A novel set of DIP-STR markers for improved analysis of challenging DNA mixtures.

Currently available molecular biology tools allow forensic scientists to characterize DNA evidence found at crime scenes for a large variety of samples, including those of limited quantity and quality, and achieve high levels of individualization. Yet, standard forensic markers provide limited or no results when applied to mixed DNA samples where the contributors are present in very different proportions (unbalanced DNA mixtures). This becomes an issue mostly for the analysis of trace samples collected on the victim or from touched objects. To this end, we recently proposed an innovative type of genetic marker, named DIP-STR that relies on pairing deletion/insertion polymorphisms (DIP) with standard short tandem repeats (STR). This novel compound marker allows detection of the minor DNA contributor in a DNA mixture of any gender and cellular origin with unprecedented resolution (beyond a DNA ratio of 1:1000). To provide a novel analytical tool useful in practice to common forensic laboratories, this article describes the first set of 10 DIP-STR markers selected according to forensic technical standards. The novel DIP-STR regions are short (between 146 and 271 bp), include only highly polymorphic tri-, tetra- and pentanucleotide tandem repeats and are located on different chromosomes or chromosomal arms to provide statistically independent results. This novel set of DIP-STR can target the amplification of 0.03-0.1 ng of DNA when mixed with a 1000-fold excess of major DNA. DIP-STR relative allele frequencies are estimated based on a survey of 103 Swiss individuals. Finally, this study provides an estimate of the occurrence of informative alleles and a calculation of the corresponding random match probability of the detected minor DIP-STR genotype assessed across 10,506 pairwise conceptual mixtures.

Exploring the relative DNA contribution of first and second object's users on mock touch DNA mixtures

Contact stains recovered at break-in crime scenes are frequently characterized by mixtures of DNA from several persons. Broad knowledge on the relative contribution of DNA left behind by different users overtime is of paramount importance. Such information might help crime investigators to robustly evaluate the possibility of detecting a specific (or known) individual's DNA profile based on the type and history of an object. To address this issue, a contact stain simulation-based protocol was designed. Fourteen volunteers either acting as first or second object's users were recruited. The first user was required to regularly handle/wear 9 different items during an 8-10-day period, whilst the second user for 5, 30 and 120 min, in three independent simulation sessions producing a total of 231 stains. Subsequently, the relative DNA profile contribution of each individual pair was investigated. Preliminary results showed a progressive increase of the percentage contribution of the second user compared to the first. Interestingly, the second user generally became the major DNA contributor when most objects were handled/worn for 120 min, Furthermore, the observation of unexpected additional alleles will then prompt the investigation of indirect DNA transfer events.

On the Rule of Mixtures for Predicting Stress-Softening and Residual Strain Effects in Biological Tissues and Biocompatible Materials

In this work, we use the rule of mixtures to develop an equivalent material model in which the total strain energy density is split into the isotropic part related to the matrix component and the anisotropic energy contribution related to the fiber effects. For the isotropic energy part, we select the amended non-Gaussian strain energy density model, while the energy fiber effects are added by considering the equivalent anisotropic volumetric fraction contribution, as well as the isotropized representation form of the eight-chain energy model that accounts for the material anisotropic effects. Furthermore, our proposed material model uses a phenomenological non-monotonous softening function that predicts stress softening effects and has an energy term, derived from the pseudo-elasticity theory, that accounts for residual strain deformations. The model’s theoretical predictions are compared with experimental data collected from human vaginal tissues, mice skin, poly(glycolide-co-caprolactone) (PGC25 3-0) and polypropylene suture materials and tracheal and brain human tissues. In all cases examined here, our equivalent material model closely follows stress-softening and residual strain effects exhibited by experimental data

Singlet oxygen reactivity in water-rich solvent mixtures

The 3-methylindole (3MI) oxygenation sensitized by psoralen (PSO) has been investigated in 100%, 20% and 5% O2-saturated water/dioxane (H2O/Dx) mixtures. The lowering of the ¹O2* chemical rate when water (k chem∆3MI = 1.4 × 109 M-1 s-1) is replaced by deuterated water (k chem∆3MI = 1.9 × 108 M-1 s-1) suggests that hydrogen abstraction is involved in the rate determining step. A high dependence of the chemical rate constant on water concentration in H2O/Dx mixtures was found showing that water molecules are absolutely essential for the success of the 3MI substrate oxidation by ¹O2* in water-rich solvent mixtures.

Reaction mixtures formed by nitrite and selected sulfa-drugs showed mutagenicity in acidic medium

Nitrite, which is present in preserved meat and can be produced in the oral cavity by reduction of nitrate taken from vegetables, could react in stomach with nitrosatable drugs, giving genotoxic-carcinogenic N-nitroso compounds (NOC). The mutagenicity of reaction mixtures formed by sodium nitrite and selected sulfa-drugs (sulfathiazole, HST; phtalylsulfathiazole, PhST; complex Co(II)-sulfathiazole, Co(II)-ST) in acidic medium was evaluated using the Salmonella typhimurium reverse mutation assay (Ames test), with TA98 and TA 100 strains. The reactions were carried out at room temperature, with a mole ratio [nitrite]/[sulfa-drug] > 1. The three reaction mixtures showed mutagenic effects in the considered range.

Thermodynamic study of the solubility of sodium naproxen in some ethanol + water mixtures

By using the van't Hoff and Gibbs equations the apparent thermodynamic functions Gibbs energy, enthalpy, and entropy of solution for sodium naproxen in ethanol + water cosolvent mixtures, were evaluated from solubility data determined at temperatures from (278.15 to 308.15) K. The drug solubility was greatest in neat water and lowest in neat ethanol at all the temperatures studied. By means of non-linear enthalpy-entropy compensation analysis, it follows that the dissolution process of this drug in ethanol-rich mixtures is entropy-driven, whereas, in water-rich mixtures the process is enthalpy-driven.

Indomethacin solubility estimation in 1,4-dioxane + water mixtures by the extended hildebrand solubility approach

Extended Hildebrand Solubility Approach (EHSA) was successfully applied to evaluate the solubility of Indomethacin in 1,4-dioxane + water mixtures at 298.15 K. An acceptable correlation-performance of EHSA was found by using a regular polynomial model in order four of the W interaction parameter vs. solubility parameter of the mixtures (overall deviation was 8.9%). Although the mean deviation obtained was similar to that obtained directly by means of an empiric regression of the experimental solubility vs. mixtures solubility parameters, the advantages of EHSA are evident because it requires physicochemical properties easily available for drugs.

Thermodynamic study of the solubility of triclocarban in ethanol + propylene glycol mixtures

By using the van't Hoff and Gibbs equations the apparent thermodynamic functions Gibbs energy, enthalpy, and entropy of solution for triclocarban in ethanol + propylene glycol mixtures were evaluated from solubility data determined at temperatures from (293.15 to 313.15) K. The drug solubility was greatest in the mixture with 0.60 in mass fraction of ethanol and lowest in neat propylene glycol at almost all the temperatures studied. Non-linear enthalpy-entropy compensation is found indicating apparently different mechanisms of the solution process according to the mixtures composition.

Solution thermodynamics of methocarbamol in some ethanol + water mixtures

Apparent thermodynamic functions, Gibbs energy, enthalpy and entropy of solution and mixing, for methocarbamol in ethanol + water mixtures, were evaluated from solubility data determined at temperatures from 293.15 K to 313.15 K and from calorimetric values of drug fusion. The drug solubility was greatest in the mixtures with 0.70 or 0.80 mass fraction of ethanol and lowest in neat water across all temperatures studied. Non-linear enthalpy-entropy compensation was found for the dissolution processes. Accordingly, solution enthalpy drives the respective processes in almost all the solvent systems analyzed.

Optimization of solvent mixtures for extraction from bark of Schinus terebinthifolius by a statistical mixture-design technique and development of a UV-Vis spectrophotometric method for analysis of total polyphenols in the extract

A statistical mixture-design technique was used to study the effects of different solvents and their mixtures on the yield, total polyphenol content, and antioxidant capacity of the crude extracts from the bark of Schinus terebinthifolius Raddi (Anacardiaceae). The experimental results and their response-surface models showed that ternary mixtures with equal portions of all the three solvents (water, ethanol and acetone) were better than the binary mixtures in generating crude extracts with the highest yield (22.04 ± 0.48%), total polyphenol content (29.39 ± 0.39%), and antioxidant capacity (6.38 ± 0.21). An analytical method was developed and validated for the determination of total polyphenols in the extracts. Optimal conditions for the various parameters in this analytical method, namely, the time for the chromophoric reaction to stabilize, wavelength of the absorption maxima to be monitored, the reference standard and the concentration of sodium carbonate were determined to be 5 min, 780 nm, pyrogallol, and 14.06% w v-1, respectively. UV-Vis spectrophotometric monitoring of the reaction under these conditions proved the method to be linear, specific, precise, accurate, reproducible, robust, and easy to perform.

Differences in competitive ability among races of Colletotrichum graminicola in mixtures

Mixtures of races of Colletotrichum graminicola, causing sorghum (Sorghum bicolor) anthracnose and differing in their virulence range, were inoculated for five and six generations on the susceptible sorghum cultivar BR009 (Tx623), in two experiments in a greenhouse. In each generation a sample of 50 single spore isolates was obtained and inoculated on a standard differential set to determine the proportion of each race in the mixture. Isolates of the race 30A, with the narrowest virulence range, predominated over isolates of the more complex races 31B, 31C and 31E indicating the existence of differences in the survival ability among races of this pathogen.

Variability of the anthracnose fungus Colletotrichum graminicola in sorghum genotype mixtures

This paper reports partial results obtained on the variability of Colletotrichum graminicola developed in response to the host diversity generated by three-line combination of sorghum (Sorghum bicolor) genotypes. Nine sorghum lines were used in this study: CMSXS210B, CMSXS112B, CMSXS215B, CMSXS221B, CMSXS169R, CMSXS180R, CMSXS182R, CMSXS227R, and CMSXS116R. A total of 39 treatments on mixtures and pure stands of the component lines were evaluated in the field for the development of anthracnose, as a natural epidemic. Samples of the single spore isolates of the pathogen of each treatment indicated a reduction in the phenotypic diversity and an increase in the frequency of more complex races in genotype mixtures in relation to the pure stands of each genotype.

Evaluation of genetic mixtures of sorghum lines for anthracnose resistance management

The main objective of this work was to evaluate the diversification of sorghum (Sorghum bicolor) populations as a way to manage resistance to the sorghum anthracnose fungus Colletotrichum graminicola. A total of 18 three-way hybrids were obtained by crossing six single cross male-sterile F1 hybrids, derived by crossing A (non restorer sterile cytoplasm) and B (non restorer normal cytoplasm) lines, with three fertile R (restorer) lines, previously evaluated for their differential reaction to the pathogen. Variation in the level of resistance was observed, as indicated by the values of the area under the disease progress curve (AUDPC) obtained for each hybrid. Lines contributed differently to the level of resistance of each hybrid. All hybrids in which CMSXS169R was the male progenitor were classified as highly resistant. Some hybrids had a level of resistance superior to the maximum levels of each line component individually.

Amphoteric behavior of di-2-pyridyl ketone benzoylhydrazone in ethanol-water mixtures

The ligand di-2-pyridyl ketone benzoylhydrazone (DPKBH) is widely used for the determination of transition metal ions in environmental samples. Due to its low solubility in water it is used in aqueous-ethanol (1:1) solvent and for higher sensitivity the pH must be properly adjusted. The properties of DPKBH solutions must be known at different ethanol-water percentages in order to achieve higher sensitivity and/or selectivity for metal analysis. The acid-base behavior of this reagent in aqueous-ethanol solvent and the dissociation/ionization constants (pK1 and pK2) of DPKBH have been determined in different aqueous-ethanol solvent mixtures (10, 20, 30 and 50 % V/V of ethanol) from potentiometric titrations at 25.0 ± 0.1° C. As the amount of ethanol increases from 10 to 30% the pK1 and pK2 values increased, but they decreased in 50% of the organic solvent. The results are correlated with the medium composition and its effects.