Application of Quantitative Real-Time Polymerase Chain Reaction for Noninvasive Genetic Monitoring

ABSTRACT Noninvasive genetic monitoring of animal populations has become a widely used method in animal conservation and wildlife management due to its known advantages in sample availability of endangered or elusive species. A variety of methods have been suggested to overcome the difficulties of collecting reliable genetic data despite poor DNA quality and quantity of samples. We used quantitative real-time polymerase chain reaction (qPCR) to quantify DNA contents and preselect extracts suitable for microsatellite genotyping of noninvasive samples from 2 carnivore species, wolf (Canis lupus) and Eurasian otter (Lutra lutra). We tested 2 concentration thresholds for DNA extracts containing either 5 pg/μL or 25 pg/μL at minimum and evaluated the effect of excluding samples from genotyping falling below either of these DNA concentrations. Depending on species and threshold concentration applied, we reduced the genotyping effort by 21% to 47% and genotyping errors by 7% to 45%, yet we could still detect 82% to 99% of available genotypes. Thus, qPCR may potentially reduce genotyping effort and enhance data reliability in noninvasive genetic studies. Genetic laboratories working on noninvasive population genetic studies could transfer this approach to other species, streamline genetic analyses and, thus, more efficiently provide wildlife managers with reliable genetic data of wild populations.     

Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials

Statistical distance dependent pair potentials are frequently used in a variety of folding, threading, and modeling studies of proteins. The applicability of these types of potentials is tightly connected to the reliability of statistical observations. We explored the possible origin and extent of false positive signals in statistical potentials by analyzing their distance dependence in a variety of randomized protein-like models. While on average potentials derived from such models are expected to equal zero at any distance, we demonstrate that systematic and significant distortions exist. These distortions originate from the limited statistical counts in local environments of proteins and from the limited size of protein structures at large distances. We suggest that these systematic errors in statistical potentials are connected to the dependence of amino acid composition on protein size and to variation in protein sizes. Additionally, atom-based potentials are dominated by a false positive signal that is due to correlation among distances measured from atoms of one residue to atoms of another residue. The significance of residue-based pairwise potentials at various spatial pair separations was assessed in this study and it was found that as few as approximately 50% of potential values were statistically significant at distances below 4 A, and only at most approximately 80% of them were significant at larger pair separations. A new definition for reference state, free of the observed systematic errors, is suggested. It has been demonstrated to generate statistical potentials that compare favorably to other publicly available ones.     

Plasma cholesterol-lowering and transient liver dysfunction in mice lacking squalene synthase in the liver

Squalene synthase (SS) catalyzes the biosynthesis of squalene, the first specific intermediate in the cholesterol biosynthetic pathway. To test the feasibility of lowering plasma cholesterol by inhibiting hepatic SS, we generated mice in which SS is specifically knocked out in the liver (L-SSKO) using Cre-loxP technology. Hepatic SS activity of L-SSKO mice was reduced by >90%. In addition, cholesterol biosynthesis in the liver slices was almost eliminated. Although the hepatic squalene contents were markedly reduced in L-SSKO mice, the hepatic contents of cholesterol and its precursors distal to squalene were indistinguishable from those of control mice, indicating the presence of sufficient centripetal flow of cholesterol and/or its precursors from the extrahepatic tissues. L-SSKO mice showed a transient liver dysfunction with moderate hepatomegaly presumably secondary to increased farnesol production. In a fed state, the plasma total cholesterol and triglyceride were significantly reduced in L-SSKO mice, primarily owing to reduced hepatic VLDL secretion. In a fasted state, the hypolipidemic effect was lost. mRNA expression of liver X receptor α target genes was reduced, while that of sterol-regulatory element binding protein 2 target genes was increased. In conclusion, liver-specific ablation of SS inhibits hepatic cholesterol biosynthesis and induces hypolipidemia without increasing significant mortality.     

Genotoxic and cytotoxic effects induced by aluminum in the lymphocytes of the common carp (Cyprinus carpio)

Few studies have been made in regard to the effect of aluminum on the molecular and cellular structure and function of aquatic organisms; therefore, in the present report we determined the genotoxic and cytotoxic effects induced by the metal on the lymphocytes of carp (Cyprinus carpio). Three groups of fish were exposed to 0.05, 120, and 239 mg/L of aluminum (Al), respectively, by using Al₂ (SO₄)₃·7H₂O, and another group was included as control. The cells obtained were studied with the comet assay, flow cytometry, and the TUNEL method. With the first method we found a concentration and time dependent, significant increase in the amount of DNA damage induced by Al, and a higher damage when we evaluated the level of oxidized DNA. By applying flow cytometry we established that the metal induced a DNA content increase and ploidy modifications as well as apoptosis and disturbances of the cell cycle progression. With the last method we determined a significant increase in the amount of apoptotic cells, mainly in the 72–96 h period. Our results established that Al caused deleterious DNA and cellular effects in the tested organism, and they suggested the pertinence of evaluating toxicity induced by the metal in organisms living in contaminated water bodies.     

Mitigating scoring errors in microsatellite data from wild populations

Microsatellite data are widely used to test ecological and evolutionary hypotheses in wild populations. In this paper, we consider three typical sources of scoring errors capable of biasing biological conclusions: stuttering, large‐allele dropout and null alleles. We describe methods to detect errors and propose conventions to mitigate scoring errors and report error rates in studies of wild populations. Finally, we discuss potential bias in ecological or evolutionary conclusions based on data sets containing these scoring errors.     

Estimation of the number of genetic markers required for individual animal identification accounting for genotyping errors

Nearly all studies that consider the power of exclusion for individual identification using genetic markers ignore the possibility of erroneous genotypes, although individual genotype error rates are approximately 1% for microsatellites. Single nucleotide polymorphisms (SNPs) have lower error rates, but because of their lower information content, more SNPs than microsatellites will be required to obtain the same power of exclusion for traceability. In this study, we accounted for genotyping mistakes by requiring at least two discrepancies to reject a match. Exclusion probabilities were computed analytically and by simulation. A microsatellite with five alleles was approximately comparable in exclusion power to 2-2.25 SNPs. At least eight SNPs were required to achieve a 99% probability of rejection for a match between two individuals, while with 25 SNPs there was a <1% chance for a match between any of five million individuals.     

Conditions for the spread of conspicuous warning signals: a numerical model with novel insights

The initial evolution of conspicuous warning signals presents an evolutionary problem because selection against rare conspicuous signals is presumed to be strong, and new signals are rare when they first arise. Several possible solutions have been offered to solve this apparent evolutionary paradox, but disagreement persists over the plausibility of some of the proposed mechanisms. In this paper, we construct a deterministic numerical simulation model that allows us to derive the strength of selection on novel warning signals in a wide range of biologically relevant situations. We study the effects of predator psychology (learning, rate of mistaken attacks, and neophobia) on selection. We also study the how prey escape, predation intensity, number of predators, and abundance of different prey types affects selection. The model provides several important results. Selection on novel warning signals is number rather than frequency dependent. In most cases, there exists a threshold number of aposematic individuals below which aposematism is selected against and above which aposematism is selected for. Signal conspicuousness (which increases detection rate) and distinctiveness (which allows predator to distinguish defended from nondefended prey) have opposing effects on evolution of warning signals. A more conspicuous warning signal cannot evolve unless it makes the prey more distinctive from palatable prey, reducing mistaken attacks by predators. A novel warning signal that is learned quickly can spread from lower abundance more easily than a signal that is learned more slowly. However, the relative rate at which the resident signal and the novel signal are learned is irrelevant for the spread of the novel signal. Long-lasting neophobia can facilitate the spread of novel warning signals. Individual selection via the ability of defended prey to escape from predator is not likely to facilitate evolution of conspicuous warning signals if both the resident (cryptic) morph and the novel morph have the same escape probability. Predation intensity (defined as the proportion of palatable prey eaten by the predator) has a strong effect on selection. More intense predation results in strong selection against rare signals, but also strong selective advantage to common signals. The threshold number of aposematic individuals is lower when predation is intense. Thus, the evolution of warning signals may be more likely in environments where predation is intense. The effect of numbers of predators depends on whether predation intensity also changes. When predation intensity is constant, increasing numbers of predators raises the threshold number of aposematic individuals, and thus makes evolution of aposematism more difficult. If predation intensity increases in parallel with number of predators, the threshold number of aposematic individuals does not change much, but selection becomes more intense on both sides of the threshold.     

Studying fatty aldehyde metabolism in living cells with pyrene-labeled compounds

The lack of fatty aldehyde dehydrogenase function in Sjögren Larsson Syndrome (SLS) patient cells not only impairs the conversion of fatty aldehydes into their corresponding fatty acid but also has an effect on connected pathways. Alteration of the lipid profile in these cells is thought to be responsible for severe symptoms such as ichtyosis, mental retardation, and spasticity. Here we present a novel approach to examine fatty aldehyde metabolism in a time-dependent manner by measuring pyrene-labeled fatty aldehyde, fatty alcohol, fatty acid, and alkylglycerol in the culture medium of living cells using HPLC separation and fluorescence detection. Our results show that in fibroblasts from SLS patients, fatty aldehyde is not accumulating but is converted readily into fatty alcohol. In control cells, in contrast, exclusively the corresponding fatty acid is formed. SLS patient cells did not display a hypersensitivity toward hexadecanal or hexadecanol, but 3-fold lower concentrations of the fatty alcohol than the corresponding fatty aldehyde were needed to induce toxicity in SLS patient and in control cells.