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.     

When can we measure stress noninvasively? Postdeposition effects on a fecal stress metric confound a multiregional assessment

Measurement of stress hormone metabolites in fecal samples has become a common method to assess physiological stress in wildlife populations. Glucocorticoid metabolite (GCM) measurements can be collected noninvasively, and studies relating this stress metric to anthropogenic disturbance are increasing. However, environmental characteristics (e.g., temperature) can alter measured GCM concentration when fecal samples cannot be collected immediately after defecation. This effect can confound efforts to separate environmental factors causing predeposition physiological stress in an individual from those acting on a fecal sample postdeposition. We used fecal samples from American pikas (Ochotona princeps) to examine the influence of environmental conditions on GCM concentration by (1) comparing GCM concentration measured in freshly collected control samples to those placed in natural habitats for timed exposure, and (2) relating GCM concentration in samples collected noninvasively throughout the western United States to local environmental characteristics measured before and after deposition. Our timed‐exposure trials clarified the spatial scale at which exposure to environmental factors postdeposition influences GCM concentration in pika feces. Also, fecal samples collected from occupied pika habitats throughout the species' range revealed significant relationships between GCM and metrics of climate during the postdeposition period (maximum temperature, minimum temperature, and precipitation during the month of sample collection). Conversely, we found no such relationships between GCM and metrics of climate during the predeposition period (prior to the month of sample collection). Together, these results indicate that noninvasive measurement of physiological stress in pikas across the western US may be confounded by climatic conditions in the postdeposition environment when samples cannot be collected immediately after defecation. Our results reiterate the importance of considering postdeposition environmental influences on this stress metric, especially in multiregional comparisons. However, measurements of fecal GCM concentration should prove useful for population monitoring within an eco‐region or when postdeposition exposure can be minimized.     

Bulked sample analysis in genetics,genomics and crop improvement

Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high‐throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker‐assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.     

Comparison of plasma sample purification by manual liquid–liquid extraction, automated 96-well liquid–liquid extraction and automated 96-well solid-phase extraction for analysis by high-performance liquid chromatography with tandem mass spectrometry

Three extraction procedures were developed for the quantitative determination of a carboxylic acid containing analyte (I) in human plasma by high-performance liquid chromatography (HPLC) with negative ion electrospray tandem mass spectrometry (MS–MS). The first procedure was based on the manual liquid–liquid extraction (LLE) of the acidified plasma samples with methyl tert.-butyl ether. The second procedure was based on the automation of the manual LLE procedure using 96-well collection plates and a robotic liquid handling system. The third approach was based on automated solid-phase extraction (SPE) using 96-well SPE plates and a robotic liquid handling system. A lower limit of quantitation of 50 pg/ml was achieved using all three extraction procedures. The total time required to prepare calibration curve standards, aliquot the standards and plasma samples, and process a total of 96 standards and samples by manual LLE was three-times longer than the time required for 96-well SPE or 96-well LLE (4 h, 50 min vs. 1 h, 43 min). Even more importantly, the time the bioanalyst physically spent on the 96-well LLE or 96-well SPE procedure was only a small fraction of the time spent on the manual LLE procedure (<10 min vs. 4 h, 10 min). It should be noted that the 96-well SPE procedure incorporated the two steps of evaporation of the eluates to dryness and subsequent reconstitution of the dried extract. The total time required for the 96-well SPE could be reduced by 50% if the eluates were injected directly, eliminating the drying and reconstitution steps, which is achievable when sensitivity is less of an issue.     

Efficient,Noninvasive Genetic Sampling for Monitoring Reintroduced Wolves

ABSTRACT Traditional methods of monitoring gray wolves (Canis lupus) are expensive and invasive and require extensive efforts to capture individual animals. Noninvasive genetic sampling (NGS) is an alternative method that can provide data to answer management questions and complement already-existing methods. In a 2-year study, we tested this approach for Idaho gray wolves in areas of known high and low wolf density. To focus sampling efforts across a large study area and increase our chances of detecting reproductive packs, we visited 964 areas with landscape characteristics similar to known wolf rendezvous sites. We collected scat or hair samples from 20% of sites and identified 122 wolves, using 8–9 microsatellite loci. We used the minimum count of wolves to accurately detect known differences in wolf density. Maximum likelihood and Bayesian single-session population estimators performed similarly and accurately estimated the population size, compared with a radiotelemetry population estimate, in both years, and an average of 1.7 captures per individual were necessary for achieving accurate population estimates. Subsampling scenarios revealed that both scat and hair samples were important for achieving accurate population estimates, but visiting 75% and 50% of the sites still gave reasonable estimates and reduced costs. Our research provides managers with an efficient and accurate method for monitoring high-density and low-density wolf populations in remote areas.     

Association between the CYP1A1 T3801C polymorphism and risk of cancer: Evidence from 268 case–control studies

T3801C is a common polymorphism in CYP1A1, showing differences in its biological functions. Case–control studies have been performed to elucidate the role of T3801C in cancer, although the results are conflicting and heterogeneous. Hence, we performed a meta-analysis to investigate the association between cancer susceptibility and T3801C (55,963 cases and 76,631 controls from 268 studies) polymorphism in different inheritance models. We used odds ratios with 95% confidence intervals to assess the strength of the association. Overall, significantly increased cancer risk was observed in any genetic model (dominant model: odds ratio [OR] = 1.14, 95% confidence interval [CI] = 1.09–1.19; recessive model: OR = 1.23, 95% CI = 1.12–1.34; CC vs. TT: OR = 1.31, 95% CI = 1.19–1.45; TC vs. TT: OR = 1.12, 95% CI = 1.07–1.18; additive model: OR = 1.14, 95% CI = 1.09–1.19) when all eligible studies were pooled into the meta-analysis. In further stratified and sensitivity analyses, the elevated risk remained for subgroups of cervical cancer, head and neck cancer, hepatocellular cancer, leukemia, lung cancer, prostate cancer and breast cancer. In addition, significantly decreased colorectal cancer risk was also observed. In summary, this meta-analysis suggests that the participation of CYP1A1 T3801C is a genetic susceptibility for some cancer types. Moreover, our work also points out the importance of new studies for T3801C association in some cancer types, such as gallbladder cancer, Asians of acute myeloid leukemia, and thyroid cancer, where at least some of the covariates responsible for heterogeneity could be controlled, to obtain a more conclusive understanding about the function of the CYP1A1 T3801C polymorphism in cancer development.     

Analysis of tissue cadmium distribution in chronic cadmium-exposed mice using in-air micro-PIXE

This study undertook the analysis of tissue cadmium (Cd) distribution using in-air micro-particle-induced X-ray emission (PIXE) and the examination of the involvement of metal ions in parenteral Cd toxicity. A mouse was injected intraperitoneally with 3 mg/kg body weight of CdCl₂ thrice weekly. After 27 wk, the liver and kidney were excised and fixed in 10% formalin solution for 4 h and then embedded in paraffin. Thin paraffin sections were used to analyze trace elements with in-air micro-PIXE and to examine metallothionein protein and histological changes. Cd distribution was determined by micro-PIXE in the liver and renal cortex of the Cd-exposed mouse, and the net Cd count was higher in the liver than in the renal cortex. The net iron (Fe) count was higher in the liver of the Cd-exposed mouse compared to the control, and an opposite tendency was observed in the renal cortex. Wide cellular Cd distribution was demonstrated in the liver and renal cortex of the chronic Cd-exposed mouse compared to the control. Metallothionein staining was increased by chronic exposure to Cd both in the liver and kidney, and nephrotoxicity was more apparent than hepatotoxicity. The modification of tissue Fe and calcium distribution by an intraperitoneal injection of Cd might be involved in Cd-induced toxicity.     

Trends in solventless sample preparation techniques for environmental analysis

The paper presents recent trends in solventless sample preparation techniques for environmental analysis. First, a general classification of solventless methods is given. Next, three of them, treated as preferable techniques, i.e. SPME, SDME and HS, are presented in detail, with respect to their usability and effectiveness for environmental samples. Examples of all discussed techniques are given in the tables.     

Hair Sampling Techniques for River Otters

ABSTRACT River otter (Lontra canadensis) populations have been difficult to monitor and information on densities is lacking throughout their range. To obtain DNA-based population estimates of river otters we developed 2 traps to capture hair; a modified body-snare and a modified foot-hold trap. Of 82 traps activated 77 captured hairs (94%). Traps snagged 3–20 guard hairs per capture. Our capture rates of otter hair ranged from one capture per 3.6 trap nights to one capture per 156.6 trap-nights. Our traps provide an effective, noninvasive technique for obtaining hair DNA from individual river otters.