Computing by polymerase chain reaction

A mathematical notation is introduced to represent, at a symbolic level, different mechanisms of DNA recombination, and a 'PCR lemma' is proven by analytically describing the combinatorial properties of the polymerase chain reaction process. This approach led to the discovery of novel techniques, based on a form of PCR which we called cross pairing PCR (briefly XPCR). They were mathematically analyzed and already experimentally proven in different contexts, such as DNA extraction and recombination. Thus, a mathematical analysis of standard methodologies may highlight novel mechanisms of DNA recombination and this can provide new technologies for DNA manipulation.     

Copulation behaviour in mammals: evidence that sperm competition is widespread

We review information on copulation behaviour and sperm competition in mammals using data primarily from the literature. Female mammals of many species regularly copulate with more than one male during each oestrous period. Such multi-male copulations are reported more often in social, compared with solitary species. In addition, the mates of males of polygynous species experience multi-male copulations as often as the mates of males or monogamous species. Male mammals attempt to increase their certainty of paternity through a number of reproductive tactics. Copulation frequency is higher in specks with multi-male copulations compared with other species. Consortships, which can br regarded as a form of mate guarding, are often absent from species in which more than one male copulates with each female during her oestrous period. Most solitary burrow-living small mammal species copulate in the open, whereas social species often copulate inside their burrows. Insurance copulations may occur in many species since high copulation rates occur in four circumstances: (i) when mates are reunited, (ii) when a new male takes over a female, (iii) when a strange male steals a copulation, and (iv) when an audience of males is present.     

A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria

We describe a novel DNA and RNA found in the mitochondria of the Varkud-1c natural isolate of Neurospora. The majority of the RNA, termed VSRNA, is an 881 nucleotide single-stranded circular molecule complementary to one strand of a low copy, double-stranded circular DNA, VSDNA. VSRNA combines some features of the human hepatitis delta virus, group I introns, retroelements, and plant viral satellite RNAs. VSRNA synthesized in vitro performs a self-cleavage reaction whose products terminate with a 5' hydroxyl and a 2',3' cyclic phosphate. This reaction may be involved in the natural processing pathway of multimeric VSRNA in vivo. VSRNA lacks a hammer-head structure or substantial sequence similarity to any other self-cleaving RNA, suggesting that the RNA structure involved in cleavage may be different from those in previously characterized catalytic RNAs.     

Estimation of the reaction efficiency in polymerase chain reaction

Polymerase chain reaction (PCR) is largely used in molecular biology for increasing the copy number of a specific DNA fragment. The succession of 20 replication cycles makes it possible to multiply the quantity of the fragment of interest by a factor of 1 million. The PCR technique has revolutionized genomics research. Several quantification methodologies are available to determine the DNA replication efficiency of the reaction which is the probability of replication of a DNA molecule at a replication cycle. We elaborate a quantification procedure based on the exponential phase and the early saturation phase of PCR. The reaction efficiency is supposed to be constant in the exponential phase, and decreasing in the saturation phase. We propose to model the PCR amplification process by a branching process which starts as a Galton-Watson branching process followed by a size-dependent process. Using this stochastic modelling and the conditional least-squares estimation method, we infer the reaction efficiency from a single PCR trajectory.     

Fellatio by Fruit Bats Prolongs Copulation Time

Oral sex is widely used in human foreplay, but rarely documented in other animals. Fellatio has been recorded in bonobos Pan paniscus, but even then functions largely as play behaviour among juvenile males. The short-nosed fruit bat Cynopterus sphinx exhibits resource defence polygyny and one sexually active male often roosts with groups of females in tents made from leaves. Female bats often lick their mate''s penis during dorsoventral copulation. The female lowers her head to lick the shaft or the base of the male''s penis but does not lick the glans penis which has already penetrated the vagina. Males never withdrew their penis when it was licked by the mating partner. A positive relationship exists between the length of time that the female licked the male''s penis during copulation and the duration of copulation. Furthermore, mating pairs spent significantly more time in copulation if the female licked her mate''s penis than if fellatio was absent. Males also show postcopulatory genital grooming after intromission. At present, we do not know why genital licking occurs, and we present four non-mutually exclusive hypotheses that may explain the function of fellatio in C. sphinx.     

Copulation type affects parturition in the guppy

In some animals, females are often compelled to mate with less desirable males due to the males' alternative mating tactics. Male guppies, Poecilia reticulata, exhibit courtship displays and cooperatively copulate with females. However, they also exhibit sneaking behaviors and coercively copulate with females. To examine the consequences of these two mating patterns, we investigated the influence of copulation type, i.e., cooperative or coercive, on parturition and brood size of females. A single female was allowed to freely contact and copulate with a single male only once. Males that cooperatively copulated with females had larger orange spot areas (an important criterion of female mate choice) than males that copulated coercively. Most females that were coerced into copulation did not give birth to offspring within 100 days after mating. The probability of parturition was high when females copulated cooperatively, and when their mates exhibited frequent postcopulatory jerking behavior. However, the results suggest that copulation type did not affect brood size. Brood size was positively influenced by both female body size and male orange spot area. These results suggest that parturient success is low when females are coerced into mating by less desirable males, whereas brood size is independent of copulation type.     

Detection of Norwalk virus in the UK by the polymerase chain reaction

Abstract We have developed a polymerase chain reaction for the detection of Norwalk virus using the published sequence of the virus RNA dependent RNA polymerase gene and have used this to clone and sequence this region of a virus from a UK outbreak. We have applied this method to a panel of UK Norwalk-like viruses using both Tet-z and Taq DNA polymerases and found that amplification produces a multiplicity of bands from stool samples. However, combination with Southern blotting. Taq polymerase amplification detected virus in 13 of a panel of 30 clinical samples known to contain these viruses and also detected astroviruses in a mixed infection. Amplification using Tet-z DNA polymerase was less efficient (6/30) and detected predominantly viruses typed as UK type 2 by solid phase immune electron microscopy.     

Diagnosis of bovine freemartinism by the polymerase chain reaction method

Summary. Using sex chromosome specific primers, leucocyte chimaerism in heterosexual bovine female twins was identified by combining polymerase chain reaction (PCR) and restriction enzyme digests.     

Copulation in the neritic chaetognath Sagitta crassa

The number of spermatophores found attached to Sagitta crassa,the dominant chateognath in Tokyo Bay, ranged from one to four.Individuals with one spermatophore were most abundant, accountingfor 70% of chaetognaths with spermatophores (A). Using the meanminimum body length of chaetognaths with spermatophores (A),those without spermatophores were subdivided into two categories:those >7 mm (B) were considered to be mature animals, andthose <7 mm (C) to be immature. The ratio of chaetognathswith spermatopbores (A) to all chaetognaths (A+B+C) varied withtime, with high values from 0040 through 0120 h as in a previousstudy. Variations in the ratio of chaetognaths with spermatophores(A) to all adults (A+B) showed a pronounced peak at 0100 h.Thus, it was confirmed that copulation of S. crassa is a periodicactivity with a peak soon after midnight. Most of the chaetognathpairs exchange one spermatophore. The frequency of copulationis considered to be two times per night at most because thechaetognaths have a single pair of seminal vesicles. However,the presence of chaetognaths with 3–4 spermatophores suggeststhat occasionally a reciprocal exchange of spermatophores doesnot occur. This could be called false copulation. It is suggestedthat copulation in S. crassa including false copulation occursat most four times per night.     

Following ionic activity by electrochemistry during the polymerase chain reaction

The most commonly used technique for gene detection is the polymerase chain reaction (PCR). PCR is associated with alterations in ionic activity because inorganic pyrophosphate (PPi) and inorganic phosphate (Pi) ions are produced during nucleotide polymerization. To maintain electro-neutrality, magnesium, potassium, and ammonium ions are bound to DNA. Deoxynucleotides are also bound to DNA during PCR. Some authors have described DNA itself as an electrically conducting polymer formed by base stapling with the formation of extensive Pi systems. In the current study, alterations in electrical conductivity determined experimentally during PCR are reported, and a model explaining the observed changes is described. During recent years, several different techniques for quantifying PCR products have been developed. The most frequently used technique is comparison of the densitometric intensities of ethidium bromide-stained PCR products separated by electrophoresis on gels. Here an alternative technique for quantifying PCR products by measuring alterations in electrical conductivity during PCR is presented.     

Quantitative determination of mRNA phenotypes by the polymerase chain reaction

A method for quantitative determination of specific cellular mRNA is described. The mRNA in a dilution series of total RNA was reverse transcribed by an oligo-dT primer and the cDNA was amplified by the polymerase chain reaction (PCR) using sets of specific primers. A 32P- or biotin-labeled specific probe was hybridized to the PCR products immobilized on nitrocellulose membrane. The intensity of the hybridization signals was evaluated for quantification of the PCR products. A standard curve was produced by the known amount of the in vitro transcribed cRNA, which contained the same sequence as the mRNA. The series of standard cRNA dilutions were reverse transcribed, amplified and hybridized in the same manner. The amount of the specific RNA was deduced by fitting to the standard curve. Two tissue specimens of intestinal tumors, evaluated on the basis of hybridization signals by three different methods, were shown to contain similar amounts of beta-actin mRNA. Furthermore, a Chinese hamster ovary (CHO) cell line transfected with platelet-derived growth factor (PDGF) beta-receptor cDNA was found to contain similar amounts of beta-actin mRNA as the untransfected CHO cell line. However, the transfected CHO cell line contained over 10(11) copies of the PDGF beta-receptor mRNA per microgram of total RNA, while the untransfected one showed no detectable RNA, indicating that the latter contained less than 10(6) copies per microgram of total RNA in this assay.     

Frankia genus-specific characterization by polymerase chain reaction.

The polymerase chain reaction (PCR) is an in vitro procedure for primer-directed enzymatic amplification of specific template nucleic acid sequences. In order to determine whether a given actinomycete isolated from an actinorhiza (nodule) belongs to the genus Frankia or is a contaminant, we have developed a test based on the PCR. Primers complementary to sequences of two DNA regions corresponding to the nif genes (nifH and nifD) and the rRNA genes (16S and 23S) were specifically chosen to differentially amplify DNAs from Frankia strains but not those from other microorganisms. A series of positive and negative controls were set up by using universal or selective primers resulting in a discriminant amplification, which could be detected after agarose gel electrophoresis. In the nif region, degenerate oligonucleotide primers were used to amplify a target common to all the nitrogen-fixing microorganisms tested, while another set of primers amplified a target with a high specificity for Frankia strains. In the rRNA gene region, universal and specific primers were characterized and tested with DNAs from a wide range of microorganisms. The efficiency of this rapid and sensitive PCR assay was tested with an isolate obtained from Alnus nepalensis nodules, confirming results obtained by nodulation tests.