Unbalanced Mixtures Research Articles

An investigation of the potential of DIP-STR markers for DNA mixture analyses.

The genetic characterization of unbalanced mixed stains remains an important area where improvement is imperative. In fact, using the standard tools of forensic DNA profiling (i.e., STR markers), the profile of the minor contributor in mixed DNA stains cannot be successfully detected if its quantitative share of DNA is less than 10% of the mixed trace. This is due to the fact that the major contributor's profile "masks" that of the minor contributor. Besides known remedies to this problem, such as Y-STR analysis, a new compound genetic marker that consists of a Deletion/Insertion Polymorphism (DIP) linked to a Short Tandem Repeat (STR) polymorphism, has recently been developed and proposed. These novel markers are called DIP-STR markers. This paper compares, from a statistical and forensic perspective, the potential usefulness of these novel DIP-STR markers (i) with traditional STR markers in cases of moderately unbalanced mixtures, and (ii) with Y-STR markers in cases of female-male mixtures. This is done through a comparison of the distribution of 100,000 likelihood ratio values obtained using each method on simulated mixtures. This procedure is performed assuming, in turn, the prosecution's and the defence's point of view.

Atom-dimer scattering amplitude for fermionic mixtures with different masses:s-wave andp-wave contributions

We study near a Feshbach resonance, as a function of the mass ratio, the fermion-dimer scattering amplitude in fermionic mixtures of two fermion species. When masses are equal the physical situation is known to be quite simple. We show that, when the mass ratio is increased, the situation becomes much more complex. For the s-wave contribution we obtain an analytical solution in the asymptotic limit of very large mass ratio. In this regime the s-wave scattering amplitude displays a large number of zeros, essentially linked to the known large value of the fermion-dimer scattering length in this regime. We find by an exact numerical calculation that a zero is still present for a mass ratio of 15. For the p-wave contribution we make our study below the mass ratio of 8.17, where a fermion-dimer bound state appears. We find that a strong p-wave resonance is present at low energy, due to a virtual bound state, in the fermion-dimer system, which is a forerunner of the real bound state. This resonance becomes prominent in the mass ratio range around the one corresponding to the $^{40}$K - $^6$Li mixtures, much studied experimentally. This resonance should affect a number of physical properties. These include the equation of state of unbalanced mixtures at very low temperature but also the equation of state of balanced mixtures at moderate or high temperature. The frequency and the damping of collective modes should also provide a convenient way to evidence this resonance. Finally it should be possible to modify the effective mass of one of the fermionic species by making use of an optical lattice. This would allow to study the strong dependence of the resonance as a function of the mass ratio of the two fermionic elements. In particular one could check if the virtual bound state is relevant for the instabilities of these mixtures.

A new thermostable DNA polymerase mixture for efficient amplification of long DNA fragments

The thermostable DNA polymerases have been used for amplification of DNA fragments since the invention of PCR. The constraint on the maximum size of the amplified fragments can be solved to certain level by the use of unbalanced mixtures of non-proofreading and proofreading thermostable DNA polymerases. In this study, we tested the use of a mixtures of N-terminal deletional variant of Taq polymerase - Klentaq278 and Tne polymerase from Thermotoga neapolitana. Klentaq278 and Tne polymerase genes were cloned and expressed in different expression vectors under tac promoter. The most efficient ratio of Klentaq278/Tne polymerase for amplification was 10 : 1. The polymerase mixture of Klentaq278 and Tne polymerase is very effective in amplification of DNA fragments for up to 8 kb and is useful addition to a DNA polymerases used in long-range PCR.

Results of the 2003–2004 GEP-ISFG collaborative study on mitochondrial DNA: Focus on the mtDNA profile of a mixed semen-saliva stain

We report here a review of the seventh mitochondrial DNA (mtDNA) exercise undertaken by the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) corresponding to the period 2003–2004. Five reference bloodstains from five donors (M1–M5), a mixed stain of saliva and semen (M6), and a hair sample (M7) were submitted to each participating laboratory for nuclear DNA (nDNA; autosomal STR and Y-STR) and mtDNA analysis. Laboratories were asked to investigate the contributors of samples M6 and M7 among the reference donors (M1–M5). A total of 34 laboratories reported total or partial mtDNA sequence data from both, the reference bloodstains (M1–M5) and the hair sample (M7) concluding a match between mtDNA profiles of M5 and M7. Autosomal STR and Y-STR profiling was the preferred strategy to investigate the contributors of the semen/saliva mixture (M6). Nuclear DNA profiles were consistent with a mixture of saliva from the donor (female) of M4 and semen from donor M5, being the semen (XY) profile the dominant component of the mixture. Strikingly, and in contradiction to the nuclear DNA analysis, mtDNA sequencing results yield a more simple result: only the saliva contribution (M4) was detected, either after preferential lysis or after complete DNA digestion. Some labs provided with several explanations for this finding and carried out additional experiments to explain this apparent contradictory result. The results pointed to the existence of different relative amounts of nuclear and mtDNAs in saliva and semen. We conclude that this circumstance could strongly influence the interpretation of the mtDNA evidence in unbalanced mixtures and in consequence lead to false exclusions. During the GEP-ISFG annual conference a validation study was planned to progress in the interpretation of mtDNA from different mixtures.

The ghost of hybridization past: niche pre-emption is not the only explanation of apparent monophyly in island endemics.

Summary 1 Published molecular phylogenies show that many plant groups in the Canary Islands are monophyletic despite the fact that the short distance between the islands and Africa should have led to many independent colonization events. 2 Low establishment rates of later migrants owing to niche pre-emption by earlier, already established, colonists could explain these patterns. The apparent monophyly is, however, also compatible with multiple colonizations, with later colonizers making only limited contributions to the total gene pool (and therefore being undetected in the molecular phylogeny) or being wiped out by stochastic processes. 3 Experimental evidence for niche pre-emption and species-specific interactions in plants is weak, with survival and establishment of a newly immigrant species depending on the overall composition of the community, rather than on the presence of a particular ‘ecologically similar’ species. 4 Although niche pre-emption might have contributed to the observed patterns of monophyly, we do not think that phylogeographical data from Macaronesia can be taken as evidence for its action in the geological past.

The role of growth form and correlated traits in competitive ranking of six perennial ruderal plant species grown in unbalanced mixtures

The competitive abilities of six perennial ruderal plants of three different growth forms were compared via yield measures using an additive diallel experimental design with unbalanced mixtures (9:3 or 3:9 plants per pot, respectively). Thus, in a given mixture species A was grown in two configurations: three individuals in centre position of the pot together with nine plants of species B in border position and vice versa. Effect competitive abilities as well as response competitive abilities of the species were significantly related to canopy height and plant biomass. The species with lower rosette growth form and smaller biomasses were weaker competitors than the species possessing elevated canopies along with higher biomasses, whereas total leaf area was not significantly correlated with competitive ability between species. Species differences in competitive ability were stronger between the plants grown in the central position than between those grown in the border position. Furthermore, interactions between species-specific traits and configuration could be observed, indicating the importance of species proportions and arrangement patterns for evaluation of competitive outcome in the field. The degree of complete transitivity of the competitive network of the six ruderal species, which was significantly higher than expected under the null model in our experimental design, also seemed to depend on species proportions in mixture. Shifts in root:shoot ratio of the centre plants when faced with competition by the border plants were in the direction of higher shoot allocation for the weak competitors with rosette growth form irrespective of the neighbour species, except for Bunias orientalis , which showed a more plastic response. The stronger competitors showed higher root allocation ( Urtica dioica ) or were hardly affected at all. Consistent with the results of our experiment, the weaker competitors occur at rather frequently disturbed and therefore transient field sites whereas the stronger competitors predominate at infrequently disturbed sites during several phases of succession.

Analysis of Tomato Root Initiation Using a Normal Mixture Distribution

We attempt to identify the number of underlying physical phenomena behind tomato lateral root initiation by using a normal mixture distribution coupled with the Box-Cox power transformation. An initial analysis of the data suggested the possibility of two (possibly more) subpopulations, but upon taking reciprocals, the data appear to be very nearly Gaussian. A simulation study explores the possibility of erroneously detecting a second subpopulation by fitting data which are improperly scaled. A power calculation suggests that only unrealistically large sample sizes can detect the unbalanced mixtures one might expect with data of this type.

Effect of Amino Acids on Liver RNA Synthesis in the Chick

Two-week-old chicks were administered orally mixtures of vari ous kinds and amounts of amino acids. The effect of these amino acids on RNA synthesis was measured by the incorporation of tritium from uridine-5-3H into RNA of the chick liver. High levels of amino acids (300 mg) administered to chicks resulted in a decrease in RNA synthesis. Of the precursors of the purine ring tested (folie acid, glycine, glutamine and asparuc acid), only aspartA­cacid had any effect on RNA synthesis. It increased the synthesis of RNA. When tested at various levels, 20 mg of aspartic acid per chick promoted the highest amount of RNA synthesis whereas 40 mg of aspartic acid decreased the synthesis of RNA. Amino acid imbalances generally lowered both RNA and protein synthesis when compared to a completely balanced amino acid mixture. Of the imbalances tested by measuring the incorporation of carbon-14 from glycine-l-1'lC into both RNA and protein, a deficiency of tryptophan seemed to have the greatest effect. The data from these experiments in general indicate that amino acids will increase the synthesis of RNA when administered at recommended dietary intakes but will decrease synthesis of RNA when fed at excessively high intakes or as certain unbalanced mixtures. J. Nutr. 102: 987-994, 1972.

Effect of dietary proteins and amino acids on the susceptibility of mice to bacterial infections.

Young mice were maintained for periods of 1 to 6 weeks on experimental diets containing all known growth factors, but differing in their protein and amino acid contents. All diets were supplemented with L-cystine. The effect of the nutritional regimen on infection was tested by inoculating the animals with either one of four pathogens (Mycobacterium tuberculosis var. bovis, Mycobacterium fortuitum, Staphylococcus aureus, Klebsiella pneumoniae type C), and by observing the survival time. The infective dose was administered by either one of three routes: intravenous, intraperitoneal, or air-borne (aerosol). In some experiments, the animals were maintained in groups of five throughout the tests. In other experiments they were housed in individual cages. This difference in housing did not affect the results in a detectable manner. Mice fed diets containing 5 or 8 per cent casein as sole source of amino acid (except for cystine supplementation) proved more susceptible to the experimental diseases than did mice fed diets containing 15 or 20 per cent of the same protein. Susceptibility to infection developed when wheat gluten, or soybean alpha-protein, was substituted for casein-even in high concentrations (15 or 20 per cent). In one experiment, mice were fed a diet containing as sole source of amino acids a mixture of soybean and rice flour, so designed as to provide a protein concentration of 15 per cent, with an amino acid pattern similar to that of casein. These animals gained weight at the same rate as those fed a diet containing 15 per cent casein and they exhibited a satisfactory level of resistance to bacterial infection. The infection-enhancing effect of low casein concentration (5 and 8 per cent) could be corrected by supplementing the diet with the proper mixture of amino acids. This could be done using either synthetic or natural amino acids. In contrast, susceptibility to infection developed when low casein diets were supplemented with unbalanced mixtures of amino acids. The infection-enhancing effect of gluten diets could not be corrected by supplementing the latter with lysine even though this supplementation markedly improved weight gains in uninfected animals. It appears in conclusion that the relative proportion of the various amino acids in the diet is as important a factor as their total amount in conditioning resistance to bacterial infections. This effect of nutrition on resistance can be detected irrespective of the route of infection: intravenous, intraperitoneal, or air-borne. Moreover, the effect has been observed with two strains of mice differing markedly in their natural resistance to bacterial infection.