Mitochondrial DNA polymorphisms in a sample of Albanian population (Tirana)

RFLPs of mtDNA for HpaI, BamHI, HaeII, MspI, AvaII and HincII were analysed in a sample of 100 from collected in Tirana (Albania). Eighteen mtDNA types were identified, four of which are new: two because of new morphs for Hpa/HincII (HpaI-9^Tir/HincII-17^Tir) and AvaII (AvaII-35Tir), and two because of new associations between morphs which were already known. Albanian data were compared with corresponding ones from Calabrians (Southern Italians) and Arbreshes (people of Albanian ancestry living in Calabria). Even though the examined mtDNA markers do not reveal important differences among the three groups, the analysis of both morphs and types shows a trend which places Arbreshes closer to Calabrians than to Albanians.     

Reflection of working memory: ERP mnemonic effects

The study of working memory often utilizes a delayed matching to sample paradigm (DMS). Typically in the matching condition, the test and sample stimuli are identical, raising the possible confound of retinotopic projections for the matching stimuli in contrast to the non-matching stimuli. In the present study, 65 healthy subjects performed a modified delayed matching to sample task while monitoring their ERP waveforms. The stimuli consisted of 60 different sample stimuli (S1) and 60 different test stimuli (S2). Half of the S2s were complementary to the sample stimuli (Fit), the other half of the S2s were not complementary (Nonfit). After S2, the subjects pressed one of the buttons to indicate whether the test stimulus fits the sample stimulus. Our statistical results indicated that the ERPs to sample stimuli differed from the ERPs to test stimuli from 200 ms poststimulus to the end of the recording epoch. The ERPs to fitting stimuli were significantly different from those to non-fitting stimuli from 200 to 400 ms poststimulus. The ERP patterns in the present study may reflect ERP mnemonic effect for working memory. Our results ruled out the retinotopic confound as a potential mediator variable, and are in agreement with other animal or human neurophysiological studies on memory.     

Effects of sample size on the performance of species distribution models

A wide range of modelling algorithms is used by ecologists, conservation practitioners, and others to predict species ranges from point locality data. Unfortunately, the amount of data available is limited for many taxa and regions, making it essential to quantify the sensitivity of these algorithms to sample size. This is the first study to address this need by rigorously evaluating a broad suite of algorithms with independent presence–absence data from multiple species and regions. We evaluated predictions from 12 algorithms for 46 species (from six different regions of the world) at three sample sizes (100, 30, and 10 records). We used data from natural history collections to run the models, and evaluated the quality of model predictions with area under the receiver operating characteristic curve (AUC). With decreasing sample size, model accuracy decreased and variability increased across species and between models. Novel modelling methods that incorporate both interactions between predictor variables and complex response shapes (i.e. GBM, MARS-INT, BRUTO) performed better than most methods at large sample sizes but not at the smallest sample sizes. Other algorithms were much less sensitive to sample size, including an algorithm based on maximum entropy (MAXENT) that had among the best predictive power across all sample sizes. Relative to other algorithms, a distance metric algorithm (DOMAIN) and a genetic algorithm (OM-GARP) had intermediate performance at the largest sample size and among the best performance at the lowest sample size. No algorithm predicted consistently well with small sample size ( n  < 30) and this should encourage highly conservative use of predictions based on small sample size and restrict their use to exploratory modelling.     

Changes in the Structure of Chromatin in Pea Shoots upon a Shift in Growth Temperature from 2C to 25C

Low temperature-resistant pea seedlings (Pisum sativum cv. Alaska),which had been kept at 2C in darkness, during which time growthhad been almost totally suppressed, were either transferredto 25C (warmed sample) or kept at 2C (chilled sample) for1 day. Rapid growth occurred at 25C. The number of nuclei inthe shoot tips of the warmed sample was twice that in the chilledsample. Nuclei prepared from the warmed and chilled samples were digestedby micrococcal nuclease at the same rate and appeared to havenucleosomal repeats of similar length, namely, approximately150 base pairs, and they generated similar patterns in termsof ladders of multimers of the basic fragment. However, significant differences in terms of chromatin structurewere observed when the chromatins isolated from the warmed andchilled samples were compared. The digestibility by DNase IIwas apparently greater in the case of chromatin prepared fromthe warmed sample. The analysis of the melting curves of thechromatins revealed three phases. The T_m of each phase was higherin the case of chromatin prepared from the chilled sample. Furthermore,an analysis by sucrose density gradient centrifugation revealedthat the chromatin prepared from the chilled sample migratedto a region of slightly higher density in the gradient thanthe chromatin from the warmed sample. Taken together, theseresults suggest that the structure of the chromatin preparedfrom the chilled sample may be more compact than that of thechromatin prepared from the warmed sample. (Received December 10, 1992; Accepted June 23, 1993)     

Theory of the effects of population structure and sampling on patterns of linkage disequilibrium applied to genomic data from humans

We develop predictions for the correlation of heterozygosity and for linkage disequilibrium between two loci using a simple model of population structure that includes migration among local populations, or demes. We compare the results for a sample of size two from the same deme (a single-deme sample) to those for a sample of size two from two different demes (a scattered sample). The correlation in heterozygosity for a scattered sample is surprisingly insensitive to both the migration rate and the number of demes. In contrast, the correlation in heterozygosity for a single-deme sample is sensitive to both, and the effect of an increase in the number of demes is qualitatively similar to that of a decrease in the migration rate: both increase the correlation in heterozygosity. These same conclusions hold for a commonly used measure of linkage disequilibrium (r(2)). We compare the predictions of the theory to genomic data from humans and show that subdivision might account for a substantial portion of the genetic associations observed within the human genome, even though migration rates among local populations of humans are relatively large. Because correlations due to subdivision rather than to physical linkage can be large even in a single-deme sample, then if long-term migration has been important in shaping patterns of human polymorphism, the common practice of disease mapping using linkage disequilibrium in "isolated" local populations may be subject to error.     

The late Neandertal supraorbital fossils from Vindija Cave,Croatia: a biased sample?

The late Neandertal sample from Vindija (Croatia) has been described as transitional between the earlier Central European Neandertals from Krapina (Croatia) and modern humans. However, the morphological differences indicating this transition may rather be the result of different sex and/or age compositions between the samples. This study tests the hypothesis that the metric differences between the Krapina and Vindija supraorbital samples are due to sampling bias. We focus upon the supraorbital region because past studies have posited this region as particularly indicative of the Vindija sample's transitional nature. Furthermore, the supraorbital region varies significantly with both age and sex.We analyzed four chords and two derived indices of supraorbital torus form as defined by Smith & Ranyard (1980, Am. J. phys. Anthrop.93, pp. 589-610). For each variable, we analyzed relative sample bias of the Krapina and Vindija samples using three sampling methods. In order to test the hypothesis that the Vindija sample contains an over-representation of females and/or young while the Krapina sample is normal or also female/young biased, we determined the probability of drawing a sample of the same size as and with a mean equal to or less than Vindija's from a Krapina-based population. In order to test the hypothesis that the Vindija sample is female/young biased while the Krapina sample is male/old biased, we determined the probability of drawing a sample of the same size as and with a mean equal or less than Vindija's from a generated population whose mean is halfway between Krapina's and Vindija's. Finally, in order to test the hypothesis that the Vindija sample is normal while the Krapina sample contains an over-representation of males and/or old, we determined the probability of drawing a sample of the same size as and with a mean equal to or greater than Krapina's from a Vindija-based population. Unless we assume that the Vindija sample is female/young and the Krapina sample is male/old biased, our results falsify the hypothesis that the metric differences between the Krapina and Vindija samples are due to sample bias.     

Influence of macroinvertebrate sample size on bioassessment of streams

In order to standardise biological assessment of surface waters in Europe, a standardised method for sampling, sorting and identification of benthic macroinvertebrates in running waters was developed during the AQEM project. The AQEM method has proved to be relatively time-consuming. Hence, this study explored the consequences of a reduction in sample size on costs and bioassessment results. Macroinvertebrate samples were collected from six different streams: four streams located in the Netherlands and two in Slovakia. In each stream 20 sampling units were collected with a pond net (25×25 cm), over a length of approximately 25 cm per sampling unit, from one or two habitats dominantly present. With the collected data, the effect of increasing sample size on variability and accuracy was examined for six metrics and a multimetric index developed for the assessment of Dutch slow running streams. By collecting samples from separate habitats it was possible to examine whether the coefficient of variation (CV; measure of variability) and the mean relative deviation from the “reference” sample (MRD; measure of accuracy) for different metrics depended only on sample size, or also on the type of habitat sampled. Time spent on sample processing (sorting and identification) was recorded for samples from the Dutch streams to assess the implications of changes in sample size on the costs of sample processing. Accuracy of metric results increased and variability decreased with increasing sample size. Accuracy and variability varied depending on the habitat and the metric, hence sample size should be based on the specific habitats present in a stream and the metric(s) used for bioassessment. The AQEM sampling method prescribes a multihabitat sample of 5 m. Our results suggest that a sample size of less than 5 m is adequate to attain a CV and MRD of ≤ 10% for the metrics ASPT (Average Score per Taxon), Saprobic Index and type Aka+Lit+Psa (%) (the percentage of individuals with a preference for the akal, littoral and psammal). The metrics number of taxa, number of individuals and EPT-taxa (%) required a multihabitat sample size of more than 5 m to attain a CV and MRD of ≤ 10%. For the metrics number of individuals and number of taxa a multihabitat sample size of 5 m is not even adequate to attain a CV and MRD of ≤ 20%. Accuracy of the multimetric index for Dutch slow running streams can be increased from ≤ 20 to ≤ 10% with an increase in labour time of 2 h. Considering this low increase in costs and the possible implications of incorrect assessment results it is recommended to strive for this ≤ 10% accuracy. To achieve an accuracy of ≤ 10% a multihabitat sample of the four habitats studied in the Netherlands would require a sample size of 2.5 m and a labour time of 26 h (excluding identification of Oligochaeta and Diptera) or 38 h (including identification of Oligochaeta and Diptera). Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Reverse Sample Genome Probing, a New Technique for Identification of Bacteria in Environmental Samples by DNA Hybridization, and Its Application to the Identification of Sulfate-Reducing Bacteria in Oil Field Samples

A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a “standard”) to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples.     

Possible genomic imprinting of three human obesity-related genetic loci

To detect potentially imprinted, obesity-related genetic loci, we performed genomewide parent-of-origin linkage analyses under an allele-sharing model for discrete traits and under a family regression model for obesity-related quantitative traits, using a European American sample of 1,297 individuals from 260 families, with 391 microsatellite markers. We also used two smaller, independent samples for replication (a sample of 370 German individuals from 89 families and a sample of 277 African American individuals from 52 families). For discrete-trait analysis, we found evidence for a maternal effect in chromosome region 10p12 across the three samples, with LOD scores of 5.69 (single-point) and 4.52 (multipoint) for the pooled sample. For quantitative-trait analysis, we found the strongest evidence for a maternal effect (single-point LOD of 2.85; multipoint LOD of 4.01 for body mass index [BMI] and 3.69 for waist circumference) in region 12q24 and for a paternal effect (single-point LOD of 4.79; multipoint LOD of 3.72 for BMI) in region 13q32, in the European American sample. The results suggest that parent-of-origin effects, perhaps including genomic imprinting, may play a role in human obesity.     

On Double Sampling Ratio-Cum-Product-Type Estimator with Independent Samples

There are two cases in double sampling; case(i) when the second sample is a sub-sample from preliminary large sample, and case(ii) when the second sample is not a sub-sample from the preliminary large sample. Recently SISODIA and DWIVEDI (1981) proposed a ratio cum product-type estimator in double sampling in which they have studied the properties of this estimator under case (i). In this paper, we have made an attempt to study the properties of the same estimator under case (ii). It is found that the estimator is superior than double sampling linear regression estimator, usual ratio estimator, product estimator and among others. The estimator is also compared with simple mean per unit for a given cost of the survey.     

A technique for optimizing sample size (replication)

Current methods for estimating sample size are not appropriate in situations where a minimum detectable difference cannot be specified a priori. For these cases, a method is proposed which incorporates resolving power as a primary factor and expended effort (feasibility) as a secondary factor. Trade-offs between resolving power and expended effort are evaluated over a range of sample sizes. The Se is used as a measure of resolving power and the greatest limiting factor on sample size is used as a measure of sample effort. Techniques for obtaining a range of sample sizes from a single large collection or from a preliminary experiment also are given.     

Sampling considerations for garden symphylans (Order: Cephalostigmata) in western Oregon

Sampling recommendations were developed for a potato bait sampling method used to estimate garden symphylan (Scutigerella immaculata Newport) densities in western Oregon. Sample size requirements were developed using Taylor's power law to describe the relationship between sample means and variances. Developed sampling recommendations performed well at sample sizes of 30 and greater, when validated by resampling a cohort of 40 independent data sets. Sample size requirements for the bait sampling method were 1.5 times greater than the requirements for the soil sampling method over densities from 1 to 20 S. immaculata per sample unit. As S. immaculata densities increased from April to May, sample size requirements decreased by 36% for fixed precision levels. For sampling in April, decreasing the damage threshold from 20, to 10 and five S. immaculata per sample unit, required a 1.6 and 2.5 times greater sample size requirement, respectively, for a fixed precision level (c) appropriate for pest management (c = 0.25). The bait sampling method provides an efficient reliable alternative to the standard soil sampling method used to monitor garden symphylan populations.     

Chiral aspects of the metabolism of ethosuximide

Ethosuximide is a chiral drug substance primarily indicated for the treatment of absence seizures. This drug is used clinically as the racemate. The urinary metabolites of ethosuximide (following i.p. administration of the racemate or individual enantiomers to rats) have been studied using chiral gas chromatography (GC) and gas chromatography-mass spectroscopy (GCMS). The metabolites identified were unchanged ethosuximide enantiomers, all four stereoisomers of 2-(1-hydroxyethyl)-2-methylsuccinimide, and a single stereoisomer of 2-ethyl-3-hydroxy-2-methylsuccinimide [derived from (R)-ethosuximide]. Preliminary quantitative studies indicate a degree of stereoselectivity in the fate of ethosuximide since the ratio of (R)- to (S)-ethosuximide in the urine was found to be 0.77:1 (0–24 h sample), 0.64:1 (24–48 h sample), and 0.83:1 (48–72 h sample). This would suggest that the (R)-isomer is preferentially metabolised. Results obtained following the administration of individual enantiomers of ethosuximide indicate that the 2-(1-hydroxyethyl)-2-methylsuccinimide diastereoisomers derived from (R)-ethosuximide are produced in approximately equal proportions [ratio 1.05:1 (0–24 h sample), 1.10:1 (24–48 h sample)], whilst those from (S)-ethosuximide are produced in unequal proportions [ratio 1.65:1 (0–24 h sample), 1.74:1 (24–48 h sample)]. © 1995 Wiley-Liss, Inc.     

Estimating the age of the common ancestor of a sample of DNA sequences

We present a simple Monte Carlo method for estimating the age of the most recent common ancestor (MRCA) of a sample of DNA sequences. We show that Templeton's (1993) estimator of the age of the MRCA based on the maximum number of nucleotide differences between two sequences in a sample is inaccurate, and we demonstrate the new method by reanalyzing a sample of DNA sequences from human Y chromosomes and a sample of human Alu sequences.      

High-Quality Exome Sequencing of Whole-Genome Amplified Neonatal Dried Blood Spot DNA

Stored neonatal dried blood spot (DBS) samples from neonatal screening programmes are a valuable diagnostic and research resource. Combined with information from national health registries they can be used in population-based studies of genetic diseases. DNA extracted from neonatal DBSs can be amplified to obtain micrograms of an otherwise limited resource, referred to as whole-genome amplified DNA (wgaDNA). Here we investigate the robustness of exome sequencing of wgaDNA of neonatal DBS samples. We conducted three pilot studies of seven, eight and seven subjects, respectively. For each subject we analysed a neonatal DBS sample and corresponding adult whole-blood (WB) reference sample. Different DNA sample types were prepared for each of the subjects. Pilot 1: wgaDNA of 2x3.2mm neonatal DBSs (DBS_2x3.2) and raw DNA extract of the WB reference sample (WB_ref). Pilot 2: DBS_2x3.2, WB_ref and a WB_ref replica sharing DNA extract with the WB_ref sample. Pilot 3: DBS_2x3.2, WB_ref, wgaDNA of 2x1.6 mm neonatal DBSs and wgaDNA of the WB reference sample. Following sequencing and data analysis, we compared pairwise variant calls to obtain a measure of similarity—the concordance rate. Concordance rates were slightly lower when comparing DBS vs WB sample types than for any two WB sample types of the same subject before filtering of the variant calls. The overall concordance rates were dependent on the variant type, with SNPs performing best. Post-filtering, the comparisons of DBS vs WB and WB vs WB sample types yielded similar concordance rates, with values close to 100%. WgaDNA of neonatal DBS samples performs with great accuracy and efficiency in exome sequencing. The wgaDNA performed similarly to matched high-quality reference—whole-blood DNA—based on concordance rates calculated from variant calls. No differences were observed substituting 2x3.2 with 2x1.6 mm discs, allowing for additional reduction of sample material in future projects.     

Evaluation of juvenile stature and body mass prediction

This investigation evaluates the performance of juvenile stature (from tibia and radius lengths) and body mass (from breadth of the femoral distal metaphysis) prediction equations based on the Denver Growth Study sample (Ruff C. 2007. Am J Phys Anthropol 133 698-716). The sample used here for evaluation is an independent sample of juveniles brought to the Franklin County (Ohio) Coroner in 1990-1991. The Ohio sample differs somewhat from the Denver reference sample: it includes approximately 25% African-Americans (rather than all European-Americans), a significant number of right limb bones were measured (rather than all left side), it includes a wider range of economic statuses and it includes individuals who died from disease and trauma. As such the composition and measures of the Ohio sample correspond more generally to that seen in skeletal samples so that the accuracy of the estimates from the present sample should approach those found in practical applications of these methods. Results indicate that both juvenile body mass and stature are estimated relatively accurately. Accuracy of body mass estimates for 1-13-year-old juveniles is similar for African-American and European-American males and females. The least accurate estimates are for individuals in the 8-13 years age class (excluding individuals with body mass indices greater than the age specific 95th percentile): n = 9, +/- 2.9 kg, 95% confidence interval 1.4-4.4 kg. Accuracy of stature estimates for 1-17-year-old juveniles is comparable for the tibia and radius and, as with body mass estimates, are similar for African-American and European-American males and females. For combined age, sex, and ancestry groups average accuracies are in the +/-3.5 to +/-6.5 cm range. Some limitations of the methods are discussed.     

A Markov chain Monte Carlo strategy for sampling from the joint posterior distribution of pedigrees and population parameters under a Fisher-Wright model with partial selfing

A simple population genetic model is presented for a hermaphrodite annual species, allowing both selfing and outcrossing. Those male gametes (pollen) responsible for outcrossing are assumed to disperse much further than seeds. Under this model, the pedigree of a sample from a single locality is loop-free. A novel Markov chain Monte Carlo strategy is presented for sampling from the joint posterior distribution of the pedigree of such a sample and the parameters of the population genetic model (including the selfing rate) given the genotypes of the sampled individuals at unlinked marker loci. The computational costs of this Markov chain Monte Carlo strategy scale well with the number of individuals in the sample, and the number of marker loci, but increase exponentially with the age (time since colonisation from the source population) of the local population. Consequently, this strategy is particularly suited to situations where the sample has been collected from a population which is the result of a recent colonisation process.     

Investigation of the distribution of deoxynivalenol and ochratoxin A contamination within a 26 t truckload of wheat kernels

A study was conducted to determine the distribution of deoxynivalenol (DON) and ochratoxin A (OTA) in a lot of 261 of wheat kernels. Within this study, two different sampling and sample preparation strategies were carried out. On the one hand, following the official commission regulation 401/2006/EC, an aggregate sample out of 100 incremental samples was build, homogenized and prepared for laboratory analysis. On the other hand each individual subsample was investigated for its deoxynivalenol and ochratoxin A content. The determined concentration of DON in the individual samples was in a range from 830 up to 2655 (μg/kg, for OTA results ranged from < 0.2 up to 8.6 μg/kg. Thus, a coefficient of variance of 25% for DON and 200% for OTA was achieved. From this, a spot formation for OTA was observed and the average value of the 100 incremental samples did not correspond to the achieved value for the aggregate sample. While the DON contamination at this concentration range seems to be more even, consequently the result of the aggregate sample was in accordance with the average value. In addition a sample communition study was performed to answer the question whether the time consuming process of grinding of the whole aggregate sample is necessary or not. The results of this study show that contamination of whole wheat kernels with DON is at the same level within a 1 kg sample (CV 16%), while OTA contamination shows high variability (CV 94%). At least for OTA this study indicated that an extensive and complete sample communition of the high volume aggregate sample is necessary.     

The effect of sample duration on the quantification of stream drift

1. We performed computer simulations and a field experiment to determine the effect that sample duration and, thus, sample volume had on estimates of drift density and sample variance. 2. In computer simulations, when the spatial arrangement of individuals in the water column approximated a random and a contagious-random distribution, estimated mean drift density was not significantly affected by sample duration, but sample variance decreased curvilinearly as sample duration increased. 3. Similar results were obtained in field experiments in habitats of high and low water velocity. 4. Our findings from an Albertan stream indicate that the relationship between sample variance (i.e. coefficient of variation) and duration of drift samples is curvilinear. This relationship affected the number of samples required to achieve a specific level of precision (i.e. a standard error within 10% of the mean). For estimates in low and high current velocities, sample variation was halved by increasing the duration of sample collections from 10 to 20 min. The increased precision obtained with samples of 20 min duration reduced the amount of drift material that needed to be processed by approximately 50% compared with an equivalent 10% level of precision for samples of 10 min duration. This reduction in the number of samples required to obtain a given level of precision has important consequences to the cost of processing drift samples. 5. Thus to optimize studies of stream invertebrate drift, both in terms of sample precision and processing effort, researchers must consider the effect that sample volume has on the variance of drift density estimates. Because researchers generally use drift nets with similar-sized apertures (>300cm²), the problem for specific field applications becomes one of optimizing sample duration relative to variance estimates for drift density.