato; NLP, and 3 lines of NewLeaf Y potato; NLY) have already been authorized as safe for use in foods and feeds. We have developed polymerase chain reaction (PCR) methods for the qualitative detection of the GM potatoes for the screening and the identification of NL, NLP and NLY. The gene encoding uridine diphosphate (UDP)-glucose pyrophosphorylase (UGPase) was used as a taxon specific gene. We designed the primer pair to detect the cryIIIA genes as a screening method for GM potatoes because the gene should be inserted in all 8 lines of the GM potatoes. For identification of NL, NLP and NLY, we further designed three specific primer pairs for the different recombinant DNAs (r-DNA) specifically introduced into NL, NLP, or NLY. In addition, to identify the 3 lines of NLY that have been introduced with the same r-DNA, the three line-specific primer pairs for the border sequence between the r-DNA and genomic DNA of NLY 3 lines were designed. Six lines of GM potato used as the test material were specifically identified using the each primer pair under the same PCR condition. The detection limits of all the GM potatoes should be approximately 0.1%. Furthermore, the specificity and reproducibility of the methods were confirmed in a six-laboratory collaborative study.
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Affiliation(s)
- Takahiro Watanabe
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan.
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17
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Abstract
Bacterial artificial chromosome (BAC) libraries are emerging as valuable tools for investigating phylogenetic relationships at the level of genome structure. To date, BAC library construction has been restricted to a fairly small number of laboratories and species that represent a not insignificant, but a fairly small, fraction of diversity in the plant kingdom. This chapter is intended to contribute to rectifying this situation by providing protocols that facilitate BAC library construction in laboratories possessing basic molecular biology skills.
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Affiliation(s)
- Andrew G McCubbin
- School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236, USA
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18
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Affiliation(s)
- Stefanie Trapmann
- European Commission, Joint Research Centre, Institute for Reference Materials and Measurements (IRMM), Retieseweg 111, Geel 2440, Belgium.
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19
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Abstract
A rapid and simple DNA extraction method is needed to detect genetically modified recombinant DNA in soybean kernels and processed foods. However, since various kernels and processed foods differ greatly in form, a uniform DNA extraction method has proved elusive. The silica-base resin DNA extraction method does not use any organic solvent, and the operation is simple and the cost per extraction is low, although the frequency of its use is very low and few domestic reports exist. We therefore studied suitable conditions for a silica-base resin method. We also developed the method to get more pure DNA from soybean kernels. The silica-base resin method was found to be adequate for extracting DNA from various processed foods for PCR amplification with endogenous gene primers. In the case of DNA extraction from soybean kernels, pure DNA could be efficiently extracted after pre-heating the soybean suspension in TNE buffer. The extracted DNA showed higher ratios of absorption at 260 nm/280 nm and 260 nm/230 nm than those for samples obtained with previous methods. Moreover, our observations suggested that the extraction time could be reduced to within 30 min for processed foods such as tofu.
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Affiliation(s)
- Akihiko Nakama
- Nutrition College, Osaka Institute of Public Health and Environmental Sciences: 8-34, Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
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20
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Affiliation(s)
- Kazutoyo Osoegawa
- BACPAC Resource Center, Children's Hospital Oakland Research Institute, CA, USA
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21
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Affiliation(s)
- Deborah A Swing
- Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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22
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23
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Affiliation(s)
- Vikki M Marshall
- The Watler and Eliza Hall Institute of Medical Resesarch, Royal Melbourne Hospital, Victoria, Australia
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24
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Gross RH. Using desktop cloning software to plan, track, and evaluate cloning projects. Methods Mol Biol 2004; 235:107-20. [PMID: 12904654 DOI: 10.1385/1-59259-409-3:107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Robert H Gross
- Department of Biological Sciences, Center for Biological and Biomedical Computing, Dartmouth College, Hanover, NH, USA
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25
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Affiliation(s)
- Nicholas Downey
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
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26
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Wang Y, Cao Z, Hood D, Townsel JG. Construction of genomic libraries in lambda-vectors. Methods Mol Biol 2004; 235:153-68. [PMID: 12904658 DOI: 10.1385/1-59259-409-3:153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yilun Wang
- Department of Biological Sciences, Tennessee State University, Nashville, USA
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27
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Powles R, Steyn LM. Creating nested DNA deletions using exonuclease III. Methods Mol Biol 2004; 235:225-31. [PMID: 12904665 DOI: 10.1385/1-59259-409-3:225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rosamund Powles
- Division of Medical Microbiology, University of Cape Town, Rondebosch, South Africa
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28
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Goranson-Siekierke J, Erbe JL. Restriction analysis of recombinant plasmids. Methods Mol Biol 2004; 235:175-81. [PMID: 12904660 DOI: 10.1385/1-59259-409-3:175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Nichols WA. Screening recombinant DNA libraries. Methods Mol Biol 2004; 235:183-94. [PMID: 12904661 DOI: 10.1385/1-59259-409-3:183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Wade A Nichols
- Department of Biological Sciences, Illinois State University, Normal, USA
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30
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Affiliation(s)
- Zhidong Xu
- Department of Surgery, Comprehensive Cancer Center, University of California, San Francisco, USA
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31
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Affiliation(s)
- Sangwei Lu
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, USA
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32
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Chen YX, Liu H, Zhang WB, Jin YF. A novel tri-primer PCR method (TP-PCR) for rapid construction of fpg gene. J Microbiol Methods 2004; 56:359-64. [PMID: 14967227 DOI: 10.1016/j.mimet.2003.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2003] [Revised: 11/03/2003] [Accepted: 11/04/2003] [Indexed: 11/30/2022]
Abstract
A novel tri-primer polymerase chain reaction method (TP-PCR) was developed for the construction of a fused fpg gene, in which no endonuclease and ligase were used. Instead, two templates and three specifically designed primers were applied. Results showed that pheB and gfp genes, which encodes the catechol 2, 3-dioxygenase and the green fluorescent protein (GFP), respectively, were successfully fused into an fpg gene through the rapid TP-PCR system, indicating that TP-PCR method could be a useful tool for DNA fragment fusion in which no proper endonuclease sites were available.
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Affiliation(s)
- Ying Xu Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, China.
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33
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Poulsen TS. Purification of BAC DNA. Methods Mol Biol 2004; 255:91-100. [PMID: 15020817 DOI: 10.1385/1-59259-752-1:091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
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34
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Heister TGH, Vögtlin A, Müller L, Heid I, Fraefel C. Construction of HSV-1 BACs and their use for packaging of HSV-1-based amplicon vectors. Methods Mol Biol 2004; 256:241-56. [PMID: 15024170 DOI: 10.1385/1-59259-753-x:241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
MESH Headings
- Animals
- Chlorocebus aethiops
- Chromosomes, Artificial, Bacterial/genetics
- Cloning, Molecular
- DNA, Recombinant/genetics
- DNA, Recombinant/isolation & purification
- DNA, Viral/genetics
- DNA, Viral/isolation & purification
- Escherichia coli/genetics
- Genetic Techniques
- Genetic Vectors
- Genome, Viral
- Herpesvirus 1, Human/genetics
- Plasmids/genetics
- Recombination, Genetic
- Vero Cells
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35
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Chen XN, Korenberg JR. BAC mapping using fluorescence in situ hybridization. Methods Mol Biol 2004; 255:131-41. [PMID: 15020820 DOI: 10.1385/1-59259-752-1:131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Xiao-Ning Chen
- Department of Human Genetics and Pediatrics, Cedars-Sinai Medical Center, University of California, Los Angeles, USA
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36
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Testa G, Vintersten K, Zhang Y, Benes V, Muyrers JPP, Stewart AF. BAC engineering for the generation of ES cell-targeting constructs and mouse transgenes. Methods Mol Biol 2004; 256:123-39. [PMID: 15024164 DOI: 10.1385/1-59259-753-x:123] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Giuseppe Testa
- BioInnovation Zentrum, University of Technology, Dresden, c/o Max-Planck Institut for Cell Biology and Genetics, Dresden, Germany
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37
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Affiliation(s)
- Bruce A Roe
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, USA
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38
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Kigawa T, Yabuki T, Matsuda N, Matsuda T, Nakajima R, Tanaka A, Yokoyama S. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. ACTA ACUST UNITED AC 2004; 5:63-8. [PMID: 15263844 DOI: 10.1023/b:jsfg.0000029204.57846.7d] [Citation(s) in RCA: 276] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
As structural genomics and proteomics research has become popular, the importance of cell-free protein synthesis systems has been realized for high-throughput expression. Our group has established a high-throughput pipeline for protein sample preparation for structural genomics and proteomics by using cell-free protein synthesis. Among the many procedures for cell-free protein synthesis, the preparation of the cell extract is a crucial step to establish a highly efficient and reproducible workflow. In this article, we describe a detailed protocol for E. coli cell extract preparation for cell-free protein synthesis, which we have developed and routinely use. The cell extract prepared according to this protocol is used for many of our cell-free synthesis applications, including high-throughput protein expression using PCR-amplified templates and large-scale protein production for structure determinations.
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Affiliation(s)
- Takanori Kigawa
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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39
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Abstract
Despite the availability of antibody libraries for the selection of receptor molecules, the large number of established and well-characterized hybridoma lines still represent a useful source for recombinant antibody genes. This protocol describes the PCR amplification, cloning, and a small-scale expression test for the generation of scFv fragments from hybridoma cell lines. Particular emphasis was placed on frequently observed problems and pitfalls of this method.
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Affiliation(s)
- Lars Toleikis
- Hospital for Women, University of Heidelberg, Germany
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40
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Möritz A. Industry perspective for biotech products. Dev Biol (Basel) 2004; 118:37-44. [PMID: 15645671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
This presentation, held at the Joint PDA/EMEA Virus Safety Forum, provided an industry perspective on virus safety for biotech products. After discussion of the various groups of biologicals for human use, the presentation focused on a specific group of biologicals, the cell-derived rDNA products. The current authority guidelines of this group of well-defined biotech products were discussed, and a representative case study addressing virus safety aspects was presented. Questions for discussion were raised which illustrated the need for discussion between regulators and industry concerning updated guidance for this group of biologicals.
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Affiliation(s)
- A Möritz
- Novartis Pharma AG, Technical Research & Development Quality Assurance, Basel, Switzerland.
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41
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Cross SH. Isolation of CpG islands from BAC clones using a methyl-CpG binding column. Methods Mol Biol 2004; 256:21-37. [PMID: 15024157 DOI: 10.1385/1-59259-753-x:021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Sally H Cross
- MRC Human Genetics Unit, Western General Hospital, Edinburgh, UK
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42
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Muyrers JPP, Zhang Y, Benes V, Testa G, Rientjes JMJ, Stewart AF. ET recombination: DNA engineering using homologous recombination in E. coli. Methods Mol Biol 2004; 256:107-21. [PMID: 15024163 DOI: 10.1385/1-59259-753-x:107] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Joep P P Muyrers
- Gene Expression Program, European Molecular Biology Laboratory, Heidelberg, Germany
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43
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Harwood JC, Phear GA. Direct sequencing of PCR products. Methods Mol Biol 2003; 58:403-12. [PMID: 8713890 DOI: 10.1385/0-89603-402-x:403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- J C Harwood
- Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, UK
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44
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Bignell GR, Evans IH. Genomic yeast DNA clone banks. Construction and gene isolation. Methods Mol Biol 2003; 53:155-87. [PMID: 8924978 DOI: 10.1385/0-89603-319-8:155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- G R Bignell
- School of Biological and Chemical Sciences, University of Greenwich, London, UK
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45
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Silverman GA. End-rescue of YAC clone inserts by inverse PCR. Methods Mol Biol 2003; 54:145-55. [PMID: 8597787 DOI: 10.1385/0-89603-313-9:145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- G A Silverman
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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46
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Snell RG. The isolation of cDNAs by hybridization of YACs to cDNA libraries. Methods Mol Biol 2003; 54:329-36. [PMID: 8597800 DOI: 10.1385/0-89603-313-9:329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- R G Snell
- Ruakura Research Centre, Hamilton, New Zealand
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47
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Affiliation(s)
- W M Strauss
- Department of Medicine, Division of Gerontology, Beth Israel Hospital, Boston, MA, USA
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48
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Affiliation(s)
- M J Page
- Department of Cell Biology, Wellcome Research Laboratories, Beckenham, Kent, UK
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49
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Hughes MA, Crampton JM. The development and use of repetitive sequences as DNA probes for parasite detection and species identification. Methods Mol Biol 2003; 21:169-89. [PMID: 8220714 DOI: 10.1385/0-89603-239-6:169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- M A Hughes
- Wolfson Unit of Molecular Genetics, Liverpool School of Tropical Medicine, UK
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50
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Affiliation(s)
- M K Trower
- Molecular Genetics Unit, MRC Centre, Cambridge, UK
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