Comparison of properties of agarose for electrophoresis of DNA

A method for high-concentration agarose gel preparation and its application in high-resolution separation of low-molecular-weight nucleic acids and proteins

Separation of nucleic acids and proteins using gels has always been a crucial part of molecular biology research. For low-molecular-weight nucleic acids and proteins, low- and medium-concentration agarose gels cannot achieve the high resolution as polyacrylamide gels. We found that 6 %-14 % high-concentration agarose gels (HAGs) could be easily dissolved in an autoclave and the vertical gel cast can be effortlessly filled using an easy-made plastic box. Coupled with the improved buffer condition, HAG electrophoresis resulted in a good resolution of DNA and protein bands. With conventional TBE buffer plus 0.2 % NaCl, DNA fragments that differ by 2-5-bp within the 50-200-bp size range can be resolved on 6 %-8 % HAGs. By using TBE without NaCl, DNA fragments that differ by 2-bp or 2-nt within the 10-100-bp size range can be well resolved on >8 % HAGs. Using a buffer system comprising 1 M Tris-Cl for gel preparation, 0.2 M Tris-Cl/0.2 % SDS as upper tank buffer, and 0.2 M Tris-Cl as the lower tank buffer, HAGs achieved good molecular weight separation of total bacterial and plant proteins in the 10-200 kDa range. In conclusion, we developed a method for HAG preparation and electrophoresis of low-molecular-weight nucleic acids and proteins.

A reassessment of several erstwhile methods for isolating DNA fragments from agarose gels

Molecular biology research often requires extraction of DNA fragments from agarose gels. In the past decades, there have been many methods developed for this purpose. Currently most researchers, especially novices, use commercial kits for this extraction, although these kits cost money and the procedures involved are not necessarily easier than some erstwhile methods. We herein reintroduce and reassess several simple and cost-free older methods. One method involves excising a slice of the gel containing the DNA fragment, followed by a thaw-and-freeze procedure to release the DNA from the gel slice into the gel-making buffer. The second method involves a dialysis tubing and requires electroelution of the DNA from the gel slice in the tubing. The third one is to centrifuge the gel slice to release the DNA. The fourth method requires electro-transfer of the DNA from the gel into a filter paper, while the fifth one includes either allowing the DNA in the slice to be dissolved into a buffer or dissolving the DNA-containing gel slice, followed by DNA precipitation with ethanol or isopropanol. The strengths and weaknesses of these methods are discussed to assist researchers in making their choice. We also point out that some of the end uses of the DNA fragment in the agarose gel may not actually require extraction of the DNA. For instance, a tiny DNA-containing gel block or filter paper can be directly used as the template in a nested or semi-nested polymerase chain reaction to preliminarily determine the identity of the DNA fragment.

Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA

Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.

New design of hydrogels with tuned electro-osmosis: a potential model system to understand electro-kinetic transport in biological tissues

A series of charged polymer gels with precisely controlled magnitude and direction of electro-osmotic flow was prepared and opens up the possibility for understanding the contribution of electro-osmosis to transport phenomenon in native biological tissues.

Chromosome sequence maps of the Giardia lamblia assemblage A isolate WB

Two genotypes, assemblages A and B, of the pathogenic gut protozoan parasite Giardia lamblia infect humans. Symptoms of infection range from asymptomatic to chronic diarrhea. Giardia chromosomes have long been characterized but not until the publication of the first Giardia genome sequence was chromosome mapping work, commenced nearly two decades ago, completed. Initial mapping studies identified and ordered Not I chromosome segments (summating to 1.8 Mb) of the estimated 2 Mb chromosome 3. The resulting map was confirmed with the release of the Giardia genome sequence and this revitalized mapping. The result is that 93% of the WB isolate genome sequence has now been assigned to one of five major chromosomes, and community access to these data has been made available through GiardiaDB, the database for Giardia genomes.

Sequence map of the 3-Mb Giardia duodenalis assemblage A chromosome

The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromosome, a library of probes specific for this chromosome was constructed. The probes were hybridised to NotI-cleaved whole chromosomes, and the combined size of different NotI segments identified by the probes was 2,225 kb indicating the probes were well distributed along the 3-Mb chromosome. Six scaffolds (CH991814, CH991779, CH991793, CH991763, CH991764, and CH991761) were identified as belonging to the 3-Mb chromosome, and these scaffolds were ordered and oriented according to scaffold features including I-PpoI sites and hybridisation pattern. However, the combined size of scaffolds was more than 4 Mb. Approximately, 1 Mb of scaffold CH991763 carrying previously identified sequences specific for the 1.5-Mb chromosome(s) including subtelomeric sequence was reassigned, and several other anomalies were addressed such that the final size of the apparently 3-Mb chromosome is estimated to be 2,885 kb. This work addresses erroneous computer-based assignment of a number of contigs and emphasises the need for alternative and confirmatory methods of scaffold construction.

Effect of the matrix on DNA electrophoretic mobility

DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.

DNA detection system using molecularly imprinted polymer as the gel matrix in electrophoresis

To develop a simple and inexpensive method for DNA detection, we prepared a molecularly imprinted polymer (MIP) for recognizing a specific double-stranded DNA (dsDNA) sequence and used it in an electrophoretic gel matrix. The MIP gel has many binding sites that are complementary in size, shape, and arrangement of functional groups of the target dsDNA sequence. During MIP gel electrophoresis (MIPGE), migration of the target dsDNA should be hindered by the capture effect of the binding sites in the MIP gel. This was confirmed by observation of deviations from the linear relationship between the migration distances of the DNA standard size markers in the polyacrylamide gel and those in the MIP gel. The migration distances of nontarget dsDNA maintained a linear relationship, however. In addition, the sequence selectivity of dsDNA in this method was investigated by using the Ha-ras gene and its point mutants. Except for A.T to T.A base pair substitution, mutant dsDNA (for example, substitution from A.T to C.G and from G.C to T.A) could be distinguished from the target (wild-type) dsDNA. Although some improvement in A.T (T.A) base pair distinction is still needed, this study is the first to demonstrate detection of a specific dsDNA sequence with MIPs and, as such, opens up a new realm for practical applications of MIPs.

Delivery of DNA vaccines by agarose hydrogel implants facilitates genetic immunization in cattle

The present study demonstrates the interest of two slow-release systems as vaccination tools in cattle. Two experiments show that a first intradermal administration of one DNA vaccine dose combined with the slow-release of a second dose conduct to a priming of the bovine herpesvirus 1-specific immune response similar to the one generated by two discrete administrations 4 weeks apart. The first experiment demonstrates the efficacy of the slow-release system with well-characterized Alzet osmotic pumps, whereas the second experiment extends the same concept with innovative agarose hydrogel implants. These latter implants are cheaper and more convenient than the osmotic pumps or repeated intradermal administrations since they contribute to an efficient priming of the immune response in a single manipulation of the animals.

Detection of a specific DNA sequence by electrophoresis through a molecularly imprinted polymer

To develop a simple and inexpensive DNA detection method, we prepared a molecularly imprinted polymer (MIP) gel for recognizing a specific double-stranded DNA (dsDNA) target sequence in MIP gel electrophoresis (MIPGE). During MIPGE, migration of the target sequence of dsDNA should be hindered by the capture effect of the binding sites in the MIP gel. This migration hindrance of target dsDNA was determined by plotting the relationship between the migration distance in the MIP gel and that in polyacrylamide gel, commonly used in gel electrophoresis. Using this plot, detection of a target dsDNA from a mixture of different-sized dsDNA fragments was achieved. Moreover, we found the detection method successfully distinguished between a target and its base-pair substitutes. These results suggest that MIPGE could be employed for detection of a target dsDNA sequence.

Structural and mechanical characterization of nanoclay-reinforced agarose nanocomposites

Nanoclay-reinforced agarose nanocomposite films with varying weight concentration ranging from 0 to 80% of nanoclay were prepared, and structurally and mechanically characterized. Structural characterization was carried out by transmission electron microscopy (TEM), scanning electron microscopy (SEM) and atomic force microscopy (AFM). It was found that pre-exfoliated clay platelets were re-aggregated into particles (stacked platelets) during the composite preparation process. Each particle consists of approximately 11 clay platelets stacked together. The nanoclay particles were homogeneously dispersed within an agarose matrix. The clay particles were oriented with a slight preference of the stacked platelets being parallel to the composite film's surface within the low loading composite films. Mechanical properties of the nanocomposite films were measured by tensile, three-point bending and nanoindentation tests. Mechanical testing results show that nanoclays provide a significant enhancement to the tensile modulus and strength. For the 60% clay nanocomposite, its elastic modulus increases up to 21.4 GPa, which is five times higher than that of the agarose matrix. Based upon the structural characterization, a theoretical model has been developed to simulate the mechanical behaviour of the nanoclay-reinforced polymer composites.

Albendazole resistance in Giardia is correlated with cytoskeletal changes but not with a mutation at amino acid 200 in beta-tubulin

Albendazole resistance was induced in three different Giardia cultures following growth in successively increasing amounts of drug. One of the lines was previously resistant to high levels of metronidazole and was able to grow in 2 microM albendazole. The other two survived exposure to 0.8 microM, while normally lethal levels of albendazole against Giardia in vitro were around 0.1-0.2 microM. Albendazole-resistant Giardia were cross-resistant to parbendazole. Major chromosome rearrangements were evident in the line resistant to 2 microM albendazole and IFA with antitubulin antibody indicated differences in the cytoskeleton, particularly the median body, between sensitive and resistant lines. This implicates the cytoskeleton in the mechanism of resistance. Substitution of Tyr for Phe is a consistent beta-tubulin amino acid change in the benzimidazole-resistant helminths and fungi so far analyzed. PCR primers were designed from the published Giardia beta-tubulin gene sequence and spanned the region encoding Phe at position 200. Sequence data from albendazole-resistant Giardia demonstrated that the beta-tubulin gene did not carry a mutation in the codon for amino acid 200. These data suggest that Phe at position 200 in beta-tubulin is not necessary for benzimidazole resistance.

Mapping variation in chromosome homologues of different Giardia strains

A landmark physical map of the 2-Mb chromosome of the Giardia duodenalis cloned line WB-1B, constructed using randomly cloned, chromosome specific markers, was used to compare the organisation and map order of the equivalent chromosome in other strains. A representative marker from each of the 13 NotI segments of the 2-Mb chromosome was hybridized to NotI cleavages of whole chromosomes of the other strains. Two strains, one isolated from a human, and one from a cat, had the same chromosome hybridization patterns as WB-1B. A strain isolated from a sheep, had one NotI chromosome 5 segment larger than WB-1B. Two additional strains isolated from a calf and a human had significantly different NotI cleavage patterns from the previous strains and shared no similar-sized chromosome NotI segment from their 2Mb chromosome homologues and only one in common with WB-1B. In one strain, two markers from the same WB-1B NotI segment did not hybridize suggesting deletion events have occurred. The order of some NotI segments within the 2Mb chromosome homologue was maintained, as determined from partial NotI chromosome cleavages, while in the most divergent of strains internal chromosome rearrangements and deletions were evident. All but one of the 2Mb WB-1B chromosome markers examined hybridized to a single chromosome band in all strains. Thus, while Giardia chromosomes vary in size, copy number and organisation, some linkage of markers is apparently maintained in isolates from disparate hosts and localities. We have therefore generated a genetic analysis system for Giardia with landmark maps using representative markers to replace the paucity of classical genetic markers and mutants. This approach is being extended to the complete genome.

Biological and genetic analysis of a longitudinal collection of Giardia samples derived from humans

Duodenal aspirates from children investigated for diarrhoea have been examined for the presence of Giardia over an eleven year period, and where possible, in vitro or in vivo Giardia cultures in mice were established. Based on biochemical characteristics of electrophoretic karyotype, RFLP analysis and rDNA hybridization studies of 40 stocks at least two major varieties, or demes, of Giardia have infected the population of South East Queensland and environs during this period. These demes carried different rDNA repeat units and differed markedly in both the electrophoretic karyotype pattern and the molar representation of chromosome bands. From 1983 to 1991 only one deme was documented. The first evidence of a new deme seen in local children occurred in 1991 and was followed by a predominance of this deme in 1993. These 40 stocks do not represent all positive samples. Other stocks established in vivo were not able to be cultured in vitro, and these probably represent other demes. Since all of the stocks established in vivo were not able to be cultured in vitro, and these probably represent other demes. Since all of the stocks were derived from children with similar chronic symptoms it appears that at least two demes of Giardia are pathogenic.

Physical map of a 2 Mb chromosome of the intestinal protozoan parasite Giardia duodenalis

The protozoan parasite, Giardia duodenalis, is regarded as the most primitive eukaryote. The two apparently identical nuclei presumably carry the same chromosomes but the number of different chromosomes in the organism is unknown. A genome map of G. duodenalis is required to resolve this issue and mapping studies were initiated using chromosome 5. This chromosome was estimated to be approximately 2 Mb when Giardia chromosomes were separated by contour-clamped homogeneous electric field gel electrophoresis. A plasmid library of chromosome 5-specific DNA sequences was constructed from gel-extracted chromosome 5 and selected probes were used as markers to identify NotI DNA segments derived from chromosome 5. Fifty-nine unique copy markers were used to identify thirteen NotI segments which ranged in size from 47 kb to 400 kb. The sum of the NotI segments was 1.78 Mb which indicated that most, if not all, of the chromosome was accounted for and that chromosome band 5 of the cloned line WB-1B, used in this study comprised only one chromosome type. The NotI segments were ordered on the map by comparison of hybridization patterns of the markers with partial NotI cleavages of whole chromosomes. Chromosome rearrangements occur readily in Giardia, and in two drug-resistant lines selected for resistance to different drugs, partial conservative duplications of chromosome 5 were observed in addition to the original, full length chromosome 5. Both duplications retained the central region of chromosome 5 but were deleted at different termini resulting in one duplication of 1.5 Mb and the other of 1.3 Mb.(ABSTRACT TRUNCATED AT 250 WORDS)