Preimplantation embryo sexing by polymerase chain reaction amplification of the sry gene on single mouse blastomeres

Accurate and rapid sex determination of preimplantation embryos has great potential both in animal breeding and in human pathology. In the past, sex determination has been accomplished by cytogenetic or immunologic means and by polymerase chain reaction amplification of Y-chromosome-specific repetitive sequences. More recently, amplification of the Y-specific single-copy ZFY gene has been used in humans for sex determination of preimplantation embryos. The experiments reported here indicate that another Y-chromosome-specific single-copy gene, the sex-determining region gene (sry) can be successfully amplified from single mouse blastomeres. Blastocysts positive for sry amplification were reimplanted to foster mothers, and six of six newborns were male. We conclude that sry gene amplification can represent a good marker for embryo sex determination.     

Livestock embryo sexing: A review of current methods, with emphasis on Y-specific DNA probes

Control of the sex ratio of domestic species is potentially of great commercial importance to agriculture. While sexing of spermatozoa would be the most advantageous approach, studies to date suggest that this technology is unlikely to be available in the near future. As an alternative, four methods of sexing embryos have been developed. The use of X-linked enzymes and a serological assay involving H-Y antigen are noninvasive methods which have the advantage of allowing all embryos to be sexed, but these methods are not always accurate. Cytogenetic analysis and the use of Y-specific DNA probes are invasive methods which are limited by the accessibility of embryonic material for biopsy, but they are highly accurate. Each method is reviewed, with an emphasis on the use of Y-linked probes, and each is seen to have both advantages and limitations; the difficulty is in achieving a method that provides both an accurate sexing procedure and an acceptable pregnancy rate after embryo transfer. While no single method currently available fulfills all the criteria for a commercial method of embryo sexing, the potential for the development of an ideal method does exist.     

Sex determination in sheep and goats using bovine Y-chromosome specific primers via polymerase chain reaction: potential for embryo sexing.

A simple and novel method, using polymerase chain reaction (PCR) has been standardized for accurate sex determination in sheep and goats. The assay utilizes a pair of bovine Y-chromosome specific primers and the genomic DNA isolated from blood samples of adult male and female sheep and goats. The primers recognize and amplify the Y-chromosome specific sequences in male goats and sheep. The assay is accurate, reliable and rapid.     

Polymerase chain reaction: a Markov process approach

A probabilistic approach to the kinetics of the polymerase chain reaction (PCR) is developed. The approach treats the primer extension step of PCR as a microscopic Markov process in which the molecules of deoxy-nucleoside triphosphate (dNTP) are bound to the 3' end of the primer strand one at a time. The binding probability rates are prescribed by combinatorial rules in accord with the microscopic chemical kinetics. As an example, a simple model based on this approach is proposed and analysed, and an exact solution for the probability distribution of lengths of synthesized DNA strands is found by analytical means. Using this solution, it is demonstrated that the model is able to reproduce the main features of PCR, such as extreme sensitivity to the variation of control parameters and the existence of an amplification plateau. A multidimensional optimization technique is used to find numerically the optimum values of control parameters which maximize the yield of the target sequence for a given PCR run while minimizing the overall run time.     

Markov chain aggregation and its applications to combinatorial reaction networks

We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk.     

Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies

In the biological sciences there have been technological advances that catapult the discipline into golden ages of discovery. For example, the field of microbiology was transformed with the advent of Anton van Leeuwenhoek''s microscope, which allowed scientists to visualize prokaryotes for the first time. The development of the polymerase chain reaction (PCR) is one of those innovations that changed the course of molecular science with its impact spanning countless subdisciplines in biology. The theoretical process was outlined by Keppe and coworkers in 1971; however, it was another 14 years until the complete PCR procedure was described and experimentally applied by Kary Mullis while at Cetus Corporation in 1985. Automation and refinement of this technique progressed with the introduction of a thermal stable DNA polymerase from the bacterium Thermus aquaticus, consequently the name Taq DNA polymerase.PCR is a powerful amplification technique that can generate an ample supply of a specific segment of DNA (i.e., an amplicon) from only a small amount of starting material (i.e., DNA template or target sequence). While straightforward and generally trouble-free, there are pitfalls that complicate the reaction producing spurious results. When PCR fails it can lead to many non-specific DNA products of varying sizes that appear as a ladder or smear of bands on agarose gels. Sometimes no products form at all. Another potential problem occurs when mutations are unintentionally introduced in the amplicons, resulting in a heterogeneous population of PCR products. PCR failures can become frustrating unless patience and careful troubleshooting are employed to sort out and solve the problem(s). This protocol outlines the basic principles of PCR, provides a methodology that will result in amplification of most target sequences, and presents strategies for optimizing a reaction. By following this PCR guide, students should be able to: ● Set up reactions and thermal cycling conditions for a conventional PCR experiment ● Understand the function of various reaction components and their overall effect on a PCR experiment ● Design and optimize a PCR experiment for any DNA template ● Troubleshoot failed PCR experiments     

Rapid sexing of preimplantation bovine embryo using consecutive and multiplex polymerase chain reaction (PCR) with biopsied single blastomere.

The objective of this study was to establish a rapid and reliable PCR method for the sexing of 8- to 16-cell stage bovine embryos. The BOV97M and bovine 1.715 satellite DNA sequences were selected for amplification of male- and bovine-specific DNA, respectively. But the unequal number of copies of these two repetitive sequences required some modification of the multiplex PCR method. In consecutive and multiplex PCR, the first 10 PCR cycles were done with male-specific primer followed by an additional 23 cycles with bovine-specific primer. In this PCR method, the appearance of male- and bovine-specific bands was independent of the DNA concentration. This PCR method was applied successfully using groups of 8, 4, 2, and 1 blastomeres dissociated from the embryos, and the sexing efficiency was 100.0, 96.3, 94.3 and 92.1%, respectively. The coincident rate of sex determination between biopsied single blastomere and matched blastocyst was 90.0%. Therefore the developmental potential from 8- to 16-cell stage embryos to the blastocyst stage was not significantly different (P>0.2) for intact embryo (42.3%) than for demi-embryos (53.8%), suggesting that trauma to the demi-embryo caused by single-blastomere aspiration using a bevelled micropipette was very small. In conclusion, we developed a rapid (within 2 hours) and effective PCR method for the sexing of 8- to 16-cell stage bovine embryos using a single blastomere.     

Polymerase chain reaction detect polymorphisms and trait association in soybean

Five sets of synthetic oligonucleotide (20-to 24-mers containing no intenal repeats) primers of known gene sequences [yellow lupin nodule specific (hydroxyl) proline-rich protein, pearl millet alcohol dehydrogenase, Pisum sativum heat shock proteins, Drosophila homeobox, and tRNA] were used to differentiate 73 soybean accessions, including 56 Glycine max (L.) Merr. and 17 G. soja Zucc. & Sieb. The amplified genetic markers revealed polymorphic bands for most genotypes studied. The χ²-analyses of the results showed that several fragments produced with these gene primers were associated non-randomly with resistance to Phytophothora, maturity, seed size, flower colour, seed coat colour, seed hilum colour, growth type, and leaf shape. These markers appear to be valuable for differentiation of G. max and G. soja species and genotypes within these species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Polymerase chain reaction fidelity and denaturing high-performance liquid chromatography

Incorporation of non-complementary nucleotides during polymerase chain reaction can result in ambiguous denaturing high-performance liquid chromatography profiles that reduce both sensitivity and specificity of mutation analysis. The use of proofreading DNA polymerases increases the fidelity of polymerase chain reaction and, consequently, reduces background noise in the chromatograms. This is demonstrated for several BRCA1 and BRCA2 mutations hat had yielded previously chromatograms of poor quality using non-proofreading enzyme for amplification. Interestingly, despite the reduced level of background heteroduplices, the ability of denaturing high-performance liquid chromatography to detect mutant alleles at a frequency <10% in pools of chromosomes did not improve significantly.     

Polymerase chain reaction: replication errors and reliability of gene diagnosis.

The impact of replication errors on the reliability of polymerase chain reaction (PCR) data is studied theoretically. Practical applications of our results to RFLP analysis and oligonucleotide probing confirm that for practical purposes replication errors can be neglected if a large number of starting templates (e.g. 100,000) is being used. For single locus analysis in single cells, however, the probability of false diagnosis due to such errors is of the order of 1 percent.     

Polymerase chain reaction in diagnosis of Borrelia burgdorferi infections and studies on taxonomic classification

Lyme borreliosis caused by the spirochete Borrelia burgdorferi is now the most common vectorborne disease in North America, Europe and Asia. It is a multisystemic infection which may cause skin, neurological, cardiac or rheumatologic disorders. The aims of the present thesis were: (i) to develop a PCR assay for direct detection of B. burgdorferi DNA and to evaluate the diagnostic utility of PCR in clinical specimens from patients with Lyme borreliosis and (ii) to study the taxonomic classification of B. burgdorferi isolates and its implications for epidemiology and clinical presentation. Laboratory diagnosis of Lyme borreliosis by direct demonstration of B. burgdorferi in clinical specimens would compared to current serology allow (i) optimal specificity, (ii) increased sensitivity during the first weeks of infection, when the antibody response is not yet detectable and (iii) discrimination between ongoing and past infection. Due to the extreme paucity of spirochetes in clinical specimens neither in vitro culture nor antigen detection had yielded a sufficient diagnostic sensitivity. Thus the recently introduced highly sensitive PCR methodology could be a solution and was thus studied. Assays for PCR amplification and subsequent identification of B. burgdorferi specific sequences were established and used. For all assays the analytical sensitivity was a few genome copies using purified DNA as template. The efficacy of PCR was initially evaluated using tissue samples from experimentally infected gerbils in order to start with biological samples a priori known to contain B. burgdorferi. B. burgdorferi DNA was detectable in 88% of the specimens. Thus the diagnostic sensitivity of PCR was comparable to and even higher than in vitro culture. PCR was significantly more sensitive than a histological B. burgdorferi specific immunophosphatase-staining method. The utility of the PCR was then tested for identification of B. burgdorferi DNA in skin biopsies from 31 patients with erythema migrans. The sensitivity of PCR was 71%, which was superior to culture and serology. Based on own and otherwise published results there is clear evidence for PCR being the most sensitive and specific test for detection of B. burgdorferi in skin biopsies from patients with both early and late dermatoborreliosis. However, since the clinical diagnosis of dermatoborreliosis in most instances is easy, an invasive procedure as a skin biopsy, will only be justified in patients with an atypical clinical presentation. The most frequent and serious manifestation of disseminated Lyme borreliosis is neuroborreliosis. PCR was applied to 190 patients with untreated and confirmed neuroborreliosis. B. burgdorferi DNA was detectable in 17-21% of CSF samples from patients with neuroborreliosis. In patients with very early neuroborreliosis (< 2 weeks), still being negative for specific intrathecal antibody synthesis, a positive PCR was more frequent than in patients with longer disease duration. PCR can be used as a diagnostic aid in these patients. However, in general the measurement of specific intrathecal antibody production in patients with neuroborreliosis was superior to PCR. In urine samples from patients with Lyme borreliosis the diagnostic sensitivity varied, generally showing a low reproducibility. Urine is thus not regarded as a suitable sample source for B. burgdorferi PCR. The reason may be the variable presence of Taq polymerase inhibitors. Based on a semi-quantitative detection system for amplicons, reflecting the input amount of specific DNA and thus the density of spirochetes in the clinical samples high amounts of DNA were found in skin biopsies whereas especially in urine the amount of DNA was low. When the present study was initiated there was no accepted classification of B. burgdorferi. A heterogeneity among B. burgdorferi strains might have important implications for understanding the epidemiology and different clinical presentations (dermatoborreliosis versus neuroborreliosis) and courses (self-limiting versus chronic disease). Furthermore, strain differences were of importance for selection of suitable antigens for diagnostic assays and for vaccine development. Since then, B. burgdorferi isolates have been studied by phenotypic and genotypic traits and have been shown to be highly heterogeneous. Our first approach was to genotype a panel of human B. burgdorferi isolates by restriction fragment length polymorphism (RFLP) of three genes. Thereafter, sequencing and dideoxy fingerprinting of ospA was applied. By RFLP the strains could be differentiated into two to five groups. The RFLP classification was compared with four different phenotypic and genotypic methods including the rRNA typing. Results obtained with the different methods correlated highly and confirmed the meanwhile accepted taxonomic classification by Baranton et al., According to this the term B. burgdorferi sensu lato comprises three different human pathogenic genospecies B. burgdorferi sensu stricto, B. garinii and B. afzelii. All three genospecies have been isolated among Danish patients with Lyme borreliosis and are thus prevalent in Denmark. Since isolation of B. burgdorferi from patients with Lyme borreliosis is laborious and often unsuccessful molecular typing methods based on PCR are recommended obviating the need for isolation by prior culture. Of special interest was to study a possible association of neuroborreliosis to certain B. burgdorferi genospecies, indicating species depended organotropism. By RFLP all six CSF isolates tested belonged to B. garinii and that 6 out of 7 isolates from patients with acrodermatitis chronica atrophicans belonged to B. afzelii. Due to the low culture yield of B. burgdorferi from CSF, the association of B. garinii and neuroborreliosis was further studied by sequence analysis and dideoxyfingerprinting analysis of ospA PCR amplicons obtained from CSF samples from patients with neuroborreliosis. Phylogenetic analysis showed that in 11 out of 13 patients B. garinii DNA was found in CSF. These data strongly supports the hypothesis that B. garinii is the principal agent of Lyme neuroborreliosis in Europe. Similarly it was shown that B. afzelii is associated with acrodermatitis chronica atrophicans and thus dermatoborreliosis. Due to a strain dependent different selection pressure in culture only PCR based methods can be used to answer whether mixed infection in patients specimens occur. Our data indicate that mixed infections in humans if ever are rare.     

Polymerase chain reaction diagnosis of fungal disease: Finally coming of age

Definitive diagnosis of invasive fungal disease (IFD) remains limited, and nonculture diagnostic tests could improve this. Serologic testing for biomarkers is standardized through commercial manufacture and is gaining widespread application and incorporation into disease-defining guidelines, whereas most molecular assays remain “in-house” with few commercial tests and limited clinical validation. Standardization of molecular testing will need to be genus-specific because different diseases present and progress in various ways, influencing the optimal specimen choice. Methodologic standardization is almost complete for Aspergillus polymerase chain reaction and will be used to determine clinical performance. The new generation of broad-range systems capable of detecting and differentiating fungi may provide the best route to covering the spectrum of IFD, but evaluation is required and will be difficult to achieve for some of the less prevalent IFDs.     

Polymerase chain reaction in polymeric microchips: DNA amplification in less than 240 seconds

There is much interest in developing methods amenable to amplifying nucleic acids by the polymerase chain reaction (PCR) in small volumes in microfabricated devices. The use of infrared-mediated temperature control to accurately thermocycle microliter volumes in microchips fabricated from polyimide is demonstrated. Amplification of a 500-base-pair fragment of lambda-phage DNA was achieved in a 1.7-microl chamber containing a thermocouple that allowed for accurate control of temperature. While previous work showed that Taq polymerase was inactivated when in direct contact with the thermocouple, this was circumvented with the polyimide chip by the addition of polyethylene glycol as a buffer additive. This, consequently, allowed for adequate amounts of PCR product to be observed after only 15 cycles, with a total time for amplification of 240 s.     

Polymerase chain reaction identification of Vibrio vulnificus in artificially contaminated oysters

DNAs extracted from Vibrio vulnificus seeded into oyster homogenates were evaluated as templates for the polymerase chain reaction. Several extraction procedures were examined, and it was determined that DNA recovered from cells lysed by guanidine isothiocyanate, extracted with chloroform, and precipitated with ethanol was most suitable for use as a polymerase chain reaction template. The region targeted was a 519-bp portion of the cytotoxin-hemolysin gene of V. vulnificus. This region was amplified only when DNA from this species was present in the homogenate. V. vulnificus seeded into oyster homogenates at an initial level of 10(2) CFU/g of oyster meat was consistently observed after 24 h of incubation in alkaline peptone water.     

Polymerase chain reaction for detection ofToxoplasma gondii in human biological samples

Using the polymerase chain reaction (PCR), Toxoplasma gondii from gene TGR1E with primers TGR1E-1, TGR1E-2 (standard PCR), and from B1 gene with primers TM1, TM2, TM3 (hemi-nested PCR) was detected in biological samples from 347 individuals (441 biological materials). Of the total of 441 biological materials, T. gondii DNA was detected in 5.2 %; it was positive in the following samples: blood (n = 6), blood from newborns (2), biopsies (2) and samples of progenitor cells (2) (from candidates for bone marrow transplantation). DNA of T. gondii was also revealed in 11 samples (8.3 %) of 120 cases of pregnant women during prenatal examinations. A positive result in the blood was also found in two cases of newborn babies from mothers who were infected in later pregnancy. The positive PCR examination was confirmed by serological methods (ELISA and complement fixation test). Agreement of PCR results and the detection of antibodies against toxoplasma was found in 83.3 %. Rapid PCR examination for the confirmation of acute parasitemia T. gondii is particularly important for the patients in whom the infection may cause serious consequences (e.g., for fetus in pregnant women or for patients suffering from imunosuppression).