Orthogonal Field Alternation Gel Electrophoresis Research Articles

Is Leishmania (Viannia) peruviana a Distinct Species? A MLEE/RAPD Evolutionary Genetics Answer

A set of 38 Leishmania stocks from the Andean valleys of Peru was characterized by both Multilocus Enzyme Electrophoresis (MLEE) and Random Amplified Polymorphic DNA (RAPD). Data were analyzed in terms of taxonomy and evolutionary genetics. Synapomorphic MLEE and RAPD characters, clear-cut clustering, and strong agreement between the phylogenies inferred from either MLEE or RAPD supported the view that Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis correspond to two closely related, but distinct monophyletic lines (clades) and can therefore be considered as "discrete typing units" (DTUs). The question whether the L. (V.) peruxviana DTU deserves species status is dependent upon the desirability of it, in terms of epidemiological and medical relevance. A previous Orthogonal Field Alternating Gel Electrophoresis (OFAGE) analysis of the same L. (V.) peruviana isolates was published by Dujardin et al. (1995b). The data from the different markers (i.e. MLEE, RAPD and OFAGE) were compared by population genetics analysis. RAPD and OFAGE provided divergent results, since RAPD showed a strong linkage disequilibrium whereas OFAGE revealed no apparent departure from panmictic expectation. MLEE showed no linkage disequilibrium. Nevertheless, contrary to OFAGE, this is most probably explainable by the limited variability revealed by this marker in L. (V.) peruviana (statistical type II error). RAPD data were consistent with the hypothesis that the present L. (V.) peruviana sample displays a basically clonal population structure with limited or no genetic exchange. Disagreement between RAPD and OFAGE can be explained either by accumulation of chromosomal rearrangements due to amplification/deletion of repeated sequences, or by pseudo-recombinational events.

Characterization of trypanosome isolates from naturally infected horses on a farm in Kenya

Following an outbreak of trypanosomosis in horses on a farm in Kenya, 18 trypanosome isolates were collected from the infected animals over a period of one and a half years and cryopreserved for characterization. The characterization was done on the basis of morphology using Giemsa-stained blood and buffy coat smears, infectivity to mice, recombinant DNA hybridization, and chromosome separation by orthogonal field alternation gel electrophoresis (OFAGE). Morphologically, all the trypanosome isolates were identified as belonging to the subgenus Nannomonas, and a total of 16 out of the 18 isolates grew in mice. Using the recombinant DNA hybridization technique, the isolates were further classified as the ‘savannah’ type of Trypanosoma congolense. Furthermore, chromosome separation by OFAGE, carried out on six clones derived from different isolates, exhibited a profile characteristic of T. congolense, ‘savannah’ type. However, there were differences in the number and positions of the medium-sized and minichromosomes indicating a diversity of serodemes within the isolates. Hence the infecting trypanosomes in this disease outbreak were T. congolense, ‘savannah’ type, and comprised several serodemes or strains.

The Characterization of Cell Death Induced by 1-(3-C-Ethynyl-β-D-ribo-Pentofuranosyl)Cytosine (ECyd) in FM3A Cells

The characterization of cell death induced by 1-(3-C-ethynyl-β-D-ribo-pentofuranosyl)cytosine(ECyd), a potent inhibitor of RNA synthesis, was performed using mouse mammary tumor FM3A cells in vitro. Accompanied with the cell death induced by ECyd (3.0 μM)-treatment, about 100–200 kbp-sized and internucleosomal DNA fragmentation were observed by orthogonal-field-alternation gel electrophoresis (OFAGE) and conventional gel electrophoresis, respectively. Protease inhibitors, carbobenzoxy-L-aspart-1-yl[(2,6-dichlorobenzoyl)oxy]methane (Z-Asp-CH2-DCB), Nα-p-tosyl-L-lysine chloromethyl ketone (TLCK) and N-p-tosyl-L-phenylalanine chloromethyl ketone (TPCK), effectively blocked the cell death, suggesting that the proteases inhibited by Z-Asp-CH2-DCB, TLCK or TPCK were involved in the process of the cell death.

The value of certain chemotaxonomic methods in the identification of food related yeasts

A total of 166 food-related yeast species were selected and used as a basis for a taxonomic study. An extensive survey has been conducted on the cellular long-chain fatty acid composition (LCFA), G+C values, coenzyme Q analyses and orthogonal field alternation gel electrophoresis (OFAGE) of yeasts associated with food in order to obtain rapid and reliable identification of the yeasts. In the above survey, the yeast strains were cultured under standardized conditions, after which the different profiles of each species were examined using the above-mentioned techniques. The chemotaxonomic data were compared with data obtained by means of standard conventional methods using a comparative model. None of the chemotaxonomic techniques proved to be solely adequate in characterizing isolated species. Our data suggest, however, that the coordinate use of all the above techniques provide a reliable approach for differentiating between food yeast species.

Electrophoretic karyotypes ofPhaffia rhodozymastrains

Electrophoretic karyotypes of strains from the astaxanthin-producing yeast Phaffia rhodozyma have been established. Intact chromosomal DNA molecules released from protoplasts were separated by orthogonal field alternation gel electrophoresis (OFAGE) and contour clamped homogeneous electric field (CHEF). Both small and large chromosomal DNA molecules were resolved simultaneously by optimizing the running conditions. Electrophoretic karyotypes among the Phaffia isolates examined differed significantly. Seven to thirteen chromosomal bands, ranging in size from 0.83 Mb to 3.50 Mb, were resolved, giving total genome sizes of about 15.4 to 23.2 Mb. Ribosomal DNA has been assigned to chromosomal bands using a heterologous gene probe.

Rodent malaria parasites: molecular karyotypes characterize species, subspecies and lines.

The molecular karyotypes of the African murine malaria parasites P. berghei (3 strains, 2 lines) P. yoeli (2 strains) P. chabaudi (3 strains, 1 line) and P. vinckei (4 strains) have been studied using orthogonal field alternation gel electrophoresis (OFAGE). The genome of each species was resolved into 9 to 11 distinct chromosomal DNA banas molecules of varying intensities which seem to represent 14 chromosomes ranging in size from 600 kb to 3500 kb. The position of certain chromosomes allowed the identification of a unique karyotype for each of the strains and lines under study. P. yoelii appears by criteria of chromosome size, chromosome numbers and localisation of DNA probes to differ considerably from the other three rodent malaria species. The chromosomal location of 5 DNA probes allowed the identification of corresponding chromosomes in rodent malaria parasites and the differentiation between species and strains. Assignment of the "PMMSA" gene of P. c. chabaudi IP-PC 1 enables the distinction of the four rodent malaria species. The molecular karyotype combined to chromosomal assignment of DNA probes provides a useful tool for a more precise characterization by a genetic definition of malaria parasites.

Halobacterial megaplasmids are negatively supercoiled

Several covalently closed circular halobacterial megaplasmids (up to more than 500 kb) from different strains of Haloferax mediterranei, have been resolved by orthogonal-field alternating gel electrophoresis (OFAGE). These molecules seem to be negatively supercoiled in vivo, as deduced from the effect of intercalating agents affecting their topology and, therefore, their electrophoretic mobility. It has also been demonstrated that the topoisomerase II inhibitor novobiocin affects the native topological state of halobacterial megaplasmids impeding their migration in OFAGE under standard conditions for resolution of large supercoiled molecules.

A small chromosome of Leishmania (Viannia) braziliensis contains multicopy sequences which are complex specific

Orthogonal Field Alternating Gel Electrophoresis (OFAGE) has been used to show a band of approximately 260 kb which is stained intensely with ethidium bromide in Leishmania (V.) braziliensis stock M2903. This small chromosome (sc-2903), as well as a 50 kb and a 200 kb chromosome seen in L. (L.) mexicana and L. (L.) amazonensis, respectively, are stably maintained and linear. When used as a hybridisation probe, sc-2903 showed homology to large chromosomal DNA bands and to a multiplicity of genomic fragments in all braziliensis stocks tested, indicating either different sequences, different copy numbers or both but no hybridisation to mexicana stocks. It is possible that these sequences are present in all members of the braziliensis complex and are not related to LD1 or any other previously published small chromosome sequences. However, at least one clone isolated from a sc-2903 library recognised genomic DNA of stocks belonging to the braziliensis, mexicana and donovani complexes. Our results suggest that the clone carries sequence(s) that are repeated and shared between stocks of different complexes but with a variable genomic distribution.

Recombinant kinetoplast DNA (kDNA) probe for identifying Leishmania tropica

The paper reports on the construction of a kDNA library with DNA isolated from the WHO reference strain of Leishmania tropica IC-305 and subsequent identification and propagation of recombinant plasmids containing L. tropica kDNA sequences. It also shows that the cloned kDNA sequences can be used as genetic markers in restriction endonuclease, Southern blot transfer, and dot blot hybridisation analysis, to identify L. tropica parasites. When the pL 305-I kDNA probe was used in hybridisation experiments with DNAs from various Leishmania reference strains, species and isolates from different host species and from different geographical locations, hybridisation was detected only with L. tropica, thereby suggesting that the insert in recombinant plasmid 305-I was species-specific. The probe is sensitive to the level of 10 3 parasites in dot blot hybridisation. Additionally, orthogonal field alternation gel electrophoresis (OFAGE) and transverse alternating field electrophoresis (TAFE) were used to characterise Leishmania reference strains and Leishmania species. The molecular karyotypes resolved by these techniques showed significant differences in the profiles of chromosomal sized-DNA molecules among species of Leishmania. The DNA karyotypes of the two reference strains of L. tropica (IC-305 and NLB-067), while similar, were nevertheless distinct.

NAM9 Nuclear Suppressor of Mitochondrial Ochre Mutations in Saccharomyces cerevisiae Codes for a Protein Homologous to S4 Ribosomal Proteins from Chloroplasts, Bacteria, and Eucaryotes

We report the genetic characterization, molecular cloning, and sequencing of a novel nuclear suppressor, the NAM9 gene from Saccharomyces cerevisiae, which acts on mutations of mitochondrial DNA. The strain NAM9-1 was isolated as a respiration-competent revertant of a mitochondrial mit mutant which carries the V25 ochre mutation in the oxi1 gene. Genetic characterization of the NAM9-1 mutation has shown that it is a nuclear dominant omnipotent suppressor alleviating several mutations in all four mitochondrial genes tested and has suggested its informational, and probably ribosomal, character. The NAM9 gene was cloned by transformation of the recipient oxi1-V25 mutant to respiration competence by using a gene bank from the NAM9-1 rho o strain. Orthogonal-field alternation gel electrophoresis analysis and genetic mapping localized the NAM9 gene on the right arm of chromosome XIV. Sequence analysis of the NAM9 gene showed that it encodes a basic protein of 485 amino acids with a presequence that could target the protein to the mitochondrial matrix. The N-terminal sequence of 200 amino acids of the deduced NAM9 product strongly resembles the S4 ribosomal proteins from chloroplasts and bacteria. Significant although less extensive similarity was found with ribosomal cytoplasmic proteins from lower eucaryotes, including S. cerevisiae. Chromosomal inactivation of the NAM9+ gene is not lethal to the cell but leads to respiration deficiency and loss of mitochondrial DNA integrity. We conclude that the NAM9 gene product is a mitochondrial ribosomal counterpart of S4 ribosomal proteins found in other systems and that the suppressor acts through decreasing the fidelity of translation.

NAM9 nuclear suppressor of mitochondrial ochre mutations in Saccharomyces cerevisiae codes for a protein homologous to S4 ribosomal proteins from chloroplasts, bacteria, and eucaryotes.

We report the genetic characterization, molecular cloning, and sequencing of a novel nuclear suppressor, the NAM9 gene from Saccharomyces cerevisiae, which acts on mutations of mitochondrial DNA. The strain NAM9-1 was isolated as a respiration-competent revertant of a mitochondrial mit mutant which carries the V25 ochre mutation in the oxi1 gene. Genetic characterization of the NAM9-1 mutation has shown that it is a nuclear dominant omnipotent suppressor alleviating several mutations in all four mitochondrial genes tested and has suggested its informational, and probably ribosomal, character. The NAM9 gene was cloned by transformation of the recipient oxi1-V25 mutant to respiration competence by using a gene bank from the NAM9-1 rho o strain. Orthogonal-field alternation gel electrophoresis analysis and genetic mapping localized the NAM9 gene on the right arm of chromosome XIV. Sequence analysis of the NAM9 gene showed that it encodes a basic protein of 485 amino acids with a presequence that could target the protein to the mitochondrial matrix. The N-terminal sequence of 200 amino acids of the deduced NAM9 product strongly resembles the S4 ribosomal proteins from chloroplasts and bacteria. Significant although less extensive similarity was found with ribosomal cytoplasmic proteins from lower eucaryotes, including S. cerevisiae. Chromosomal inactivation of the NAM9+ gene is not lethal to the cell but leads to respiration deficiency and loss of mitochondrial DNA integrity. We conclude that the NAM9 gene product is a mitochondrial ribosomal counterpart of S4 ribosomal proteins found in other systems and that the suppressor acts through decreasing the fidelity of translation.

Cloning and disruption of the LEU2 gene of Kluyveromyces marxianus CBS 6556

The LEU2 gene, coding for beta-isopropylmalate dehydrogenase, of the yeast Kluyveromyces marxianus was isolated and sequenced. An open reading frame, coding for a protein with a molecular weight of 38 kDa was found. Comparison of the deduced amino acid sequence of the LEU2 gene with the corresponding enzymes of three other yeasts and two thermophilic bacteria, revealed extensive sequence similarities. The cloned gene could complement a leuB mutation of Escherichia coli and a leu2 mutation of Saccharomyces cerevisiae. Using orthogonal field alternation gel electrophoresis, the genomic copy of the gene was found to be located at chromosome VI or VII. Analysis of the 5'-untranslated region indicated the presence of a putative binding site for the LEU3 protein, which is involved in the leucine-specific regulation of transcription. We show that the cloned gene can be used for the construction of a non-reverting K. marxianus leu2 mutant.

Virulence determinants of Escherichia coli O6 extraintestinal isolates analysed by Southern hybridizations and DNA long range mapping techniques

A total of 16 Escherichia coli O6 strains isolated from cases of extraintestinal infections were analysed for the genetic presence and phenotypic expression of fimbrial adhesins (P, S/FIC, type I), aerobactin and hemolysin. In addition restriction fragment length polymorphisms (RFLPs) of Xbal-cleaved genomic DNA of seven selected strains, separated by orthogonal field alternation gel electrophoresis (OFAGE) were determined and virulence-associated DNA probes were used for Southern hybridization studies of the Xbal-cleaved genomic DNAs. The virulence characteristics and hybridization patterns obtained differed between the various isolates. In three isolates hemolysin genes and P fimbrial determinants were located on the same Xbal fragments. Furthermore, multiple copies of FIC determinants ( foc) could be detected in two strains. Our data show that the new technique of pulse field electrophoresis together with Southern hybridization represents a powerful tool for the genetic analysis of pathogenic bacteria.

Theoretical studies of DNA during orthogonal field alternating gel electrophoresis

We perform numerical simulations on a model of DNA molecules during gel electrophoresis in which the effect of periodically changing the applied field by 90° is examined. A random gel is used in this simulation. We find a scaling relationship between mobility and the ratio of the chain length to pulse time for 100 and 200 link chains. Also presented are results for the orientation, with respect to the new field direction, of chains being subjected to periodically varying orthogonal fields. We find no overshoot in this orientation. Results supporting the existence of persistence in the orientation of a chain over several field changes is presented for 400 link chains.

Genome analysis of Legionella ssp. by orthogonal field alternation gel electrophoresis (OFAGE)

Various Legionella isolates from different sources and origins were analysed by orthogonal field alternation gel electrophoresis of NotI cleaved genomic DNA. The genome of L. pneumophila Philadelphia I, the original isolate of the epidemics in 1976, exhibits only five NotI fragments. Two virulent derivatives, derived from L. pneumophila Philadelphia I, which were obtained by prolonged passage on artificial culture media, did not differ from their isogenic virulent strain according the NotI fragment pattern. By summing the lengths of the NotI fragments, the genome size of L. pneumophila Philadelphia I was calculated as approximately 3.9 Mb. Environmental L. pneumophila strains exhibited different NotI patterns, as did Legionella Strains not belonging to the species pneumophila. The usefulness of DNA long range mapping of Legionella ssp. with NotI for epidemiology and evaluation of their evolutionary relationships is discussed.

Giardia sp.: Comparison of electrophoretic karyotypes

Species in the genus Giardia have been named on the basis of host specificity, cell dimensions, and median body morphology. Despite these criteria, the species taxonomy of Giardia is still in question. To investigate Giardia taxonomy on a molecular level, Giardia chromosomal DNA was analyzed by orthogonal-field-alternation gel electrophoresis (OFAGE) and transverse alternating field electrophoresis (TAFE). Chromosomal DNA of G. duodenalis isolates (human, muskrat, sheep, dog, beaver), G. muris (mouse), and G. ardeae (great blue heron) were subjected to OFAGE and TAFE analyses. Comparable DNA patterns were obtained by both electrophoretic methods, but OFAGE required 8 days while TAFE required only 3 days. DNA patterns among all G. duodenalis isolates, although quite similar to each other, were distinctly different from those of G. muris and G. ardeae; G. muris and G. ardeae DNA patterns were distinctly different from each other. A G. duodenalis (Portland 1) total DNA probe hybridized to the DNA of all G. duodenalis isolates on Southern blots, but not detectably to G. muris and G. ardeae DNA. Similarly, G. muris and G. ardeae total DNA probes only hybridized detectably to their respective DNA. One probe that appears to hybridize to the DNA of all G. duodenalis and to G. ardeae DNA rather than G. muris DNA has been developed. Another probe that hybridizes only to G. muris and G. ardeae DNA has been developed. These data suggest that the differentiation of Giardia isolated from host and environmental samples may eventually be accomplished by DNA probes. Additionally, these techniques perhaps combined with other criteria may lead to the establishment of a sound taxonomic scheme for this genus.

Observation of single DNA molecules during pulsed-field gel electrophoresis by fluorescence microscopy

The dynamics of single DNA molecules undergoing steady-state and pulsed-field gel electrophoresis have been studied using T2 DNA molecules labeled with acridine orange and visualized with a fluorescence microscope. It was observed that DNA molecules moving through the gel display an extension-contraction motion, and they tend to bunch up in their leading ends. Furthermore, the molecules often remain hooked around obstacles assuming U-shape conformations and then slip off, with the longer arm driving the chain. In field-inversion gel electrophoresis molecules of intermediate size show a substantially reduced mobility compared to both small- and large-size molecules. In orthogonal field alternating gel electrophoresis (OFAGE) the formation of kinks is promoted when time is allowed between the application of the two orthogonal fields so that the molecule attains a partially relaxed configuration. The formation of kinks provides a significant retardation of the reorientation of the molecules and appears to play an important role in the fractionation attained with OFAGE.

Increased resolution of large DNA fragments by a two dimensional pulse field gel electrophoresis

An electrophoretic method for separating well-defined large DNA fragments from higher and lower molecular weight molecules is described. It combines in a first dimension either a contour-clamped homogeneous electric field or an orthogonal field alternation gel electrophoresis technique followed by a perpendicular field inversion gel electrophoresis (FIGE) in a second dimension. A complex migration curve after the FIGE run is obtained depending on the applied pulse time, the forward/reverse ratio being kept constant at 3. However, a part of the curve appears as a straight line where the migration is inversely proportional to the molecular weight of the DNA fragments. In this zone, DNA molecules are particularly well separated from other fragments. When the forward pulse time increases, this part is displaced toward the higher molecular weights. Moreover a simple relationship between the middle part of the straight line and forward pulse time has been established.

An Electrophoretic Karyotype Comparison of the Yeast Genera Dipodascopsis Batra et Millner, Lipomyces Lodder et Kreger-van Rij, Myxozyma van der Walt et von Arx

The chromosomal DNA banding patterns of twenty-nine strains representing the family Lipomycetaceae and the associated anamorph genus Myxozyma, were determined by orthogonal-field-alternation gel electrophoresis (OFAGE). In order to evaluate this genomic character, the results obtained were compared with carbon source utilization and coenzyme Q systems. Species within a genus produced the same number of chromosomal bands but not necessarily the same chromosome sizes, except for members of the anamorph genus Myxozyma, which produced different numbers of DNA bands. On the basis of the chromosomal DNA band number, it was possible to distinguish between the genera Dipodascopsis (one DNA band), Lipomyces and Waltomyces (two DNA bands), Zygozyma (three DNA bands) and Myxozyma (five DNA bands and more). It was however impossible to differentiate between the representative species of Dipodascopsis, Lipomyces or Myxozyma, on this basis. We found that the more complex hyphal species (characterized by the utilization of a large amount of carbon sources and the presence of a CoQ9 system) produced only one heavy DNA band, while the less complex budding forms (characterized by the utilization of a small amount of carbon sources and the presence of a CoQ8 system) produced five or more smaller chromosomal bands. No teleomorph/anamorph relations between the genus Myxozyma and the genera Dipodascopsis, Lipomyces and Waltomyces were found on the basis of OFAGE, CoQ system or physiological characteristics.

Imaging of kinked configurations of DNA molecules undergoing orthogonal field alternating gel electrophoresis by fluorescence microscopy

The dynamics of individual DNA molecules undergoing orthogonal field alternating gel electrophoresis (OFAGE) have been studied by use of T2 DNA molecules labeled with a dye and visualized with a fluorescence microscope. The mechanism of reorientation used by a molecule to align itself in the direction of the new orthogonal field depends on the degree of extension of the chain immediately before the application of this field. The formation of kinks is promoted when time is allowed between the application of the two orthogonal fields so that the molecule attains a partially relaxed configuration. In this case, the chain appears bunched up in domains moving along the contour of the molecule. These regions are found to be the locations where the kinks are formed upon application of the second field perpendicular to the chain. The formation of kinks provides a significant retardation of the reorientation of the molecules, relative to molecules that do not form kinks, and appears to play an important role in the fractionation attained with OFAGE. A classification of various reorientation mechanisms observed in molecules that form kinks is presented.