Diagnostic Restriction Sites Research Articles

Using indCAPS to Detect CRISPR/Cas9 Induced Mutations.

Cleaved amplified polymorphic sequences (CAPS) assays are useful tools for detecting small mutations such as single nucleotide polymorphisms (SNPs) or insertion/deletions (indels) present in an amplified DNA fragment. A mutation that disrupts or creates a restriction site will prevent cleavage by a restriction enzyme, allowing discrimination of wild-type and mutant alleles. In cases where no convenient restriction site is present, a derived Cleaved Amplified Polymorphic Sequence (dCAPS) assay can be used, where mismatches in the primer are used to create a diagnostic restriction site. No special design constraints are present for a CAPS assay, but cases where CAPS assays can be used are infrequent. A dCAPS assay can be burdensome to design by hand, but it is more broadly applicable. This protocol will describe the use of the indCAPS tool for the design of CAPS and dCAPS primers. The indCAPS tool was designed to be compatible with indel alleles, which prior tools struggled with but have increased importance since the rise of CRISPR/Cas9 mutagenesis methods.

Rapid mutagenesis-based analysis of phosphorylation sites in mitogen-activated protein kinase substrates.

In eukaryotes, mitogen-activated protein kinases (MAPKs) are one of the best studied pathways for posttranslational modification-mediated regulation of protein functions. Here, we describe a rapid in vitro method to screen potential protein phosphorylation sites targeted by MAPKs. The method is based on PCR-mediated mutagenesis together with a type IIs restriction digest. Screening for the successfully mutated clones is further facilitated through introduction of a second diagnostic restriction site. Besides time-saving, this reduces the cost for sequencing confirmation of the positive clones, which are used for subsequent recombinant protein production and kinase assay validation.

British Society for Gene and Cell Therapy (BSGCT) Conference AbstractsRoyal HollowayUniversity of London17–19 April, 2013

British Society for Gene and Cell Therapy (BSGCT) Conference AbstractsRoyal HollowayUniversity of London17–19 April, 2013

Species identification method for Scombrops boops and Scombrops gilberti based on polymerase chain reaction–restriction fragment length polymorphism analysis of mitochondrial DNA

Gnomefish Scombrops boops and Scombrops gilberti are commercially important fishes in Japan, but these species are often confused in the markets because of their morphological similarity. To identify these two species, we performed nucleotide sequencing and restriction fragment length polymorphism (RFLP) analysis on 16S ribosomal RNA (rRNA) gene and the control region in mitochondrial DNA. Five and 12 nucleotide substitutions were observed between species in the 777-bp 16S rRNA gene and 471-bp control region, respectively. Diagnostic restriction sites for discriminating between S. boops and S. gilberti were found in the 16S rRNA gene, but not in the control region. Polymerase chain reaction (PCR)-RFLP analysis using two enzymes, EcoNI and Mval, clearly discriminated between S. boops and S. gilberti identified by meristic characters. The PCR-RFLP analysis identified most of the 168 Scombrops young caught in the coastal waters of the Izu and Miura peninsulas as S. boops, suggesting that S. gilberti juveniles are rare in this area.

Interspecific phylogenetic analysis enhances intraspecific phylogeographical inference: a case study in Pinus lambertiana

Pinus lambertiana (sugar pine) is an economically and ecologically important conifer with a 1600-km latitudinal range extending from Oregon, USA, to northern Baja California, Mexico. Like all North American white pines (subsect. Strobus), sugar pine is highly susceptible to white pine blister rust, a disease caused by the fungus Cronartium ribicola. We conducted a chloroplast DNA (cpDNA) survey of Pinus subsect. Strobus with comprehensive geographical sampling of P. lambertiana. Sequence analysis of 12 sugar pine individuals revealed strong geographical differentiation for two chloroplast haplotypes. A diagnostic restriction site survey of an additional 72 individuals demarcated a narrow 150-km contact zone in northeastern California. In the contact zone, maternal (megagametophtye) and paternal (embryo) haplotypes were identified in 31 single seeds, demonstrating bidirectional pollen flow extending beyond the range of maternal haplotypes. The frequencies of the Cr1 allele for white pine blister rust major gene resistance, previously determined for 41 seed zones, differ significantly among seed zones that are fixed for the alternate haplotypes, or contain a mixture of both haplotypes. Interspecific phylogenetic analysis reveals that the northern sugar pine haplotype belongs to a clade that includes Pinus albicaulis (whitebark pine) and all of the East Asian white pines. Furthermore, there is little cpDNA divergence between northern sugar pine and whitebark pine (dS = 0.00058). These results are consistent with a Pleistocene migration of whitebark pine into North America and subsequent chloroplast introgression from whitebark pine to sugar pine. This study demonstrates the importance of placing phylogeographical results in a broader phylogenetic context.

Documentation of Hybridization Between Californian Cypresses: Cupressus macnabiana &times sargentii

Abstract It has been suggested in the literature that limited hybridization occurs between Cupressus macnabiana and C. sargentii where the species occur in sympatry. This study confirmed the hybrid origin of specimens from a sympatric population using an objective analysis of morphological and DNA evidence. Fifty–eight individuals from three populations (two pure stands and one mixed population) were sampled. Variation in diagnostic restriction sites within ITS (nrDNA), matK (cpDNA), and NEEDLY intron two (nDNA) were used in combination with 20 quantitative morphological characters to detect and characterize putative hybrids. ITS and NEEDLY were uninformative with respect to hybrid detection, but matK demonstrated species–specific polymorphism. Anomalous combinations of plastid type, Discriminant Function identification, and position in a pictorialized scatter diagram were used to identify putative hybrids. Intermediacy of the putative hybrids was demonstrated statistically (p = 0.005) with 13 out of the ...

Specific detection of Lettuce mosaic virus isolates belonging to the “Most” type

Lettuce mosaic virus (LMV)-Most isolates can infect and are seed-borne in cultivars containing the mo1 gene. A reverse transcription and polymerase chain reaction (RT-PCR)-based test was developed for the specific detection of LMV-Most isolates. Based on the complete genome sequences of three LMV isolates belonging respectively to the Most type, the Common type and neither of these two types, three different assays were compared: (i) presence of a diagnostic restriction site in the region of the genome encoding the variable N-terminus of the capsid protein, in the 3′ end of the genome, (ii) RT-PCR using primers designed to amplify a cDNA corresponding to a portion of the P1 coding region, in the 5′ end of the genome and (iii) RT-PCR using primers designed to amplify a central region of the genome. The assays were performed against a collection of 21 isolates from different geographical origins and representing the molecular variability of LMV. RT-PCR of the central region of the genome was preferred because its results are expected to be less affected by natural recombination between LMV isolates, and it allows sensitive detection of LMV-Most in situations of single as well as mixed contamination.

PCR-RFLP analysis of mitochondrial DNA ND5/6 region among 3 subspecies of common carp (Cyprinus carpio L.) and its application to genetic discrimination of subspecies

Mitochondrial DNA ND5/6 region was studied by PCR-RFLP analysis among ten representative strains belonging to three subspecies (Cyprinus carpio carpio, Cyprinus carpio haematopterus and Cyprinus carpio rubrofuscus) of common carp (Cyprinus carpio L.). A total of 2.4 kb fragment was amplified and subjected to restriction endonuclease analysis with nine restriction endonucleases subsequently. The results indicated that each subspecies owned one hyplotype and four restriction enzymes (Dde I, HaeIII, Taq I and Mbo I) produced diagnostic restriction sites which could be used for discriminating the three subspecies and as molecular genetic markers for assistant selective breeding of common carp.

PCR–RFLP analysis of the mitochondrial ND-3/4 and ND-5/6 gene polymorphisms in the European and East Asian subspecies of common carp ( Cyprinus carpio L.)

Polymorphism within the mitochondrial NADH-3,4 dehydrogenase ( ND-3/4) and NADH-5,6 dehydrogenase ( ND-5/6) gene regions was studied by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis among common carp populations belonging to the European (two farmed strains and three wild populations) and East Asian (Amur wild carp, Vietnamese wild carp and Japanese Koi carp) subspecies, Cyprinus carpio carpio and C. c. haematopterus, respectively. Polymorphism was detected using eight and six restriction enzymes, respectively, and a total of seven composite haplotypes were identified. Both distance-based and maximum likelihood phylogenetic inference methods clustered the haplotypes into four distinct groups—the European (two haplotypes), Amur (two haplotypes), Vietnamese (two haplotypes) and Koi (one haplotype), and their distributions strictly follow the geographic origin of populations. The populations are clustered into two highly divergent groups (average net nucleotide divergence, 2.4%), the European and the East Asian populations, suggesting an ancient separation. Six enzymes ( HinfI, AluI, HpaII and TaqI at ND-3/4; Eco47I and BsuRI at ND-5/6) yielded diagnostic restriction sites for discriminating between the European and East Asian maternal lineages that can be applied to monitoring of genetic purity of the European farmed strains.

The T911C (F304S) substitution in the human ALG6 gene is a common polymorphism and not a causal mutation of CDG-Ic.

A T911C (F304S) substitution in the ALG6 gene involved in congenital disorder of glycosylation type Ic (OMIM 603147) has been described. However, whether the F304S substitution is a common polymorphism or a causal mutation remains unclear. We screened for the T911C substitution in the ALG6 gene in 54 unrelated healthy French individuals. We developed a restriction fragment length polymorphism assay with a mutagenic primer introducing a diagnostic DdeI restriction site. We found 23 heterozygotes (42.6%) and 3 homozygous individuals (5.5%). This result indicates that T911C is a common polymorphism with an allele frequency of 27% in a French population and not a causal mutation of congenital disorder of glycosylation type Ic.

Mitochondrial DNA haplogroups in Amerindian populations from the Gran Chaco.

Mitochondrial DNA from 141 individuals was typed for diagnostic restriction sites and the 9-bp region V deletion to examine the distribution of the founding mtDNA lineage haplotypes in three Amerindian populations (Mataco, Toba, and Pilagá) who currently inhabit the Argentinian part of the Gran Chaco. All four lineages were identified in the three tribes and four population samples studied. Disregarding ethnic or geographic origin, haplogroups B and D exhibit high incidence among the Gran Chaco inhabitants, whereas haplogroups A and C are present in a lower frequency. Three individuals possess none of the characteristic markers and, therefore, could not be assigned to one of those lineages. A neighbor-joining representation of F(ST) distances reflects the current geographic location of the populations, and this also corresponds to their historic distribution. After separating South America into four major regions (Tropical Forest, Andes, Gran Chaco, and Patagonia-Tierra del Fuego), the Gran Chaco populations present the highest average intragroup variability (Hs = 0.64) as well as the lowest intergroup diversity (G(')(ST) = 0.06). These findings suggest high levels of gene flow among the Chaco tribes, as well as with neighbor populations from outside the region.

Characterization of the screwworm flies Cochliomyia hominivorax and Cochliomyia macellaria by PCR-RFLP of mitochondrial DNA.

The primary screwworm fly Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae) is one of the most important insect pests of livestock in neotropical regions, whereas Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae), the secondary screwworm, is of medical and sanitary importance because of its role in the dissemination of pathogens. These two species share morphological similarities and both may occur in the same myiasis, but in different developmental stages. In this work, the usefulness of PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism) of mitochondrial DNA (mtDNA) for the unambiguous identification of C. hominivorax and C. macellaria was investigated. Two specific regions of mtDNA were amplified: 870bp from Cytochrome oxidase subunit I and 2100bp from the A+T rich/12S region from C. hominivorax and C. macellaria specimens from different areas of Brazil. Reliable species-specific PCR-RFLP results were obtained for the CO I region and the A+T rich/12S region using the restriction enzymes Dra I and Ssp I. These results confirm the conservation of CO I diagnostic restriction sites previously reported and demonstrate the usefulness of the control region sequences as an efficient marker for PCR-RFLP identification of Brazilian screwworm flies. The occurrences of intraspecific polymorphic patterns are discussed based on frequencies and potential conflicts for species identification. PCR-RFLP provides a potentially useful method for identifying samples from the areas where these species are monitored.

The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor

The dihydroxyacetone kinase (DhaK) of Escherichia coli consists of three soluble protein subunits. DhaK (YcgT; 39.5 kDa) and DhaL (YcgS; 22.6 kDa) are similar to the N- and C-terminal halves of the ATP-dependent DhaK ubiquitous in bacteria, animals and plants. The homodimeric DhaM (YcgC; 51.6 kDa) consists of three domains. The N-terminal dimerization domain has the same fold as the IIA domain (PDB code 1PDO) of the mannose transporter of the bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS). The middle domain is similar to HPr and the C-terminus is similar to the N-terminal domain of enzyme I (EI) of the PTS. DhaM is phosphorylated three times by phosphoenolpyruvate in an EI- and HPr-dependent reaction. DhaK and DhaL are not phosphorylated. The IIA domain of DhaM, instead of ATP, is the phosphoryl donor to dihydroxyacetone (Dha). Unlike the carbohydrate-specific transporters of the PTS, DhaK, DhaL and DhaM have no transport activity.

The mitochondrial genome of the primary screwworm fly Cochliomyia hominivorax (Diptera: Calliphoridae).

The complete sequence of the mitochondrial genome of the screwworm Cochliomyia hominivorax was determined. This genome is 16,022 bp in size and corresponds to a typical Brachycera mtDNA. A Serine start codon for COI and incomplete termination codons for COII, NADH 5 and NADH 4 genes were described. The nucleotide composition of C. hominivorax mtDNA is 77% AT-rich, reflected in the predominance of AT-rich codons in protein-coding genes. Non-optimal codon usage was commonly observed in C. hominivorax mitochondrial genes. Phylogenetic analysis distributed the Acalypterate species as a monophyletic group and assembled the C. hominivorax (Calyptratae) and the Acalyptratae in a typical Brachycera cluster. The identification of diagnostic restriction sites on the sequenced mitochondrial genome and the correlation with previous RFLP analysis are discussed.

A New Molecular Phylogenetic Hypothesis for the Evolution of Freshwater Eels

Phylogenetic analysis of a segment of the mitochondrial 16S rDNA of eight Anguilla species from the Indo–Pacific region and from the North Atlantic revealed that the genus Anguilla appears to be surprisingly young, based upon the small observed maximum genetic distance of 4.8% and the high degree of morphological similarity among the species. The placement of A. marmorata as the most ancestral lineage suggests that the genus is likely to have originated in the Indo–Malayian region, from which it quickly spread. Two Pacific species, A. obscura and A. japonica, branched next. A. japonica was placed as sister group to all remaining species, which formed three clades: the first comprising A. australis, the second A. reinhardti and A. mossambica, and the third A. anguilla and A. rostrata. All analyzed specimens of A. rostrata originating from southern New Jersey to Nova Scotia had identical mitotypes, while five mitochondrial genotypes were found in Europe differing by zero to two substitutions. The two Atlantic eel species are very closely related; all surveyed specimens of A. anguilla differ by three to five substitutions from their American allies, corroborating the existence of two distinct biological species. This was also confirmed by restriction analysis of a 350-bp segment of the cytochrome b, in which American specimens were distinct in sharing a single diagnostic restriction site of HinfI. Our results suggest little to no gene flow between the two nominal Atlantic eel species.

Haemochromatosis: Automated Detection of the Two Point Mutations in the HFE Gene: Cys282Tyr and His63Asp

Hereditary haemochromatosis (HH) is one of the most common inherited diseases among Caucasians. Two mutations in the HFE gene have been implicated in HH: 80 to 90% of the patients with HH are homozygous for the point mutation CYS282Tyr, while the majority of the remaining patients displays either a compound heterozygosity for the mutation CYS282Tyr and the point mutation HIS63Asp, or are homozygous for HIS63Asp. Though the disease can be treated easily, symptoms are non-specific, and onset and severity are influenced by environmental factors, and therefore the disease can remain undetected until decades of iron overload lead to irreversible damage in a variety of organs, which may result in their failure. In order to detect patients with HH, simple and cost-effective tests are needed. We have developed a rapid, automated, PCR-based test which makes use of a diagnostic restriction site in each of two amplified fragments. The test employs off-the-shelf chemistry and uses the automated detection process of an immunoassay analyzer that is available in many clinical laboratories, thus avoiding an additional investment in a more specialized PCR analyzer. Because of its low costs and easy handling, the assay is particularly suited for the routine clinical laboratories.

Turkish honeybees: genetic variation and evidence for a fourth lineage of Apis mellifera mtDNA.

The mtDNA of bees from 84 colonies of Turkish honeybees (Apis mellifera) was surveyed for variation at four diagnostic restriction sites and the sequence of a noncoding intergenic region. These colonies came from 16 locations, ranging from European Turkey and the western Mediterranean coast to the Caucasus Mountains along the Georgian border, the eastern Lake Van region, and the extreme south. Combined restriction site and sequence data revealed four haplotypes. Three haplotypes belonged to the eastern Mediterranean mtDNA lineage. The fourth haplotype, which had a novel restriction site pattern and noncoding sequence, was found in samples from the extreme south, near the Syrian border. We found two different noncoding sequences among the eastern Mediterranean haplotypes. The "Caucasian" sequence matches that described from A. m. caucasica, and the "Anatolian" sequence matches that of A. m. carnica. The frequency of the "Caucasian" sequence was highest (98-100%) in sites near the Georgian border and decreased steeply to the south and west. Elsewhere the Anatolian sequence was found. In European Turkey (Thrace) a restriction site polymorphism previously reported from A. m. carnica in Austria and the Balkans was present at high frequency. A novel mtDNA haplotype with a unique restriction site pattern and noncoding sequence was found among bees from Hatay, in the extreme south near the Syrian border. This haplotype differed from the three previously known lineages of honeybee mtDNA--African, western European, and eastern Mediterranean-and may represent a fourth mitochondrial lineage.

Mitochondrial Gene Markers for the Hybridizing ToadsBufo microscaphusandBufo woodhousiiin Arizona

Three restriction site markers from the mitochondrial genome are described for the toads Bufo microscaphus and B. woodhousii. Markers were resolved from DNA sequence data representing segments of cytochrome b (cytb) and 16S ribosomal genes. Two diagnostic restriction sites (BsmA I; SfaN I) characterize B. microscaphus for cytb, whereas a third restriction site (Tsp509 I) distinguishes B. woodhousii for 16S. Restriction digests of PCR-amplified cytb and 16S segments provide an economical, nondestructive assay with which to identify mtDNA haplotypes for these toads and their hybrids. The mtDNA markers complement diagnostic allozyme and call characters, offering an additional approach to examine hybridization between the two species in central Arizona.

Development and usefulness of new polymerase chain reaction-based tests for detection of different alleles at codons 136 and 171 of the ovine prion protein gene

Abstract Objective To develop new and improved tests to detect alleles at codons 136 and 171 of the ovine prion protein locus and to evaluate the frequency of these alleles. Animals 159 Suffolk sheep belonging to 3 flocks. Procedure Polymerase chain reaction (PCR) analysis that contained diagnostic restriction site variation for each allele were developed for the relevant gene regions. Alleles were determined by analyzing DNA isolated from buccal swab specimens or blood samples. Results At codon 136, frequencies of the alanine and valine alleles were found to be 97 and 3%, respectively. At codon 171, frequencies of the glutamine, arginine, and histidine alleles were found to be 57, 41, and 2%, respectively. Conclusions Little variation was detected in codon 136, whereas noteworthy variation was found in codon 171; > 40% of the alleles at this locus coded for glutamine. Because the glutamine allele at codon 171 confers susceptibility to scrapie, reduction of its frequency is of importance to management of sheep flocks. Clinical Relevance Genotyping of sheep, using the tests reported here, should facilitate selective breeding programs designed to decrease the risk of scrapie. (Am J Vet Res 1999;60:884–887)

An evaluation of introgression of Atlantic coast striped bass mitochondrial DNA in a Gulf of Mexico population using formalin-preserved museum collections.

Striped bass Morone saxatilis populations in drainages along the Gulf of Mexico coast (Gulf) were depleted in the 1950s and 1960s, probably because of anthropogenic influences. It is believed that only the Apalachicola-Chattahoochee-Flint (A-C-F) river system continually supported a naturally reproducing population of Gulf lineage. Striped bass juveniles of Atlantic coast (Atlantic) ancestry were introduced to restore population abundances in the A-C-F from the late 1960s to the mid 1970s and in many other Gulf rivers from the 1960s to the present. We previously identified mtDNA polymorphisms that were unique to approximately 60% of striped bass from the A-C-F and which confirmed the continued successful natural reproduction of striped bass of Gulf maternal ancestry within the system. However, the genetic relatedness of the extant A-C-F population to 'pure' Gulf striped bass was not addressed. In this study, we determined the frequency of a diagnostic mtDNA XbaI polymorphism in samples of 'pure' Gulf striped bass that were collected from the A-C-F prior to the introduction of Atlantic fish, that were obtained from museum collections, and that were originally preserved in formalin. PCR primers were developed that allowed for amplification of a 191-bp mtDNA fragment that contained the diagnostic XbaI restriction site. Using RFLP and direct sequence analyses of the PCR amplicons, we found no significant differences in mtDNA XbaI genotype frequencies between the archived samples and extant A-C-F samples collected over a 15-year period. This indicates that significant maternally mediated introgression of Atlantic mtDNA genomes into the A-C-F gene pool has not occurred. Additionally, we found no evidence of the unique Gulf mtDNA genotype in striped bass from extant populations in Texas, Louisiana and the Mississippi River. These results highlight the importance of the A-C-F as a repository of striped bass to restore extirpated Gulf populations and the potential use of museum collections in retrospective population studies.