Prey capture by harbour porpoises

DEFF Research Database (Denmark)

Verfuss, Ursula; Miller, Lee; Pilz, Peter

their ultrasonic clicks as biosonar for orientation and detection of prey (mostly smaller pelagic and bottom dwelling fish), and for communication.  For studying wild animals, hydrophone arrays [Villadsgaard et al. J.Exp.Biol. 210 (2007)] and acoustic (time/depth) tags [Akamatsu et al. Deep Sea Research II 54...... (2007)] have been used.  For studying captive animals, arrays and video techniques [Verfuß et al. J.Exp.Biol. 208 (2005)] as well as miniature acoustic-behavioral tags [Deruiter et al. JASA 123 (2008)] have been used.  While searching for prey, harbor porpoises use clicks at long intervals (>50 ms......) that progressively decrease when closing on a landmark.  The source levels of captive animals reduce by about half for each halving of the distance to the target.  After detecting the prey, the click interval first stabilizes at about 50 ms and then becomes progressively shorter while approaching the prey...

Molecular detection of Anaplasma phagocytophilum DNA in the lesser horseshoe bat (Rhinolophus hipposideros) guano.

Science.gov (United States)

Afonso, E; Goydadin, A-C

2018-05-30

Although bats are increasingly recognised as potential reservoir hosts of human zoonotic pathogens, bacteria in bats are still poorly studied. To investigate the DNA faecal prevalence of the bacterium Anaplasma phagocytophilum, we sampled 23 lesser horseshoe bat (Rhinolophus hipposideros) maternity colonies located in buildings (churches, barns) in rural villages of eastern France. A total of 552 faecal samples were collected from 278 individuals. Anaplasma phagocytophilum DNA was detected in the faeces of 63 individuals (22.7%). Such high prevalence might suggest persistent infection in bats and/or a frequent consumption of insect preys carrying bacteria. Faecal DNA prevalence varied highly among colonies but was not related to the colony size. Faecal DNA prevalence was the highest in the Jura Department, where the density of ticks is known to be the highest across the study area. Because the sampled bats live in close proximity to humans, we discuss how concerning the presence of A. phagocytophilum DNA in bat guano is for humans frequenting places of worship that shelter bats. We also advocate future research to understand what a high faecal DNA prevalence in bat guano really implicates in terms of bacteria transmission.

Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding.

Science.gov (United States)

Aizpurua, Ostaizka; Budinski, Ivana; Georgiakakis, Panagiotis; Gopalakrishnan, Shyam; Ibañez, Carlos; Mata, Vanessa; Rebelo, Hugo; Russo, Danilo; Szodoray-Parádi, Farkas; Zhelyazkova, Violeta; Zrncic, Vida; Gilbert, M Thomas P; Alberdi, Antton

2018-02-01

The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study, we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary niche is shaped by the extension and type of agricultural fields. We employed a dual-primer DNA metabarcoding approach to characterize arthropod 16S and COI DNA sequences within bat faecal pellets collected across 16 Southern European localities, to first characterize the bat species' dietary niche, second measure the incidence of agricultural pests across their ranges and third assess whether geographical dietary variation responds to climatic, landscape diversity, agriculture type and vegetation productivity factors. We detected 12 arthropod orders, among which lepidopterans were predominant. We identified >200 species, 44 of which are known to cause agricultural damage. Pest species were detected at all but one sampling site and in 94% of the analysed samples. Furthermore, the dietary diversity of M. schreibersii exhibited a negative linear relation with the area of intensive agricultural fields, thus suggesting crops restrict the dietary niche of bats to prey taxa associated with agricultural production within their foraging range. Overall, our results imply that M. schreibersii might be a valuable asset for biological pest suppression in a variety of agricultural productions and highlight the dynamic interplay between wildlife and agricultural systems. © 2017 John Wiley & Sons Ltd.

Water velocity influences prey detection and capture by drift-feeding juvenile coho salmon (Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss irideus)

Science.gov (United States)

John J. Piccolo; Nicholas F. Hughes; Mason D. Bryant

2008-01-01

We examined the effects of water velocity on prey detection and capture by drift-feeding juvenile coho salmon (Oncorhynchus kisutch) and steelhead (sea-run rainbow trout,Oncorhynchus mykiss irideus) in laboratory experiments. We used repeated-measures analysis of variance to test the effects of velocity, species, and the velocity x species interaction on prey capture...

Are all prey created equal? A review and synthesis of differential predation on prey in substandard condition

Science.gov (United States)

Mesa, Matthew G.; Poe, Thomas P.; Gadomski, Dena M.; Petersen, James H.

1994-01-01

Our understanding of predator-prey interactions in fishes has been influenced largely by research assuming that the condition of the participants is normal. However, fish populations today often reside in anthropogenically altered environments and are subjected to many kinds of stressors, which may reduce their ecological performance by adversely affecting their morphology, physiology, or behaviour. One consequence is that either the predator or prey, or both, may be in a substandard condition at the time of an interaction. We reviewed the literature on predator-prey interactions in fishes where substandard prey were used as experimental groups. Although most of this research indicates that such prey are significantly more vulnerable to predation, prey condition has rarely been considered in ecological theory regarding predator-prey interactions. The causal mechanisms for increased vulnerability of substandard prey to predation include a failure to detect predators, lapses in decision-making, poor fast-start performance, inability to shoal effectively, and increased prey conspicuousness. Despite some problems associated with empirical predator-prey studies using substandard prey, their results can have theoretical and applied uses, such as in ecological modelling or justification of corrective measures to be implemented in the wild. There is a need for more corroborative field experimentation, a better understanding of the causal mechanisms behind differential predation, and increased incorporation of prey condition into the research of predator-prey modellers and theoreticians. If the concept of prey condition is considered in predator-prey interactions, our understanding of how such interactions influence the structure and dynamics of fish communities is likely to change, which should prove beneficial to aquatic ecosystems.

Detection of Non-Amplified Genomic DNA

CERN Document Server

Corradini, Roberto

2012-01-01

This book offers a state-of-the-art overview on non amplified DNA detection methods and provides chemists, biochemists, biotechnologists and material scientists with an introduction to these methods. In fact all these fields have dedicated resources to the problem of nucleic acid detection, each contributing with their own specific methods and concepts. This book will explain the basic principles of the different non amplified DNA detection methods available, highlighting their respective advantages and limitations. The importance of non-amplified DNA sequencing technologies will be also discussed. Non-amplified DNA detection can be achieved by adopting different techniques. Such techniques have allowed the commercialization of innovative platforms for DNA detection that are expected to break into the DNA diagnostics market. The enhanced sensitivity required for the detection of non amplified genomic DNA has prompted new strategies that can achieve ultrasensitivity by combining specific materials with specifi...

Optimal intermittent search strategies: smelling the prey

International Nuclear Information System (INIS)

Revelli, J A; Wio, H S; Rojo, F; Budde, C E

2010-01-01

We study the kinetics of the search of a single fixed target by a searcher/walker that performs an intermittent random walk, characterized by different states of motion. In addition, we assume that the walker has the ability to detect the scent left by the prey/target in its surroundings. Our results, in agreement with intuition, indicate that the prey's survival probability could be strongly reduced (increased) if the predator is attracted (or repelled) by the trace left by the prey. We have also found that, for a positive trace (the predator is guided towards the prey), increasing the inhomogeneity's size reduces the prey's survival probability, while the optimal value of α (the parameter that regulates intermittency) ceases to exist. The agreement between theory and numerical simulations is excellent.

Optimal intermittent search strategies: smelling the prey

Energy Technology Data Exchange (ETDEWEB)

Revelli, J A; Wio, H S [Instituto de Fisica de Cantabria, Universidad de Cantabria and CSIC, E-39005 Santander (Spain); Rojo, F; Budde, C E [Fa.M.A.F., Universidad Nacional de Cordoba, Ciudad Universitaria, X5000HUA Cordoba (Argentina)

2010-05-14

We study the kinetics of the search of a single fixed target by a searcher/walker that performs an intermittent random walk, characterized by different states of motion. In addition, we assume that the walker has the ability to detect the scent left by the prey/target in its surroundings. Our results, in agreement with intuition, indicate that the prey's survival probability could be strongly reduced (increased) if the predator is attracted (or repelled) by the trace left by the prey. We have also found that, for a positive trace (the predator is guided towards the prey), increasing the inhomogeneity's size reduces the prey's survival probability, while the optimal value of {alpha} (the parameter that regulates intermittency) ceases to exist. The agreement between theory and numerical simulations is excellent.

Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

Science.gov (United States)

McCutchen-Maloney, Sandra L.

2002-01-01

Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

Toxoplasmosis in prey species and consequences for prevalence in feral cats: not all prey species are equal.

Science.gov (United States)

Afonso, E; Thulliez, P; Pontier, D; Gilot-Fromont, E

2007-12-01

Toxoplasma gondii is largely transmitted to definitive felid hosts through predation. Not all prey species represent identical risks of infection for cats because of differences in prey susceptibility, exposure and/or lifespan. Previously published studies have shown that prevalence in rodent and lagomorph species is positively correlated with body mass. We tested the hypothesis that different prey species have different infection risks by comparing infection dynamics of feral cats at 4 sites in the sub-Antarctic Kerguelen archipelago which differed in prey availability. Cats were trapped from 1994 to 2004 and anti-T. gondii IgG antibodies were detected using the modified agglutination test (> or =1:40). Overall seroprevalence was 51.09%. Antibody prevalence differed between sites, depending on diet and also on sex, after taking into account the effect of age. Males were more often infected than females and the difference between the sexes tended to be more pronounced in the site where more prey species were available. A difference in predation efficiency between male and female cats may explain this result. Overall, our results suggest that the composition of prey items in cat diet influences the risk of T. gondii infection. Prey compositon should therefore be considered important in any understanding of infection dynamics of T. gondii.

Assessment of prey overlap between a native (Polistes humilis) and an introduced (Vespula germanica) social wasp using morphology and phylogenetic analyses of 16S rDNA.

Science.gov (United States)

Kasper, Marta L; Reeson, Andrew F; Cooper, Steven J B; Perry, Kym D; Austin, Andrew D

2004-07-01

Abstract In newly invaded communities, interspecific competition is thought to play an important role in determining the success of the invader and its impact on the native community. In southern Australia, the native Polistes humilis was the predominant social wasp prior to the arrival of the exotic Vespula germanica (Hymenoptera: Vespidae). Both species forage for similar resources (water, pulp, carbohydrate and protein prey), and concerns have arisen about potential competition between them. The aim of this study was to identify the protein foods that these wasps feed on. As many prey items are masticated by these wasps to the degree that they cannot be identified using conventional means, morphological identification was complemented by sequencing fragments of the mitochondrial 16S rRNA gene. GenBank searches using blast and phylogenetic analyses were used to identify prey items to at least order level. The results were used to construct complete prey inventories for the two species. These indicate that while P. humilis is restricted to feeding on lepidopteran larvae, V. germanica collects a variety of prey of invertebrate and vertebrate origin. Calculated values of prey overlap between the two species are used to discuss the implications of V. germanica impacting on P. humilis. Results obtained are compared to those gained by solely 'conventional' methods, and the advantages of using DNA-based taxonomy in ecological studies are emphasized.

Penguin head movement detected using small accelerometers: a proxy of prey encounter rate.

Science.gov (United States)

Kokubun, Nobuo; Kim, Jeong-Hoon; Shin, Hyoung-Chul; Naito, Yasuhiko; Takahashi, Akinori

2011-11-15

Determining temporal and spatial variation in feeding rates is essential for understanding the relationship between habitat features and the foraging behavior of top predators. In this study we examined the utility of head movement as a proxy of prey encounter rates in medium-sized Antarctic penguins, under the presumption that the birds should move their heads actively when they encounter and peck prey. A field study of free-ranging chinstrap and gentoo penguins was conducted at King George Island, Antarctica. Head movement was recorded using small accelerometers attached to the head, with simultaneous monitoring for prey encounter or body angle. The main prey was Antarctic krill (>99% in wet mass) for both species. Penguin head movement coincided with a slow change in body angle during dives. Active head movements were extracted using a high-pass filter (5 Hz acceleration signals) and the remaining acceleration peaks (higher than a threshold acceleration of 1.0 g) were counted. The timing of head movements coincided well with images of prey taken from the back-mounted cameras: head movement was recorded within ±2.5 s of a prey image on 89.1±16.1% (N=7 trips) of images. The number of head movements varied largely among dive bouts, suggesting large temporal variations in prey encounter rates. Our results show that head movement is an effective proxy of prey encounter, and we suggest that the method will be widely applicable for a variety of predators.

First experimental evidence that a harvestman (Arachnida: Opiliones detects odors of non-rotten dead prey by olfaction

Directory of Open Access Journals (Sweden)

Thaiany Miranda Costa

2013-06-01

Full Text Available Harvestmen feed on live, dead and fresh, or decomposing animals, fungi, and plant matter, being very dependent on chemoreception to find food. Herein we performed an experiment to test if individuals of Discocyrtus pectinifemur Mello-Leitão, 1937 (Gonyleptidae (n = 23 behave differently when in contact with olfactory cues from different sources (rotten prey, non-rotten prey and a control. Using dead crickets in a box covered with a mesh, and recording the time the harvestmen spent in the vicinities of the box, we show that D. pectinifemur detects non-rotten prey and stays longer on it than on the other two treatments. Our results contrast with a previous study on another species, showing that we should not generalize results obtained for one species. Our data also suggest that olfactory receptors occur on the legs of these harvestmen and that D. pectinifemur might choose dietary items based on olfaction.

Detectability matters: conspicuous nestling mouth colours make prey transfer easier for parents in a cavity nesting bird.

Science.gov (United States)

Dugas, Matthew B

2015-11-01

An often underappreciated function of signals is to notify receivers of the presence and position of senders. The colours that ornament the mouthparts of nestling birds, for example, have been hypothesized to evolve via selective pressure generated by parents' inability to efficiently detect and feed nestlings without such visually conspicuous targets. This proposed mechanism has primarily been evaluated with comparative studies and experimental tests for parental allocation bias, leaving untested the central assumption of this detectability hypothesis, that provisioning offspring is a visually challenging task for avian parents and conspicuous mouths help. To test this assumption, I manipulated the mouths of nestling house sparrows to appear minimally and maximally conspicuous, and quantified prey transfer difficulty as the total duration of a feeding event and the number of transfer attempts required. Prey transfer to inconspicuous nestlings was, as predicted, more difficult. While this suggests that detectability constraints could shape nestling mouth colour evolution, even minimally conspicuous nestlings were not prohibitively difficult for parents to feed, indicating that a more nuanced explanation for interspecific diversity in this trait is needed. © 2015 The Author(s).

[Single-molecule detection and characterization of DNA replication based on DNA origami].

Science.gov (United States)

Wang, Qi; Fan, Youjie; Li, Bin

2014-08-01

To investigate single-molecule detection and characterization of DNA replication. Single-stranded DNA (ssDNA) as the template of DNA replication was attached to DNA origami by a hybridization reaction based on the complementary base-pairing principle. DNA replication catalyzed by E.coli DNA polymerase I Klenow Fragment (KF) was detected using atomic force microscopy (AFM). The height variations between the ssDNA and the double-stranded DNA (dsDNA), the distribution of KF during DNA replication and biotin-streptavidin (BA) complexes on the DNA strand after replication were detected. Agarose gel electrophoresis was employed to analyze the changes in the DNA after replication. The designed ssDNA could be anchored on the target positions of over 50% of the DNA origami. The KF was capable of binding to the ssDNA fixed on DNA origami and performing its catalytic activities, and was finally dissociated from the DNA after replication. The height of DNA strand increased by about 0.7 nm after replication. The addition of streptavidin also resulted in an DNA height increase to about 4.9 nm due to the formation of BA complexes on the biotinylated dsDNA. The resulting dsDNA and BA complex were subsequently confirmed by agarose gel electrophoresis. The combination of AFM and DNA origami allows detection and characterization of DNA replication at the single molecule level, and this approach provides better insights into the mechanism of DNA polymerase and the factors affecting DNA replication.

Acoustic shadows help gleaning bats find prey, but may be defeated by prey acoustic camouflage on rough surfaces.

Science.gov (United States)

Clare, Elizabeth L; Holderied, Marc W

2015-09-01

Perceptual abilities of animals, like echolocating bats, are difficult to study because they challenge our understanding of non-visual senses. We used novel acoustic tomography to convert echoes into visual representations and compare these cues to traditional echo measurements. We provide a new hypothesis for the echo-acoustic basis of prey detection on surfaces. We propose that bats perceive a change in depth profile and an 'acoustic shadow' cast by prey. The shadow is more salient than prey echoes and particularly strong on smooth surfaces. This may explain why bats look for prey on flat surfaces like leaves using scanning behaviour. We propose that rather than forming search images for prey, whose characteristics are unpredictable, predators may look for disruptions to the resting surface (acoustic shadows). The fact that the acoustic shadow is much fainter on rougher resting surfaces provides the first empirical evidence for 'acoustic camouflage' as an anti-predator defence mechanism.

Detection of HBV Covalently Closed Circular DNA

Directory of Open Access Journals (Sweden)

Xiaoling Li

2017-06-01

Full Text Available Chronic hepatitis B virus (HBV infection affects approximately 240 million people worldwide and remains a serious public health concern because its complete cure is impossible with current treatments. Covalently closed circular DNA (cccDNA in the nucleus of infected cells cannot be eliminated by present therapeutics and may result in persistence and relapse. Drug development targeting cccDNA formation and maintenance is hindered by the lack of efficient cccDNA models and reliable cccDNA detection methods. Southern blotting is regarded as the gold standard for quantitative cccDNA detection, but it is complicated and not suitable for high-throughput drug screening, so more sensitive and simple methods, including polymerase chain reaction (PCR-based methods, Invader assays, in situ hybridization and surrogates, have been developed for cccDNA detection. However, most methods are not reliable enough, and there are no unified standards for these approaches. This review will summarize available methods for cccDNA detection. It is hoped that more robust methods for cccDNA monitoring will be developed and that standard operation procedures for routine cccDNA detection in scientific research and clinical monitoring will be established.

Prey aggregation is an effective olfactory predator avoidance strategy

Directory of Open Access Journals (Sweden)

Asa Johannesen

2014-05-01

Full Text Available Predator–prey interactions have a major effect on species abundance and diversity, and aggregation is a well-known anti-predator behaviour. For immobile prey, the effectiveness of aggregation depends on two conditions: (a the inability of the predator to consume all prey in a group and (b detection of a single large group not being proportionally easier than that of several small groups. How prey aggregation influences predation rates when visual cues are restricted, such as in turbid water, has not been thoroughly investigated. We carried out foraging (predation experiments using a fish predator and (dead chironomid larvae as prey in both laboratory and field settings. In the laboratory, a reduction in visual cue availability (in turbid water led to a delay in the location of aggregated prey compared to when visual cues were available. Aggregated prey suffered high mortality once discovered, leading to better survival of dispersed prey in the longer term. We attribute this to the inability of the dead prey to take evasive action. In the field (where prey were placed in feeding stations that allowed transmission of olfactory but not visual cues, aggregated (large groups and semi-dispersed prey survived for longer than dispersed prey—including long term survival. Together, our results indicate that similar to systems where predators hunt using vision, aggregation is an effective anti-predator behaviour for prey avoiding olfactory predators.

Detection of parvovirus B19 DNA in blood: Viruses or DNA remnants?

Science.gov (United States)

Molenaar-de Backer, M W A; Russcher, A; Kroes, A C M; Koppelman, M H G M; Lanfermeijer, M; Zaaijer, H L

2016-11-01

Parvovirus B19 (B19V) DNA can be detected in blood over a long period after acute infection. Several reports associate the presence of B19V DNA with disease, irrespective of timing of the initial B19V infection. This study aims to analyze the properties of B19V DNA in blood, differentiating between bare, non-infectious strands of DNA and B19V DNA in viable virions. Ten blood donors with asymptomatic acute B19V infection were followed and sampled up to 22 months after infection. The samples were treated with and without an endonuclease and tested for B19V DNA, to distinguish between DNA in virions and naked DNA. In the acute phase of infection, high levels of B19V DNA were detected, concurrent with B19V IgM antibodies. B19V DNA apparently was encapsidated, as indicated by resistance to endonuclease degradation. Subsequently, B19V DNA remained detectable for more than one year in all donors at low levels (<10 5 IU/mL). Approximately 150days after infection B19V DNA became degradable by an endonuclease, indicating that this concerned naked DNA. In some donors a second endonuclease-resistant peak occurred. Detection of B19V DNA in blood by PCR does not necessarily imply that B19V replication takes place and that infectious B19V virions are present. We propose that remnant B19V DNA strands can be released from tissues without active replication. This finding urges to reconsider an assumed role of B19V infection mainly based on B19V DNA detection in blood, a much debated subject in clinical syndromes such as myocarditis and arthritis. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessing environmental DNA detection in controlled lentic systems.

Science.gov (United States)

Moyer, Gregory R; Díaz-Ferguson, Edgardo; Hill, Jeffrey E; Shea, Colin

2014-01-01

Little consideration has been given to environmental DNA (eDNA) sampling strategies for rare species. The certainty of species detection relies on understanding false positive and false negative error rates. We used artificial ponds together with logistic regression models to assess the detection of African jewelfish eDNA at varying fish densities (0, 0.32, 1.75, and 5.25 fish/m3). Our objectives were to determine the most effective water stratum for eDNA detection, estimate true and false positive eDNA detection rates, and assess the number of water samples necessary to minimize the risk of false negatives. There were 28 eDNA detections in 324, 1-L, water samples collected from four experimental ponds. The best-approximating model indicated that the per-L-sample probability of eDNA detection was 4.86 times more likely for every 2.53 fish/m3 (1 SD) increase in fish density and 1.67 times less likely for every 1.02 C (1 SD) increase in water temperature. The best section of the water column to detect eDNA was the surface and to a lesser extent the bottom. Although no false positives were detected, the estimated likely number of false positives in samples from ponds that contained fish averaged 3.62. At high densities of African jewelfish, 3-5 L of water provided a >95% probability for the presence/absence of its eDNA. Conversely, at moderate and low densities, the number of water samples necessary to achieve a >95% probability of eDNA detection approximated 42-73 and >100 L, respectively. Potential biases associated with incomplete detection of eDNA could be alleviated via formal estimation of eDNA detection probabilities under an occupancy modeling framework; alternatively, the filtration of hundreds of liters of water may be required to achieve a high (e.g., 95%) level of certainty that African jewelfish eDNA will be detected at low densities (i.e., <0.32 fish/m3 or 1.75 g/m3).

Inferring predator behavior from attack rates on prey-replicas that differ in conspicuousness.

Directory of Open Access Journals (Sweden)

Yoel E Stuart

Full Text Available Behavioral ecologists and evolutionary biologists have long studied how predators respond to prey items novel in color and pattern. Because a predatory response is influenced by both the predator's ability to detect the prey and a post-detection behavioral response, variation among prey types in conspicuousness may confound inference about post-prey-detection predator behavior. That is, a relatively high attack rate on a given prey type may result primarily from enhanced conspicuousness and not predators' direct preference for that prey. Few studies, however, account for such variation in conspicuousness. In a field experiment, we measured predation rates on clay replicas of two aposematic forms of the poison dart frog Dendrobates pumilio, one novel and one familiar, and two cryptic controls. To ask whether predators prefer or avoid a novel aposematic prey form independently of conspicuousness differences among replicas, we first modeled the visual system of a typical avian predator. Then, we used this model to estimate replica contrast against a leaf litter background to test whether variation in contrast alone could explain variation in predator attack rate. We found that absolute predation rates did not differ among color forms. Predation rates relative to conspicuousness did, however, deviate significantly from expectation, suggesting that predators do make post-detection decisions to avoid or attack a given prey type. The direction of this deviation from expectation, though, depended on assumptions we made about how avian predators discriminate objects from the visual background. Our results show that it is important to account for prey conspicuousness when investigating predator behavior and also that existing models of predator visual systems need to be refined.

Environmental DNA (eDNA) Detection Probability Is Influenced by Seasonal Activity of Organisms.

Science.gov (United States)

de Souza, Lesley S; Godwin, James C; Renshaw, Mark A; Larson, Eric

2016-01-01

Environmental DNA (eDNA) holds great promise for conservation applications like the monitoring of invasive or imperiled species, yet this emerging technique requires ongoing testing in order to determine the contexts over which it is effective. For example, little research to date has evaluated how seasonality of organism behavior or activity may influence detection probability of eDNA. We applied eDNA to survey for two highly imperiled species endemic to the upper Black Warrior River basin in Alabama, US: the Black Warrior Waterdog (Necturus alabamensis) and the Flattened Musk Turtle (Sternotherus depressus). Importantly, these species have contrasting patterns of seasonal activity, with N. alabamensis more active in the cool season (October-April) and S. depressus more active in the warm season (May-September). We surveyed sites historically occupied by these species across cool and warm seasons over two years with replicated eDNA water samples, which were analyzed in the laboratory using species-specific quantitative PCR (qPCR) assays. We then used occupancy estimation with detection probability modeling to evaluate both the effects of landscape attributes on organism presence and season of sampling on detection probability of eDNA. Importantly, we found that season strongly affected eDNA detection probability for both species, with N. alabamensis having higher eDNA detection probabilities during the cool season and S. depressus have higher eDNA detection probabilities during the warm season. These results illustrate the influence of organismal behavior or activity on eDNA detection in the environment and identify an important role for basic natural history in designing eDNA monitoring programs.

DNA Origami-Graphene Hybrid Nanopore for DNA Detection.

Science.gov (United States)

Barati Farimani, Amir; Dibaeinia, Payam; Aluru, Narayana R

2017-01-11

DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami-graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami-graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases. The specific interactions (hydrogen bonds) between DNA origami and the translocating DNA strand yield different residence times and ionic currents. We also conclude that the speed of DNA translocation decreases due to the friction between the dangling bases at the pore mouth and the sequencing DNA strands.

A universal DNA-based protein detection system.

Science.gov (United States)

Tran, Thua N N; Cui, Jinhui; Hartman, Mark R; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C; Lis, John T; Cui, Haixin; Luo, Dan

2013-09-25

Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability.

ctDNA DLBCL Detection Lancet Oncology

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Measurement of circulating tumor DNA in blood can be used to detect disease recurrence in patients with a curable form of cancer known as diffuse large B-cell lymphoma (DLBCL). In most patients, measurement of ctDNA enabled detection of microscopic diseas

The foraging ecology of the mountain long-eared bat Plecotus macrobullaris revealed with DNA mini-barcodes.

Directory of Open Access Journals (Sweden)

Antton Alberdi

Full Text Available Molecular analysis of diet overcomes the considerable limitations of traditional techniques for identifying prey remains in bat faeces. We collected faeces from individual Mountain Long-eared Bats Plecotus macrobullaris trapped using mist nets during the summers of 2009 and 2010 in the Pyrenees. We analysed their diet using DNA mini-barcodes to identify prey species. In addition, we inferred some basic features of the bat's foraging ecology that had not yet been addressed. P. macrobullaris fed almost exclusively on moths (97.8%. As prey we detected one dipteran genus (Tipulidae and 29 moth taxa: 28 were identified at species level (23 Noctuidae, 1 Crambidae, 1 Geometridae, 1 Pyralidae, 1 Sphingidae, 1 Tortricidae, and one at genus level (Rhyacia sp., Noctuidae. Known ecological information about the prey species allowed us to determine that bats had foraged at elevations between 1,500 and 2,500 m amsl (above mean sea level, mostly in subalpine meadows, followed by other open habitats such as orophilous grasslands and alpine meadows. No forest prey species were identified in the diet. As 96.4% of identified prey species were tympanate moths and no evidence of gleaning behaviour was revealed, we suggest P. macrobullaris probably forages by aerial hawking using faint echolocation pulses to avoid detection by hearing moths. As we could identify 87.8% of the analysed sequences (64.1% of the MOTUs, Molecular Operational Taxonomic Units at species level, we conclude that DNA mini-barcodes are a very useful tool to analyse the diet of moth-specialist bats.

Prey-mediated avoidance of an intraguild predator by its intraguild prey

Science.gov (United States)

Wilson, R.R.; Blankenship, T.L.; Hooten, M.B.; Shivik, J.A.

2010-01-01

Intraguild (IG) predation is an important factor influencing community structure, yet factors allowing coexistence of IG predator and IG prey are not well understood. The existence of spatial refuges for IG prey has recently been noted for their importance in allowing coexistence. However, reduction in basal prey availability might lead IG prey to leave spatial refuges for greater access to prey, leading to increased IG predation and fewer opportunities for coexistence. We determined how the availability of prey affected space-use patterns of bobcats (Lynx rufus, IG prey) in relation to coyote space-use patterns (Canis latrans, IG predators). We located animals from fall 2007 to spring 2009 and estimated bobcat home ranges and core areas seasonally. For each bobcat relocation, we determined intensity of coyote use, distance to water, small mammal biomass, and mean small mammal biomass of the home range during the season the location was collected. We built generalized linear mixed models and used Akaike Information Criteria to determine which factors best predicted bobcat space use. Coyote intensity was a primary determinant of bobcat core area location. In bobcat home ranges with abundant prey, core areas occurred where coyote use was low, but shifted to areas intensively used by coyotes when prey declined. High spatial variability in basal prey abundance allowed some bobcats to avoid coyotes while at the same time others were forced into more risky areas. Our results suggest that multiple behavioral strategies associated with spatial variation in basal prey abundance likely allow IG prey and IG predators to coexist. ?? 2010 Springer-Verlag.

Ultraviolet absorption detection of DNA in gels

International Nuclear Information System (INIS)

Mahon, A.R.

1998-01-01

A method and apparatus for the detection and quantification of large fragments of unlabelled deoxyribonucleic acid (DNA) in agarose gels is presented. The technique is based on ultra-violet (UV) absorption by nucleotides. A deuterium lamp was used to illuminate regions of an electrophoresis gel. As DNA bands passed through the illuminated region of the gel the amount of UV light transmitted was reduced due to DNA absorption. Two detection systems were investigated. In the first system, synthetic chemical vapour deposition (CVD) diamond strip detectors were used to locate regions of DNA in the gels by detecting the transmitted light. CVD diamond has a high indirect band gap of 5.45 eV and is therefore sensitive to UV photons of wavelengths < 224 nm. A number of CVD diamond samples were characterised to investigate their suitability as detectors for this application. The detectors' quantum efficiency, UV response and time response were measured. DNA bands containing as little as 20 ng were detected by the diamond. In a second system, a deuterium lamp was used to illuminate individual sample lanes of an electrophoresis gel via an array of optical fibres. During electrophoresis the regions of DNA were detected with illumination at 260 nm, using a UV-sensitive charge coupled device (CCD). As the absorption coefficient of a DNA sample is approximately proportional to its mass, the technique is inherently quantitative. This system had a detection limit of 0.25 ng compared with 2-10 ng for the most popular conventional technique, ethidium bromide (EtBr) staining. Using this detection technique, the DNA sample remains in its native state. The removal of carcinogenic dyes from the detection procedure greatly reduces associated biological hazards. (author)

Environmental DNA (eDNA sampling improves occurrence and detection estimates of invasive burmese pythons.

Directory of Open Access Journals (Sweden)

Margaret E Hunter

Full Text Available Environmental DNA (eDNA methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR for the Burmese python (Python molurus bivittatus, Northern African python (P. sebae, boa constrictor (Boa constrictor, and the green (Eunectes murinus and yellow anaconda (E. notaeus. Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive

Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive burmese pythons.

Science.gov (United States)

Hunter, Margaret E; Oyler-McCance, Sara J; Dorazio, Robert M; Fike, Jennifer A; Smith, Brian J; Hunter, Charles T; Reed, Robert N; Hart, Kristen M

2015-01-01

Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors

Foraging efficiency of a predator flock for randomly moving prey: A simulation study

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Lee, Sang-Hee; Kwon, Ohsung

2016-03-01

Flocking behavior of animals is highly advantageous for taking food resources. The degree of the advantage is related to the ability of flock members to detect their prey and the mobility of prey individuals. In this study, to explore the relation, we constructed a model to simulate a predator flock and its randomly moving prey. The predator members have the prey detection ability, which was characterized as sensing distance, R, and a sensing angle, θ. The mobility of the prey individuals was characterized as the maximum traveling distance of an iteration time step, L. The relative flock foraging efficiency, ɛ, was defined as ɛ = 1 - (Td/Tup). Tup and Td represent the spent time for the flock to eat all prey individuals and to uptake the last remaining 10% prey, respectively. Simulation results showed that ɛ increased, maximized, and decreased with the increase of R, regardless of L. As the number of prey, N, increased, the tendency of the increasing and decreasing was diluted. The result was briefly discussed in relation to the flock foraging behavior and the development of the model toward applications for real ecosystems.

Prey capture by harbor porpoises

DEFF Research Database (Denmark)

Miller, Lee; Verfuss, Ursula

2009-01-01

their ultrasonic clicks as biosonar for orientation and detection of prey (mostly smaller pelagic and bottom dwelling fish), and for communication. For studying wild animals, hydrophone arrays and acoustic (time/depth) tags have been used. For studying captive animals, arrays and video techniques as well...

Infomechanical specializations for prey capture in knifefish

Science.gov (United States)

Maciver, Malcolm; Patankar, Neelesh; Curet, Oscar; Shirgaonkar, Anup

2007-11-01

How does an animal's mechanics and its information acquisition system work together to solve crucial behavioral tasks? We examine this question for the black ghost weakly electric knifefish (Apteronotus albifrons), which is a leading model system for the study of sensory processing in vertebrates. These animals hunt at night by detecting perturbations of a self-generated electric field caused by prey. While the fish searches for prey, it pitches at 30 . Fully resolved Navier-Stokes simulations of their swimming, which occurs through undulations of a long ribbon-like fin along the bottom edge of the body, indicates that this configuration enables maximal thrust while minimizing pitch moment. However, pitching the body also increases drag. Our analysis of the sensory volume for detection of prey shows this volume to be similar to a cylinder around the body. Thus, pitching the body enables a greater swept volume of scanned fluid. Examining the mechanical and information acquisition demands on the animal in this task gives insight into how these sometimes conflicting demands are resolved.

Optical Detection of Non-amplified Genomic DNA

Science.gov (United States)

Li, Di; Fan, Chunhai

Nucleic acid sequences are unique to every living organisms including animals, plants and even bacteria and virus, which provide a practical molecular target for the identification and diagnosis of various diseases. DNA contains heterocyclic rings that has inherent optical absorbance at 260 nm, which is widely used to quantify single and double stranded DNA in biology. However, this simple quantification method could not differentiate sequences; therefore it is not suitable for sequence-specific analyte detection. In addition to a few exceptions such as chiral-related circular dichroism spectra, DNA hybridization does not produce significant changes in optical signals, thus an optical label is generally needed for sequence-specific DNA detection with optical means. During the last two decades, we have witnessed explosive progress in the area of optical DNA detection, especially with the help of simultaneously rapidly developed nanomaterials. In this chapter, we will summarize recent advances in optical DNA detection including colorimetric, fluorescent, luminescent, surface plasmon resonance (SPR) and Raman scattering assays. Challenges and problems remained to be addressed are also discussed.

Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus)

Science.gov (United States)

Nevers, Meredith; Byappanahalli, Muruleedhara; Morris, Charles C.; Shively, Dawn; Przybyla-Kelly, Katarzyna; Spoljaric, Ashley M.; Dickey, Joshua; Roseman, Edward

2018-01-01

Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, occupancy estimates, and real-time detections of invasive species. In the Great Lakes, the round goby (Neogobius melanostomus), an invasive benthic fish from the Black Sea, has spread to encompass all five lakes and many tributaries, outcompeting or consuming native species; however, estimates of round goby abundance are confounded by behavior and habitat preference, which impact reliable methods for estimating their population. By integrating eDNA into round goby monitoring, improved estimates of biomass may be obtainable. We conducted mesocosm experiments to estimate rates of goby DNA shedding and decay. Further, we compared eDNA with several methods of traditional field sampling to compare its use as an alternative/complementary monitoring method. Environmental DNA decay was comparable to other fish species, and first-order decay was lower at 12°C (k = 0.043) than at 19°C (k = 0.058). Round goby eDNA was routinely detected in known invaded sites of Lake Michigan and its tributaries (range log10 4.8–6.2 CN/L), but not upstream of an artificial fish barrier. Traditional techniques (mark-recapture, seining, trapping) in Lakes Michigan and Huron resulted in fewer, more variable detections than eDNA, but trapping and eDNA were correlated (Pearson R = 0.87). Additional field testing will help correlate round goby abundance with eDNA, providing insight on its role as a prey fish and its impact on food webs.

Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms.

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Brown, David S; Jarman, Simon N; Symondson, William O C

2012-03-01

Little quantitative ecological information exists on the diets of most invertebrate feeding reptiles, particularly nocturnal or elusive species that are difficult to observe. In the UK and elsewhere, reptiles are legally required to be relocated before land development can proceed, but without knowledge of their dietary requirements, the suitability of receptor sites cannot be known. Here, we tested the ability of non-invasive DNA-based molecular diagnostics (454 pyrosequencing) to analyse reptile diets, with the specific aims of determining which earthworm species are exploited by slow worms (the legless lizard Anguis fragilis) and whether they feed on the deeper-living earthworm species that only come to the surface at night. Slow worm faecal samples from four different habitats were analysed using earthworm-specific PCR primers. We found that 86% of slow worms (N=80) had eaten earthworms. In lowland heath and marshy/acid grassland, Lumbricus rubellus, a surface-dwelling epigeic species, dominated slow worm diet. In two other habitats, riverside pasture and calciferous coarse grassland, diet was dominated by deeper-living anecic and endogeic species. We conclude that all species of earthworm are exploited by these reptiles and lack of specialization allows slow worms to thrive in a wide variety of habitats. Pyrosequencing of prey DNA in faeces showed promise as a practical, rapid and relatively inexpensive means of obtaining detailed and valuable ecological information on the diets of reptiles. © 2011 Blackwell Publishing Ltd.

Echolocating bats cry out loud to detect their prey

DEFF Research Database (Denmark)

Surlykke, Annemarie; Kalko, Elisabeth K V

2008-01-01

Echolocating bats have successfully exploited a broad range of habitats and prey. Much research has demonstrated how time-frequency structure of echolocation calls of different species is adapted to acoustic constraints of habitats and foraging behaviors. However, the intensity of bat calls has b...

A tiger beetle’s pursuit of prey depends on distance

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Noest, R. M.; Wang, Z. Jane

2017-04-01

Tiger beetles pursue prey by adjusting their heading according to a time-delayed proportional control law that minimizes the error angle (Haselsteiner et al 2014 J. R. Soc. Interface 11 20140216). This control law can be further interpreted in terms of mechanical actuation: to catch prey, tiger beetles exert a sideways force by biasing their tripod gait in proportion to the error angle measured half a stride earlier. The proportional gain was found to be nearly optimal in the sense that it minimizes the time to point directly toward the prey. For a time-delayed linear proportional controller, the optimal gain, k, is inversely proportional to the time delay, τ, and satisfies kτ =1/e . Here we present evidence that tiger beetles adjust their control gain during their pursuit of prey. Our analysis shows two critical distances: one corresponding to the beetle’s final approach to the prey, and the second, less expected, occurring at a distance around 10 cm for a prey size of 4.5 mm. The beetle initiates its chase using a sub-critical gain and increases the gain to the optimal value once the prey is within this critical distance. Insects use a variety of methods to detect distance, often involving different visual cues. Here we examine two such methods: one based on motion parallax and the other based on the prey’s elevation angle. We show that, in order for the motion parallax method to explain the observed data, the beetle needs to correct for the ratio of the prey’s sideways velocity relative to its own. On the other hand, the simpler method based on the elevation angle can detect both the distance and the prey’s size. Moreover we find that the transition distance corresponds to the accuracy required to distinguish small prey from large predators.

Effects of prey abundance, distribution, visual contrast and morphology on selection by a pelagic piscivore

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Hansen, Adam G.; Beauchamp, David A.

2014-01-01

Most predators eat only a subset of possible prey. However, studies evaluating diet selection rarely measure prey availability in a manner that accounts for temporal–spatial overlap with predators, the sensory mechanisms employed to detect prey, and constraints on prey capture.We evaluated the diet selection of cutthroat trout (Oncorhynchus clarkii) feeding on a diverse planktivore assemblage in Lake Washington to test the hypothesis that the diet selection of piscivores would reflect random (opportunistic) as opposed to non-random (targeted) feeding, after accounting for predator–prey overlap, visual detection and capture constraints.Diets of cutthroat trout were sampled in autumn 2005, when the abundance of transparent, age-0 longfin smelt (Spirinchus thaleichthys) was low, and 2006, when the abundance of smelt was nearly seven times higher. Diet selection was evaluated separately using depth-integrated and depth-specific (accounted for predator–prey overlap) prey abundance. The abundance of different prey was then adjusted for differences in detectability and vulnerability to predation to see whether these factors could explain diet selection.In 2005, cutthroat trout fed non-randomly by selecting against the smaller, transparent age-0 longfin smelt, but for the larger age-1 longfin smelt. After adjusting prey abundance for visual detection and capture, cutthroat trout fed randomly. In 2006, depth-integrated and depth-specific abundance explained the diets of cutthroat trout well, indicating random feeding. Feeding became non-random after adjusting for visual detection and capture. Cutthroat trout selected strongly for age-0 longfin smelt, but against similar sized threespine stickleback (Gasterosteus aculeatus) and larger age-1 longfin smelt in 2006. Overlap with juvenile sockeye salmon (O. nerka) was minimal in both years, and sockeye salmon were rare in the diets of cutthroat trout.The direction of the shift between random and non-random selection

Prey size spectra and prey availability of larval and small juvenile cod

DEFF Research Database (Denmark)

Munk, Peter

1997-01-01

The aim of the present study is to describe the prey preference characteristics of cod larvae and assess preference variability in relation to species and size composition of copepod prey. A further aim is to examine the hypothesis that dietary prey size spectra remain the same during the larval ...... were indicated, dependent on location. The findings illustrate the usefulness of coupling dietary prey size spectra and biomass spectra of available prey sizes during studies of ichthyoplankton feeding ecology. (C) 1997 The Fisheries Society of the British Isles....

What you need is what you eat? Prey selection by the bat Myotis daubentonii.

Science.gov (United States)

Vesterinen, Eero J; Ruokolainen, Lasse; Wahlberg, Niklas; Peña, Carlos; Roslin, Tomas; Laine, Veronika N; Vasko, Ville; Sääksjärvi, Ilari E; Norrdahl, Kai; Lilley, Thomas M

2016-04-01

Optimal foraging theory predicts that predators are selective when faced with abundant prey, but become less picky when prey gets sparse. Insectivorous bats in temperate regions are faced with the challenge of building up fat reserves vital for hibernation during a period of decreasing arthropod abundances. According to optimal foraging theory, prehibernating bats should adopt a less selective feeding behavior--yet empirical studies have revealed many apparently generalized species to be composed of specialist individuals. Targeting the diet of the bat Myotis daubentonii, we used a combination of molecular techniques to test for seasonal changes in prey selectivity and individual-level variation in prey preferences. DNA metabarcoding was used to characterize both the prey contents of bat droppings and the insect community available as prey. To test for dietary differences among M. daubentonii individuals, we used ten microsatellite loci to assign droppings to individual bats. The comparison between consumed and available prey revealed a preference for certain prey items regardless of availability. Nonbiting midges (Chironomidae) remained the most highly consumed prey at all times, despite a significant increase in the availability of black flies (Simuliidae) towards the end of the season. The bats sampled showed no evidence of individual specialization in dietary preferences. Overall, our approach offers little support for optimal foraging theory. Thus, it shows how novel combinations of genetic markers can be used to test general theory, targeting patterns at both the level of prey communities and individual predators. © 2016 John Wiley & Sons Ltd.

Effect of sublethal levels of ionizing radiation on a predator-prey interaction

International Nuclear Information System (INIS)

Chee, P.C.

1976-01-01

The predator-prey interaction studied was that between the largemouth bass (Micropterus salmoides) and the fathead minnow (Pimephales promelas) in an artificial test environment. Experiments were first conducted to determine the 50% lethal dose at 30 days of the minnow. Three different dose rates were used to test the effect of dose rate on the 50% lethal dose value. After the 50% lethal dose was determined the predator-prey interaction experiment was conducted using 30% of the 50% lethal dose as the highest radiation dose, this dose being considered the upper limit to sublethal radiation levels. A 4 x 4 Latin square design was chosen for the experiment, with four treatment levels (control plus three radiation levels) and four replicates. In each test 10 prey minnow were offered to one predator bass and the number of prey left after 14 days was the parameter of interest. A predator-prey interaction experiment using a single high level of radiation and two types of controls as conducted to ascertain the ability of the test environment to detect changes in the predator-prey interaction. The two types of controls were irradiated prey not exposed to predation and non-irradiated prey exposed to predation. An experiment was also conducted to test the correlation between the physical activity patterns of minnow and different doses of radiation. At a dose rate of 37.8 rad/min the 50% lethal dose at 30 days for minnow was found to be 2650 rad. It was found that dose rate had a strong influence on the 50% lethal dose. In the predator-prey interaction test it was found that the 14-day survival rate of prey was unaffected by sublethal levels of ionizing radiation. No significant correlation was detected between the physical activity patterns of minnow and radiation dose

Interspecific variation in prey capture behavior by co-occurring Nepenthes pitcher plants

Science.gov (United States)

Chin, Lijin; Chung, Arthur YC; Clarke, Charles

2014-01-01

Pitcher plants of the genus Nepenthes capture a wide range of arthropod prey for nutritional benefit, using complex combinations of visual and olfactory signals and gravity-driven pitfall trapping mechanisms. In many localities throughout Southeast Asia, several Nepenthes different species occur in mixed populations. Often, the species present at any given location have strongly divergent trap structures and preliminary surveys indicate that different species trap different combinations of arthropod prey, even when growing at the same locality. On this basis, it has been proposed that co-existing Nepenthes species may be engaged in niche segregation with regards to arthropod prey, avoiding direct competition with congeners by deploying traps that have modifications that enable them to target specific prey types. We examined prey capture among 3 multi-species Nepenthes populations in Borneo, finding that co-existing Nepenthes species do capture different combinations of prey, but that significant interspecific variations in arthropod prey combinations can often be detected only at sub-ordinal taxonomic ranks. In all lowland Nepenthes species examined, the dominant prey taxon is Formicidae, but montane Nepenthes trap few (or no) ants and 2 of the 3 species studied have evolved to target alternative sources of nutrition, such as tree shrew feces. Using similarity and null model analyses, we detected evidence for niche segregation with regards to formicid prey among 5 lowland, sympatric Nepenthes species in Sarawak. However, we were unable to determine whether these results provide support for the niche segregation hypothesis, or whether they simply reflect unquantified variation in heterogeneous habitats and/or ant communities in the study sites. These findings are used to propose improvements to the design of field experiments that seek to test hypotheses about targeted prey capture patterns in Nepenthes. PMID:24481246

Prey preference of snow leopard (Panthera uncia in South Gobi, Mongolia.

Directory of Open Access Journals (Sweden)

Wasim Shehzad

Full Text Available Accurate information about the diet of large carnivores that are elusive and inhabit inaccessible terrain, is required to properly design conservation strategies. Predation on livestock and retaliatory killing of predators have become serious issues throughout the range of the snow leopard. Several feeding ecology studies of snow leopards have been conducted using classical approaches. These techniques have inherent limitations in their ability to properly identify both snow leopard feces and prey taxa. To examine the frequency of livestock prey and nearly-threatened argali in the diet of the snow leopard, we employed the recently developed DNA-based diet approach to study a snow leopard population located in the Tost Mountains, South Gobi, Mongolia. After DNA was extracted from the feces, a region of ∼100 bp long from mitochondrial 12S rRNA gene was amplified, making use of universal primers for vertebrates and a blocking oligonucleotide specific to snow leopard DNA. The amplicons were then sequenced using a next-generation sequencing platform. We observed a total of five different prey items from 81 fecal samples. Siberian ibex predominated the diet (in 70.4% of the feces, followed by domestic goat (17.3% and argali sheep (8.6%. The major part of the diet was comprised of large ungulates (in 98.8% of the feces including wild ungulates (79% and domestic livestock (19.7%. The findings of the present study will help to understand the feeding ecology of the snow leopard, as well as to address the conservation and management issues pertaining to this wild cat.

Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

Directory of Open Access Journals (Sweden)

Eveson J Paige

2006-08-01

Full Text Available Abstract Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide. This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will

DNA-based species detection capabilities using laser transmission spectroscopy.

Science.gov (United States)

Mahon, A R; Barnes, M A; Li, F; Egan, S P; Tanner, C E; Ruggiero, S T; Feder, J L; Lodge, D M

2013-01-06

Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications.

DNA microarray technique for detecting food-borne pathogens

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Xing GAO

2012-08-01

Full Text Available Objective To study the application of DNA microarray technique for screening and identifying multiple food-borne pathogens. Methods The oligonucleotide probes were designed by Clustal X and Oligo 6.0 at the conserved regions of specific genes of multiple food-borne pathogens, and then were validated by bioinformatic analyses. The 5' end of each probe was modified by amino-group and 10 Poly-T, and the optimized probes were synthesized and spotted on aldehyde-coated slides. The bacteria DNA template incubated with Klenow enzyme was amplified by arbitrarily primed PCR, and PCR products incorporated into Aminoallyl-dUTP were coupled with fluorescent dye. After hybridization of the purified PCR products with DNA microarray, the hybridization image and fluorescence intensity analysis was acquired by ScanArray and GenePix Pro 5.1 software. A series of detection conditions such as arbitrarily primed PCR and microarray hybridization were optimized. The specificity of this approach was evaluated by 16 different bacteria DNA, and the sensitivity and reproducibility were verified by 4 food-borne pathogens DNA. The samples of multiple bacteria DNA and simulated water samples of Shigella dysenteriae were detected. Results Nine different food-borne bacteria were successfully discriminated under the same condition. The sensitivity of genomic DNA was 102 －103pg/ μl, and the coefficient of variation (CV of the reproducibility of assay was less than 15%. The corresponding specific hybridization maps of the multiple bacteria DNA samples were obtained, and the detection limit of simulated water sample of Shigella dysenteriae was 3.54×105cfu/ml. Conclusions The DNA microarray detection system based on arbitrarily primed PCR can be employed for effective detection of multiple food-borne pathogens, and this assay may offer a new method for high-throughput platform for detecting bacteria.

A Universal Fast Colorimetric Method for DNA Signal Detection with DNA Strand Displacement and Gold Nanoparticles

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Xin Li

2015-01-01

Full Text Available DNA or gene signal detection is of great significance in many fields including medical examination, intracellular molecular monitoring, and gene disease signal diagnosis, but detection of DNA or gene signals in a low concentration with instant visual results remains a challenge. In this work, a universal fast and visual colorimetric detection method for DNA signals is proposed. Specifically, a DNA signal amplification “circuit” based on DNA strand displacement is firstly designed to amplify the target DNA signals, and then thiol modified hairpin DNA strands and gold nanoparticles are used to make signal detection results visualized in a colorimetric manner. If the target DNA signal exists, the gold nanoparticles aggregate and settle down with color changing from dark red to grey quickly; otherwise, the gold nanoparticles’ colloids remain stable in dark red. The proposed method provides a novel way to detect quickly DNA or gene signals in low concentrations with instant visual results. When applied in real-life, it may provide a universal colorimetric method for gene disease signal diagnosis.

Dynamics analysis of a predator-prey system with harvesting prey and disease in prey species.

Science.gov (United States)

Meng, Xin-You; Qin, Ni-Ni; Huo, Hai-Feng

2018-12-01

In this paper, a predator-prey system with harvesting prey and disease in prey species is given. In the absence of time delay, the existence and stability of all equilibria are investigated. In the presence of time delay, some sufficient conditions of the local stability of the positive equilibrium and the existence of Hopf bifurcation are obtained by analysing the corresponding characteristic equation, and the properties of Hopf bifurcation are given by using the normal form theory and centre manifold theorem. Furthermore, an optimal harvesting policy is investigated by applying the Pontryagin's Maximum Principle. Numerical simulations are performed to support our analytic results.

Interface Layering Phenomena in Capacitance Detection of DNA with Biochips

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Sandro Carrara

2007-02-01

Full Text Available Reliable DNA detection is of great importance for the development of the Lab-on-chip technology. The effort of the most recent projects on this field is to integrate all necessary operations, such as sample preparation (mixing, PCR amplification together with the sensor user for DNA detection. Among the different ways to sense the DNA hybridization, fluorescence based detection has been favored by the market. However, fluorescence based approaches require that the DNA targets are labeled by means of chromophores. As an alternative label-free DNA detection method, capacitance detection was recently proposed by different authors. While this effect has been successfully demonstrated by several groups, the model used for data analysis is far too simple to describe the real behavior of a DNA sensor. The aim of the present paper is to propose a different electrochemical model to describe DNA capacitance detection.

Chemical basis of prey recognition in thamnophiine snakes: the unexpected new roles of parvalbumins.

Directory of Open Access Journals (Sweden)

Maïté Smargiassi

Full Text Available Detecting and locating prey are key to predatory success within trophic chains. Predators use various signals through specialized visual, olfactory, auditory or tactile sensory systems to pinpoint their prey. Snakes chemically sense their prey through a highly developed auxiliary olfactory sense organ, the vomeronasal organ (VNO. In natricine snakes that are able to feed on land and water, the VNO plays a critical role in predatory behavior by detecting cues, known as vomodors, which are produced by their potential prey. However, the chemical nature of these cues remains unclear. Recently, we demonstrated that specific proteins-parvalbumins-present in the cutaneous mucus of the common frog (Rana temporaria may be natural chemoattractive proteins for these snakes. Here, we show that parvalbumins and parvalbumin-like proteins, which are mainly intracellular, are physiologically present in the epidermal mucous cells and mucus of several frog and fish genera from both fresh and salt water. These proteins are located in many tissues and function as Ca(2+ buffers. In addition, we clarified the intrinsic role of parvalbumins present in the cutaneous mucus of amphibians and fishes. We demonstrate that these Ca(2+-binding proteins participate in innate bacterial defense mechanisms by means of calcium chelation. We show that these parvalbumins are chemoattractive for three different thamnophiine snakes, suggesting that these chemicals play a key role in their prey-recognition mechanism. Therefore, we suggest that recognition of parvalbumin-like proteins or other calcium-binding proteins by the VNO could be a generalized prey-recognition process in snakes. Detecting innate prey defense mechanism compounds may have driven the evolution of this predator-prey interaction.

Ultrasonic predator-prey interactions in water-convergent evolution with insects and bats in air?

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Wilson, Maria; Wahlberg, Magnus; Surlykke, Annemarie; Madsen, Peter Teglberg

2013-01-01

Toothed whales and bats have independently evolved biosonar systems to navigate and locate and catch prey. Such active sensing allows them to operate in darkness, but with the potential cost of warning prey by the emission of intense ultrasonic signals. At least six orders of nocturnal insects have independently evolved ears sensitive to ultrasound and exhibit evasive maneuvers when exposed to bat calls. Among aquatic prey on the other hand, the ability to detect and avoid ultrasound emitting predators seems to be limited to only one subfamily of Clupeidae: the Alosinae (shad and menhaden). These differences are likely rooted in the different physical properties of air and water where cuticular mechanoreceptors have been adapted to serve as ultrasound sensitive ears, whereas ultrasound detection in water have called for sensory cells mechanically connected to highly specialized gas volumes that can oscillate at high frequencies. In addition, there are most likely differences in the risk of predation between insects and fish from echolocating predators. The selection pressure among insects for evolving ultrasound sensitive ears is high, because essentially all nocturnal predation on flying insects stems from echolocating bats. In the interaction between toothed whales and their prey the selection pressure seems weaker, because toothed whales are by no means the only marine predators placing a selection pressure on their prey to evolve specific means to detect and avoid them. Toothed whales can generate extremely intense sound pressure levels, and it has been suggested that they may use these to debilitate prey. Recent experiments, however, show that neither fish with swim bladders, nor squid are debilitated by such signals. This strongly suggests that the production of high amplitude ultrasonic clicks serve the function of improving the detection range of the toothed whale biosonar system rather than debilitation of prey.

Ultrasonic predator-prey interactions in water– convergent evolution with insects and bats in air?

Directory of Open Access Journals (Sweden)

Maria eWilson

2013-06-01

Full Text Available Toothed whales and bats have independently evolved biosonar systems to navigate and locate and catch prey. Such active sensing allows them to operate in darkness, but with the potential cost of warning prey by the emission of intense ultrasonic signals. At least six orders of nocturnal insects have independently evolved ears sensitive to ultrasound and exhibit evasive maneuvers when exposed to bat calls. Among aquatic prey on the other hand, the ability to detect and avoid ultrasound emitting predators seems to be limited to only one subfamily of Clupeidae: the Alosinae (shad and menhaden. These differences are likely rooted in the different physical properties of air and water where cuticular mechanoreceptors have been adapted to serve as ultrasound sensitive ears, whereas ultrasound detection in water have called for sensory cells mechanically connected to highly specialized gas volumes that can oscillate at high frequencies. In addition, there are most likely differences in the risk of predation between insects and fish from echolocating predators. The selection pressure among insects for evolving ultrasound sensitive ears is high, because essentially all nocturnal predation on flying insects stems from echolocating bats. In the interaction between toothed whales and their prey the selection pressure seems weaker, because toothed whales are by no means the only marine predators placing a selection pressure on their prey to evolve specific means to detect and avoid them.Toothed whales can generate extremely intense sound pressure levels, and it has been suggested that they may use these to debilitate prey. Recent experiments however, show that neither fish with swim bladder, nor squid are debilitated by such signals. This strongly suggests that the production of high amplitude ultrasonic clicks serve the function of improving the detection range of the toothed whale biosonar system rather than debilitation of prey.

Electrochemical DNA sandwich assay with a lipase label for attomole detection of DNA

DEFF Research Database (Denmark)

Ferapontova, Elena; Hansen, Majken Nørgaard; Saunders, Aaron Marc

2010-01-01

A fast and sensitive electrochemical lipase-based sandwich hybridization assay for detection of attomole levels of DNA has been developed. A combination of magnetic beads, used for pre-concentration and bioseparation of the analyte with a lipase catalyst label allowed detection of DNA with a limi...

Prey-Predator Model with a Nonlocal Bistable Dynamics of Prey

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Malay Banerjee

2018-03-01

Full Text Available Spatiotemporal pattern formation in integro-differential equation models of interacting populations is an active area of research, which has emerged through the introduction of nonlocal intra- and inter-specific interactions. Stationary patterns are reported for nonlocal interactions in prey and predator populations for models with prey-dependent functional response, specialist predator and linear intrinsic death rate for predator species. The primary goal of our present work is to consider nonlocal consumption of resources in a spatiotemporal prey-predator model with bistable reaction kinetics for prey growth in the absence of predators. We derive the conditions of the Turing and of the spatial Hopf bifurcation around the coexisting homogeneous steady-state and verify the analytical results through extensive numerical simulations. Bifurcations of spatial patterns are also explored numerically.

An evaluation of the efficacy of using environmental DNA (eDNA) to detect giant gartersnakes (Thamnophis gigas)

Science.gov (United States)

Halstead, Brian J.; Wood, Dustin A.; Bowen, Lizabeth; Waters, Shannon C.; Vandergast, Amy G.; Ersan, Julia S.; Skalos, Shannon M.; Casazza, Michael L.

2017-09-28

Detecting populations of rare or cryptic species is essential for their conservation. For species like giant gartersnakes (Thamnophis gigas), conventional survey methods can be expensive and inefficient. These sampling difficulties might be overcome by modern techniques that detect deoxyribonucleic acid (DNA) shed by organisms into the environment (eDNA). We evaluated the efficacy of detecting giant gartersnake eDNA in water samples from the laboratory and at locations with known giant gartersnake populations in the Sacramento Valley of California, and failed to detect giant gartersnake DNA in most laboratory and all field samples. Aspects of giant gartersnake biology—such as highly keratinized skin and spending extensive time in the terrestrial environment, as well as hot, sunny, and turbid conditions in wetlands and canals of the Sacramento Valley—likely contributed to low detection probabilities. Although detection of eDNA shows promise under many conditions, further development is needed before sampling for eDNA is a viable option for detecting giant gartersnake populations.

Detection of an enigmatic plethodontid Salamander using Environmental DNA

Science.gov (United States)

Pierson, Todd W.; Mckee, Anna; Spear, Stephen F.; Maerz, John C.; Camp, Carlos D.; Glenn, Travis C.

2016-01-01

The isolation and identification of environmental DNA (eDNA) offers a non-invasive and efficient method for the detection of rare and secretive aquatic wildlife, and it is being widely integrated into inventory and monitoring efforts. The Patch-Nosed Salamander (Urspelerpes brucei) is a tiny, recently discovered species of plethodontid salamander known only from headwater streams in a small region of Georgia and South Carolina. Here, we present results of a quantitative PCR-based eDNA assay capable of detecting Urspelerpes in more than 75% of 33 samples from five confirmed streams. We deployed the method at 31 additional streams and located three previously undocumented populations of Urspelerpes. We compare the results of our eDNA assay with our attempt to use aquatic leaf litterbags for the rapid detection of Urspelerpes and demonstrate the relative efficacy of the eDNA assay. We suggest that eDNA offers great potential for use in detecting other aquatic and semi-aquatic plethodontid salamanders.

Prey responses to predator chemical cues: disentangling the importance of the number and biomass of prey consumed.

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Michael W McCoy

Full Text Available To effectively balance investment in predator defenses versus other traits, organisms must accurately assess predation risk. Chemical cues caused by predation events are indicators of risk for prey in a wide variety of systems, but the relationship between how prey perceive risk in relation to the amount of prey consumed by predators is poorly understood. While per capita predation rate is often used as the metric of relative risk, studies aimed at quantifying predator-induced defenses commonly control biomass of prey consumed as the metric of risk. However, biomass consumed can change by altering either the number or size of prey consumed. In this study we determine whether phenotypic plasticity to predator chemical cues depends upon prey biomass consumed, prey number consumed, or both. We examine the growth response of red-eyed treefrog tadpoles (Agalychnis callidryas to cues from a larval dragonfly (Anax amazili. Biomass consumed was manipulated by either increasing the number of prey while holding individual prey size constant, or by holding the number of prey constant and varying individual prey size. We address two questions. (i Do prey reduce growth rate in response to chemical cues in a dose dependent manner? (ii Does the magnitude of the response depend on whether prey consumption increases via number or size of prey? We find that the phenotypic response of prey is an asymptotic function of prey biomass consumed. However, the asymptotic response is higher when more prey are consumed. Our findings have important implications for evaluating past studies and how future experiments should be designed. A stronger response to predation cues generated by more individual prey deaths is consistent with models that predict prey sensitivity to per capita risk, providing a more direct link between empirical and theoretical studies which are often focused on changes in population sizes not individual biomass.

Performance of mitochondrial DNA mutations detecting early stage cancer

International Nuclear Information System (INIS)

Jakupciak, John P; Srivastava, Sudhir; Sidransky, David; O'Connell, Catherine D; Maragh, Samantha; Markowitz, Maura E; Greenberg, Alissa K; Hoque, Mohammad O; Maitra, Anirban; Barker, Peter E; Wagner, Paul D; Rom, William N

2008-01-01

Mutations in the mitochondrial genome (mtgenome) have been associated with cancer and many other disorders. These mutations can be point mutations or deletions, or admixtures (heteroplasmy). The detection of mtDNA mutations in body fluids using resequencing microarrays, which are more sensitive than other sequencing methods, could provide a strategy to measure mutation loads in remote anatomical sites. We determined the mtDNA mutation load in the entire mitochondrial genome of 26 individuals with different early stage cancers (lung, bladder, kidney) and 12 heavy smokers without cancer. MtDNA was sequenced from three matched specimens (blood, tumor and body fluid) from each cancer patient and two matched specimens (blood and sputum) from smokers without cancer. The inherited wildtype sequence in the blood was compared to the sequences present in the tumor and body fluid, detected using the Affymetrix Genechip ® Human Mitochondrial Resequencing Array 1.0 and supplemented by capillary sequencing for noncoding region. Using this high-throughput method, 75% of the tumors were found to contain mtDNA mutations, higher than in our previous studies, and 36% of the body fluids from these cancer patients contained mtDNA mutations. Most of the mutations detected were heteroplasmic. A statistically significantly higher heteroplasmy rate occurred in tumor specimens when compared to both body fluid of cancer patients and sputum of controls, and in patient blood compared to blood of controls. Only 2 of the 12 sputum specimens from heavy smokers without cancer (17%) contained mtDNA mutations. Although patient mutations were spread throughout the mtDNA genome in the lung, bladder and kidney series, a statistically significant elevation of tRNA and ND complex mutations was detected in tumors. Our findings indicate comprehensive mtDNA resequencing can be a high-throughput tool for detecting mutations in clinical samples with potential applications for cancer detection, but it is

The Allometry of Prey Preferences

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Kalinkat, Gregor; Rall, Björn Christian; Vucic-Pestic, Olivera; Brose, Ulrich

2011-01-01

The distribution of weak and strong non-linear feeding interactions (i.e., functional responses) across the links of complex food webs is critically important for their stability. While empirical advances have unravelled constraints on single-prey functional responses, their validity in the context of complex food webs where most predators have multiple prey remain uncertain. In this study, we present conceptual evidence for the invalidity of strictly density-dependent consumption as the null model in multi-prey experiments. Instead, we employ two-prey functional responses parameterised with allometric scaling relationships of the functional response parameters that were derived from a previous single-prey functional response study as novel null models. Our experiments included predators of different sizes from two taxonomical groups (wolf spiders and ground beetles) simultaneously preying on one small and one large prey species. We define compliance with the null model predictions (based on two independent single-prey functional responses) as passive preferences or passive switching, and deviations from the null model as active preferences or active switching. Our results indicate active and passive preferences for the larger prey by predators that are at least twice the size of the larger prey. Moreover, our approach revealed that active preferences increased significantly with the predator-prey body-mass ratio. Together with prior allometric scaling relationships of functional response parameters, this preference allometry may allow estimating the distribution of functional response parameters across the myriads of interactions in natural ecosystems. PMID:21998724

The allometry of prey preferences.

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Gregor Kalinkat

Full Text Available The distribution of weak and strong non-linear feeding interactions (i.e., functional responses across the links of complex food webs is critically important for their stability. While empirical advances have unravelled constraints on single-prey functional responses, their validity in the context of complex food webs where most predators have multiple prey remain uncertain. In this study, we present conceptual evidence for the invalidity of strictly density-dependent consumption as the null model in multi-prey experiments. Instead, we employ two-prey functional responses parameterised with allometric scaling relationships of the functional response parameters that were derived from a previous single-prey functional response study as novel null models. Our experiments included predators of different sizes from two taxonomical groups (wolf spiders and ground beetles simultaneously preying on one small and one large prey species. We define compliance with the null model predictions (based on two independent single-prey functional responses as passive preferences or passive switching, and deviations from the null model as active preferences or active switching. Our results indicate active and passive preferences for the larger prey by predators that are at least twice the size of the larger prey. Moreover, our approach revealed that active preferences increased significantly with the predator-prey body-mass ratio. Together with prior allometric scaling relationships of functional response parameters, this preference allometry may allow estimating the distribution of functional response parameters across the myriads of interactions in natural ecosystems.

Gluttonous predators: how to estimate prey size when there are too many prey

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MS. Araújo

Full Text Available Prey size is an important factor in food consumption. In studies of feeding ecology, prey items are usually measured individually using calipers or ocular micrometers. Among amphibians and reptiles, there are species that feed on large numbers of small prey items (e.g. ants, termites. This high intake makes it difficult to estimate prey size consumed by these animals. We addressed this problem by developing and evaluating a procedure for subsampling the stomach contents of such predators in order to estimate prey size. Specifically, we developed a protocol based on a bootstrap procedure to obtain a subsample with a precision error of at the most 5%, with a confidence level of at least 95%. This guideline should reduce the sampling effort and facilitate future studies on the feeding habits of amphibians and reptiles, and also provide a means of obtaining precise estimates of prey size.

Prey preferences of the jaguar Panthera onca reflect the post-Pleistocene demise of large prey.

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Matt W Hayward

2016-01-01

Full Text Available Documenting the impacts of the Pleistocene megafaunal extinctions on predator-prey interactions is a challenge because of the incomplete fossil record and depauperate extant community structure. We used a comparative ecological approach to investigate whether the existing prey preference patterns of jaguars Panthera onca were potentially affected by the Pleistocene extinctions in the Americas compared with large felids in Africa and Asia. We reviewed the literature and found 25 studies reporting 3214 jaguar kills recorded throughout the species’ distribution. We found that jaguars significantly preferred capybara Hydrochaeris hydrochaeris and giant anteater Myrmecophaga tridactyla, and avoided agoutis, carnivorans, primates, black-eared opossum Didelphis marsupialis and tapirs. Generalised linear models showed that jaguars select prey primarily based on socio-ecological and behavioural traits (abundance and herd size, rather than morphological characteristics (body size. Nonetheless, their accessible prey weight range was 6-60 kg, preferred prey weight range was 45-85 kg, and mean mass of significantly preferred prey was 32 ± 13 kg leading to a predator to prey body mass ratio of 1:0.53, which is much less than that of other solitary felids. Compared with other large, solitary felids, jaguars have an unusual predator to prey body mass ratio, show limited effect of prey morphology as a driver of prey selection, lack evidence of optimal foraging beyond their preferred prey, and an absence of preferentially hunting on Cetartiodactyla herbivores. These features, coupled with the reduction in jaguar body mass since the Pleistocene, suggest that the loss of larger potential prey items within the preferred and accessible weight ranges at the end-Pleistocene still affects jaguar predatory behaviour. It may be that jaguars survived this mass extinction event by preferentially preying on relatively small species.

Rapid, highly sensitive and highly specific gene detection by combining enzymatic amplification and DNA chip detection simultaneously

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Koji Hashimoto

2016-05-01

Full Text Available We have developed a novel gene detection method based on the loop-mediated isothermal amplification (LAMP reaction and the DNA dissociation reaction on the same DNA chip surface to achieve a lower detection limit, broader dynamic range and faster detection time than are attainable with a conventional DNA chip. Both FAM- and thiol-labeled DNA probe bound to the complementary sequence accompanying Dabcyl was immobilized on the gold surface via Au/thiol bond. The LAMP reaction was carried out on the DNA probe fixed gold surface. At first, Dabcyl molecules quenched the FAM fluorescence. According to the LAMP reaction, the complementary sequence with Dabcyl was competitively reacted with the amplified targeted sequence. As a result, the FAM fluorescence increased owing to dissociation of the complementary sequence from the DNA probe. The simultaneous reaction of LAMP and DNA chip detection was achieved, and 103 copies of the targeted gene were detected within an hour by measuring fluorescence intensity of the DNA probe. Keywords: Biosensor, DNA chip, Loop-mediated isothermal amplification (LAMP, Fluorescence detection, Gold substrate, Au/thiol bond

Interactive effects of prey refuge and additional food for predator in a diffusive predator-prey system

DEFF Research Database (Denmark)

Chakraborty, Subhendu; Tiwari, P. K.; Sasmal, S.K.

2017-01-01

a predator-prey system with prey refuge and additional food for predator apart from the focal prey in the presence of diffusion. Our main aim is to study the interactive effects of prey refuge and additional food on the system dynamics and especially on the controllability of prey (pest). Different types......Additional food for predators has been considered as one of the best established techniques in integrated pest management and biological conservation programs. In natural systems, there are several other factors, e.g., prey refuge, affect the success of pest control. In this paper, we analyze...... of Turing patterns such as stripes, spots, holes, and mixtures of them are obtained. It is found that the supply of additional food to the predator is unable to control the prey (pest) population when prey refuge is high. Moreover, when both prey refuge and additional food are low, spatial distribution...

Detecting in situ copepod diet diversity using molecular technique: development of a copepod/symbiotic ciliate-excluding eukaryote-inclusive PCR protocol.

Science.gov (United States)

Hu, Simin; Guo, Zhiling; Li, Tao; Carpenter, Edward J; Liu, Sheng; Lin, Senjie

2014-01-01

Knowledge of in situ copepod diet diversity is crucial for accurately describing pelagic food web structure but is challenging to achieve due to lack of an easily applicable methodology. To enable analysis with whole copepod-derived DNAs, we developed a copepod-excluding 18S rDNA-based PCR protocol. Although it is effective in depressing amplification of copepod 18S rDNA, its applicability to detect diverse eukaryotes in both mono- and mixed-species has not been demonstrated. Besides, the protocol suffers from the problem that sequences from symbiotic ciliates are overrepresented in the retrieved 18S rDNA libraries. In this study, we designed a blocking primer to make a combined primer set (copepod/symbiotic ciliate-excluding eukaryote-common: CEEC) to depress PCR amplification of symbiotic ciliate sequences while maximizing the range of eukaryotes amplified. We firstly examined the specificity and efficacy of CEEC by PCR-amplifying DNAs from 16 copepod species, 37 representative organisms that are potential prey of copepods and a natural microplankton sample, and then evaluated the efficiency in reconstructing diet composition by detecting the food of both lab-reared and field-collected copepods. Our results showed that the CEEC primer set can successfully amplify 18S rDNA from a wide range of isolated species and mixed-species samples while depressing amplification of that from copepod and targeted symbiotic ciliate, indicating the universality of CEEC in specifically detecting prey of copepods. All the predetermined food offered to copepods in the laboratory were successfully retrieved, suggesting that the CEEC-based protocol can accurately reconstruct the diets of copepods without interference of copepods and their associated ciliates present in the DNA samples. Our initial application to analyzing the food composition of field-collected copepods uncovered diverse prey species, including those currently known, and those that are unsuspected, as copepod prey

Dendrimer-based biosensor for chemiluminescent detection of DNA hybridization

International Nuclear Information System (INIS)

Liu, P.; Hun, X.; Qing, H.

2011-01-01

We report on a highly sensitive chemiluminescent (CL) biosensor for the sequence-specific detection of DNA using a novel bio barcode DNA probe modified with gold nanoparticles that were covered with a dendrimer. The modified probe is composed of gold nanoparticles, a dendrimer, the CL reagent, and the DNA. The capture probe DNA was immobilized on magnetic beads covered with gold. It first hybridizes with the target DNA and then with one terminal end of the signal DNA on the barcoded DNA probe. CL was generated by adding H 2 O 2 and Co(II) ions as the catalyst. The immobilization of dendrimer onto the gold nanoparticles can significantly enhance sensitivity and gives a detection limit of 6 fmol L -1 of target DNA. (author)

Patterns of detection and capture are associated with cohabiting predators and prey.

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Billie T Lazenby

Full Text Available Avoidance behaviour can play an important role in structuring ecosystems but can be difficult to uncover and quantify. Remote cameras have great but as yet unrealized potential to uncover patterns arising from predatory, competitive or other interactions that structure animal communities by detecting species that are active at the same sites and recording their behaviours and times of activity. Here, we use multi-season, two-species occupancy models to test for evidence of interactions between introduced (feral cat Felis catus and native predator (Tasmanian devil Sarcophilus harrisii and predator and small mammal (swamp rat Rattus lutreolus velutinus combinations at baited camera sites in the cool temperate forests of southern Tasmania. In addition, we investigate the capture rates of swamp rats in traps scented with feral cat and devil faecal odours. We observed that one species could reduce the probability of detecting another at a camera site. In particular, feral cats were detected less frequently at camera sites occupied by devils, whereas patterns of swamp rat detection associated with devils or feral cats varied with study site. Captures of swamp rats were not associated with odours on traps, although fewer captures tended to occur in traps scented with the faecal odour of feral cats. The observation that a native carnivorous marsupial, the Tasmanian devil, can suppress the detectability of an introduced eutherian predator, the feral cat, is consistent with a dominant predator-mesopredator relationship. Such a relationship has important implications for the interaction between feral cats and the lower trophic guilds that form their prey, especially if cat activity increases in places where devil populations are declining. More generally, population estimates derived from devices such as remote cameras need to acknowledge the potential for one species to change the detectability of another, and incorporate this in assessments of numbers

Patterns of Detection and Capture Are Associated with Cohabiting Predators and Prey

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Lazenby, Billie T.; Dickman, Christopher R.

2013-01-01

Avoidance behaviour can play an important role in structuring ecosystems but can be difficult to uncover and quantify. Remote cameras have great but as yet unrealized potential to uncover patterns arising from predatory, competitive or other interactions that structure animal communities by detecting species that are active at the same sites and recording their behaviours and times of activity. Here, we use multi-season, two-species occupancy models to test for evidence of interactions between introduced (feral cat Felis catus) and native predator (Tasmanian devil Sarcophilus harrisii) and predator and small mammal (swamp rat Rattus lutreolus velutinus) combinations at baited camera sites in the cool temperate forests of southern Tasmania. In addition, we investigate the capture rates of swamp rats in traps scented with feral cat and devil faecal odours. We observed that one species could reduce the probability of detecting another at a camera site. In particular, feral cats were detected less frequently at camera sites occupied by devils, whereas patterns of swamp rat detection associated with devils or feral cats varied with study site. Captures of swamp rats were not associated with odours on traps, although fewer captures tended to occur in traps scented with the faecal odour of feral cats. The observation that a native carnivorous marsupial, the Tasmanian devil, can suppress the detectability of an introduced eutherian predator, the feral cat, is consistent with a dominant predator – mesopredator relationship. Such a relationship has important implications for the interaction between feral cats and the lower trophic guilds that form their prey, especially if cat activity increases in places where devil populations are declining. More generally, population estimates derived from devices such as remote cameras need to acknowledge the potential for one species to change the detectability of another, and incorporate this in assessments of numbers and survival

Tumor‐associated DNA mutation detection in individuals undergoing colonoscopy

OpenAIRE

Fleshner, Phillip; Braunstein, Glenn D.; Ovsepyan, Gayane; Tonozzi, Theresa R.; Kammesheidt, Anja

2017-01-01

Abstract The majority of colorectal cancers (CRC) harbor somatic mutations and epigenetic modifications in the tumor tissue, and some of these mutations can be detected in plasma as circulating tumor DNA (ctDNA). Precancerous colorectal lesions also contain many of these same mutations. This study examined plasma for ctDNA from patients undergoing a screening or diagnostic colonoscopy to determine the sensitivity and specificity of the ctDNA panel for detecting CRC and precancerous lesions. T...

Detection of DNA hybridizations using solid-state nanopores

International Nuclear Information System (INIS)

Balagurusamy, Venkat S K; Weinger, Paul; Sean Ling, Xinsheng

2010-01-01

We report an experimental study of using DNA translocation through solid-state nanopores to detect the sequential arrangement of two double-stranded 12-mer hybridization segments on a single-stranded DNA molecule. The sample DNA is a trimer molecule formed by hybridizing three single-stranded oligonucleotides. A polystyrene bead is attached to the end of the trimer DNA, providing a mechanism in slowing down the translocation and suppressing the thermal diffusion, thereby allowing the detection of short features of DNA by standard patch-clamp electronics. The electrical signature of the translocation of a trimer molecule through a nanopore has been identified successfully in the temporal traces of ionic current. The results reported here represent the first successful attempt in using a solid-state nanopore as an ionic scanning device in resolving individual hybridization segments (or 'probes') on a DNA molecule.

Detection of DNA hybridizations using solid-state nanopores

Energy Technology Data Exchange (ETDEWEB)

Balagurusamy, Venkat S K; Weinger, Paul; Sean Ling, Xinsheng, E-mail: Xinsheng_Ling@brown.edu [Department of Physics, Brown University, Providence, RI 02912 (United States)

2010-08-20

We report an experimental study of using DNA translocation through solid-state nanopores to detect the sequential arrangement of two double-stranded 12-mer hybridization segments on a single-stranded DNA molecule. The sample DNA is a trimer molecule formed by hybridizing three single-stranded oligonucleotides. A polystyrene bead is attached to the end of the trimer DNA, providing a mechanism in slowing down the translocation and suppressing the thermal diffusion, thereby allowing the detection of short features of DNA by standard patch-clamp electronics. The electrical signature of the translocation of a trimer molecule through a nanopore has been identified successfully in the temporal traces of ionic current. The results reported here represent the first successful attempt in using a solid-state nanopore as an ionic scanning device in resolving individual hybridization segments (or 'probes') on a DNA molecule.

The Dynamics of a Nonautonomous Predator-Prey Model with Infertility Control in the Prey

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Xiaomei Feng

2014-01-01

Full Text Available A nonautonomous predator-prey model with infertility control in the prey is formulated and investigated. Threshold conditions for the permanence and extinction of fertility prey and infertility prey are established. Some new threshold values of integral form are obtained. For the periodic cases, these threshold conditions act as sharp threshold values for the permanence and extinction of fertility prey and infertility prey. There are also mounting concerns that the quantity of biological sterile drug is obtained in the process of the prevention and control of pest in the grasslands and farmland. Finally, two examples are given to illustrate the main results of this paper. The numerical simulations shown that, when the pest population is permanet, different dynamic behaviors may be found in this model, such as the global attractivity and the chaotic attractor.

Can species-specific prey responses to chemical cues explain prey susceptibility to predation?

Science.gov (United States)

Šmejkal, Marek; Ricard, Daniel; Sajdlová, Zuzana; Čech, Martin; Vejřík, Lukáš; Blabolil, Petr; Vejříková, Ivana; Prchalová, Marie; Vašek, Mojmír; Souza, Allan T; Brönmark, Christer; Peterka, Jiří

2018-05-01

The perception of danger represents an essential ability of prey for gaining an informational advantage over their natural enemies. Especially in complex environments or at night, animals strongly rely on chemoreception to avoid predators. The ability to recognize danger by chemical cues and subsequent adaptive responses to predation threats should generally increase prey survival. Recent findings suggest that European catfish ( Silurus glanis ) introduction induce changes in fish community and we tested whether the direction of change can be attributed to differences in chemical cue perception. We tested behavioral response to chemical cues using three species of freshwater fish common in European water: rudd ( Scardinius erythrophthalmus ), roach ( Rutilus rutilus ), and perch ( Perca fluviatilis ). Further, we conducted a prey selectivity experiment to evaluate the prey preferences of the European catfish. Roach exhibited the strongest reaction to chemical cues, rudd decreased use of refuge and perch did not alter any behavior in the experiment. These findings suggest that chemical cue perception might be behind community data change and we encourage collecting more community data of tested prey species before and after European catfish introduction to test the hypothesis. We conclude that used prey species can be used as a model species to verify whether chemical cue perception enhances prey survival.

Insectivorous birds eavesdrop on the pheromones of their prey.

Science.gov (United States)

Saavedra, Irene; Amo, Luisa

2018-01-01

Chemical cues play a fundamental role in mate attraction and mate choice. Lepidopteran females, such as the winter moth (Operophtera brumata), emit pheromones to attract males in the reproductive period. However, these chemical cues could also be eavesdropped by predators. To our knowledge, no studies have examined whether birds can detect pheromones of their prey. O. brumata adults are part of the winter diet of some insectivorous tit species, such as the great tit (Parus major) and blue tit (Cyanistes caeruleus). We performed a field experiment aimed to disentangle whether insectivorous birds can exploit the pheromones emitted by their prey for prey location. We placed artificial larvae and a dispenser on branches of Pyrenean oak trees (Quercus pyrenaica). In half of the trees we placed an O. brumata pheromone dispenser and in the other half we placed a control dispenser. We measured the predation rate of birds on artificial larvae. Our results show that more trees had larvae with signs of avian predation when they contained an O. brumata pheromone than when they contained a control dispenser. Furthermore, the proportion of artificial larvae with signs of avian predation was greater in trees that contained the pheromone than in control trees. Our results indicate that insectivorous birds can exploit the pheromones emitted by moth females to attract males, as a method of prey detection. These results highlight the potential use of insectivorous birds in the biological control of insect pests.

Sub-indicator: Prey fish

Science.gov (United States)

Weidel, Brian C.; Dunlop, Erin

2017-01-01

Prey fish communities across the Great Lakes continue to change, although the direction and magnitude of those changes are not consistent across the lakes. The metrics used to categorize prey fish status in this and previous periods are based on elements that are common among each of the lake’s Fish Community Objectives and include diversity and the relative role of native species in the prey fish communities. The diversity index categorized three of lakes as ‘fair’, while Superior and Erie were ‘good’ (Table 1). The short term trend, from the previous period (2008-2010) to the current period (2011-2014) found diversity in Erie and Superior to be unchanging, but the other three lakes to be ‘deteriorating’, resulting in an overall trend categorization of ‘undetermined’ (Table 1). The long term diversity trend suggested Lakes Superior and Erie have the most diverse prey communities although the index for those prey fish have been quite variable over time (Figure 1). In Lake Huron, where non-native alewife have substantially declined, the diversity index has also declined. The continued dominance of alewife in Lake Ontario (96% of the prey fish biomass) resulted in the lowest diversity index value (Figure 1). The proportion of native species within the community was judged as ‘good’ in Lakes Superior and Huron, ‘fair’ in Michigan and Erie and ‘poor’ in Ontario (Table 2). The short term trend was improving in in all lakes except Michigan (‘deteriorating’) and Ontario (‘unchanging’), resulting in an overall short term trend of ‘undetermined’ (Table 2). Over the current period, Lake Superior consistently had the highest proportion native prey fish (87%) while Lake Ontario had the lowest (1%) (Figure 2). Lake Michigan’s percent native has declined as round goby increase and comprises a greater proportion of the community. Native prey fish make up 51% of Lake Erie, although basin-specific values differed (Figure 2). Most notably

Adelie penguin population diet monitoring by analysis of food DNA in scats.

Directory of Open Access Journals (Sweden)

Simon N Jarman

Full Text Available The Adélie penguin is the most important animal currently used for ecosystem monitoring in the Southern Ocean. The diet of this species is generally studied by visual analysis of stomach contents; or ratios of isotopes of carbon and nitrogen incorporated into the penguin from its food. There are significant limitations to the information that can be gained from these methods. We evaluated population diet assessment by analysis of food DNA in scats as an alternative method for ecosystem monitoring with Adélie penguins as an indicator species. Scats were collected at four locations, three phases of the breeding cycle, and in four different years. A novel molecular diet assay and bioinformatics pipeline based on nuclear small subunit ribosomal RNA gene (SSU rDNA sequencing was used to identify prey DNA in 389 scats. Analysis of the twelve population sample sets identified spatial and temporal dietary change in Adélie penguin population diet. Prey diversity was found to be greater than previously thought. Krill, fish, copepods and amphipods were the most important food groups, in general agreement with other Adélie penguin dietary studies based on hard part or stable isotope analysis. However, our DNA analysis estimated that a substantial portion of the diet was gelatinous groups such as jellyfish and comb jellies. A range of other prey not previously identified in the diet of this species were also discovered. The diverse prey identified by this DNA-based scat analysis confirms that the generalist feeding of Adélie penguins makes them a useful indicator species for prey community composition in the coastal zone of the Southern Ocean. Scat collection is a simple and non-invasive field sampling method that allows DNA-based estimation of prey community differences at many temporal and spatial scales and provides significant advantages over alternative diet analysis approaches.

An objective approach to determining the weight ranges of prey preferred by and accessible to the five large African carnivores.

Directory of Open Access Journals (Sweden)

Hayley S Clements

Full Text Available Broad-scale models describing predator prey preferences serve as useful departure points for understanding predator-prey interactions at finer scales. Previous analyses used a subjective approach to identify prey weight preferences of the five large African carnivores, hence their accuracy is questionable. This study uses a segmented model of prey weight versus prey preference to objectively quantify the prey weight preferences of the five large African carnivores. Based on simulations of known predator prey preference, for prey species sample sizes above 32 the segmented model approach detects up to four known changes in prey weight preference (represented by model break-points with high rates of detection (75% to 100% of simulations, depending on number of break-points and accuracy (within 1.3±4.0 to 2.7±4.4 of known break-point. When applied to the five large African carnivores, using carnivore diet information from across Africa, the model detected weight ranges of prey that are preferred, killed relative to their abundance, and avoided by each carnivore. Prey in the weight ranges preferred and killed relative to their abundance are together termed "accessible prey". Accessible prey weight ranges were found to be 14-135 kg for cheetah Acinonyx jubatus, 1-45 kg for leopard Panthera pardus, 32-632 kg for lion Panthera leo, 15-1600 kg for spotted hyaena Crocuta crocuta and 10-289 kg for wild dog Lycaon pictus. An assessment of carnivore diets throughout Africa found these accessible prey weight ranges include 88±2% (cheetah, 82±3% (leopard, 81±2% (lion, 97±2% (spotted hyaena and 96±2% (wild dog of kills. These descriptions of prey weight preferences therefore contribute to our understanding of the diet spectrum of the five large African carnivores. Where datasets meet the minimum sample size requirements, the segmented model approach provides a means of determining, and comparing, the prey weight range preferences of any carnivore

An objective approach to determining the weight ranges of prey preferred by and accessible to the five large African carnivores.

Science.gov (United States)

Clements, Hayley S; Tambling, Craig J; Hayward, Matt W; Kerley, Graham I H

2014-01-01

Broad-scale models describing predator prey preferences serve as useful departure points for understanding predator-prey interactions at finer scales. Previous analyses used a subjective approach to identify prey weight preferences of the five large African carnivores, hence their accuracy is questionable. This study uses a segmented model of prey weight versus prey preference to objectively quantify the prey weight preferences of the five large African carnivores. Based on simulations of known predator prey preference, for prey species sample sizes above 32 the segmented model approach detects up to four known changes in prey weight preference (represented by model break-points) with high rates of detection (75% to 100% of simulations, depending on number of break-points) and accuracy (within 1.3±4.0 to 2.7±4.4 of known break-point). When applied to the five large African carnivores, using carnivore diet information from across Africa, the model detected weight ranges of prey that are preferred, killed relative to their abundance, and avoided by each carnivore. Prey in the weight ranges preferred and killed relative to their abundance are together termed "accessible prey". Accessible prey weight ranges were found to be 14-135 kg for cheetah Acinonyx jubatus, 1-45 kg for leopard Panthera pardus, 32-632 kg for lion Panthera leo, 15-1600 kg for spotted hyaena Crocuta crocuta and 10-289 kg for wild dog Lycaon pictus. An assessment of carnivore diets throughout Africa found these accessible prey weight ranges include 88±2% (cheetah), 82±3% (leopard), 81±2% (lion), 97±2% (spotted hyaena) and 96±2% (wild dog) of kills. These descriptions of prey weight preferences therefore contribute to our understanding of the diet spectrum of the five large African carnivores. Where datasets meet the minimum sample size requirements, the segmented model approach provides a means of determining, and comparing, the prey weight range preferences of any carnivore species.

"Prey Play": Learning about Predators and Prey through an Interactive, Role-Play Game

Science.gov (United States)

Deaton, Cynthia C. M.; Dodd, Kristen; Drennon, Katherine; Nagle, Jack

2012-01-01

"Prey Play" is an interactive role-play activity that provides fifth-grade students with opportunities to examine predator-prey interactions. This four-part, role-play activity allows students to take on the role of a predator and prey as they reflect on the behaviors animals exhibit as they collect food and interact with one another, as well as…

Detection of environmental carcinogens-DNA

International Nuclear Information System (INIS)

Pfohl-Leszkowicz, A.; Guillemaut, G.; Rether, B.; Masfaraud, J.F.; Haguenoer, J.M.

1995-01-01

It has been estimated that majority of human cancer is due to environmental factors including pollutants in air, soil, water and food, work places exposure and personal habits such as smoking. After penetration in organism, xenobiotics could be directly excreted or are bio transformed by oxidation or reduction in more hydrophilic compounds which could be conjugate and then eliminated in urine. But in some case, the biotransformation leads to electrophilic compounds which interact with macromolecules such as DNA, forming addition products named adduct. The 32 P post-labelling method, inspired by recent developments in the methodology for sequencing nucleic acids, is an extremely sensitive method for assessing and quantifying DNA adducts and is applicable to structurally diverse classes of chemicals. In the first study, we have analysed hepatic DNA from fish living in the River Rhone downstream and upstream from a polychlorinated biphenyl incineration plant. Our results suggest that fish are exposed to genotoxic chemicals. In another study, leave DNA from healthy and declining hop were analysed. The total adduct level is 3 time higher in declining hop. A comparison between DNA adducts from several vegetal cells cultured in presence of heptachlor and DNA adduct in declining hop, confirmed the implication of heptachlor. In these examples, our data indicate the usefulness of the 32 P-post labelling method to assess the contamination of the environment by genotoxic pollutants. Epidemiological data suggested that increasing exposure to airborne PAH contributes to increase risk cancer in this population. Exposure-dependent adducts were detected in while blood cells in coke oven workers. The adduct levels is function of the level of pollutant. In the last example we have analysed lung tissue from patient with cancer. We observed many adducts in peritumoral tissue, while few adducts could be detected in tumoral tissues. (author)

Prey-predator dynamics with prey refuge providing additional food to predator

International Nuclear Information System (INIS)

Ghosh, Joydev; Sahoo, Banshidhar; Poria, Swarup

2017-01-01

Highlights: • The effects of interplay between prey refugia and additional food are reported. • Hopf bifurcation conditions are derived analytically. • Existence of unique limit cycle is shown analytically. • Predator extinction may be possible at very high prey refuge ecological systems. - Abstract: The impacts of additional food for predator on the dynamics of a prey-predator model with prey refuge are investigated. The equilibrium points and their stability behaviours are determined. Hopf bifurcation conditions are derived analytically. Most significantly, existence conditions for unique stable limit cycle in the phase plane are shown analytically. The analytical results are in well agreement with the numerical simulation results. Effects of variation of refuge level as well as the variation of quality and quantity of additional food on the dynamics are reported with the help of bifurcation diagrams. It is found that high quality and high quantity of additional food supports oscillatory coexistence of species. It is observed that predator extinction possibility in high prey refuge ecological systems may be removed by supplying additional food to predator population. The reported theoretical results may be useful to conservation biologist for species conservation in real world ecological systems.

A novel SERRS sandwich-hybridization assay to detect specific DNA target.

Directory of Open Access Journals (Sweden)

Cécile Feuillie

Full Text Available In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR. In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

Sensitive detection of mercury and copper ions by fluorescent DNA/Ag nanoclusters in guanine-rich DNA hybridization.

Science.gov (United States)

Peng, Jun; Ling, Jian; Zhang, Xiu-Qing; Bai, Hui-Ping; Zheng, Liyan; Cao, Qiu-E; Ding, Zhong-Tao

2015-02-25

In this work, we designed a new fluorescent oligonucleotides-stabilized silver nanoclusters (DNA/AgNCs) probe for sensitive detection of mercury and copper ions. This probe contains two tailored DNA sequence. One is a signal probe contains a cytosine-rich sequence template for AgNCs synthesis and link sequence at both ends. The other is a guanine-rich sequence for signal enhancement and link sequence complementary to the link sequence of the signal probe. After hybridization, the fluorescence of hybridized double-strand DNA/AgNCs is 200-fold enhanced based on the fluorescence enhancement effect of DNA/AgNCs in proximity of guanine-rich DNA sequence. The double-strand DNA/AgNCs probe is brighter and stable than that of single-strand DNA/AgNCs, and more importantly, can be used as novel fluorescent probes for detecting mercury and copper ions. Mercury and copper ions in the range of 6.0-160.0 and 6-240 nM, can be linearly detected with the detection limits of 2.1 and 3.4 nM, respectively. Our results indicated that the analytical parameters of the method for mercury and copper ions detection are much better than which using a single-strand DNA/AgNCs. Copyright © 2014 Elsevier B.V. All rights reserved.

21 CFR 864.7280 - Factor V Leiden DNA mutation detection systems.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Factor V Leiden DNA mutation detection systems....7280 Factor V Leiden DNA mutation detection systems. (a) Identification. Factor V Leiden deoxyribonucleic acid (DNA) mutation detection systems are devices that consist of different reagents and...

Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction

Science.gov (United States)

Xiong, Yanxiang; Wei, Min; Wei, Wei; Yin, Lihong; Pu, Yuepu; Liu, Songqin

2014-01-01

DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag+-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science.

Coexistence for an Almost Periodic Predator-Prey Model with Intermittent Predation Driven by Discontinuous Prey Dispersal

Directory of Open Access Journals (Sweden)

Yantao Luo

2017-01-01

Full Text Available An almost periodic predator-prey model with intermittent predation and prey discontinuous dispersal is studied in this paper, which differs from the classical continuous and impulsive dispersal predator-prey models. The intermittent predation behavior of the predator species only happens in the channels between two patches where the discontinuous migration movement of the prey species occurs. Using analytic approaches and comparison theorems of the impulsive differential equations, sufficient criteria on the boundedness, permanence, and coexistence for this system are established. Finally, numerical simulations demonstrate that, for an intermittent predator-prey model, both the intermittent predation and intrinsic growth rates of the prey and predator species can greatly impact the permanence, extinction, and coexistence of the population.

Fluorescent carbon nanoparticle-based lateral flow biosensor for ultrasensitive detection of DNA.

Science.gov (United States)

Takalkar, Sunitha; Baryeh, Kwaku; Liu, Guodong

2017-12-15

We report a fluorescent carbon nanoparticle (FCN)-based lateral flow biosensor for ultrasensitive detection of DNA. Fluorescent carbon nanoparticle with a diameter of around 15nm was used as a tag to label a detection DNA probe, which was complementary with the part of target DNA. A capture DNA probe was immobilized on the test zone of the lateral flow biosensor. Sandwich-type hybridization reactions among the FCN-labeled DNA probe, target DNA and capture DNA probe were performed on the lateral flow biosensor. In the presence of target DNA, FCNs were captured on the test zone of the biosensor and the fluorescent intensity of the captured FCNs was measured with a portable fluorescent reader. After systematic optimizations of experimental parameters (the components of running buffers, the concentration of detection DNA probe used in the preparation of FCN-DNA conjugates, the amount of FCN-DNA dispensed on the conjugate pad and the dispensing cycles of the capture DNA probes on the test-zone), the biosensor could detect a minimum concentration of 0.4 fM DNA. This study provides a rapid and low-cost approach for DNA detection with high sensitivity, showing great promise for clinical application and biomedical diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Parasites as prey

NARCIS (Netherlands)

Goedknegt, M.A.; Welsh, J.E.; Thieltges, D.W.

2012-01-01

Parasites are usually considered to use their hosts as a resource for energy. However, there is increasing awareness that parasites can also become a resource themselves and serve as prey for other organisms. Here we describe various types of predation in which parasites act as prey for other

Facile preparation of a DNA sensor for rapid herpes virus detection

Energy Technology Data Exchange (ETDEWEB)

Tam, Phuong Dinh, E-mail: tampd-hast@mail.hut.edu.vn [Hanoi Advanced School of Science and Technology, Hanoi University of Technology (Viet Nam); Tuan, Mai Anh, E-mail: tuanma-itims@mail.hut.edu.vn [International Training Institute for Materials Science, Hanoi University of Technology (Viet Nam); Huy, Tran Quang [National Institute of Hygiene and Epidemiology (NIHE), 01 Yersin, Hai Ba Trung District, Hanoi (Viet Nam); Le, Anh-Tuan [Hanoi Advanced School of Science and Technology, Hanoi University of Technology (Viet Nam); Hieu, Nguyen Van, E-mail: hieu@itims.edu.vn [International Training Institute for Materials Science, Hanoi University of Technology (Viet Nam)

2010-10-12

In this paper, a simple DNA sensor platform was developed for rapid herpes virus detection in real samples. The deoxyribonucleic acid (DNA) sequences of the herpes simplex virus (DNA probe) were directly immobilized on the surface of interdigitated electrodes by electrochemical polymerization along with pyrrole monomers. The potential was scanned from - 0.7 to + 0.6 V, and the scanning rate was 100 mV/s. Fourier transform infrared spectroscopy was employed to verify specific DNA sequence binding and the conducting polymer. The morphology of the conducting polymer doped with DNA strands was characterized using a field emission scanning electron microscope. As-obtained DNA sensor was used to detect the herpes virus DNA in the real samples. The results show that the current DNA sensors detected the lowest DNA concentration of 2 nM. This sensitivity appears to be better than that of the DNA sensors prepared by immobilization of the DNA probe on the 3-aminopropyl-triethoxy-silance (APTS) membrane.

Facile preparation of a DNA sensor for rapid herpes virus detection

International Nuclear Information System (INIS)

Tam, Phuong Dinh; Tuan, Mai Anh; Huy, Tran Quang; Le, Anh-Tuan; Hieu, Nguyen Van

2010-01-01

In this paper, a simple DNA sensor platform was developed for rapid herpes virus detection in real samples. The deoxyribonucleic acid (DNA) sequences of the herpes simplex virus (DNA probe) were directly immobilized on the surface of interdigitated electrodes by electrochemical polymerization along with pyrrole monomers. The potential was scanned from - 0.7 to + 0.6 V, and the scanning rate was 100 mV/s. Fourier transform infrared spectroscopy was employed to verify specific DNA sequence binding and the conducting polymer. The morphology of the conducting polymer doped with DNA strands was characterized using a field emission scanning electron microscope. As-obtained DNA sensor was used to detect the herpes virus DNA in the real samples. The results show that the current DNA sensors detected the lowest DNA concentration of 2 nM. This sensitivity appears to be better than that of the DNA sensors prepared by immobilization of the DNA probe on the 3-aminopropyl-triethoxy-silance (APTS) membrane.

Factors influencing detection of eDNA from a stream-dwelling amphibian

Science.gov (United States)

Pilliod, David S.; Goldberg, Caren S.; Arkle, Robert S.; Waits, Lisette P.

2013-01-01

Environmental DNA (eDNA) methods for detecting and estimating abundance of aquatic species are emerging rapidly, but little is known about how processes such as secretion rate, environmental degradation, and time since colonization or extirpation from a given site affect eDNA measurements. Using stream-dwelling salamanders and quantitative PCR (qPCR) analysis, we conducted three experiments to assess eDNA: (i) production rate; (ii) persistence time under different temperature and light conditions; and (iii) detectability and concentration through time following experimental introduction and removal of salamanders into previously unoccupied streams. We found that 44–50 g individuals held in aquaria produced 77 ng eDNA/h for 2 h, after which production either slowed considerably or began to equilibrate with degradation. eDNA in both full-sun and shaded treatments degraded exponentially to 2) and when samples were collected within 5 m of the animals. Concentrations of eDNA detected were very low and increased steadily from 6–24 h after introduction, reaching 0.0022 ng/L. Within 1 h of removing salamanders from the stream, eDNA was no longer detectable. These results suggest that eDNA detectability and concentration depend on production rates of individuals, environmental conditions, density of animals, and their residence time.

Sensitive Leptospira DNA detection using tapered optical fiber sensor.

Science.gov (United States)

Zainuddin, Nurul H; Chee, Hui Y; Ahmad, Muhammad Z; Mahdi, Mohd A; Abu Bakar, Muhammad H; Yaacob, Mohd H

2018-03-23

This paper presents the development of tapered optical fiber sensor to detect a specific Leptospira bacteria DNA. The bacteria causes Leptospirosis, a deadly disease but with common early flu-like symptoms. Optical single mode fiber (SMF) of 125 μm diameter is tapered to produce 12 μm waist diameter and 15 cm length. The novel DNA-based optical fiber sensor is functionalized by incubating the tapered region with sodium hydroxide (NaOH), (3-Aminopropyl) triethoxysilane and glutaraldehyde. Probe DNA is immobilized onto the tapered region and subsequently hybridized by its complementary DNA (cDNA). The transmission spectra of the DNA-based optical fiber sensor are measured in the 1500 to 1600 nm wavelength range. It is discovered that the shift of the wavelength in the SMF sensor is linearly proportional with the increase in the cDNA concentrations from 0.1 to 1.0 nM. The sensitivity of the sensor toward DNA is measured to be 1.2862 nm/nM and able to detect as low as 0.1 fM. The sensor indicates high specificity when only minimal shift is detected for non-cDNA testing. The developed sensor is able to distinguish between actual DNA of Leptospira serovars (Canicola and Copenhageni) against Clostridium difficile (control sample) at very low (femtomolar) target concentrations. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gold-silver-alloy nanoprobes for one-pot multiplex DNA detection

Energy Technology Data Exchange (ETDEWEB)

Doria, G; Larguinho, M; Dias, J T; Baptista, P V [Centro de Investigacao em Genetica Molecular Humana (CIGMH), Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Pereira, E [Rede de Quimica e Tecnologia (REQUIMTE), Departamento de Quimica, Faculdade de Ciencias, Universidade do Porto, 4169-007 Porto (Portugal); Franco, R, E-mail: pmvb@fct.unl.pt [Rede de Quimica e Tecnologia (REQUIMTE), Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal)

2010-06-25

A specific colorimetric DNA detection method based on oligonucleotide functionalized gold-silver-alloy nanoparticles (AuAg-alloy-nanoprobes) is presented. The AuAg-alloy-nanoprobes were then used for the specific detection of a DNA sequence from TP53-a gene involved in cancer development. The AuAg-alloy-nanoprobes were then used in combination with Au-nanoprobes for a one-pot dual-colour detection strategy that allowed for the simultaneous differential detection of two distinct target sequences. This system poses an unprecedented opportunity to explore the combined use of metal nanoparticles with different composition towards the development of a multiplex one-pot colorimetric assay for DNA detection.

Gold-silver-alloy nanoprobes for one-pot multiplex DNA detection

International Nuclear Information System (INIS)

Doria, G; Larguinho, M; Dias, J T; Baptista, P V; Pereira, E; Franco, R

2010-01-01

A specific colorimetric DNA detection method based on oligonucleotide functionalized gold-silver-alloy nanoparticles (AuAg-alloy-nanoprobes) is presented. The AuAg-alloy-nanoprobes were then used for the specific detection of a DNA sequence from TP53-a gene involved in cancer development. The AuAg-alloy-nanoprobes were then used in combination with Au-nanoprobes for a one-pot dual-colour detection strategy that allowed for the simultaneous differential detection of two distinct target sequences. This system poses an unprecedented opportunity to explore the combined use of metal nanoparticles with different composition towards the development of a multiplex one-pot colorimetric assay for DNA detection.

The strategies of DNA immobilization and hybridization detection mechanism in the construction of electrochemical DNA sensor: A review

Directory of Open Access Journals (Sweden)

Jahwarhar Izuan Abdul Rashid

2017-11-01

Full Text Available In recent years, electrochemical deoxyribonucleic acid (DNA sensor has recently emerged as promising alternative clinical diagnostic devices especially for infectious disease by exploiting DNA recognition events and converting them into an electrochemical signal. This is because the existing DNA diagnostic method possesses certain drawbacks such as time-consuming, expensive, laborious, low selectivity and sensitivity. DNA immobilization strategies and mechanism of electrochemical detection are two the most important aspects that should be considered before developing highly selective and sensitive electrochemical DNA sensor. Here, we focus on some recent strategies for DNA probes immobilization on the surface of electrochemical transducer such as adsorption, covalent bonding and Avidin/Streptavidin-Biotin interaction on the electrode surface for specific interaction with its complementary DNA target. A numerous approach for DNA hybridization detection based electrochemical technique that frequently used including direct DNA electrochemical detection and label based electrochemical (redox-active indicator, enzyme label and nanoparticles were also discussed in aiming to provide general guide for the design of electrochemical DNA sensor. We also discussed the challenges and suggestions to improve the application of electrochemical DNA sensor at point-care setting. Keywords: Electrochemical DNA sensor, DNA immobilization, DNA hybridization, Electrochemical mechanism

Enzyme-free and label-free ultrasensitive electrochemical detection of DNA and adenosine triphosphate by dendritic DNA concatamer-based signal amplification.

Science.gov (United States)

Liu, Shufeng; Lin, Ying; Liu, Tao; Cheng, Chuanbin; Wei, Wenji; Wang, Li; Li, Feng

2014-06-15

Hybridization chain reaction (HCR) strategy has been well developed for the fabrication of various biosensing platforms for signal amplification. Herein, a novel enzyme-free and label-free ultrasensitive electrochemical DNA biosensing platform for the detection of target DNA and adenosine triphosphate (ATP) was firstly proposed, in which three auxiliary DNA probes were ingeniously designed to construct the dendritic DNA concatamer via HCR strategy and used as hexaammineruthenium(III) chloride (RuHex) carrier for signal amplification. With the developed dendritic DNA concatamer-based signal amplification strategy, the DNA biosensor could achieve an ultrasensitive electrochemical detection of DNA and ATP with a superior detection limit as low as 5 aM and 20 fM, respectively, and also demonstrate a high selectivity for DNA and ATP detection. The currently proposed dendritic DNA concatamer opens a promising direction to construct ultrasensitive DNA biosensing platform for biomolecular detection in bioanalysis and clinical biomedicine, which offers the distinct advantages of simplicity and cost efficiency owing to no need of any kind of enzyme, chemical modification or labeling. Copyright © 2014 Elsevier B.V. All rights reserved.

Adélie penguin population diet monitoring by analysis of food DNA in scats.

Science.gov (United States)

Jarman, Simon N; McInnes, Julie C; Faux, Cassandra; Polanowski, Andrea M; Marthick, James; Deagle, Bruce E; Southwell, Colin; Emmerson, Louise

2013-01-01

The Adélie penguin is the most important animal currently used for ecosystem monitoring in the Southern Ocean. The diet of this species is generally studied by visual analysis of stomach contents; or ratios of isotopes of carbon and nitrogen incorporated into the penguin from its food. There are significant limitations to the information that can be gained from these methods. We evaluated population diet assessment by analysis of food DNA in scats as an alternative method for ecosystem monitoring with Adélie penguins as an indicator species. Scats were collected at four locations, three phases of the breeding cycle, and in four different years. A novel molecular diet assay and bioinformatics pipeline based on nuclear small subunit ribosomal RNA gene (SSU rDNA) sequencing was used to identify prey DNA in 389 scats. Analysis of the twelve population sample sets identified spatial and temporal dietary change in Adélie penguin population diet. Prey diversity was found to be greater than previously thought. Krill, fish, copepods and amphipods were the most important food groups, in general agreement with other Adélie penguin dietary studies based on hard part or stable isotope analysis. However, our DNA analysis estimated that a substantial portion of the diet was gelatinous groups such as jellyfish and comb jellies. A range of other prey not previously identified in the diet of this species were also discovered. The diverse prey identified by this DNA-based scat analysis confirms that the generalist feeding of Adélie penguins makes them a useful indicator species for prey community composition in the coastal zone of the Southern Ocean. Scat collection is a simple and non-invasive field sampling method that allows DNA-based estimation of prey community differences at many temporal and spatial scales and provides significant advantages over alternative diet analysis approaches.

Benefits of Group Foraging Depend on Prey Type in a Small Marine Predator, the Little Penguin.

Science.gov (United States)

Sutton, Grace J; Hoskins, Andrew J; Arnould, John P Y

2015-01-01

Group foraging provides predators with advantages in over-powering prey larger than themselves or in aggregating small prey for efficient exploitation. For group-living predatory species, cooperative hunting strategies provide inclusive fitness benefits. However, for colonial-breeding predators, the benefit pay-offs of group foraging are less clear due to the potential for intra-specific competition. We used animal-borne cameras to determine the prey types, hunting strategies, and success of little penguins (Eudyptula minor), a small, colonial breeding air-breathing marine predator that has recently been shown to display extensive at-sea foraging associations with conspecifics. Regardless of prey type, little penguins had a higher probability of associating with conspecifics when hunting prey that were aggregated than when prey were solitary. In addition, success was greater when individuals hunted schooling rather than solitary prey. Surprisingly, however, success on schooling prey was similar or greater when individuals hunted on their own than when with conspecifics. These findings suggest individuals may be trading-off the energetic gains of solitary hunting for an increased probability of detecting prey within a spatially and temporally variable prey field by associating with conspecifics.

Two-prey one-predator model

International Nuclear Information System (INIS)

Elettreby, M.F.

2009-01-01

In this paper we propose a new multi-team prey-predator model, in which the prey teams help each other. We study its local stability. In the absence of predator, there is no help between the prey teams. So, we study the global stability and persistence of the model without help.

Multicolour probes for sequence-specific DNA detection based on graphene oxide.

Science.gov (United States)

Zhu, Qing; Xiang, Dongshan; Zhang, Cuiling; Ji, Xinghu; He, Zhike

2013-09-21

The bifunctionality of graphene oxide (GO) which can highly adsorb single-stranded DNA (ssDNA) and effectively quench the emission of organic dyes is reasonably utilized in a multiplexed DNA detection system, achieving sensitive and selective detection of HIV, VV and EV, respectively.

Irradiation detection of food by DNA Comet Assay

International Nuclear Information System (INIS)

Khan, A.A.; Delincee, H.

1999-01-01

Microgel electrophoresis of single cells or nuclei (DNA Comet Assay) has been investigated to detect irradiation treatment of more than 50 food commodities e.g. meats, seafood, cereals, pulses, nuts, fruits and vegetables, and spices. The foodstuffs have been exposed to radiation doses covering the range of potential commercial irradiation for inactivation of pathogenic and spoilage micro-organisms, for insect disinfestation and for shelf-life extension. The Comet Assay is based on detection of DNA fragments presumptive to irradiation. For most of the food items investigated, the assay can be applied successfully for irradiation detection by working out different conditions of the assay. However, with some of the foods difficulties arose due to - lack of discrimination between the irradiated and unirradiated food samples due to the presence of the same kinds of comets in both cases and the total absence of the typical intact cells in unirradiated samples. - Sufficient DNA material was not available from some of the foods. - Insufficient lysis of the cell walls in case of some plant foods. In conclusion, the DNA Comet Assay can help to detect the irradiation treatment of several varieties of foods using low-cost equipment in a short time of analysis. (orig.)

Electrochemical DNA probe for Hg(2+) detection based on a triple-helix DNA and Multistage Signal Amplification Strategy.

Science.gov (United States)

Wang, Huan; Zhang, Yihe; Ma, Hongmin; Ren, Xiang; Wang, Yaoguang; Zhang, Yong; Wei, Qin

2016-12-15

In this work, an ultrasensitive electrochemical sensor was developed for detection of Hg(2+). Gold nanoparticles decorated bovine serum albumin reduction of graphene oxide (AuNP-BSA-rGO) were used as subsurface material for the immobilization of triple-helix DNA. The triple-helix DNA containing a thiol labelled single-stranded DNA (sDNA) and a thymine-rich DNA (T-rich DNA), which could be unwinded in the present of Hg(2+) to form more stable thymine-Hg(2+)-thymine (T-Hg(2+)-T) complex. T-Hg(2+)-T complex was then removed and the sDNA was left on the electrode. At this time, gold nanoparticle carrying thiol labelled cytosine-rich complementary DNA (cDNA-AuNP) could bind with the free sDNA. Meanwhile, the other free cDNA on AuNP could bind with each other in the present of Ag(+) to form the stable cytosine-Ag(+)-cytosine (C-Ag(+)-C) complex and circle amplification. Plenty of C-Ag(+)-C could form silver nanoclusters by electrochemical reduction and the striping signal of Ag could be measured for purpose of the final electrochemical detection of Hg(2+). This sensor could detect Hg(2+) over a wide concentration range from 0.1 to 130nM with a detection limit of 0.03nM. Copyright © 2016 Elsevier B.V. All rights reserved.

Harvesting policy for a delayed stage-structured Holling II predator-prey model with impulsive stocking prey

International Nuclear Information System (INIS)

Jiao Jianjun; Meng Xinzhu; Chen Lansun

2009-01-01

A predator-prey model with a stage structure for the predator, which improves the assumption that each individual predator has the same ability to capture prey, is proposed by Wang et al. [Wang W, Mulone G, Salemi F, Salone V. Permanence and stability of a stage-structured predator-prey model. J Math Anal Appl 2001;262:499-528]. It is assumed that immature individuals and mature individuals of the predator are divided by a fixed age and that immature predators do not have the ability to attack prey. We do economic management behavior for Wang model [Wang et al., 2001] by continuous harvesting on predator and impulsive stocking on prey. Then, a delayed stage-structured Holling type II predator-prey model with impulsive stocking prey and continuous harvesting predator is established. It is also assumed that the predating products of the predator is only to increase its bearing ability. We obtain the sufficient conditions of the global attractivity of predator-extinction boundary periodic solution and the permanence of the system. Our results show that the behavior of impulsive stocking prey plays an important role for the permanence of the system, and provide tactical basis for the biological resource management. Further, the numerical analysis is also inserted to illuminate the dynamics of the system.

Effect of sample storage time on detection of hybridization signals in Checkerboard DNA-DNA hybridization.

Science.gov (United States)

do Nascimento, Cássio; Muller, Katia; Sato, Sandra; Albuquerque Junior, Rubens Ferreira

2012-04-01

Long-term sample storage can affect the intensity of the hybridization signals provided by molecular diagnostic methods that use chemiluminescent detection. The aim of this study was to evaluate the effect of different storage times on the hybridization signals of 13 bacterial species detected by the Checkerboard DNA-DNA hybridization method using whole-genomic DNA probes. Ninety-six subgingival biofilm samples were collected from 36 healthy subjects, and the intensity of hybridization signals was evaluated at 4 different time periods: (1) immediately after collecting (n = 24) and (2) after storage at -20 °C for 6 months (n = 24), (3) for 12 months (n = 24), and (4) for 24 months (n = 24). The intensity of hybridization signals obtained from groups 1 and 2 were significantly higher than in the other groups (p  0.05). The Checkerboard DNA-DNA hybridization method was suitable to detect hybridization signals from all groups evaluated, and the intensity of signals decreased significantly after long periods of sample storage.

Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets.

Science.gov (United States)

Rant, Ulrich; Arinaga, Kenji; Scherer, Simon; Pringsheim, Erika; Fujita, Shozo; Yokoyama, Naoki; Tornow, Marc; Abstreiter, Gerhard

2007-10-30

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 x 10(8) bound targets per cm(2) sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.

Environmental DNA for Detection of Endangered Grouper Species (Epinephelus spp.

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Servet A. Doğdu

2016-09-01

Full Text Available Marine ecosystems nestle species or populations known to be threatened due to human overexploitation. Reliable detection and monitoring of threatened organisms is crucial for data-driven conservation actions. Furthermore, misidentification of species represents a major problem. Here, we investigate the potential of using metabarcoding of environmental DNA (eDNA obtained directly from seawater samples to detect endangered grouper species (Epinephelus spp.. Cytochrome c oxidase subunit I (COI fragment of mtDNA was used to detect groupers species in the Mediterranean Coasts. We conducted eDNA sampling at sites by underwater diving across the range of the Grouper species habitats in Northeastern Mediterranean (Antalya-Kas Region and Iskenderun Bay. eDNA was isolated from 2 liter seawater samples which were vacuum-filtered onto 0.45-mm membrane filters. Filters were then folded inwards, placed in 2 ml tubes and stored at -20 oC until DNA extraction, which took place within 24 hours. DNA was extracted from the water sample filters using the DNeasy Blood and Tissue Kit (Qiagen, USA. Manufacturer’s protocols were used during all steps. PCR amplification of eDNA samples were done using selective primers of COI region of mitochondrial DNA, and next-generation DNA sequencing of PCR application was conducted. For the successfully obtained COI sequences, maximum matching rates were revealed as 80% for Epinephelus marginatus, 78,95% for Epinephelus aeneus, 73,48% for Epinephelus costae, 63,45% for Epinephelus caninus, 60,12% for Mycteroperca rubra and 57,12% for Hyporthodus haifensis. Despite the methodological challenges inherent in eDNA analysis, the results demonstrated that eDNA method may be proved to step towards a new beginning to detect and monitor endangered grouper species.

Modified DNA extraction for rapid PCR detection of methicillin-resistant staphylococci

International Nuclear Information System (INIS)

Japoni, A.; Alborzi, A.; Rasouli, M.; Pourabbas, B.

2004-01-01

Nosocomial infection caused by methicillin-resistant staphylococci poses a serious problem in many countries. The aim of this study was to rapidly and reliably detect methicillin-resistant-staphylococci in order to suggest appropriate therapy. The presence or absence of the methicillin-resistance gene in 115 clinical isolates of staphylococcus aureus and 50 isolates of coagulase negative staphylococci was examined by normal PCR. DNA extraction for PCR performance was then modified by omission of achromopeptadiase and proteinase K digestion, phenol/chloroform extraction and ethanol precipitation. All isolates with Mic>8 μ g/ml showed positive PCR. No differences in PCR detection have been observed when normal and modified DNA extractions have been performed. Our modified DNA extraction can quickly detect methicillin-resistant staphylococci by PCR. The advantage of rapid DNA extraction extends to both reduction of time and cost of PCR performance. This modified DNA extraction is suitable for different PCR detection, when staphylococci are the subject of DNA analysis

Turing-Hopf bifurcations in a predator-prey model with herd behavior, quadratic mortality and prey-taxis

Science.gov (United States)

Liu, Xia; Zhang, Tonghua; Meng, Xinzhu; Zhang, Tongqian

2018-04-01

In this paper, we propose a predator-prey model with herd behavior and prey-taxis. Then, we analyze the stability and bifurcation of the positive equilibrium of the model subject to the homogeneous Neumann boundary condition. By using an abstract bifurcation theory and taking prey-tactic sensitivity coefficient as the bifurcation parameter, we obtain a branch of stable nonconstant solutions bifurcating from the positive equilibrium. Our results show that prey-taxis can yield the occurrence of spatial patterns.

Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species.

Science.gov (United States)

Huh, Iksoo; Wu, Xin; Park, Taesung; Yi, Soojin V

2017-07-21

DNA methylation is one of the most extensively studied epigenetic modifications of genomic DNA. In recent years, sequencing of bisulfite-converted DNA, particularly via next-generation sequencing technologies, has become a widely popular method to study DNA methylation. This method can be readily applied to a variety of species, dramatically expanding the scope of DNA methylation studies beyond the traditionally studied human and mouse systems. In parallel to the increasing wealth of genomic methylation profiles, many statistical tools have been developed to detect differentially methylated loci (DMLs) or differentially methylated regions (DMRs) between biological conditions. We discuss and summarize several key properties of currently available tools to detect DMLs and DMRs from sequencing of bisulfite-converted DNA. However, the majority of the statistical tools developed for DML/DMR analyses have been validated using only mammalian data sets, and less priority has been placed on the analyses of invertebrate or plant DNA methylation data. We demonstrate that genomic methylation profiles of non-mammalian species are often highly distinct from those of mammalian species using examples of honey bees and humans. We then discuss how such differences in data properties may affect statistical analyses. Based on these differences, we provide three specific recommendations to improve the power and accuracy of DML and DMR analyses of invertebrate data when using currently available statistical tools. These considerations should facilitate systematic and robust analyses of DNA methylation from diverse species, thus advancing our understanding of DNA methylation. © The Author 2017. Published by Oxford University Press.

Ultrasensitive DNA sequence detection using nanoscale ZnO sensor arrays

Energy Technology Data Exchange (ETDEWEB)

Kumar, Nitin; Dorfman, Adam; Hahm, Jong-in [Department of Chemical Engineering, Pennsylvania State University, 160 Fenske Laboratory, University Park, PA 16802 (United States)

2006-06-28

We report that engineered nanoscale zinc oxide structures can be effectively used for the identification of the biothreat agent, Bacillus anthracis by successfully discriminating its DNA sequence from other genetically related species. We explore both covalent and non-covalent linking schemes in order to couple probe DNA strands to the zinc oxide nanostructures. Hybridization reactions are performed with various concentrations of target DNA strands whose sequence is unique to Bacillus anthracis. The use of zinc oxide nanomaterials greatly enhances the fluorescence signal collected after carrying out duplex formation reaction. Specifically, the covalent strategy allows detection of the target species at sample concentrations at a level as low as a few femtomolar as compared to the detection sensitivity in the tens of nanomolar range when using the non-covalent scheme. The presence of the underlying zinc oxide nanomaterials is critical in achieving increased fluorescence detection of hybridized DNA and, therefore, accomplishing rapid and extremely sensitive identification of the biothreat agent. We also demonstrate the easy integration potential of nanoscale zinc oxide into high density arrays by using various types of zinc oxide sensor prototypes in the DNA sequence detection. When combined with conventional automatic sample handling apparatus and computerized fluorescence detection equipment, our approach can greatly promote the use of zinc oxide nanomaterials as signal enhancing platforms for rapid, multiplexed, high-throughput, highly sensitive, DNA sensor arrays.

Ultrasensitive DNA sequence detection using nanoscale ZnO sensor arrays

International Nuclear Information System (INIS)

Kumar, Nitin; Dorfman, Adam; Hahm, Jong-in

2006-01-01

We report that engineered nanoscale zinc oxide structures can be effectively used for the identification of the biothreat agent, Bacillus anthracis by successfully discriminating its DNA sequence from other genetically related species. We explore both covalent and non-covalent linking schemes in order to couple probe DNA strands to the zinc oxide nanostructures. Hybridization reactions are performed with various concentrations of target DNA strands whose sequence is unique to Bacillus anthracis. The use of zinc oxide nanomaterials greatly enhances the fluorescence signal collected after carrying out duplex formation reaction. Specifically, the covalent strategy allows detection of the target species at sample concentrations at a level as low as a few femtomolar as compared to the detection sensitivity in the tens of nanomolar range when using the non-covalent scheme. The presence of the underlying zinc oxide nanomaterials is critical in achieving increased fluorescence detection of hybridized DNA and, therefore, accomplishing rapid and extremely sensitive identification of the biothreat agent. We also demonstrate the easy integration potential of nanoscale zinc oxide into high density arrays by using various types of zinc oxide sensor prototypes in the DNA sequence detection. When combined with conventional automatic sample handling apparatus and computerized fluorescence detection equipment, our approach can greatly promote the use of zinc oxide nanomaterials as signal enhancing platforms for rapid, multiplexed, high-throughput, highly sensitive, DNA sensor arrays

New applications of CRISPR/Cas9 system on mutant DNA detection.

Science.gov (United States)

Jia, Chenqiang; Huai, Cong; Ding, Jiaqi; Hu, Lingna; Su, Bo; Chen, Hongyan; Lu, Daru

2018-01-30

The detection of mutant DNA is critical for precision medicine, but low-frequency DNA mutation is very hard to be determined. CRISPR/Cas9 is a robust tool for in vivo gene editing, and shows the potential for precise in vitro DNA cleavage. Here we developed a DNA mutation detection system based on CRISPR/Cas9 that can detect gene mutation efficiently even in a low-frequency condition. The system of CRISPR/Cas9 cleavage in vitro showed a high accuracy similar to traditional T7 endonuclease I (T7E1) assay in estimating mutant DNA proportion in the condition of normal frequency. The technology was further used for low-frequency mutant DNA detection of EGFR and HBB somatic mutations. To the end, Cas9 was employed to cleave the wild-type (WT) DNA and to enrich the mutant DNA. Using amplified fragment length polymorphism analysis (AFLPA) and Sanger sequencing, we assessed the sensitivity of CRISPR/Cas9 cleavage-based PCR, in which mutations at 1%-10% could be enriched and detected. When combined with blocker PCR, its sensitivity reached up to 0.1%. Our results suggested that this new application of CRISPR/Cas9 system is a robust and potential method for heterogeneous specimens in the clinical diagnosis and treatment management. Copyright © 2017 Elsevier B.V. All rights reserved.

Prey preferences and prey acceptance in juvenile Brown Treesnakes (Boiga irregularis)

Science.gov (United States)

Lardner, Bjorn; Savidge, Julie A.; Rodda, Gordon H.; Reed, Robert N.

2009-01-01

On the Pacific island of Guam, control of the invasive Brown Treesnake (Boiga irregularis) relies largely on methods that use mice as bait. Juvenile B. irregularis feed primarily on lizards and their eggs, but little is known about their prey preference. We conducted an experiment to investigate preferences for, and acceptance of, dead geckos, skinks, and neonatal mice, in juvenile B. irregularis ranging from 290 mm to ca. 700 mm snout-vent length (SVL). Snakes of all sizes showed a preference for geckos over skinks and neonatal mice. Geckos were the first prey chosen in 87% of 224 initial trials (56 snakes subjected to four trials each; 33% would be expected from a random choice). The smallest snakes had the most pronounced preference. Although many of the snakes accepted neonatal mice and/or skinks, some snakes of all sizes were reluctant to feed on anything but geckos, especially when well fed. We also addressed the hypothesis that repeated encounters with a particular prey type increase a snake's preference for that prey. Our study does not support this hypothesis. Our results suggest that control methods relying solely on rodent bait may be inefficient for targeting snakes < 700 mm SVL and that individual heterogeneity in prey preference may cause a significant part of this juvenile cohort to be completely refractory to capture with rodent bait, even if the bait is dead and small enough to be readily swallowed.

Surface-enhanced Raman scattering based nonfluorescent probe for multiplex DNA detection.

Science.gov (United States)

Sun, Lan; Yu, Chenxu; Irudayaraj, Joseph

2007-06-01

To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive, and multiplex format, an alternative surface-enhanced Raman scattering based probe was designed and fabricated to covalently attach both DNA probing sequence and nonfluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the nonfluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). Excellent multiplexing capability of the DNA-AuP-RTag scheme was demonstrated by simultaneous identification of up to eight probes in a mixture. Detection of hybridization of single-stranded DNA to its complementary targets was successfully accomplished with a long-term goal to use nonfluorescent RTags in a Raman-based DNA microarray platform.

Stochastic Predator-Prey Dynamics of Transposons in the Human Genome

Science.gov (United States)

Xue, Chi; Goldenfeld, Nigel

2016-11-01

Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic, relying on the enzymes produced by the regular transposons. In this case, we show that a stochastic model, which takes into account the small copy numbers of the active transposons in a cell, predicts noise-induced predator-prey oscillations with a characteristic time scale that is much longer than the cell replication time, indicating that the state of the predator-prey oscillator is stored in the genome and transmitted to successive generations. Our work demonstrates the important role of the number fluctuations in the expression of mobile genetic elements, and shows explicitly how ecological concepts can be applied to the dynamics and fluctuations of living genomes.

Disturbed flow in an aquatic environment may create a sensory refuge for aggregated prey

Directory of Open Access Journals (Sweden)

Asa Johannesen

2017-03-01

Full Text Available Predators use olfactory cues moved within water and air to locate prey. Because prey aggregations may produce more cue and be easier to detect, predation could limit aggregation size. However, disturbance in the flow may diminish the reliability of odour as a prey cue, impeding predator foraging success and efficiency. We explore how different cue concentrations (as a proxy for prey group size affect risk to prey by fish predators in disturbed (more turbulent or mixed and non-disturbed (less mixed flowing water. We find that increasing odour cue concentration increases predation risk and disturbing the flow reduces predation risk. At high cue concentration fish were able to locate the cue source in both disturbed and non-disturbed flow, but at medium concentrations, predators only located the cue source more often than expected by chance in non-disturbed flow. This suggests that objects disturbing flow provide a sensory refuge allowing prey to form larger groups, but that group sizes may be limited by level of disturbance to the flow.

A direct detection of Escherichia coli genomic DNA using gold nanoprobes

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Padmavathy

2012-02-01

Full Text Available Abstract Background In situation like diagnosis of clinical and forensic samples there exists a need for highly sensitive, rapid and specific DNA detection methods. Though conventional DNA amplification using PCR can provide fast results, it is not widely practised in diagnostic laboratories partially because it requires skilled personnel and expensive equipment. To overcome these limitations nanoparticles have been explored as signalling probes for ultrasensitive DNA detection that can be used in field applications. Among the nanomaterials, gold nanoparticles (AuNPs have been extensively used mainly because of its optical property and ability to get functionalized with a variety of biomolecules. Results We report a protocol for the use of gold nanoparticles functionalized with single stranded oligonucleotide (AuNP- oligo probe as visual detection probes for rapid and specific detection of Escherichia coli. The AuNP- oligo probe on hybridization with target DNA containing complementary sequences remains red whereas test samples without complementary DNA sequences to the probe turns purple due to acid induced aggregation of AuNP- oligo probes. The color change of the solution is observed visually by naked eye demonstrating direct and rapid detection of the pathogenic Escherichia coli from its genomic DNA without the need for PCR amplification. The limit of detection was ~54 ng for unamplified genomic DNA. The method requires less than 30 minutes to complete after genomic DNA extraction. However, by using unamplified enzymatic digested genomic DNA, the detection limit of 11.4 ng was attained. Results of UV-Vis spectroscopic measurement and AFM imaging further support the hypothesis of aggregation based visual discrimination. To elucidate its utility in medical diagnostic, the assay was validated on clinical strains of pathogenic Escherichia coli obtained from local hospitals and spiked urine samples. It was found to be 100% sensitive and proves to

Detection of human papillomavirus DNA in urine. A review of the literature.

Science.gov (United States)

Vorsters, A; Micalessi, I; Bilcke, J; Ieven, M; Bogers, J; Van Damme, P

2012-05-01

The detection of human papillomavirus (HPV) DNA in urine, a specimen easily obtained by a non-invasive self-sampling method, has been the subject of a considerable number of studies. This review provides an overview of 41 published studies; assesses how different methods and settings may contribute to the sometimes contradictory outcomes; and discusses the potential relevance of using urine samples in vaccine trials, disease surveillance, epidemiological studies, and specific settings of cervical cancer screening. Urine sampling, storage conditions, sample preparation, DNA extraction, and DNA amplification may all have an important impact on HPV DNA detection and the form of viral DNA that is detected. Possible trends in HPV DNA prevalence in urine could be inferred from the presence of risk factors or the diagnosis of cervical lesions. HPV DNA detection in urine is feasible and may become a useful tool but necessitates further improvement and standardization.

Novel DNA sequence detection method based on fluorescence energy transfer

International Nuclear Information System (INIS)

Kobayashi, S.; Tamiya, E.; Karube, I.

1987-01-01

Recently the detection of specific DNA sequence, DNA analysis, has been becoming more important for diagnosis of viral genomes causing infections disease and human sequences related to inherited disorders. These methods typically involve electrophoresis, the immobilization of DNA on a solid support, hybridization to a complementary probe, the detection using labeled with /sup 32/P or nonisotopically with a biotin-avidin-enzyme system, and so on. These techniques are highly effective, but they are very time-consuming and expensive. A principle of fluorescene energy transfer is that the light energy from an excited donor (fluorophore) is transferred to an acceptor (fluorophore), if the acceptor exists in the vicinity of the donor and the excitation spectrum of donor overlaps the emission spectrum of acceptor. In this study, the fluorescence energy transfer was applied to the detection of specific DNA sequence using the hybridization method. The analyte, single-stranded DNA labeled with the donor fluorophore is hybridized to a probe DNA labeled with the acceptor. Because of the complementary DNA duplex formation, two fluorophores became to be closed to each other, and the fluorescence energy transfer was occurred

Non-webbuilding spiders: prey specialists or generalists?

Science.gov (United States)

Nentwig, Wolfgang

1986-07-01

Feeding experiments were performed with seven species of non-webbuilding spiders and a variety of prey taxa. Some species were generally polyphagous whereas other spiders restricted their prey to a few groups. At one end of the spectrum of prey specialization the thomisid Misumena vatia is limited to a few taxa of possible prey (Table 1). The literature of prey records of non-webbuilding spiders is reviewed (Table 2) with special emphasis on oligophagous or monophagous spiders. Monophagous spiders are generally rare and have specialized on only a few prey taxa: social insects (ants, bees, termites) and spiders.

Synthesis of streptavidin-conjugated magnetic nanoparticles for DNA detection

International Nuclear Information System (INIS)

Gong Peijun; Peng Zheyang; Wang Yao; Qiao Ru; Mao Weixing; Qian Haisheng; Zhang Mengya; Li Congcong; Shi Shenyuan

2013-01-01

In this paper, we report a fabrication of streptavidin-coated magnetic nanoparticles used for DNA detection. Initially, amino-functionalized Fe 3 O 4 nanoparticles with high saturation magnetization are prepared by a photopolymerization method using allylamine as monomer. It is followed by covalent immobilization of streptavidin onto the particle surface via a two-step reaction using glutaraldehyde as coupling agent. Streptavidin-coated magnetic nanoparticles are characterized and further tested for their ability to capture DNA target after binding biotinylated oligonucleotide probes. The results show that the products (∼27.2 nm) have a maximum biotin-binding capacity of 0.71 nmol mg −1 when the immobilization reaction is conducted with a mass ratio of streptavidin to magnetic carriers above 0.2 in phosphate buffered saline (pH 7.4) for 24 h. In addition, highly negative ζ-potential and good magnetic susceptibility of the nanocomposites make them applicable for DNA collection and detection, which is verified by the results from the preliminary application of streptavidin-coated magnetic nanoparticles in DNA detection. Therefore, the magnetic nanoparticles provide a promising approach for rapid collection and detection of gene.

Quantitative detection of DNA by autocatalytic enlargement of hybridized gold nanoprobes

DEFF Research Database (Denmark)

Zhan, Zongrui; Cao, Cuong; Sim, Sang Jun

2010-01-01

Quantitative detection of specific viral DNA has become a pressing issue for the earlier clinical diagnosis of viral infectious diseases. Therefore, in this paper, we report a simple, sensitive, and inexpensive quantitative approach for DNA detection based on the autocatalytic Au deposition of go...... to the concentration of the target DNA, could easily be confirmed by a UV–vis scanning spectrophotometer. Limit of detection could be obtained as low as 1.0 fM by this simple method....

Colorimetric Detection of Specific DNA Segments Amplified by Polymerase Chain Reactions

Science.gov (United States)

Kemp, David J.; Smith, Donald B.; Foote, Simon J.; Samaras, N.; Peterson, M. Gregory

1989-04-01

The polymerase chain reaction (PCR) procedure has many potential applications in mass screening. We describe here a general assay for colorimetric detection of amplified DNA. The target DNA is first amplified by PCR, and then a second set of oligonucleotides, nested between the first two, is incorporated by three or more PCR cycles. These oligonucleotides bear ligands: for example, one can be biotinylated and the other can contain a site for a double-stranded DNA-binding protein. After linkage to an immobilized affinity reagent (such as a cloned DNA-binding protein, which we describe here) and labeling with a second affinity reagent (for example, avidin) linked to horseradish peroxidase, reaction with a chromogenic substrate allows detection of the amplified DNA. This amplified DNA assay (ADA) is rapid, is readily applicable to mass screening, and uses routine equipment. We show here that it can be used to detect human immunodeficiency virus sequences specifically against a background of human DNA.

Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

Science.gov (United States)

Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

2013-01-01

Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry. PMID:23435052

Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

Directory of Open Access Journals (Sweden)

Yuji Miyahara

2013-02-01

Full Text Available Peptide nucleic acid (PNA has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

PCR-based detection of a rare linear DNA in cell culture

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Saveliev Sergei V.

2002-01-01

Full Text Available The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 107 or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

PCR-based detection of a rare linear DNA in cell culture.

Science.gov (United States)

Saveliev, Sergei V.

2002-11-11

The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 10(7) or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

Enzyme-enhanced fluorescence detection of DNA on etched optical fibers.

Science.gov (United States)

Niu, Shu-yan; Li, Quan-yi; Ren, Rui; Zhang, Shu-sheng

2009-05-15

A novel DNA biosensor based on enzyme-enhanced fluorescence detection on etched optical fibers was developed. The hybridization complex of DNA probe and biotinylated target was formed on the etched optical fiber, and was then bound with streptavidin labeled horseradish peroxidase (streptavidin-HRP). The target DNA was quantified through the fluorescent detection of bi-p,p'-4-hydroxyphenylacetic acid (DBDA) generated from the substrate 4-hydroxyphenylacetic acid (p-HPA) under the catalysis of HRP, with a detection limit of 1 pM and a linear range from 1.69 pM to 169 pM. It is facile to regenerate this sensor through surface treatment with concentrated urea solution. It was discovered that the sensor can retain 70% of its original activity after three detection-regeneration cycles.

RADIA: RNA and DNA integrated analysis for somatic mutation detection.

Directory of Open Access Journals (Sweden)

Amie J Radenbaugh

Full Text Available The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on comparing the normal and tumor genomes from the same individual. In recent years, it has become routine for projects like The Cancer Genome Atlas (TCGA to also sequence the tumor RNA. Here we present RADIA (RNA and DNA Integrated Analysis, a novel computational method combining the patient-matched normal and tumor DNA with the tumor RNA to detect somatic mutations. The inclusion of the RNA increases the power to detect somatic mutations, especially at low DNA allelic frequencies. By integrating an individual's DNA and RNA, we are able to detect mutations that would otherwise be missed by traditional algorithms that examine only the DNA. We demonstrate high sensitivity (84% and very high precision (98% and 99% for RADIA in patient data from endometrial carcinoma and lung adenocarcinoma from TCGA. Mutations with both high DNA and RNA read support have the highest validation rate of over 99%. We also introduce a simulation package that spikes in artificial mutations to patient data, rather than simulating sequencing data from a reference genome. We evaluate sensitivity on the simulation data and demonstrate our ability to rescue back mutations at low DNA allelic frequencies by including the RNA. Finally, we highlight mutations in important cancer genes that were rescued due to the incorporation of the RNA.

Failure to detect circulating DNA-anti-DNA complexes by four radioimmunological methods in patients with systemic lupus erythematosus

International Nuclear Information System (INIS)

Izui, S.; Lambert, P.H.; Miescher, P.A.

1977-01-01

The presence of DNA-anti-DNA complexes in sera from patients with systemic lupus erythematosus (SLE) was investigated by two new radioimmunoassays (RIA) developed for this purpose and by measuring the CLq and DNA binding activity of serum before and after treatment with DNAse. Two direct RIA developed in this study were based on the reactivity of [ 3 H]actinomycin D ([ 3 H]ACT-D) or solid-phase methylated bovine serum albumin (mBSA) with DNA-anti-DNA complexes. DNA-anti-DNA complexes prepared in vitro could be efficiently detected at various antigen-antibody ratios by these two RIA. Increased levels of circulating immune complexes as indicated by the CLq binding test were found in 52% of SLE sera. However, the frequency of specific DNA-anti-DNA complexes detected in SLE sera was very low. Only 6% of sera exhibited an increased value deviating by more than three s.d. from the normal mean when tested with the [ 3 H]ACT-D binding RIA or the solid-phase mBSA RIA. On the other hand, there was no significant difference in the serum CLq or DNA binding activity after treatment with DNAse. These results suggest that DNA-anti-DNA complexes do not occur frequently in circulating blood and represent only a very small portion of the immune complexes detected in serum from patients with SLE. (author)

Detection of DNA via the fluorescence quenching of Mn-doped ZnSe D-dots/doxorubicin/DNA ternary complexes system.

Science.gov (United States)

Gao, Xue; Niu, Lu; Su, Xingguang

2012-01-01

This manuscript reports a method for the detection of double-stranded DNA, based on Mn:ZnSe d-dots and intercalating agent doxorubicin (DOX). DOX can quench the photoluminescence (PL) of Mn:ZnSe d-dots through photoinduced electron transfer process, after binding with Mn:ZnSe d-dots. The addition of DNA can result in the formation of the Mn:ZnSe d-dots-DOX-DNA ternary complexes, the fluorescence of the Mn:ZnSe d-dots-DOX complexes would be further quenched by the addition of DNA, thus allowing the detection of DNA. The formation mechanism of the Mn:ZnSe d-dots-DOX-DNA ternary complexes was studied in detail in this paper. Under optimal conditions, the quenched fluorescence intensity of Mn:ZnSe d-dots-DOX system are perfectly described by Stern-Volmer equation with the concentration of hsDNA ranging from 0.006 μg mL(-1) to 6.4 μg mL(-1). The detection limit (S/N = 3) for hsDNA is 0.5 ng mL(-1). The proposed method was successfully applied to the detection of DNA in synthetic samples and the results were satisfactory.

Eggshell membrane: A natural substrate for immobilization and detection of DNA

Energy Technology Data Exchange (ETDEWEB)

Ray, Preetam Guha; Roy, Somenath, E-mail: sroy@cgcri.res.in

2016-02-01

Chemically modified eggshell membranes (ESM) have been explored as potentially novel platforms for immobilization of oligonucleotides and subsequent detection of target DNA. The fibrous network of the native ESM as well those functionalized with acetic acid or n-butyl acetate has been examined by field-emission scanning electron microscopy (FESEM). The formation of surface functional moieties has been confirmed by Fourier-transform infrared spectroscopy (FTIR). DNA molecules, with an end terminal − NH{sub 2} group (at 5′ end) have been immobilized on the chemically modified ESM surface. The effect of surface modification on the DNA immobilization efficiency has been investigated using fluorescence microscopy and atomic force microscopy (AFM). The above studies concurrently suggest that functionalization of ESM with n-butyl acetate causes a better homogeneity of the DNA probes on the membrane surface. On-chip hybridization of the target DNA with the surface bound capture probes has been performed on the functionalized membranes. It is observed that n-butyl acetate modification of ESM pushes the limit of detection (LOD) of the DNA sensors by at least an order of magnitude compared to the other modification method. - Graphical abstract: Eggshell membranes (ESM) have been chemically modified with acetic acid or n-butyl acetate for immobilization of aminated capture probes and subsequent detection of fluorophore-tagged target DNA molecules. n-Butyl acetate modified ESM exhibits superior homogeneity of capture probe immobilization and lower limit of detection for the target DNA molecules. - Highlights: • Eggshell membranes (ESM) have been explored as potentially novel platforms for immobilization of oligonucleotides. • Compared to native ESM, those modified with acetic acid or n-butyl acetate have shown more efficient loading of DNA probes. • ESM modified with n-butyl acetate pushed the lower limit of detection (LOD) of the sensor down to 10 nM of target DNA

Direct detection of chicken genomic DNA for gender determination by thymine-DNA glycosylase.

Science.gov (United States)

Porat, N; Bogdanov, K; Danielli, A; Arie, A; Samina, I; Hadani, A

2011-02-01

1. Birds, especially nestlings, are generally difficult to sex by morphology and early detection of chick gender in ovo in the hatchery would facilitate removal of unwanted chicks and diminish welfare objections regarding culling after hatch. 2. We describe a method to determine chicken gender without the need for PCR via use of Thymine-DNA Glycosylase (TDG). TDG restores thymine (T)/guanine (G) mismatches to cytosine (C)/G. We show here, that like DNA Polymerase, TDG can recognise, bind and function on a primer hybridised to chicken genomic DNA. 3. The primer contained a T to mismatch a G in a chicken genomic template and the T/G was cleaved with high fidelity by TDG. Thus, the chicken genomic DNA can be identified without PCR amplification via direct and linear detection. Sensitivity was increased using gender specific sequences from the chicken genome. 4. Currently, these are laboratory results, but we anticipate that further development will allow this method to be used in non-laboratory settings, where PCR cannot be employed.

Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection.

Science.gov (United States)

Velders, Aldrik H; Schoen, Cor; Saggiomo, Vittorio

2018-02-01

Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap and easy, one-button device that can perform LAMP experiments. Here we show how to build and program an Arduino shield for a LAMP and detection of DNA. The here described Arduino Shield is cheap, easy to assemble, to program and use, it is battery operated and the detection of DNA is done by naked-eye so that it can be used in field.

The Dynamical Analysis of a Prey-Predator Model with a Refuge-Stage Structure Prey Population

Directory of Open Access Journals (Sweden)

Raid Kamel Naji

2016-01-01

Full Text Available We proposed and analyzed a mathematical model dealing with two species of prey-predator system. It is assumed that the prey is a stage structure population consisting of two compartments known as immature prey and mature prey. It has a refuge capability as a defensive property against the predation. The existence, uniqueness, and boundedness of the solution of the proposed model are discussed. All the feasible equilibrium points are determined. The local and global stability analysis of them are investigated. The occurrence of local bifurcation (such as saddle node, transcritical, and pitchfork near each of the equilibrium points is studied. Finally, numerical simulations are given to support the analytic results.

Detection of dopamine in dopaminergic cell using nanoparticles-based barcode DNA analysis.

Science.gov (United States)

An, Jeung Hee; Kim, Tae-Hyung; Oh, Byung-Keun; Choi, Jeong Woo

2012-01-01

Nanotechnology-based bio-barcode-amplification analysis may be an innovative approach to dopamine detection. In this study, we evaluated the efficacy of this bio-barcode DNA method in detecting dopamine from dopaminergic cells. Herein, a combination DNA barcode and bead-based immunoassay for neurotransmitter detection with PCR-like sensitivity is described. This method relies on magnetic nanoparticles with antibodies and nanoparticles that are encoded with DNA, and antibodies that can sandwich the target protein captured by the nanoparticle-bound antibodies. The aggregate sandwich structures are magnetically separated from solution, and treated in order to remove the conjugated barcode DNA. The DNA barcodes were then identified via PCR analysis. The dopamine concentration in dopaminergic cells can be readily and rapidly detected via the bio-barcode assay method. The bio-barcode assay method is, therefore, a rapid and high-throughput screening tool for the detection of neurotransmitters such as dopamine.

Predicting prey population dynamics from kill rate, predation rate and predator-prey ratios in three wolf-ungulate systems.

Science.gov (United States)

Vucetich, John A; Hebblewhite, Mark; Smith, Douglas W; Peterson, Rolf O

2011-11-01

1. Predation rate (PR) and kill rate are both fundamental statistics for understanding predation. However, relatively little is known about how these statistics relate to one another and how they relate to prey population dynamics. We assess these relationships across three systems where wolf-prey dynamics have been observed for 41 years (Isle Royale), 19 years (Banff) and 12 years (Yellowstone). 2. To provide context for this empirical assessment, we developed theoretical predictions of the relationship between kill rate and PR under a broad range of predator-prey models including predator-dependent, ratio-dependent and Lotka-Volterra dynamics. 3. The theoretical predictions indicate that kill rate can be related to PR in a variety of diverse ways (e.g. positive, negative, unrelated) that depend on the nature of predator-prey dynamics (e.g. structure of the functional response). These simulations also suggested that the ratio of predator-to-prey is a good predictor of prey growth rate. That result motivated us to assess the empirical relationship between the ratio and prey growth rate for each of the three study sites. 4. The empirical relationships indicate that PR is not well predicted by kill rate, but is better predicted by the ratio of predator-to-prey. Kill rate is also a poor predictor of prey growth rate. However, PR and ratio of predator-to-prey each explained significant portions of variation in prey growth rate for two of the three study sites. 5. Our analyses offer two general insights. First, Isle Royale, Banff and Yellowstone are similar insomuch as they all include wolves preying on large ungulates. However, they also differ in species diversity of predator and prey communities, exploitation by humans and the role of dispersal. Even with the benefit of our analysis, it remains difficult to judge whether to be more impressed by the similarities or differences. This difficulty nicely illustrates a fundamental property of ecological

Allele-Specific DNA Methylation Detection by Pyrosequencing®

DEFF Research Database (Denmark)

Kristensen, Lasse Sommer; Johansen, Jens Vilstrup; Grønbæk, Kirsten

2015-01-01

DNA methylation is an epigenetic modification that plays important roles in healthy as well as diseased cells, by influencing the transcription of genes. In spite the fact that human somatic cells are diploid, most of the currently available methods for the study of DNA methylation do not provide......-effective protocol for allele-specific DNA methylation detection based on Pyrosequencing(®) of methylation-specific PCR (MSP) products including a single nucleotide polymorphism (SNP) within the amplicon....

Constructing and detecting a cDNA library for mites.

Science.gov (United States)

Hu, Li; Zhao, YaE; Cheng, Juan; Yang, YuanJun; Li, Chen; Lu, ZhaoHui

2015-10-01

RNA extraction and construction of complementary DNA (cDNA) library for mites have been quite challenging due to difficulties in acquiring tiny living mites and breaking their hard chitin. The present study is to explore a better method to construct cDNA library for mites that will lay the foundation on transcriptome and molecular pathogenesis research. We selected Psoroptes cuniculi as an experimental subject and took the following steps to construct and verify cDNA library. First, we combined liquid nitrogen grinding with TRIzol for total RNA extraction. Then, switching mechanism at 5' end of the RNA transcript (SMART) technique was used to construct full-length cDNA library. To evaluate the quality of cDNA library, the library titer and recombination rate were calculated. The reliability of cDNA library was detected by sequencing and analyzing positive clones and genes amplified by specific primers. The results showed that the RNA concentration was 836 ng/μl and the absorbance ratio at 260/280 nm was 1.82. The library titer was 5.31 × 10(5) plaque-forming unit (PFU)/ml and the recombination rate was 98.21%, indicating that the library was of good quality. In the 33 expressed sequence tags (ESTs) of P. cuniculi, two clones of 1656 and 1658 bp were almost identical with only three variable sites detected, which had an identity of 99.63% with that of Psoroptes ovis, indicating that the cDNA library was reliable. Further detection by specific primers demonstrated that the 553-bp Pso c II gene sequences of P. cuniculi had an identity of 98.56% with those of P. ovis, confirming that the cDNA library was not only reliable but also feasible.

Do lions Panthera leo actively select prey or do prey preferences simply reflect chance responses via evolutionary adaptations to optimal foraging?

Directory of Open Access Journals (Sweden)

Matt W Hayward

Full Text Available Research on coursing predators has revealed that actions throughout the predatory behavioral sequence (using encounter rate, hunting rate, and kill rate as proxy measures of decisions drive observed prey preferences. We tested whether similar actions drive the observed prey preferences of a stalking predator, the African lion Panthera leo. We conducted two 96 hour, continuous follows of lions in Addo Elephant National Park seasonally from December 2003 until November 2005 (16 follows, and compared prey encounter rate with prey abundance, hunt rate with prey encounter rate, and kill rate with prey hunt rate for the major prey species in Addo using Jacobs' electivity index. We found that lions encountered preferred prey species far more frequently than expected based on their abundance, and they hunted these species more frequently than expected based on this higher encounter rate. Lions responded variably to non-preferred and avoided prey species throughout the predatory sequence, although they hunted avoided prey far less frequently than expected based on the number of encounters of them. We conclude that actions of lions throughout the predatory behavioural sequence, but particularly early on, drive the prey preferences that have been documented for this species. Once a hunt is initiated, evolutionary adaptations to the predator-prey interactions drive hunting success.

Do lions Panthera leo actively select prey or do prey preferences simply reflect chance responses via evolutionary adaptations to optimal foraging?

Science.gov (United States)

Hayward, Matt W; Hayward, Gina J; Tambling, Craig J; Kerley, Graham I H

2011-01-01

Research on coursing predators has revealed that actions throughout the predatory behavioral sequence (using encounter rate, hunting rate, and kill rate as proxy measures of decisions) drive observed prey preferences. We tested whether similar actions drive the observed prey preferences of a stalking predator, the African lion Panthera leo. We conducted two 96 hour, continuous follows of lions in Addo Elephant National Park seasonally from December 2003 until November 2005 (16 follows), and compared prey encounter rate with prey abundance, hunt rate with prey encounter rate, and kill rate with prey hunt rate for the major prey species in Addo using Jacobs' electivity index. We found that lions encountered preferred prey species far more frequently than expected based on their abundance, and they hunted these species more frequently than expected based on this higher encounter rate. Lions responded variably to non-preferred and avoided prey species throughout the predatory sequence, although they hunted avoided prey far less frequently than expected based on the number of encounters of them. We conclude that actions of lions throughout the predatory behavioural sequence, but particularly early on, drive the prey preferences that have been documented for this species. Once a hunt is initiated, evolutionary adaptations to the predator-prey interactions drive hunting success.

Selective olfactory attention of a specialised predator to intraspecific chemical signals of its prey.

Science.gov (United States)

Cárdenas, Manuel; Jiroš, Pavel; Pekár, Stano

2012-08-01

Prey-specialised predators have evolved specific cognitive adaptations that increase their prey searching efficiency. In particular, when the prey is social, selection probably favours the use of prey intraspecific chemical signals by predatory arthropods. Using a specialised ant-eating zodariid spider, Zodarion rubidum, which is known to prey on several ant species and possesses capture and venom adaptations more effective on Formicinae ants, we tested its ability to recognise chemical cues produced by several ant species. Using an olfactometer, we tested the response of Z. rubidum towards air with chemical cues from six different ant species: Camponotus ligniperda, Lasius platythorax and Formica rufibarbis (all Formicinae); and Messor structor, Myrmica scabrinodis and Tetramorium caespitum (all Myrmicinae). Z. rubidum was attracted to air carrying chemical cues only from F. rufibarbis and L. platythorax. Then, we identified that the spiders were attracted to airborne cues coming from the F. rufibarbis gaster and Dufour's gland, in particular. Finally, we found that among several synthetic blends, the decyl acetate and undecane mixture produced significant attraction of spiders. These chemicals are produced only by three Formicine genera. Furthermore, we investigated the role of these chemical cues in the communication of F. rufibarbis and found that this blend reduces their movement. This study demonstrates the chemical cognitive capacity of Z. rubidum to locate its ant prey using chemical signals produced by the ants. The innate capacity of Z. rubidum to olfactory detect different ant species is narrow, as it includes only two ant genera, confirming trophic specialisation at lower than subfamily level. The olfactory cue detected by Zodarion spiders is probably a component of the recruitment or trail pheromone.

When attempts at robbing prey turn fatal

Science.gov (United States)

Dejean, Alain; Corbara, Bruno; Azémar, Frédéric; Carpenter, James M.

2012-07-01

Because group-hunting arboreal ants spread-eagle insect prey for a long time before retrieving them, these prey can be coveted by predatory flying insects. Yet, attempting to rob these prey is risky if the ant species is also an effective predator. Here, we show that trying to rob prey from Azteca andreae workers is a fatal error as 268 out of 276 potential cleptobionts (97.1 %) were captured in turn. The ant workers hunt in a group and use the "Velcro®" principle to cling firmly to the leaves of their host tree, permitting them to capture very large prey. Exceptions were one social wasp, plus some Trigona spp. workers and flies that landed directly on the prey and were able to take off immediately when attacked. We conclude that in this situation, previously captured prey attract potential cleptobionts that are captured in turn in most of the cases.

DNA Barcoding of Marine Metazoa

Science.gov (United States)

Bucklin, Ann; Steinke, Dirk; Blanco-Bercial, Leocadio

2011-01-01

More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may outpace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a ˜648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.

Failure to detect circulating DNA-anti-DNA complexes by four radioimmunological methods in patients with systemic lupus erythematosus

Energy Technology Data Exchange (ETDEWEB)

Izui, S; Lambert, P H; Miescher, P A [Hopital Cantonal Geneve (Switzerland)

1977-12-01

The presence of The DNA-anti-DNA complexes in sera from patients with systemic lupus erythematosus (SLE) was investigated by two new radioimmunoassays (RIA) developed for this purpose and by measuring the CLq and DNA binding activity of serum before and after treatment with DNAse. Two direct RIA developed in this study were based on the reactivity of (/sup 3/H)actinomycin D ((/sup 3/H)ACT-D) or solid-phase methylated bovine serum albumin (mBSA) with DNA-anti-DNA complexes. DNA-anti-DNA complexes prepared in vitro could be efficiently detected at various antigen-antibody ratios by these two RIA. Increased levels of circulating immune complexes as indicated by the CLq binding test were found in 52% of the SLE sera. However, the frequency of specific DNA-anti-DNA complexes detected in the SLE sera was very low. Only 6% of the sera exhibited an increased value deviating by more than three s.d. from the normal mean when tested with the (/sup 3/H)ACT-D binding RIA or the solid-phase mBSA RIA. On the other hand, there was no significant difference in the serum CLq or DNA binding activity after treatment with DNAse. These results suggest that DNA-anti-DNA complexes do not occur frequently in circulating blood and represent only a very small portion of the immune complexes detected in serum from patients with SLE.

Ultrasensitive Electrochemical Detection of Clostridium perfringens DNA Based Morphology-Dependent DNA Adsorption Properties of CeO2 Nanorods in Dairy Products

Directory of Open Access Journals (Sweden)

Xingcan Qian

2018-06-01

Full Text Available Foodborne pathogens such as Clostridium perfringens can cause diverse illnesses and seriously threaten to human health, yet far less attention has been given to detecting these pathogenic bacteria. Herein, two morphologies of nanoceria were synthesized via adjusting the concentration of NaOH, and CeO2 nanorod has been utilized as sensing material to achieve sensitive and selective detection of C. perfringens DNA sequence due to its strong adsorption ability towards DNA compared to nanoparticle. The DNA probe was tightly immobilized on CeO2/chitosan modified electrode surface via metal coordination, and the DNA surface density was 2.51 × 10−10 mol/cm2. Under optimal experimental conditions, the electrochemical impedance biosensor displays favorable selectivity toward target DNA in comparison with base-mismatched and non-complementary DNA. The dynamic linear range of the proposed biosensor for detecting oligonucleotide sequence of Clostridium perfringens was from 1.0 × 10−14 to 1.0 × 10−7 mol/L. The detection limit was 7.06 × 10−15 mol/L. In comparison, differential pulse voltammetry (DPV method quantified the target DNA with a detection limit of 1.95 × 10−15 mol/L. Moreover, the DNA biosensor could detect C. perfringens extracted DNA in dairy products and provided a potential application in food quality control.

Modelling landscape-level numerical responses of predators to prey: the case of cats and rabbits.

Directory of Open Access Journals (Sweden)

Jennyffer Cruz

Full Text Available Predator-prey systems can extend over large geographical areas but empirical modelling of predator-prey dynamics has been largely limited to localised scales. This is due partly to difficulties in estimating predator and prey abundances over large areas. Collection of data at suitably large scales has been a major problem in previous studies of European rabbits (Oryctolagus cuniculus and their predators. This applies in Western Europe, where conserving rabbits and predators such as Iberian lynx (Lynx pardinus is important, and in other parts of the world where rabbits are an invasive species supporting populations of introduced, and sometimes native, predators. In pastoral regions of New Zealand, rabbits are the primary prey of feral cats (Felis catus that threaten native fauna. We estimate the seasonal numerical response of cats to fluctuations in rabbit numbers in grassland-shrubland habitat across the Otago and Mackenzie regions of the South Island of New Zealand. We use spotlight counts over 1645 km of transects to estimate rabbit and cat abundances with a novel modelling approach that accounts simultaneously for environmental stochasticity, density dependence and varying detection probability. Our model suggests that cat abundance is related consistently to rabbit abundance in spring and summer, possibly through increased rabbit numbers improving the fecundity and juvenile survival of cats. Maintaining rabbits at low abundance should therefore suppress cat numbers, relieving predation pressure on native prey. Our approach provided estimates of the abundance of cats and rabbits over a large geographical area. This was made possible by repeated sampling within each season, which allows estimation of detection probabilities. A similar approach could be applied to predator-prey systems elsewhere, and could be adapted to any method of direct observation in which there is no double-counting of individuals. Reliable estimates of numerical

Detection of Toxoplasma gondii DNA in sera samples of mice experimentally infected

Directory of Open Access Journals (Sweden)

H. Langoni

2006-04-01

Full Text Available Detection of Toxoplasma gondii (T. gondii DNA in blood can help to diagnose the disease in its acute phase; however, it must be considered that hemoglobin, present in blood, can inhibit polymerase activity, making impracticable the detection of DNA in samples. Mice were experimentally infected via oral route with ME49 and BTU2 strains cysts and RH strain tachyzoites; polymerase chain reaction was used to detect T. gondii DNA in mice sera 18, 24, 48, 96, and 192 hours post infection (PI. Toxoplama gondii DNA was detected in only one animal infected with BTU2 strain, genotype III (isolated from a dog with neurological signs 18 hours PI. The agent's DNA was not detected in any sample of the other experimental groups. New studies must be carried out to verify the technique sensitivity in researches on this agent's genetic material using sera samples of acute-phase toxoplasmosis patients, especially in cases of immunosuppression.

Detection of TTV-DNA in PBMC using digoxigenin labelled probe by in situ hybridization

International Nuclear Information System (INIS)

Liu Yang; Qi Qige

2002-01-01

To determine TTV-DNA in PBMC in patients with viral hepatitis, a study of in situ hybridization using digoxigenin labelled probe by PCR method to the TTV ORF1 region was performed on PBMC. Results showed that the detection rate of TTV-DNA using double-stranded probe in TTV-DNA positive group in sera was 58.06 (18/31), and the detection rate of TTV-DNA using double-stranded probe in TTV-DNA negative group in sera was 27.59 (8/29). For TTV-DNA positive group detected by double- stranded probe, then we use negative- stranded probe to detect their replication. The detection rate was 22.2%(4/18). Conclusions: TTV can infect PBMC and replicate in PBMC

Behavioral response races, predator-prey shell games, ecology of fear, and patch use of pumas and their ungulate prey.

Science.gov (United States)

Laundré, John W

2010-10-01

The predator-prey shell game predicts random movement of prey across the landscape, whereas the behavioral response race and landscape of fear models predict that there should be a negative relationship between the spatial distribution of a predator and its behaviorally active prey. Additionally, prey have imperfect information on the whereabouts of their predator, which the predator should incorporate in its patch use strategy. I used a one-predator-one-prey system, puma (Puma concolor)-mule deer (Odocoileus hemionus) to test the following predictions regarding predator-prey distribution and patch use by the predator. (1) Pumas will spend more time in high prey risk/low prey use habitat types, while deer will spend their time in low-risk habitats. Pumas should (2) select large forage patches more often, (3) remain in large patches longer, and (4) revisit individual large patches more often than individual smaller ones. I tested these predictions with an extensive telemetry data set collected over 16 years in a study area of patchy forested habitat. When active, pumas spent significantly less time in open areas of low intrinsic predation risk than did deer. Pumas used large patches more than expected, revisited individual large patches significantly more often than smaller ones, and stayed significantly longer in larger patches than in smaller ones. The results supported the prediction of a negative relationship in the spatial distribution of a predator and its prey and indicated that the predator is incorporating the prey's imperfect information about its presence. These results indicate a behavioral complexity on the landscape scale that can have far-reaching impacts on predator-prey interactions.

High-speed detection of DNA translocation in nanopipettes

Science.gov (United States)

Fraccari, Raquel L.; Ciccarella, Pietro; Bahrami, Azadeh; Carminati, Marco; Ferrari, Giorgio; Albrecht, Tim

2016-03-01

We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface.We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface. Electronic supplementary information (ESI) available: Gel electrophoresis confirming lengths and purity of DNA samples, comparison between Axopatch 200B and custom-built setup, comprehensive low-noise amplifier characterization, representative I-V curves of nanopipettes used, typical scatter plots of τ vs. peak amplitude for the four LDNA's used, table of most probable τ values, a comparison between different fitting models for the DNA translocation time distribution, further details on the stochastic numerical simulation of the scaling statistics and the derivation of the extended

Detection of DNA hybridization using graphene-coated black phosphorus surface plasmon resonance sensor

Science.gov (United States)

Pal, Sarika; Verma, Alka; Raikwar, S.; Prajapati, Y. K.; Saini, J. P.

2018-05-01

In this paper, graphene-coated black phosphorus at the metal surface for the detection of DNA hybridization event is numerically demonstrated. The strategy consists of placing the sensing medium on top of black phosphorus-graphene-coated SPR which interfaces with phosphate-buffered saline solution carrying single-stranded DNA. Upon hybridization with its complementary DNA, desorption of the nanostructures takes place and thus enables the sensitive detection of the DNA hybridization event. The proposed sensor exhibits a sensitivity (125 ο/RIU), detection accuracy (0.95) and quality factor (13.62 RIU-1) for complementary DNA. In comparison with other reported papers, our suggested sensor provides much better performance. Thus, this label-free DNA detection platform should spur off new interest towards the use of black phosphorus-graphene-coated SPR interfaces.

CLINICAL-EVALUATION OF A MODIFIED ELISA, USING PHOTOBIOTINYLATED DNA, FOR THE DETECTION OF ANTI-DNA ANTIBODIES

NARCIS (Netherlands)

HYLKEMA, MN; HUYGEN, H; KRAMERS, C; VANDERWAL, TJ; DEJONG, J; VANBRUGGEN, MCJ; SWAAK, AJG; BERDEN, JHM; SMEENK, RJT; Hylkema, Machteld

1994-01-01

The measurement of anti-dsDNA antibodies is important for the diagnosis and the follow-up of patients with systemic lupus erythematosus (SLE). For routine detection of anti-dsDNA, the Farr assay and the immunofluorescence technique (IFT) on Crithidia luciliae proved to be very useful. The anti-dsDNA

Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA) from Patients with Non-Small Cell Lung Cancer (NSCLC)

Science.gov (United States)

Sherwood, James L.; Corcoran, Claire; Brown, Helen; Sharpe, Alan D.; Musilova, Milena; Kohlmann, Alexander

2016-01-01

Introduction Non-invasive mutation testing using circulating tumour DNA (ctDNA) is an attractive premise. This could enable patients without available tumour sample to access more treatment options. Materials & Methods Peripheral blood and matched tumours were analysed from 45 NSCLC patients. We investigated the impact of pre-analytical variables on DNA yield and/or KRAS mutation detection: sample collection tube type, incubation time, centrifugation steps, plasma input volume and DNA extraction kits. Results 2 hr incubation time and double plasma centrifugation (2000 x g) reduced overall DNA yield resulting in lowered levels of contaminating genomic DNA (gDNA). Reduced “contamination” and increased KRAS mutation detection was observed using cell-free DNA Blood Collection Tubes (cfDNA BCT) (Streck), after 72 hrs following blood draw compared to EDTA tubes. Plasma input volume and use of different DNA extraction kits impacted DNA yield. Conclusion This study demonstrated that successful ctDNA recovery for mutation detection in NSCLC is dependent on pre-analytical steps. Development of standardised methods for the detection of KRAS mutations from ctDNA specimens is recommended to minimise the impact of pre-analytical steps on mutation detection rates. Where rapid sample processing is not possible the use of cfDNA BCT tubes would be advantageous. PMID:26918901

Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA from Patients with Non-Small Cell Lung Cancer (NSCLC.

Directory of Open Access Journals (Sweden)

James L Sherwood

Full Text Available Non-invasive mutation testing using circulating tumour DNA (ctDNA is an attractive premise. This could enable patients without available tumour sample to access more treatment options.Peripheral blood and matched tumours were analysed from 45 NSCLC patients. We investigated the impact of pre-analytical variables on DNA yield and/or KRAS mutation detection: sample collection tube type, incubation time, centrifugation steps, plasma input volume and DNA extraction kits.2 hr incubation time and double plasma centrifugation (2000 x g reduced overall DNA yield resulting in lowered levels of contaminating genomic DNA (gDNA. Reduced "contamination" and increased KRAS mutation detection was observed using cell-free DNA Blood Collection Tubes (cfDNA BCT (Streck, after 72 hrs following blood draw compared to EDTA tubes. Plasma input volume and use of different DNA extraction kits impacted DNA yield.This study demonstrated that successful ctDNA recovery for mutation detection in NSCLC is dependent on pre-analytical steps. Development of standardised methods for the detection of KRAS mutations from ctDNA specimens is recommended to minimise the impact of pre-analytical steps on mutation detection rates. Where rapid sample processing is not possible the use of cfDNA BCT tubes would be advantageous.

Detection of excretory Entamoeba histolytica DNA in the urine, and detection of E. histolytica DNA and lectin antigen in the liver abscess pus for the diagnosis of amoebic liver abscess

Directory of Open Access Journals (Sweden)

Khairnar Krishna

2007-05-01

Full Text Available Abstract Background Amoebic liver abscess (ALA and pyogenic liver abscesses (PLA appear identical by ultrasound and other imaging techniques. Collection of blood or liver abscess pus for diagnosis of liver abscesses is an invasive procedure, and the procedure requires technical expertise and disposable syringes. Collection of urine is a noninvasive procedure. Therefore, there has been much interest shown towards the use of urine as an alternative clinical specimen for the diagnosis of some parasitic infections. Here, we report for the first time the detection of E. histolytica DNA excreted in the urine for diagnosis of the cases of ALA. Results E. histolytica DNA was detected in liver abscess pus specimen of 80.4% of ALA patients by a nested multiplex polymerase chain reaction (PCR targeting 16S-like r RNA gene. The nested PCR detected E. histolytica DNA in all 37 (100% liver abscess pus specimens collected prior to metronidazole treatment, but were detected in only 53 of 75 (70.6% pus specimens collected after therapy with metronidazole. Similarly, the PCR detected E. histolytica DNA in 21 of 53 (39.6% urine specimens of ALA patients. The test detected E. histolytica DNA in only 4 of 23 (17.4% urine specimens collected prior to metronidazole treatment, but were detected in 17 of 30 (56.7% urine specimens collected after treatment with metronidazole. The enzyme-linked immunosorbent assay (ELISA for the detection of lectin E. histolytica antigen in the liver abscess pus showed a sensitivity of 50% and the indirect haemagglutination (IHA test for detection of amoebic antibodies in the serum showed a sensitivity of 76.8% for the diagnosis of the ALA. Conclusion The present study for the first time shows that the kidney barrier in ALA patients is permeable to E. histolytica DNA molecule resulting in excretion of E. histolytica DNA in urine which can be detected by PCR. The study also shows that the PCR for detection of E. histolytica DNA in urine of

The effect of structural complexity, prey density, and "predator-free space" on prey survivorship at created oyster reef mesocosms

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Humphries, Austin T.; La Peyre, Megan K.; Decossas, Gary A.

2011-01-01

Interactions between predators and their prey are influenced by the habitat they occupy. Using created oyster (Crassostrea virginica) reef mesocosms, we conducted a series of laboratory experiments that created structure and manipulated complexity as well as prey density and “predator-free space” to examine the relationship between structural complexity and prey survivorship. Specifically, volume and spatial arrangement of oysters as well as prey density were manipulated, and the survivorship of prey (grass shrimp, Palaemonetes pugio) in the presence of a predator (wild red drum, Sciaenops ocellatus) was quantified. We found that the presence of structure increased prey survivorship, and that increasing complexity of this structure further increased survivorship, but only to a point. This agrees with the theory that structural complexity may influence predator-prey dynamics, but that a threshold exists with diminishing returns. These results held true even when prey density was scaled to structural complexity, or the amount of “predator-free space” was manipulated within our created reef mesocosms. The presence of structure and its complexity (oyster shell volume) were more important in facilitating prey survivorship than perceived refugia or density-dependent prey effects. A more accurate indicator of refugia might require “predator-free space” measures that also account for the available area within the structure itself (i.e., volume) and not just on the surface of a structure. Creating experiments that better mimic natural conditions and test a wider range of “predator-free space” are suggested to better understand the role of structural complexity in oyster reefs and other complex habitats.

DNA biosensor by self-assembly of carbon nanotubes and DNA to detect riboflavin

Energy Technology Data Exchange (ETDEWEB)

Li Jing [College of Chemistry and Chemical Engineering. Chongqing University, ChongQing, 400044 (China); Zhang Yunhuai, E-mail: xp2031@163.com [College of Chemistry and Chemical Engineering. Chongqing University, ChongQing, 400044 (China); Yang Tongyi [School of Life Science. NanJing University, Nanjing, 210093 (China); Zhang Huai [Liming Research Institute of Chemical Industry, LuoYang, 471001 (China); Yang Yixuan [State Key Laboratory of Chemical Resource Engineering. Beijing University of Chemical Technology, Beijing 100029 (China); Xiao Peng [College of Mathematics and Physics, Chongqing University, Chongqing 400044 (China)

2009-10-15

The fabrication of biosensors via self-assembly of single-walled carbon nanotubes (SWNTs) and DNA on a platinum electrode was presented in this paper. The carboxylic SWNTs were assembled on an amine-modified platinum electrode surface and followed by the assembly of NH{sub 2}-DNA with the carboxyl-amine coupling. The decorated surface was characterized by Field Emission Electron Microscopy (FEG-SEM) and electrochemical experiments, which showed that the reaction of DNA-SWNTs biosensor was quasi-reversible. The mechanism of DNA and riboflavin (VB{sub 2}) was studied by cyclic voltammetry and UV-Vis spectroscopy. The fabricated SWNTs-reinforced biosensor exhibits high sensitivity and low detection limit for the tested VB{sub 2} compared to the reported methods.

Optimization of HPV DNA detection in urine by improving collection, storage, and extraction.

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Vorsters, A; Van den Bergh, J; Micalessi, I; Biesmans, S; Bogers, J; Hens, A; De Coster, I; Ieven, M; Van Damme, P

2014-11-01

The benefits of using urine for the detection of human papillomavirus (HPV) DNA have been evaluated in disease surveillance, epidemiological studies, and screening for cervical cancers in specific subgroups. HPV DNA testing in urine is being considered for important purposes, notably the monitoring of HPV vaccination in adolescent girls and young women who do not wish to have a vaginal examination. The need to optimize and standardize sampling, storage, and processing has been reported.In this paper, we examined the impact of a DNA-conservation buffer, the extraction method, and urine sampling on the detection of HPV DNA and human DNA in urine provided by 44 women with a cytologically normal but HPV DNA-positive cervical sample. Ten women provided first-void and midstream urine samples. DNA analysis was performed using real-time PCR to allow quantification of HPV and human DNA.The results showed that an optimized method for HPV DNA detection in urine should (a) prevent DNA degradation during extraction and storage, (b) recover cell-free HPV DNA in addition to cell-associated DNA, (c) process a sufficient volume of urine, and (d) use a first-void sample.In addition, we found that detectable human DNA in urine may not be a good internal control for sample validity. HPV prevalence data that are based on urine samples collected, stored, and/or processed under suboptimal conditions may underestimate infection rates.

Potential use of DNA adducts to detect mutagenic compounds in soil

International Nuclear Information System (INIS)

Hua Guoxiong; Lyons, Brett; Killham, Ken; Singleton, Ian

2009-01-01

In this study, three different soils with contrasting features, spiked with 300 mg benzo[a]pyrene (BaP)/kg dry soil, were incubated at 20 deg. C and 60% water holding capacity for 540 days. At different time points, BaP and DNA were extracted and quantified, and DNA adducts were quantified by 32 P-postlabelling. After 540 days incubation, 69.3, 81.6 and 83.2% of initial BaP added remained in Cruden Bay, Boyndie and Insch soils, respectively. Meanwhile, a significantly different amount of DNA-BaP adducts were found in the three soils exposed to BaP over time. The work demonstrates the concept that DNA adducts can be detected on DNA extracted from soil. Results suggest the technique is not able to directly reflect bioavailability of BaP transformation products. However, this new method provides a potential way to detect mutagenic compounds in contaminated soil and to assess the outcomes of soil remediation. - A novel DNA adduct assay may provide a potential technique to detect mutagenic compounds in contaminated soil

Inspecting Targeted Deep Sequencing of Whole Genome Amplified DNA Versus Fresh DNA for Somatic Mutation Detection: A Genetic Study in Myelodysplastic Syndrome Patients.

Science.gov (United States)

Palomo, Laura; Fuster-Tormo, Francisco; Alvira, Daniel; Ademà, Vera; Armengol, María Pilar; Gómez-Marzo, Paula; de Haro, Nuri; Mallo, Mar; Xicoy, Blanca; Zamora, Lurdes; Solé, Francesc

2017-08-01

Whole genome amplification (WGA) has become an invaluable method for preserving limited samples of precious stock material and has been used during the past years as an alternative tool to increase the amount of DNA before library preparation for next-generation sequencing. Myelodysplastic syndromes (MDS) are a group of clonal hematopoietic stem cell disorders characterized by presenting somatic mutations in several myeloid-related genes. In this work, targeted deep sequencing has been performed on four paired fresh DNA and WGA DNA samples from bone marrow of MDS patients, to assess the feasibility of using WGA DNA for detecting somatic mutations. The results of this study highlighted that, in general, the sequencing and alignment statistics of fresh DNA and WGA DNA samples were similar. However, after variant calling and when considering variants detected at all frequencies, there was a high level of discordance between fresh DNA and WGA DNA (overall, a higher number of variants was detected in WGA DNA). After proper filtering, a total of three somatic mutations were detected in the cohort. All somatic mutations detected in fresh DNA were also identified in WGA DNA and validated by whole exome sequencing.

Perceptual advertisement by the prey of stalking or ambushing predators.

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Broom, Mark; Ruxton, Graeme D

2012-12-21

There has been previous theoretical explorations of the stability of signals by prey that they have detected a stalking or ambush predator, where such perceptual advertisement dissuades the predator from attacking. Here we use a game theoretical model to extend the theory to consider some empirically-motivated complexities: (i) many perceptual advertisement signals appear to have the potential to vary in intensity, (ii) higher intensity signals are likely to be most costly to produce, and (iii) some high-cost signals (such as staring directly at the predator) can only be utilised if the prey is very confident of the existence of a nearby predator (that is, there are reserved or unfakable signals). We demonstrate that these complexities still allow for stable signalling. However, we do not find solutions where prey use a range of signal intensities to signal different degrees of confidence in the proximity of a predator; with prey simply adopting a binary response of not signalling or always signalling at the same fixed level. However this fixed level will not always be the cheapest possible signal, and we predict that prey that require more certainty about proximity of a predator will use higher-cost signals. The availability of reserved signals does not prohibit the stability of signalling based on lower-cost signals, but we also find circumstances where only the reserved signal is used. We discuss the potential to empirically test our model predictions, and to develop theory further to allow perceptual advertisement to be combined with other signalling functions. Copyright © 2012 Elsevier Ltd. All rights reserved.

The detection of great crested newts year round via environmental DNA analysis.

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Rees, Helen C; Baker, Claire A; Gardner, David S; Maddison, Ben C; Gough, Kevin C

2017-07-26

Analysis of environmental DNA (eDNA) is a method that has been used for the detection of various species within water bodies. The great crested newt (Triturus cristatus) has a short eDNA survey season (mid-April to June). Here we investigate whether this season could be extended into other months using the current methodology as stipulated by Natural England. Here we present data to show that in monthly water samples taken from two ponds (March 2014-February 2015) we were able to detect great crested newt DNA in all months in at least one of the ponds. Similar levels of great crested newt eDNA (i.e. highly positive identification) were detected through the months of March-August, suggesting it may be possible to extend the current survey window. In order to determine how applicable these observations are for ponds throughout the rest of the UK, further work in multiple other ponds over multiple seasons is suggested. Nevertheless, the current work clearly demonstrates, in two ponds, the efficacy and reproducibility of eDNA detection for determining the presence of great crested newts.

Patient-Specific Circulating Tumor DNA Detection during Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer.

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Riva, Francesca; Bidard, Francois-Clement; Houy, Alexandre; Saliou, Adrien; Madic, Jordan; Rampanou, Aurore; Hego, Caroline; Milder, Maud; Cottu, Paul; Sablin, Marie-Paule; Vincent-Salomon, Anne; Lantz, Olivier; Stern, Marc-Henri; Proudhon, Charlotte; Pierga, Jean-Yves

2017-03-01

In nonmetastatic triple-negative breast cancer (TNBC) patients, we investigated whether circulating tumor DNA (ctDNA) detection can reflect the tumor response to neoadjuvant chemotherapy (NCT) and detect minimal residual disease after surgery. Ten milliliters of plasma were collected at 4 time points: before NCT; after 1 cycle; before surgery; after surgery. Customized droplet digital PCR (ddPCR) assays were used to track tumor protein p53 ( TP53 ) mutations previously characterized in tumor tissue by massively parallel sequencing (MPS). Forty-six patients with nonmetastatic TNBC were enrolled. TP53 mutations were identified in 40 of them. Customized ddPCR probes were validated for 38 patients, with excellent correlation with MPS ( r = 0.99), specificity (≥2 droplets/assay), and sensitivity (at least 0.1%). At baseline, ctDNA was detected in 27/36 patients (75%). Its detection was associated with mitotic index ( P = 0.003), tumor grade ( P = 0.003), and stage ( P = 0.03). During treatment, we observed a drop of ctDNA levels in all patients but 1. No patient had detectable ctDNA after surgery. The patient with rising ctDNA levels experienced tumor progression during NCT. Pathological complete response (16/38 patients) was not correlated with ctDNA detection at any time point. ctDNA positivity after 1 cycle of NCT was correlated with shorter disease-free ( P < 0.001) and overall ( P = 0.006) survival. Customized ctDNA detection by ddPCR achieved a 75% detection rate at baseline. During NCT, ctDNA levels decreased quickly and minimal residual disease was not detected after surgery. However, a slow decrease of ctDNA level during NCT was strongly associated with shorter survival. © 2016 American Association for Clinical Chemistry.

Methodological considerations for detection of terrestrial small-body salamander eDNA and implications for biodiversity conservation

Science.gov (United States)

Walker, Donald M.; Leys, Jacob E.; Dunham, Kelly E.; Oliver, Joshua C.; Schiller, Emily E.; Stephenson, Kelsey S.; Kimrey, John T.; Wooten, Jessica; Rogers, Mark W.

2017-01-01

Environmental DNA (eDNA) can be used as an assessment tool to detect populations of threatened species and provide fine-scale data required to make management decisions. The objectives of this project were to use quantitative PCR (qPCR) to: (i) detect spiked salamander DNA in soil, (ii) quantify eDNA degradation over time, (iii) determine detectability of salamander eDNA in a terrestrial environment using soil, faeces, and skin swabs, (iv) detect salamander eDNA in a mesocosm experiment. Salamander eDNA was positively detected in 100% of skin swabs and 66% of faecal samples and concentrations did not differ between the two sources. However, eDNA was not detected in soil samples collected from directly underneath wild-caught living salamanders. Salamander genomic DNA (gDNA) was detected in all qPCR reactions when spiked into soil at 10.0, 5.0, and 1.0 ng/g soil and spike concentration had a significant effect on detected concentrations. Only 33% of samples showed recoverable eDNA when spiked with 0.25 ng/g soil, which was the low end of eDNA detection. To determine the rate of eDNA degradation, gDNA (1 ng/g soil) was spiked into soil and quantified over seven days. Salamander eDNA concentrations decreased across days, but eDNA was still amplifiable at day 7. Salamander eDNA was detected in two of 182 mesocosm soil samples over 12 weeks (n = 52 control samples; n = 65 presence samples; n = 65 eviction samples). The discrepancy in detection success between experiments indicates the potential challenges for this method to be used as a monitoring technique for small-bodied wild terrestrial salamander populations.

Assessing diet compositions of Lake Ontario predators using fatty acid profiles of prey fishes

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Happell, Austin; Pattridge, Robert; Rinchard, Jacques; Walsh, Maureen

2017-01-01

Fatty acid profiles are used in food web studies to assess trophic interactions between predator and prey. The present study provides the first comprehensive fatty acid dataset for important prey and predator species in Lake Ontario. Three major prey fish (alewife, rainbow smelt, and round goby) were collected at three sites along the southern shore of Lake Ontario during the spring and fall of 2013, and predator species were collected in similar locations during the summer of 2013. Fatty acid compositions were compared among all prey species, all predator species, and information from both predator and prey was used to infer foraging differences among predators. Seasonal differences in fatty acids were found within each prey species studied. Differences among prey species were greater than any spatio-temporal differences detected within species. Fatty acids of predators revealed species-specific differences that matched known foraging habits. Chinook and Coho salmon, which are known to select alewife as their dominant prey item, had relatively little variation in fatty acid profiles. Conversely, brown trout, lake trout, yellow perch and esocids had highly variable fatty acid profiles and likely highly variable diet compositions. In general, our data suggested three dominant foraging patterns: 1) diet composed of nearly exclusively alewife for Chinook and Coho Salmon; 2) a mixed diet of alewife and round goby for brown and lake trout, and both rock and smallmouth bass; 3) a diet that is likely comprised of forage fishes other than those included in our study for northern pike and chain pickerel.

A simple colorimetric assay for detection of amplified Mycobacterium leprae DNA

NARCIS (Netherlands)

van der Vliet, G. M.; de Wit, M. Y.; Klatser, P. R.

1993-01-01

A colorimetric assay for the detection of PCR-products is described. The assay is based on amplification of DNA in the presence of digoxigenin-dUTP. After immobilization of the PCR products to a microtitre plate, amplified DNA could be detected colorimetrically. The sensitivity of this colorimetric

Whole genomic DNA probe for detection of Porphyromonas endodontalis.

Science.gov (United States)

Nissan, R; Makkar, S R; Sela, M N; Stevens, R

2000-04-01

The purpose of the present study was to develop a DNA probe for Porphyromonas endodontalis. Pure cultures of P. endodontalis were grown in TYP medium, in an anaerobic chamber. DNA was extracted from the P. endodontalis and labeled using the Genius System by Boehringer Mannheim. The labeled P. endodontalis DNA was used in dot-blot hybridization reactions with homologous (P. endodontalis) and unrelated bacterial samples. To determine specificity, strains of 40 other oral bacterial species (e.g. Porphyromonas gingivalis, Porphyromonas asaccharolytica, and Prevotella intermedia) were spotted and reacted with the P. endodontalis DNA probe. None of the panel of 40 oral bacteria hybridized with the P. endodontalis probe, whereas the blot of the homologous organism showed a strong positive reaction. To determine the sensitivity of the probe, dilutions of a P. endodontalis suspension of known concentration were blotted onto a nylon membrane and reacted with the probe. The results of our investigation indicate that the DNA probe that we have prepared specifically detects only P. endodontalis and can detect at least 3 x 10(4) cells.

Molecular prey identification in Central European piscivores

OpenAIRE

Thalinger, Bettina; Oehm, Johannes; Mayr, Hannes; Obwexer, Armin; Zeisler, Christiane; Traugott, Michael

2015-01-01

Abstract Diet analysis is an important aspect when investigating the ecology of fish?eating animals and essential for assessing their functional role in food webs across aquatic and terrestrial ecosystems. The identification of fish remains in dietary samples, however, can be time?consuming and unsatisfying using conventional morphological analysis of prey remains. Here, we present a two?step multiplex PCR system, comprised of six assays, allowing for rapid, sensitive and specific detection o...

Facilitating the indirect detection of genomic DNA in an electrochemical DNA biosensor using magnetic nanoparticles and DNA ligase

Directory of Open Access Journals (Sweden)

Roozbeh Hushiarian

2015-12-01

This technique was found to be reliably repeatable. The indirect detection of genomic DNA using this method is significantly improved and showed high efficiency in small amounts of samples with the detection limit of 5.37 × 10−14 M.

Critical considerations for the application of environmental DNA methods to detect aquatic species

Science.gov (United States)

Goldberg, Caren S.; Turner, Cameron R.; Deiner, Kristy; Klymus, Katy E.; Thomsen, Philip Francis; Murphy, Melanie A.; Spear, Stephen F.; McKee, Anna; Oyler-McCance, Sara J.; Cornman, Robert S.; Laramie, Matthew B.; Mahon, Andrew R.; Lance, Richard F.; Pilliod, David S.; Strickler, Katherine M.; Waits, Lisette P.; Fremier, Alexander K.; Takahara, Teruhiko; Herder, Jelger E.; Taberlet, Pierre

2016-01-01

Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed.Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms.Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA.We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

Potential utility of environmental DNA for early detection of Eurasian watermilfoil (Myriophyllum spicatum)

Science.gov (United States)

Newton, Jeremy; Sepulveda, Adam; Sylvester, K; Thum, Ryan

2016-01-01

Considering the harmful and irreversible consequences of many biological invasions, early detection of an invasive species is an important step toward protecting ecosystems (Sepulveda et al. 2012). Early detection increases the probability that suppression or eradication efforts will be successful because invasive populations are small and localized (Vander Zanden et al. 2010). However, most invasive species are not detected early because current tools have low detection probabilities when target species are rare and the sampling effort required to achieve acceptable detection capabilities with current tools is seldom tractable (Jerde et al. 2011). As a result, many invasive species go undetected until they are abundant and suppression efforts become costly. Novel DNA-based surveillance tools have recently revolutionized early detection abilities using environmental DNA (eDNA) present in the water (Darling and Mahon 2011, Bohmann et al. 2014). In brief, eDNA monitoring enables the identification of organisms from DNA present and collected in water samples. Aquatic and semiaquatic organisms release DNA contained in sloughed, damaged, or partially decomposed tissue and waste products into the water and molecular techniques allow this eDNA in the water column to be identified from simple and easy-tocollect water samples (Darling and Mahon 2011). Despite limited understanding of the production, persistence, and spread of DNA in water (Barnes et al. 2014), eDNA monitoring has been applied not only to invasive species (Jerde et al. 2011), but also to species that are rare, endangered, or highly elusive (Spear et al. 2014). However, most eDNA research and monitoring has focused on detection of invertebrates and vertebrates and less attentionhas been given to developing eDNA techniques for detecting aquatic invasive plants. Eurasian watermilfoil (EWM; Myriophyllum spicatum L.) is an invasive species for which improved early detection would be particularly helpful. Advanced

Selective Predation of a Stalking Predator on Ungulate Prey.

Directory of Open Access Journals (Sweden)

Marco Heurich

Full Text Available Prey selection is a key factor shaping animal populations and evolutionary dynamics. An optimal forager should target prey that offers the highest benefits in terms of energy content at the lowest costs. Predators are therefore expected to select for prey of optimal size. Stalking predators do not pursue their prey long, which may lead to a more random choice of prey individuals. Due to difficulties in assessing the composition of available prey populations, data on prey selection of stalking carnivores are still scarce. We show how the stalking predator Eurasian lynx (Lynx lynx selects prey individuals based on species identity, age, sex and individual behaviour. To address the difficulties in assessing prey population structure, we confirm inferred selection patterns by using two independent data sets: (1 data of 387 documented kills of radio-collared lynx were compared to the prey population structure retrieved from systematic camera trapping using Manly's standardized selection ratio alpha and (2 data on 120 radio-collared roe deer were analysed using a Cox proportional hazards model. Among the larger red deer prey, lynx selected against adult males-the largest and potentially most dangerous prey individuals. In roe deer lynx preyed selectively on males and did not select for a specific age class. Activity during high risk periods reduced the risk of falling victim to a lynx attack. Our results suggest that the stalking predator lynx actively selects for size, while prey behaviour induces selection by encounter and stalking success rates.

Integrating feeding behavior, ecological data, and DNA barcoding to identify developmental differences in invertebrate foraging strategies in wild white-faced capuchins (Cebus capucinus).

Science.gov (United States)

Mallott, Elizabeth K; Garber, Paul A; Malhi, Ripan S

2017-02-01

Invertebrate foraging strategies in nonhuman primates often require complex extractive foraging or prey detection techniques. As these skills take time to master, juveniles may have reduced foraging efficiency or concentrate their foraging efforts on easier to acquire prey than adults. We use DNA barcoding, behavioral observations, and ecological data to assess age-based differences in invertebrate prey foraging strategies in a group of white-faced capuchins (Cebus capucinus) in northeastern Costa Rica. Invertebrate availability was monitored using canopy traps and sweep netting. Fecal samples were collected from adult female, adult male, and juvenile white-faced capuchins (n = 225). COI mtDNA sequences were compared with known sequences in GenBank and the Barcode of Life Database. Frequencies of Lepidoptera and Hymenoptera consumption were higher in juveniles than in adults. A significantly smaller proportion of juvenile fecal samples contained Gryllidae and Cercopidae sequences, compared with adults (0% and 4.2% vs. 4.6% and 12.5%), and a significantly larger proportion contained Tenthredinidae, Culicidae, and Crambidae (5.6%, 9.7%, and 5.6% vs. 1.3%, 0.7%, and 1.3%). Juveniles spent significantly more time feeding and foraging than adults, and focused their foraging efforts on prey that require different skills to capture or extract. Arthropod availability was not correlated with foraging efficiency, and the rate of consumption of specific orders of invertebrates was not correlated with the availability of those same taxa. Our data support the hypothesis that juveniles are concentrating their foraging efforts on different prey than adults, potentially focusing their foraging efforts on more easily acquired types of prey. © 2016 Wiley Periodicals, Inc.

Augmentation of French grunt diet description using combined visual and DNA-based analyses

Science.gov (United States)

Hargrove, John S.; Parkyn, Daryl C.; Murie, Debra J.; Demopoulos, Amanda W.J.; Austin, James D.

2012-01-01

Trophic linkages within a coral-reef ecosystem may be difficult to discern in fish species that reside on, but do not forage on, coral reefs. Furthermore, dietary analysis of fish can be difficult in situations where prey is thoroughly macerated, resulting in many visually unrecognisable food items. The present study examined whether the inclusion of a DNA-based method could improve the identification of prey consumed by French grunt, Haemulon flavolineatum, a reef fish that possesses pharyngeal teeth and forages on soft-bodied prey items. Visual analysis indicated that crustaceans were most abundant numerically (38.9%), followed by sipunculans (31.0%) and polychaete worms (5.2%), with a substantial number of unidentified prey (12.7%). For the subset of prey with both visual and molecular data, there was a marked reduction in the number of unidentified sipunculans (visual – 31.1%, combined &ndash 4.4%), unidentified crustaceans (visual &ndash 15.6%, combined &ndash 6.7%), and unidentified taxa (visual &ndash 11.1%, combined &ndash 0.0%). Utilising results from both methodologies resulted in an increased number of prey placed at the family level (visual &ndash 6, combined &ndash 33) and species level (visual &ndash 0, combined &ndash 4). Although more costly than visual analysis alone, our study demonstrated the feasibility of DNA-based identification of visually unidentifiable prey in the stomach contents of fish.

Templated Chemistry for Sequence-Specific Fluorogenic Detection of Duplex DNA

Science.gov (United States)

Li, Hao; Franzini, Raphael M.; Bruner, Christopher; Kool, Eric T.

2015-01-01

We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple helix formation at adjacent positions on a specific purine-rich target sequence of duplex DNA. One fluorescein-labeled probe contains an α-azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine, designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of ca. 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably, demonstrating high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and may allow detection of double stranded DNA, at least for homopurine-homopyrimidine target sites, under native, non-disturbing conditions. PMID:20859985

Competition and Dispersal in Predator-Prey Waves

NARCIS (Netherlands)

Savill, N.J.; Hogeweg, P.

1998-01-01

Dispersing predators and prey can exhibit complex spatio-temporal wave-like patterns if the interactions between them cause oscillatory dynamics. We study the effect of these predator- prey density waves on the competition between prey populations and between predator popu- lations with different

Evaluating prey switching in wolf-ungulate systems.

Science.gov (United States)

Garrott, Robert A; Bruggeman, Jason E; Becker, Matthew S; Kalinowski, Steven T; White, P J

2007-09-01

Wolf restoration has become a widely accepted conservation and management practice throughout North America and Europe, though the ecosystem effects of returning top carnivores remain both scientific and societal controversies. Mathematical models predicting and describing wolf-ungulate interactions are typically limited to the wolves' primary prey, with the potential for prey switching in wolf-multiple-ungulate systems only suggested or assumed by a number of investigators. We used insights gained from experiments on small taxa and field data from ongoing wolf-ungulate studies to construct a model of predator diet composition for a wolf-elk-bison system in Yellowstone National Park, Wyoming, USA. The model explicitly incorporates differential vulnerability of the ungulate prey types to predation, predator preference, differences in prey biomass, and the possibility of prey switching. Our model demonstrates wolf diet shifts with changes in relative abundance of the two prey, with the dynamics of this shift dependent on the combined influences of preference, differential vulnerability, relative abundances of prey, and whether or not switching occurs. Differences in vulnerability between elk and bison, and strong wolf preference for elk, result in an abrupt dietary shift occurring only when elk are very rare relative to bison, whereas incorporating switching initiates the dietary shift more gradually and at higher bison-elk ratios. We demonstrate how researchers can apply these equations in newly restored wolf-two-prey systems to empirically evaluate whether prey switching is occurring. Each coefficient in the model has a biological interpretation, and most can be directly estimated from empirical data collected from field studies. Given the potential for switching to dramatically influence predator-prey dynamics and the wide range of expected prey types and abundances in some systems where wolves are present and/or being restored, we suggest that this is an

Non-Enzymatic Detection of Bacterial Genomic DNA Using the Bio-Barcode Assay

Science.gov (United States)

Hill, Haley D.; Vega, Rafael A.; Mirkin, Chad A.

2011-01-01

The detection of bacterial genomic DNA through a non-enzymatic nanomaterials based amplification method, the bio-barcode assay, is reported. The assay utilizes oligonucleotide functionalized magnetic microparticles to capture the target of interest from the sample. A critical step in the new assay involves the use of blocking oligonucleotides during heat denaturation of the double stranded DNA. These blockers bind to specific regions of the target DNA upon cooling, and prevent the duplex DNA from re-hybridizing, which allows the particle probes to bind. Following target isolation using the magnetic particles, oligonucleotide functionalized gold nanoparticles act as target recognition agents. The oligonucleotides on the nanoparticle (barcodes) act as amplification surrogates. The barcodes are then detected using the Scanometric method. The limit of detection for this assay was determined to be 2.5 femtomolar, and this is the first demonstration of a barcode type assay for the detection of double stranded, genomic DNA. PMID:17927207

Assessment of environmental DNA for detecting presence of imperiled aquatic amphibian species in isolated wetlands

Science.gov (United States)

Mckee, Anna; Calhoun, Daniel L.; Barichivich, William J.; Spear, Stephen F.; Goldberg, Caren S.; Glenn, Travis C

2015-01-01

Environmental DNA (eDNA) is an emerging tool that allows low-impact sampling for aquatic species by isolating DNA from water samples and screening for DNA sequences specific to species of interest. However, researchers have not tested this method in naturally acidic wetlands that provide breeding habitat for a number of imperiled species, including the frosted salamander (Ambystoma cingulatum), reticulated flatwoods salamanders (Ambystoma bishopi), striped newt (Notophthalmus perstriatus), and gopher frog (Lithobates capito). Our objectives for this study were to develop and optimize eDNA survey protocols and assays to complement and enhance capture-based survey methods for these amphibian species. We collected three or more water samples, dipnetted or trapped larval and adult amphibians, and conducted visual encounter surveys for egg masses for target species at 40 sites on 12 different longleaf pine (Pinus palustris) tracts. We used quantitative PCRs to screen eDNA from each site for target species presence. We detected flatwoods salamanders at three sites with eDNA but did not detect them during physical surveys. Based on the sample location we assumed these eDNA detections to indicate the presence of frosted flatwoods salamanders. We did not detect reticulated flatwoods salamanders. We detected striped newts with physical and eDNA surveys at two wetlands. We detected gopher frogs at 12 sites total, three with eDNA alone, two with physical surveys alone, and seven with physical and eDNA surveys. We detected our target species with eDNA at 9 of 11 sites where they were present as indicated from traditional surveys and at six sites where they were not detected with traditional surveys. It was, however, critical to use at least three water samples per site for eDNA. Our results demonstrate eDNA surveys can be a useful complement to traditional survey methods for detecting imperiled pond-breeding amphibians. Environmental DNA may be particularly useful in situations

Measuring the Electronic Properties of DNA-Specific Schottky Diodes Towards Detecting and Identifying Basidiomycetes DNA

Science.gov (United States)

Periasamy, Vengadesh; Rizan, Nastaran; Al-Ta’ii, Hassan Maktuff Jaber; Tan, Yee Shin; Tajuddin, Hairul Annuar; Iwamoto, Mitsumasa

2016-01-01

The discovery of semiconducting behavior of deoxyribonucleic acid (DNA) has resulted in a large number of literatures in the study of DNA electronics. Sequence-specific electronic response provides a platform towards understanding charge transfer mechanism and therefore the electronic properties of DNA. It is possible to utilize these characteristic properties to identify/detect DNA. In this current work, we demonstrate a novel method of DNA-based identification of basidiomycetes using current-voltage (I-V) profiles obtained from DNA-specific Schottky barrier diodes. Electronic properties such as ideality factor, barrier height, shunt resistance, series resistance, turn-on voltage, knee-voltage, breakdown voltage and breakdown current were calculated and used to quantify the identification process as compared to morphological and molecular characterization techniques. The use of these techniques is necessary in order to study biodiversity, but sometimes it can be misleading and unreliable and is not sufficiently useful for the identification of fungi genera. Many of these methods have failed when it comes to identification of closely related species of certain genus like Pleurotus. Our electronics profiles, both in the negative and positive bias regions were however found to be highly characteristic according to the base-pair sequences. We believe that this simple, low-cost and practical method could be useful towards identifying and detecting DNA in biotechnology and pathology. PMID:27435636

Rapid and label-free electrochemical DNA biosensor for detecting hepatitis A virus.

Science.gov (United States)

Manzano, Marisa; Viezzi, Sara; Mazerat, Sandra; Marks, Robert S; Vidic, Jasmina

2018-02-15

Diagnostic systems that can deliver highly specific and sensitive detection of hepatitis A virus (HAV) in food and water are of particular interest in many fields including food safety, biosecurity and control of outbreaks. Our aim was the development of an electrochemical method based on DNA hybridization to detect HAV. A ssDNA probe specific for HAV (capture probe) was designed and tested on DNAs from various viral and bacterial samples using Nested-Reverse Transcription Polymerase Chain Reaction (nRT-PCR). To develop the electrochemical device, a disposable gold electrode was functionalized with the specific capture probe and tested on complementary ssDNA and on HAV cDNA. The DNA hybridization on the electrode was measured through the monitoring of the oxidative peak potential of the indicator tripropylamine by cyclic voltammetry. To prevent non-specific binding the gold surface was treated with 3% BSA before detection. High resolution atomic force microscopy (AFM) confirmed the efficiency of electrode functionalization and on-electrode hybridization. The proposed device showed a limit of detection of 0.65pM for the complementary ssDNA and 6.94fg/µL for viral cDNA. For a comparison, nRT-PCR quantified the target HAV cDNA with a limit of detection of 6.4fg/µL. The DNA-sensor developed can be adapted to a portable format to be adopted as an easy-to- use and low cost method for screening HAV in contaminated food and water. In addition, it can be useful for rapid control of HAV infections as it takes only a few minutes to provide the results. Copyright © 2017. Published by Elsevier B.V.

Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique.

OpenAIRE

Noll, W W; Collins, M

1987-01-01

Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. We have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and th...

Estimating HPV DNA Deposition Between Sexual Partners Using HPV Concordance, Y Chromosome DNA Detection, and Self-reported Sexual Behaviors.

Science.gov (United States)

Malagón, Talía; Burchell, Ann N; El-Zein, Mariam; Guénoun, Julie; Tellier, Pierre-Paul; Coutlée, François; Franco, Eduardo L

2017-12-05

Detection of human papillomavirus (HPV) DNA in genital samples may not always represent true infections but may be depositions from infected sexual partners. We examined whether sexual risk factors and a biomarker (Y chromosome DNA) were associated with genital HPV partner concordance and estimated the fraction of HPV detections potentially attributable to partner deposition. The HITCH study enrolled young women attending a university or college in Montréal, Canada, and their male partners, from 2005 to 2010. We tested baseline genital samples for Y chromosome DNA and HPV DNA using polymerase chain reaction. Type-specific HPV concordance was 42.4% in partnerships where at least one partner was HPV DNA positive. Y chromosome DNA predicted type-specific HPV concordance in univariate analyses, but in multivariable models the independent predictors of concordance were days since last vaginal sex (26.5% higher concordance 0-1 vs 8-14 days after last vaginal sex) and condom use (22.6% higher concordance in never vs always users). We estimated that 14.1% (95% confidence interval [CI], 6.3-21.9%) of HPV DNA detections in genital samples were attributable to vaginal sex in the past week. A substantial proportion of HPV DNA detections may be depositions due to recent unprotected vaginal sex. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Detection of DNA nucleotides on pretreated boron doped diamond electrodes

Energy Technology Data Exchange (ETDEWEB)

Garbellini, Gustavo S.; Uliana, Carolina V.; Yamanaka, Hideko [UNESP, Araraquara, SP (Brazil). Inst. de Quimica

2011-07-01

The individual detection and equimolar mixture of DNA nucleotides guanosine monophosphate (GMP), adenosine monophosphate (AMP), thymidine (TMP) and cytidine (CMP) 5'-monophosphate using square wave voltammetry was performed on boron doped diamond (BDD) electrodes cathodically (Red-DDB) and anodically (Oxi-DDB) pretreated. The oxidation of individual DNA nucleotides was more sensitive on Oxi-BDD electrode. In a simultaneous detection of nucleotides, the responses of GMP, AMP, TMP and CMP were very adequate on both treated electrodes. Particularly, more sensitive and separate peaks for TMP and CMP on Oxi-BDD and Red-BDD electrodes, respectively, were observed after deconvolution procedure. The detection of nucleotides in aqueous solutions will certainly contribute for genotoxic evaluation of substances and hybridization reactions by immobilizing ss or ds-DNA on BDD surface. (author)

Development of an Automated Microfluidic System for DNA Collection, Amplification, and Detection of Pathogens

Energy Technology Data Exchange (ETDEWEB)

Hagan, Bethany S.; Bruckner-Lea, Cynthia J.

2002-12-01

This project was focused on developing and testing automated routines for a microfluidic Pathogen Detection System. The basic pathogen detection routine has three primary components; cell concentration, DNA amplification, and detection. In cell concentration, magnetic beads are held in a flow cell by an electromagnet. Sample liquid is passed through the flow cell and bacterial cells attach to the beads. These beads are then released into a small volume of fluid and delivered to the peltier device for cell lysis and DNA amplification. The cells are lysed during initial heating in the peltier device, and the released DNA is amplified using polymerase chain reaction (PCR) or strand displacement amplification (SDA). Once amplified, the DNA is then delivered to a laser induced fluorescence detection unit in which the sample is detected. These three components create a flexible platform that can be used for pathogen detection in liquid and sediment samples. Future developments of the system will include on-line DNA detection during DNA amplification and improved capture and release methods for the magnetic beads during cell concentration.

Detection of Adult Green Sturgeon Using Environmental DNA Analysis.

Directory of Open Access Journals (Sweden)

Paul S Bergman

Full Text Available Environmental DNA (eDNA is an emerging sampling method that has been used successfully for detection of rare aquatic species. The Identification of sampling tools that are less stressful for target organisms has become increasingly important for rare and endangered species. A decline in abundance of the Southern Distinct Population Segment (DPS of North American Green Sturgeon located in California's Central Valley has led to its listing as Threatened under the Federal Endangered Species Act in 2006. While visual surveys of spawning Green Sturgeon in the Central Valley are effective at monitoring fish densities in concentrated pool habitats, results do not scale well to the watershed level, providing limited spatial and temporal context. Unlike most traditional survey methods, environmental DNA analysis provides a relatively quick, inexpensive tool that could efficiently monitor the presence and distribution of aquatic species. We positively identified Green Sturgeon DNA at two locations of known presence in the Sacramento River, proving that eDNA can be effective for monitoring the presence of adult sturgeon. While further study is needed to understand uncertainties of the sampling method, our study represents the first documented detection of Green Sturgeon eDNA, indicating that eDNA analysis could provide a new tool for monitoring Green Sturgeon distribution in the Central Valley, complimenting traditional on-going survey methods.

Interspecific variation in prey capture behavior by co-occurring Nepenthes pitcher plants: evidence for resource partitioning or sampling-scheme artifacts?

Science.gov (United States)

Chin, Lijin; Chung, Arthur Y C; Clarke, Charles

2014-01-01

Pitcher plants of the genus Nepenthes capture a wide range of arthropod prey for nutritional benefit, using complex combinations of visual and olfactory signals and gravity-driven pitfall trapping mechanisms. In many localities throughout Southeast Asia, several Nepenthes different species occur in mixed populations. Often, the species present at any given location have strongly divergent trap structures and preliminary surveys indicate that different species trap different combinations of arthropod prey, even when growing at the same locality. On this basis, it has been proposed that co-existing Nepenthes species may be engaged in niche segregation with regards to arthropod prey, avoiding direct competition with congeners by deploying traps that have modifications that enable them to target specific prey types. We examined prey capture among 3 multi-species Nepenthes populations in Borneo, finding that co-existing Nepenthes species do capture different combinations of prey, but that significant interspecific variations in arthropod prey combinations can often be detected only at sub-ordinal taxonomic ranks. In all lowland Nepenthes species examined, the dominant prey taxon is Formicidae, but montane Nepenthes trap few (or no) ants and 2 of the 3 species studied have evolved to target alternative sources of nutrition, such as tree shrew feces. Using similarity and null model analyses, we detected evidence for niche segregation with regards to formicid prey among 5 lowland, sympatric Nepenthes species in Sarawak. However, we were unable to determine whether these results provide support for the niche segregation hypothesis, or whether they simply reflect unquantified variation in heterogeneous habitats and/or ant communities in the study sites. These findings are used to propose improvements to the design of field experiments that seek to test hypotheses about targeted prey capture patterns in Nepenthes.

Detection of irradiation induced modifications in foodstuff DNA using 32p post-labelling

International Nuclear Information System (INIS)

Hoey, B.M.; Swallow, A.J.; Margison, G.P.

1991-01-01

DNA post-labelling has been used successfully to detect damage to DNA caused by a range of damaging agents. The assay results in a fingerprint of changes induced in DNA which might, in principle, be useful as a test for the detection of the irradiation of foods. The authors present their DNA extraction and 32 p post-labelling methods from chicken or cooked prawn samples and their analysis method (High Performance liquid chromatography). It's hoped that these results could form the basis of a test to detect if foods have been irradiated

Detection of a diverse marine fish fauna using environmental DNA from seawater samples

DEFF Research Database (Denmark)

Thomsen, Philip Francis; Kielgast, Jos; Iversen, Lars Lønsmann

2012-01-01

eDNA from 15 different fish species, including both important consumption species, as well as species rarely or never recorded by conventional monitoring. We also detect eDNA from a rare vagrant species in the area; European pilchard (Sardina pilchardus). Additionally, we detect four bird species....... Records in national databases confirmed the occurrence of all detected species. To investigate the efficiency of the eDNA approach, we compared its performance with 9 methods conventionally used in marine fish surveys. Promisingly, eDNA covered the fish diversity better than or equal to any of the applied...

A novel fluorescent DNA sensor for ultrasensitive detection of Helicobacter pylori.

Science.gov (United States)

Liu, Ziping; Su, Xingguang

2017-01-15

In this work, a novel fluorescent DNA sensor for ultrasensitive detection of Helicobacter pylori (H. pylori) DNA was developed. This strategy took advantage of DNA hybridization between single-stranded DNA (ssDNA, which had been designed as an aptamer specific for H. pylori DNA) and the complementary target H. pylori DNA, and the feature that ssDNA bound to graphene oxide (GO) with significantly higher affinity than double-stranded DNA (dsDNA). ssDNA were firstly covalent conjugated with CuInS 2 quantum dots (QDs) by reaction between the carboxy group of QDs and amino group modified ssDNA, forming ssDNA-QDs genosensor. In the absence of the complementary target H. pylori DNA, GO could adsorb ssDNA-QDs DNA sensor and efficiently quench the fluorescence of ssDNA-QDs. While the complementary target H. pylori DNA was introduced, the ssDNA-QDs preferentially bound with the H. pylori DNA. The formation of dsDNA would alter the conformation of ssDNA and disturb the interaction between ssDNA and GO. Thus, the dsDNA-QDs/GO system exhibited a stronger fluorescence emission than that of the ssDNA-QDs/GO system. Under the optimized conditions, a linear correlation was established between the fluorescence intensity ratio I/I 0 and the concentration of H. pylori DNA in the range of 1.25-875pmolL -1 with a detection limit of 0.46pmolL -1 . The proposed method was applied to the determination of H. pylori DNA sequence in milk samples with satisfactory results. Copyright © 2016 Elsevier B.V. All rights reserved.

Rapid on-site detection of Acidovorax avenae subsp. citrulli by gold-labeled DNA strip sensor.

Science.gov (United States)

Zhao, Wenjun; Lu, Jie; Ma, Wenwei; Xu, Chuanlai; Kuang, Hua; Zhu, Shuifang

2011-06-15

Acidovorax avenae subsp. citrulli (AAC) is one of the most harmful diseases in cucurbit production. A rapid and sensitive DNA strip sensor was constructed based on gold nanoparticle-labeled oligonucleotide probes for the detection of AAC. Both the qualitative and semi-quantitative detections of target DNA were successfully achieved using the developed DNA strip sensor. The qualitative limit of detection (LOD) of the strip sensor was determined as 4 nM. The LOD for the semi-quantitative detection was calculated to be 0.48 nM in the range of 0-10 nM. The genomic DNA was detected directly using the DNA strip sensor without any further treatment. This DNA strip sensor is a potentially useful tool for rapid on-site DNA screening. Copyright © 2011 Elsevier B.V. All rights reserved.

Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors

Science.gov (United States)

Star, Alexander; Tu, Eugene; Niemann, Joseph; Gabriel, Jean-Christophe P.; Joiner, C. Steve; Valcke, Christian

2006-01-01

We report carbon nanotube network field-effect transistors (NTNFETs) that function as selective detectors of DNA immobilization and hybridization. NTNFETs with immobilized synthetic oligonucleotides have been shown to specifically recognize target DNA sequences, including H63D single-nucleotide polymorphism (SNP) discrimination in the HFE gene, responsible for hereditary hemochromatosis. The electronic responses of NTNFETs upon single-stranded DNA immobilization and subsequent DNA hybridization events were confirmed by using fluorescence-labeled oligonucleotides and then were further explored for label-free DNA detection at picomolar to micromolar concentrations. We have also observed a strong effect of DNA counterions on the electronic response, thus suggesting a charge-based mechanism of DNA detection using NTNFET devices. Implementation of label-free electronic detection assays using NTNFETs constitutes an important step toward low-cost, low-complexity, highly sensitive and accurate molecular diagnostics. hemochromatosis | SNP | biosensor

Foraging mechanisms of siscowet lake trout (Salvelinus namaycush siscowet) on pelagic prey

Science.gov (United States)

Keyler, Trevor D.; Hrabik, Thomas R.; Austin, C. Lee; Gorman, Owen T.; Mensinger, Allen F.

2015-01-01

The reaction distance, angle of attack, and foraging success were determined for siscowet lake trout (Salvelinus namaycush siscowet) during laboratory trials under lighting conditions that approximated downwelling spectral irradiance and intensity (9.00 × 108–1.06 × 1014 photons m− 2 s− 1) at daytime depths. Siscowet reaction distance in response to golden shiners (Notemigonus crysoleucas) was directly correlated with increasing light intensity until saturation at 1.86 × 1011 photons m− 2 s− 1, above which reaction distance was constant within the range of tested light intensities. At the lowest tested light intensity, sensory detection was sufficient to locate prey at 25 ± 2 cm, while increasing light intensities increased reaction distance up to 59 ± 2 cm at 1.06 × 1014 photons m− 2 s− 1. Larger prey elicited higher reaction distances than smaller prey at all light intensities while moving prey elicited higher reaction distances than stationary prey at the higher light intensities (6.00 × 109 to 1.06 × 1014 photons m− 2 s− 1). The capture and consumption of prey similarly increased with increasing light intensity while time to capture decreased with increasing light intensity. The majority of orientations toward prey occurred within 120° of the longitudinal axis of the siscowet's eyes, although reaction distances among 30° increments along the entire axis were not significantly different. The developed predictive model will help determine reaction distances for siscowet in various photic environments and will help identify the mechanisms and behavior that allow for low light intensity foraging within freshwater systems.

Social Fingerprinting: detection of spambot groups through DNA-inspired behavioral modeling

DEFF Research Database (Denmark)

Cresci, Stefano; Di Pietro, Roberto; Petrocchi, Marinella

2017-01-01

Spambot detection in online social networks is a long-lasting challenge involving the study and design of detection techniques capable of efficiently identifying ever-evolving spammers. Recently, a new wave of social spambots has emerged, with advanced human-like characteristics that allow them...... to go undetected even by current state-of-the-art algorithms. In this paper, we show that efficient spambots detection can be achieved via an in-depth analysis of their collective behaviors exploiting the digital DNA technique for modeling the behaviors of social network users. Inspired by its...... biological counterpart, in the digital DNA representation the behavioral lifetime of a digital account is encoded in a sequence of characters. Then, we define a similarity measure for such digital DNA sequences. We build upon digital DNA and the similarity between groups of users to characterize both genuine...

Modifications of alkaline microgel electrophoresis for sensitive detection of DNA damage

International Nuclear Information System (INIS)

Singh, N.P.; Stephens, R.E.; Schneider, E.L.

1994-01-01

The alkaline microgel electrophoresis technique was modified to achieve a substantial increase in sensitivity for the detection of radiation-induced DNA damage in human lymphocytes. This increased sensitivity was achieved through: (1) the addition of free radical scavengers to the electrophoresis solution to reduce DNA damage generated during alkaline unwinding and electrophoresis; (2) the modification of the electrophoresis unit to achieve a more uniform electric field; (3) the use of YOYO-1, a DNA dye, producing fluorescence 500-fold more intense than ethidium bromide; and (4) the introduction of an image analysis system for the quantitation of DNA migration. In human lymphocytes, these modifications have resulted in an increased sensitivity of several fold, allowing the detection of DNA damage in the range of 50 mGy. (author)

2-Aminopurine hairpin probes for the detection of ultraviolet-induced DNA damage

International Nuclear Information System (INIS)

El-Yazbi, Amira F.; Loppnow, Glen R.

2012-01-01

Highlights: ► Molecular beacon with 2AP bases detects DNA damage in a simple mix-and-read assay. ► Molecular beacons with 2AP bases detect damage at a 17.2 nM limit of detection. ► The 2AP molecular beacon is linear over a 0–3.5 μM concentration range for damage. - Abstract: Nucleic acid exposure to radiation and chemical insults leads to damage and disease. Thus, detection and understanding DNA damage is important for elucidating molecular mechanisms of disease. However, current methods of DNA damage detection are either time-consuming, destroy the sample, or are too specific to be used for generic detection of damage. In this paper, we develop a fluorescence sensor of 2-aminopurine (2AP), a fluorescent analogue of adenine, incorporated in the loop of a hairpin probe for the quantification of ultraviolet (UV) C-induced nucleic acid damage. Our results show that the selectivity of the 2AP hairpin probe to UV-induced nucleic acid damage is comparable to molecular beacon (MB) probes of DNA damage. The calibration curve for the 2AP hairpin probe shows good linearity (R 2 = 0.98) with a limit of detection of 17.2 nM. This probe is a simple, fast and economic fluorescence sensor for the quantification of UV-induced damage in DNA.

Ratiometric FRET-based detection of DNA and micro-RNA on the surface using TIRF detection

International Nuclear Information System (INIS)

Matveeva, Evgenia G.; Gryczynski, Zygmunt; Stewart, Donald R.; Gryczynski, Ignacy

2010-01-01

A new FRET-based method for the ratiometric detection of DNA oligomers on a surface using TIRF detection mode is reported. The dual-labeled system consisting of two hybridized oligomers, Cy3oligoY:Cy5oligoX was immobilized on the surface, and the total internal reflection fluorescence (TIRF) was used to detect emission signals from the surface. Two signals, green and red, which originated from the green donor Cy3 and the red acceptor Cy5, have been simultaneously detected. When the target single-stranded complimentary oligomer was present in the solution, this oligomer replaced the Cy3oligoY in the donor:acceptor complex on the surface and the ratio of red-to-green signal was dramatically changed. This detection scheme is generally applicable to the detection of DNA or RNA on a surface.

Non-invasive prenatal detection of achondroplasia using circulating fetal DNA in maternal plasma.

Science.gov (United States)

Lim, Ji Hyae; Kim, Mee Jin; Kim, Shin Young; Kim, Hye Ok; Song, Mee Jin; Kim, Min Hyoung; Park, So Yeon; Yang, Jae Hyug; Ryu, Hyun Mee

2011-02-01

To perform a reliable non-invasive detection of the fetal achondroplasia using maternal plasma. We developed a quantitative fluorescent-polymerase chain reaction (QF-PCR) method suitable for detection of the FGFR3 mutation (G1138A) causing achondroplasia. This method was applied in a non-invasive detection of the fetal achondroplasia using circulating fetal-DNA (cf-DNA) in maternal plasma. Maternal plasmas were obtained at 27 weeks of gestational age from women carrying an achondroplasia fetus or a normal fetus. Two percent or less achondroplasia DNA was reliably detected by QF-PCR. In a woman carrying a normal fetus, analysis of cf-DNA showed only one peak of the wild-type G allele. In a woman expected an achondroplasia fetus, analysis of cf-DNA showed the two peaks of wild-type G allele and mutant-type A allele and accurately detected the fetal achondroplasia. The non-invasive method using maternal plasma and QF-PCR may be useful for diagnosis of the fetal achondroplasia.

Feeding rates in the chaetognath Sagitta elegans : effects of prey size, prey swimming behaviour and small-scale turbulence

DEFF Research Database (Denmark)

Saito, H.; Kiørboe, Thomas

2001-01-01

distances. We develop a simple prey encounter rate model by describing the swimming prey as a 'force dipole' and assuming that a critical signal strength is required to elicit an attack. By fitting the model to the observations, a critical signal strength of 10(-2) cm s(-1) is estimated; this is very...... at rates up to an order of magnitude higher than similarly sized females, probably owing to differences in swimming behaviour. Sagitta elegans is an ambush predator that perceives its prey by hydromechanical signals. Faster swimming prey generates stronger signals and is, hence, perceived at longer...

DNA polymorphism sensitive impedimetric detection on gold-nanoislands modified electrodes.

Science.gov (United States)

Bonanni, Alessandra; Pividori, Maria Isabel; del Valle, Manel

2015-05-01

Nanocomposite materials are being increasingly used in biosensing applications as they can significantly improve biosensor performance. Here we report the use of a novel impedimetric genosensor based on gold nanoparticles graphite-epoxy nanocomposite (nanoAu-GEC) for the detection of triple base mutation deletion in a cystic-fibrosis (CF) related human DNA sequence. The developed platform consists of chemisorbing gold nano-islands surrounded by rigid, non-chemisorbing, and conducting graphite-epoxy composite. The ratio of the gold nanoparticles in the composite was carefully optimized by electrochemical and microscopy studies. Such platform allows the very fast and stable thiol immobilization of DNA probes on the gold islands, thus minimizing the steric and electrostatic repulsion among the DNA probes and improving the detection of DNA polymorphism down to 2.25fmol by using electrochemical impedance spectroscopy. These findings are very important in order to develop new and renewable platforms to be used in point-of-care devices for the detection of biomolecules. Copyright © 2015 Elsevier B.V. All rights reserved.

Prey switching behaviour in the planktonic copepod Acartia tonsa

DEFF Research Database (Denmark)

Kiørboe, Thomas; Saiz, E.; Viitasalo, M.

1996-01-01

The copepod Acartia tonsa has 2 different prey encounter strategies. It can generate a feeding current to encounter and capture immobile prey (suspension feeding) or it can sink slowly and perceive motile prey by means of mechanoreceptors on the antennae (ambush feeding). We hypothesized that A....... tonsa adopts the feeding mode that generates the highest energy intake rate; i.e. that prey selection changes according to the relative concentrations of alternative prey (prey switching) and that the copepods spend disproportionately more time in the feeding mode that provides the greatest reward...... be captured by suspension feeding copepods. Finally, we demonstrate that turbulence favours the selection of ciliates as prey. We suggest that prey switching by copepods may provide survival windows for microzooplankters during blooms of net phytoplankton because predation pressure from the copepods...

Amplified Detection of the Aptamer-Vanillin Complex with the Use of Bsm DNA Polymerase.

Science.gov (United States)

Andrianova, Mariia; Komarova, Natalia; Grudtsov, Vitaliy; Kuznetsov, Evgeniy; Kuznetsov, Alexander

2017-12-26

The electrochemical detection of interactions between aptamers and low-molecular-weight targets often lacks sensitivity. Signal amplification improves the detection of the aptamer-analyte complex; Bsm DNA polymerase was used to amplify the signal from the interaction of vanillin and its aptamer named Van_74 on an ion-sensitive field-effect transistor (ISFET)-based biosensor. The aptamer was immobilized on the ISFET sensitive surface. A short DNA probe was hybridized with the aptamer and dissociated from it upon vanillin addition. A free probe interacted with a special DNA molecular beacon initiated the Bsm DNA polymerase reaction that was detected by ISFET. A buffer solution suitable for both aptamer action and Bsm DNA polymerase activity was determined. The ISFET was shown to detect the Bsm DNA polymerase reaction under the selected conditions. Vanillin at different concentrations (1 × 10 -6 -1 × 10 -8 M) was detected using the biosensor with signal amplification. The developed detection system allowed for the determination of vanillin, starting at a 10 -8 M concentration. Application of the Bsm DNA polymerase resulted in a 15.5 times lower LoD when compared to the biosensor without signal amplification (10.1007/s00604-017-2586-4).

Rapid detection of cancer related DNA nanoparticulate biomarkers and nanoparticles in whole blood

Science.gov (United States)

Heller, Michael J.; Krishnan, Raj; Sonnenberg, Avery

2010-08-01

The ability to rapidly detect cell free circulating (cfc) DNA, cfc-RNA, exosomes and other nanoparticulate disease biomarkers as well as drug delivery nanoparticles directly in blood is a major challenge for nanomedicine. We now show that microarray and new high voltage dielectrophoretic (DEP) devices can be used to rapidly isolate and detect cfc-DNA nanoparticulates and nanoparticles directly from whole blood and other high conductance samples (plasma, serum, urine, etc.). At DEP frequencies of 5kHz-10kHz both fluorescent-stained high molecular weight (hmw) DNA, cfc-DNA and fluorescent nanoparticles separate from the blood and become highly concentrated at specific DEP highfield regions over the microelectrodes, while blood cells move to the DEP low field-regions. The blood cells can then be removed by a simple fluidic wash while the DNA and nanoparticles remain highly concentrated. The hmw-DNA could be detected at a level of <260ng/ml and the nanoparticles at <9.5 x 109 particles/ml, detection levels that are well within the range for viable clinical diagnostics and drug nanoparticle monitoring. Disease specific cfc-DNA materials could also be detected directly in blood from patients with Chronic Lymphocytic Leukemia (CLL) and confirmed by PCR genotyping analysis.

Absence of frequent herpesvirus transmission in a nonhuman primate predator-prey system in the wild.

Science.gov (United States)

Murthy, Sripriya; Couacy-Hymann, Emmanuel; Metzger, Sonja; Nowak, Kathrin; De Nys, Helene; Boesch, Christophe; Wittig, Roman; Jarvis, Michael A; Leendertz, Fabian H; Ehlers, Bernhard

2013-10-01

Emergence of viruses into the human population by transmission from nonhuman primates (NHPs) represents a serious potential threat to human health that is primarily associated with the increased bushmeat trade. Transmission of RNA viruses across primate species appears to be relatively frequent. In contrast, DNA viruses appear to be largely host specific, suggesting low transmission potential. Herein, we use a primate predator-prey system to study the risk of herpesvirus transmission between different primate species in the wild. The system was comprised of western chimpanzees (Pan troglodytes verus) and their primary (western red colobus, Piliocolobus badius badius) and secondary (black-and-white colobus, Colobus polykomos) prey monkey species. NHP species were frequently observed to be coinfected with multiple beta- and gammaherpesviruses (including new cytomegalo- and rhadinoviruses). However, despite frequent exposure of chimpanzees to blood, organs, and bones of their herpesvirus-infected monkey prey, there was no evidence for cross-species herpesvirus transmission. These findings suggest that interspecies transmission of NHP beta- and gammaherpesviruses is, at most, a rare event in the wild.

Colorimetric detection of DNA damage by using hemin-graphene nanocomposites

Science.gov (United States)

Wei, W.; Zhang, D. M.; Yin, L. H.; Pu, Y. P.; Liu, S. Q.

2013-04-01

A colorimetric method for detection of DNA damage was developed by using hemin-graphene nanosheets (H-GNs). H-GNs were skillfully synthesized by adsorping of hemin on graphene through π-π interactions. The as-prepared H-GNs possessed both the ability of graphene to differentiate the damage DNA from intact DNA and the catalytic action of hemin. The damaged DNA made H-GNs coagulated to different degrees from the intact DNA because there were different amount of negative charge exposed on their surface, which made a great impact on the solubility of H-GNs. As a result, the corresponding centrifugal supernatant of H-GNs solution showed different color in the presence of 3,3',5,5'-tetramethylbenzidine (TMB) and H2O2, which could be discriminated by naked eyes or by ultraviolet (UV)-visible spectrometer. Based on this, the damaged effects of styrene oxide (SO), NaAsO2 and UV radiation on DNA were studied. Results showed that SO exerted most serious damage effect on DNA although all of them damaged DNA seriously. The new method for detection of DNA damage showed good prospect in the evaluation of genotoxicity of new compounds, the maximum limit of pesticide residue, food additives, and so on, which is important in the fields of food science, pharmaceutical science and pesticide science.

Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

Science.gov (United States)

Wilcox, Taylor M; Mckelvey, Kevin S.; Young, Michael K.; Sepulveda, Adam; Shepard, Bradley B.; Jane, Stephen F; Whiteley, Andrew R.; Lowe, Winsor H.; Schwartz, Michael K.

2016-01-01

Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout (Salvelinus fontinalis) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection > 0.99 at densities of ≥ 3 fish per 100 m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.

When prey provide more than food: mammalian predators appropriating the refugia of their prey

Science.gov (United States)

Bill Zielinski

2015-01-01

Some mammalian predators acquire both food and shelter from their prey, by eating them and using the refugia the prey construct. I searched the literature for examples of predators that exhibit this behavior and summarize their taxonomic affiliations, relative sizes, and distributions. I hypothesized that size ratios of species involved in this dynamic would be near 1....

Plant DNA Detection from Grasshopper Guts: A Step-by-Step Protocol, from Tissue Preparation to Obtaining Plant DNA Sequences

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Alina Avanesyan

2014-02-01

Full Text Available Premise of the study: A PCR-based method of identifying ingested plant DNA in gut contents of Melanoplus grasshoppers was developed. Although previous investigations have focused on a variety of insects, there are no protocols available for plant DNA detection developed for grasshoppers, agricultural pests that significantly influence plant community composition. Methods and Results: The developed protocol successfully used the noncoding region of the chloroplast trnL (UAA gene and was tested in several feeding experiments. Plant DNA was obtained at seven time points post-ingestion from whole guts and separate gut sections, and was detectable up to 12 h post-ingestion in nymphs and 22 h post-ingestion in adult grasshoppers. Conclusions: The proposed protocol is an effective, relatively quick, and low-cost method of detecting plant DNA from the grasshopper gut and its different sections. This has important applications, from exploring plant “movement” during food consumption, to detecting plant–insect interactions.

A snail-eating snake recognizes prey handedness.

Science.gov (United States)

Danaisawadi, Patchara; Asami, Takahiro; Ota, Hidetoshi; Sutcharit, Chirasak; Panha, Somsak

2016-04-05

Specialized predator-prey interactions can be a driving force for their coevolution. Southeast Asian snail-eating snakes (Pareas) have more teeth on the right mandible and specialize in predation on the clockwise-coiled (dextral) majority in shelled snails by soft-body extraction. Snails have countered the snakes' dextral-predation by recurrent coil reversal, which generates diverse counterclockwise-coiled (sinistral) prey where Pareas snakes live. However, whether the snake predator in turn evolves any response to prey reversal is unknown. We show that Pareas carinatus living with abundant sinistrals avoids approaching or striking at a sinistral that is more difficult and costly to handle than a dextral. Whenever it strikes, however, the snake succeeds in predation by handling dextral and sinistral prey in reverse. In contrast, P. iwasakii with little access to sinistrals on small peripheral islands attempts and frequently misses capturing a given sinistral. Prey-handedness recognition should be advantageous for right-handed snail-eating snakes where frequently encountering sinistrals. Under dextral-predation by Pareas snakes, adaptive fixation of a prey population for a reversal gene instantaneously generates a sinistral species because interchiral mating is rarely possible. The novel warning, instead of sheltering, effect of sinistrality benefitting both predators and prey could further accelerate single-gene ecological speciation by left-right reversal.

Direct colorimetric detection of unamplified pathogen DNA by dextrin-capped gold nanoparticles.

Science.gov (United States)

Baetsen-Young, Amy M; Vasher, Matthew; Matta, Leann L; Colgan, Phil; Alocilja, Evangelyn C; Day, Brad

2018-03-15

The interaction between gold nanoparticles (AuNPs) and nucleic acids has facilitated a variety of diagnostic applications, with further diversification of synthesis match bio-applications while reducing biotoxicity. However, DNA interactions with unique surface capping agents have not been fully defined. Using dextrin-capped AuNPs (d-AuNPs), we have developed a novel unamplified genomic DNA (gDNA) nanosensor, exploiting dispersion and aggregation characteristics of d-AuNPs, in the presence of gDNA, for sequence-specific detection. We demonstrate that d-AuNPs are stable in a five-fold greater salt concentration than citrate-capped AuNPs and the d-AuNPs were stabilized by single stranded DNA probe (ssDNAp). However, in the elevated salt concentrations of the DNA detection assay, the target reactions were surprisingly further stabilized by the formation of a ssDNAp-target gDNA complex. The results presented herein lead us to propose a mechanism whereby genomic ssDNA secondary structure formation during ssDNAp-to-target gDNA binding enables d-AuNP stabilization in elevated ionic environments. Using the assay described herein, we were successful in detecting as little as 2.94 fM of pathogen DNA, and using crude extractions of a pathogen matrix, as few as 18 spores/µL. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection of Target ssDNA Using a Microfabricated Hall Magnetometer with Correlated Optical Readout

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Steven M. Hira

2012-01-01

Full Text Available Sensing biological agents at the genomic level, while enhancing the response time for biodetection over commonly used, optics-based techniques such as nucleic acid microarrays or enzyme-linked immunosorbent assays (ELISAs, is an important criterion for new biosensors. Here, we describe the successful detection of a 35-base, single-strand nucleic acid target by Hall-based magnetic transduction as a mimic for pathogenic DNA target detection. The detection platform has low background, large signal amplification following target binding and can discriminate a single, 350 nm superparamagnetic bead labeled with DNA. Detection of the target sequence was demonstrated at 364 pM (<2 target DNA strands per bead target DNA in the presence of 36 μM nontarget (noncomplementary DNA (<10 ppm target DNA using optical microscopy detection on a GaAs Hall mimic. The use of Hall magnetometers as magnetic transduction biosensors holds promise for multiplexing applications that can greatly improve point-of-care (POC diagnostics and subsequent medical care.

A dynamic bead-based microarray for parallel DNA detection

International Nuclear Information System (INIS)

Sochol, R D; Lin, L; Casavant, B P; Dueck, M E; Lee, L P

2011-01-01

A microfluidic system has been designed and constructed by means of micromachining processes to integrate both microfluidic mixing of mobile microbeads and hydrodynamic microbead arraying capabilities on a single chip to simultaneously detect multiple bio-molecules. The prototype system has four parallel reaction chambers, which include microchannels of 18 × 50 µm 2 cross-sectional area and a microfluidic mixing section of 22 cm length. Parallel detection of multiple DNA oligonucleotide sequences was achieved via molecular beacon probes immobilized on polystyrene microbeads of 16 µm diameter. Experimental results show quantitative detection of three distinct DNA oligonucleotide sequences from the Hepatitis C viral (HCV) genome with single base-pair mismatch specificity. Our dynamic bead-based microarray offers an effective microfluidic platform to increase parallelization of reactions and improve microbead handling for various biological applications, including bio-molecule detection, medical diagnostics and drug screening

How to evaluate PCR assays for the detection of low-level DNA

DEFF Research Database (Denmark)

Banch-Clausen, Frederik; Urhammer, Emil; Rieneck, Klaus

2015-01-01

distribution describing parameters for singleplex real-time PCR-based detection of low-level DNA. The model was tested against experimental data of diluted cell-free foetal DNA. Also, the model was compared with a simplified formula to enable easy predictions. The model predicted outcomes that were...... not significantly different from experimental data generated by testing of cell-free foetal DNA. Also, the simplified formula was applicable for fast and accurate assay evaluation. In conclusion, the model can be applied for evaluation of sensitivity of real-time PCR-based detection of low-level DNA, and may also......High sensitivity of PCR-based detection of very low copy number DNA targets is crucial. Much focus has been on design of PCR primers and optimization of the amplification conditions. Very important are also the criteria used for determining the outcome of a PCR assay, e.g. how many replicates...

DNA extraction methods for panbacterial and panfungal PCR detection in intraocular fluids.

Science.gov (United States)

Mazoteras, Paloma; Bispo, Paulo José Martins; Höfling-Lima, Ana Luisa; Casaroli-Marano, Ricardo P

2015-07-01

Three different methods of DNA extraction from intraocular fluids were compared with subsequent detection for bacterial and fungal DNA by universal PCR amplification. Three DNA extraction methods, from aqueous and vitreous humors, were evaluated to compare their relative efficiency. Bacterial (Gram positive and negative) and fungal strains were used in this study: Escherichia coli, Staphylococcus epidermidis and Candida albicans. The quality, quantification, and detection limit for DNA extraction and PCR amplification were analyzed. Validation procedures for 13 aqueous humor and 14 vitreous samples, from 20 patients with clinically suspected endophthalmitis were carried out. The column-based extraction method was the most time-effective, achieving DNA detection limits ≥10(2) and 10(3 )CFU/100 µL for bacteria and fungi, respectively. PCR amplification detected 100 fg, 1 pg and 10 pg of genomic DNA of E. coli, S. epidermidis and C. albicans respectively. PCR detected 90.0% of the causative agents from 27 intraocular samples collected from 20 patients with clinically suspected endophthalmitis, while standard microbiological techniques could detect only 60.0%. The most frequently found organisms were Streptococcus spp. in 38.9% (n = 7) of patients and Staphylococcus spp. found in 22.2% (n = 4). The column-based extraction method for very small inocula in small volume samples (50-100 µL) of aqueous and/or vitreous humors allowed PCR amplification in all samples with sufficient quality for subsequent sequencing and identification of the microorganism in the majority of them.

A new method to extract dental pulp DNA: application to universal detection of bacteria.

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Lam Tran-Hung

Full Text Available BACKGROUND: Dental pulp is used for PCR-based detection of DNA derived from host and bacteremic microorganims. Current protocols require odontology expertise for proper recovery of the dental pulp. Dental pulp specimen exposed to laboratory environment yields contaminants detected using universal 16S rDNA-based detection of bacteria. METHODOLOGY/PRINCIPAL FINDINGS: We developed a new protocol by encasing decontaminated tooth into sterile resin, extracting DNA into the dental pulp chamber itself and decontaminating PCR reagents by filtration and double restriction enzyme digestion. Application to 16S rDNA-based detection of bacteria in 144 teeth collected in 86 healthy people yielded a unique sequence in only 14 teeth (9.7% from 12 individuals (14%. Each individual yielded a unique 16S rDNA sequence in 1-2 teeth per individual. Negative controls remained negative. Bacterial identifications were all confirmed by amplification and sequencing of specific rpoB sequence. CONCLUSIONS/SIGNIFICANCE: The new protocol prevented laboratory contamination of the dental pulp. It allowed the detection of bacteria responsible for dental pulp colonization from blood and periodontal tissue. Only 10% such samples contained 16S rDNA. It provides a new tool for the retrospective diagnostic of bacteremia by allowing the universal detection of bacterial DNA in animal and human, contemporary or ancient tooth. It could be further applied to identification of host DNA in forensic medicine and anthropology.

The modeling of predator-prey interactions

OpenAIRE

Muhammad Shakil; H. A. Wahab; Muhammad Naeem, et al.

2015-01-01

In this paper, we aim to study the interactions between the territorial animals like foxes and the rabbits. The territories for the foxes are considered to be the simple cells. The interactions between predator and its prey are represented by the chemical reactions which obey the mass action law. In this sense, we apply the mass action law for predator prey models and the quasi chemical approach is applied for the interactions between the predator and its prey to develop the modeled equations...

A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures.

Science.gov (United States)

Liu, Zhizhen; Liu, Jinding; Wang, Jiaqi; Chen, Deqing; Liu, Zidong; Shi, Jie; Li, Zeqin; Li, Wenyan; Zhang, Gengqian; Du, Bing

2018-03-04

Unbalanced DNA mixture is still a difficult problem for forensic practice. DIP-STRs are useful markers for detection of minor DNA but they are not widespread in the human genome and having long amplicons. In this study, we proposed a novel type of genetic marker, termed DIP-SNP. DIP-SNP refers to the combination of INDEL and SNP in less than 300bp length of human genome. The multiplex PCR and SNaPshot assay were established for 14 DIP-SNP markers in a Chinese Han population from Shanxi, China. This novel compound marker allows detection of the minor DNA contributor with sensitivity from 1:50 to 1:1000 in a DNA mixture of any gender with 1 ng-10 ng DNA template. Most of the DIP-SNP markers had a relatively high probability of informative alleles with an average I value of 0.33. In all, we proposed DIP-SNP as a novel kind of genetic marker for detection of minor contributor from unbalanced DNA mixture and established the detection method by associating the multiplex PCR and SNaPshot assay. DIP-SNP polymorphisms are promising markers for forensic or clinical mixture examination because they are shorter, widespread and higher sensitive. Copyright © 2018 Elsevier Inc. All rights reserved.

Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide.

Science.gov (United States)

Zhou, Jie; Lu, Qian; Tong, Ying; Wei, Wei; Liu, Songqin

2012-09-15

A hairpin molecular beacon tagged with carboxyfluorescein in combination with graphene oxide as a quencher reagent was used to detect the DNA damage by chemical reagents. The fluorescence of molecular beacon was quenched sharply by graphene oxide; while in the presence of its complementary DNA the quenching efficiency decreased because their hybridization prevented the strong adsorbability of molecular beacon on graphene oxide. If the complementary DNA was damaged by a chemical reagent and could not form intact duplex structure with molecular beacon, more molecular beacon would adsorb on graphene oxide increasing the quenching efficiency. Thus, damaged DNA could be detected based on different quenching efficiencies afforded by damaged and intact complementary DNA. The damage effects of chlorpyrifos-methyl and three metabolites of styrene such as mandelieaeids, phenylglyoxylieaeids and epoxystyrene on DNA were studied as models. The method for detection of DNA damage was reliable, rapid and simple compared to the biological methods. Copyright © 2012 Elsevier B.V. All rights reserved.

Detection of genetically modified organisms (GMOs using isothermal amplification of target DNA sequences

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La Mura Maurizio

2009-02-01

Full Text Available Abstract Background The most common method of GMO detection is based upon the amplification of GMO-specific DNA amplicons using the polymerase chain reaction (PCR. Here we have applied the loop-mediated isothermal amplification (LAMP method to amplify GMO-related DNA sequences, 'internal' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene junctions. Results We have tested the specificity and sensitivity of the technique for use in GMO studies. Results show that detection of 0.01% GMO in equivalent background DNA was possible and dilutions of template suggest that detection from single copies of the template may be possible using LAMP. Conclusion This work shows that GMO detection can be carried out using LAMP for routine screening as well as for specific events detection. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection.

Detection of genetically modified organisms (GMOs) using isothermal amplification of target DNA sequences.

Science.gov (United States)

Lee, David; La Mura, Maurizio; Allnutt, Theo R; Powell, Wayne

2009-02-02

The most common method of GMO detection is based upon the amplification of GMO-specific DNA amplicons using the polymerase chain reaction (PCR). Here we have applied the loop-mediated isothermal amplification (LAMP) method to amplify GMO-related DNA sequences, 'internal' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene) junctions. We have tested the specificity and sensitivity of the technique for use in GMO studies. Results show that detection of 0.01% GMO in equivalent background DNA was possible and dilutions of template suggest that detection from single copies of the template may be possible using LAMP. This work shows that GMO detection can be carried out using LAMP for routine screening as well as for specific events detection. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection.

Amplified Detection of the Aptamer–Vanillin Complex with the Use of Bsm DNA Polymerase

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Mariia Andrianova

2017-12-01

Full Text Available The electrochemical detection of interactions between aptamers and low-molecular-weight targets often lacks sensitivity. Signal amplification improves the detection of the aptamer-analyte complex; Bsm DNA polymerase was used to amplify the signal from the interaction of vanillin and its aptamer named Van_74 on an ion-sensitive field-effect transistor (ISFET-based biosensor. The aptamer was immobilized on the ISFET sensitive surface. A short DNA probe was hybridized with the aptamer and dissociated from it upon vanillin addition. A free probe interacted with a special DNA molecular beacon initiated the Bsm DNA polymerase reaction that was detected by ISFET. A buffer solution suitable for both aptamer action and Bsm DNA polymerase activity was determined. The ISFET was shown to detect the Bsm DNA polymerase reaction under the selected conditions. Vanillin at different concentrations (1 × 10−6–1 × 10−8 M was detected using the biosensor with signal amplification. The developed detection system allowed for the determination of vanillin, starting at a 10−8 M concentration. Application of the Bsm DNA polymerase resulted in a 15.5 times lower LoD when compared to the biosensor without signal amplification (10.1007/s00604-017-2586-4.

Detection of carcinogen-DNA adducts by radioimmunoassay

International Nuclear Information System (INIS)

Poirier, M.C.; Yuspa, S.H.; Weinstein, I.B.; Blobstein, S.

1977-01-01

Covalent binding of carcinogen to nucleic acids is believed to be an essential component of the carcinogenic process, so it is desirable to have highly sensitive and specific methods for detecting such adducts in cells and tissues exposed to known and suspected carcinogens. A radioimmunoassay is here described capable of detecting nanogram amounts of DNA adducts resulting from the covalent binding of the carcinogen N-2-acetylaminofluorene and its activated N-acetoxy derivative. (author)

Predation as a landscape effect: the trading off by prey species between predation risks and protection benefits.

Science.gov (United States)

Mönkkönen, M; Husby, M; Tornberg, R; Helle, P; Thomson, R L

2007-05-01

1. Predators impose costs on their prey but may also provide benefits such as protection against other (e.g. nest) predators. The optimal breeding location in relation to the distance from a nesting raptor varies so as to minimize the sum of costs of adult and nest predation. We provide a conceptual model to account for variation in the relative predation risks and derive qualitative predictions for how different prey species should respond to the distance from goshawk Accipiter gentilis nests. 2. We test the model predictions using a comprehensive collection of data from northern Finland and central Norway. First, we carried out a series of experiments with artificial bird nests to test if goshawks may provide protection against nest predation. Second, we conducted standard bird censuses and nest-box experiments to detect how the density or territory occupancy of several prey species varies with distance from the nearest goshawk nest. 3. Nest predation rate increased with distance from goshawk nest indicating that goshawks may provide protection for birds' nests against nest predation. Abundance (or probability of presence) of the main prey species of goshawks peaked at intermediate distances from goshawk nests, reflecting the trade-off. The abundance of small songbird species decreased with distance from goshawk nests. The goshawk poses little risk to small songbirds and they may benefit from goshawk proximity in protection against nest predation. Finally, no pattern with distance in pied flycatcher territory (nest box) occupation rate or the onset of egg-laying was detected. This is expected, as flycatchers neither suffer from marked nest predation risk nor are favoured goshawk prey. 4. Our results suggest that territory location in relation to the nest of a predator is a trade-off situation where adult birds weigh the risk of themselves being predated against the benefits accrued from increased nest survival. Prey species appear able to detect and measure

Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples

International Nuclear Information System (INIS)

Sayler, G.S.; Shields, M.S.; Tedford, E.T.; Breen, A.; Hooper, S.W.; Sirotkin, K.M.; Davis, J.W.

1985-01-01

The application of preexisting DNA hybridization techniques was investigated for potential in determining populations of specific gene sequences in environmental samples. Cross-hybridizations among two degradative plasmids, TOL and NAH, and two cloning vehicles, pLAFR1 and RSF1010, were determined. The detection limits for the TOL plasmid against a nonhomologous plasmid-bearing bacterial background was ascertained. The colony hybridization technique allowed detection of one colony containing TOL plasmid among 10(6) Escherichia coli colonies of nonhomologous DNA. Comparisons between population estimates derived from growth on selective substrates and from hybridizations were examined. Findings indicated that standard sole carbon source enumeration procedures for degradative populations lead to overestimations due to nonspecific growth of other bacteria on the microcontaminant carbon sources present in the media. Population estimates based on the selective growth of a microcosm population on two aromatic substrates (toluene and naphthalene) and estimates derived from DNA-DNA colony hybridizations, using the TOL or NAH plasmid as a probe, corresponded with estimates of substrate mineralization rates and past exposure to environmental contaminants. The applications of such techniques are hoped to eventually allow enumeration of any specific gene sequences in the environment, including both anabolic and catabolic genes. In addition, this procedure should prove useful in monitoring recombinant DNA clones released into environmental situations

Detecting the effects of toxic agents on spermatogenesis using DNA probes

International Nuclear Information System (INIS)

Hecht, N.B.

1987-01-01

Advances in the molecular biology of spermatogenesis suggest that DNA probes can be used to monitor the effects of toxic agents in male germ cells of mammals. Molecular hybridization analyses with DNA probes can provide a reproducible methodology capable of detecting changes ranging from massive deletions to single base pair substitutions in the genome of exposed individuals. A constantly increasing number of DNA probes that can be used to detect such alterations in human sperm DNA exist for both ubiquitously expressed proteins and for genes solely expressed in the testis. In this chapter, the currently available testicular stage-specific and/or cell type-specific DNA probes and the techniques by which they can be utilized in reproductive toxicology studies are discussed. The advantages, limitations, and future technological advances of this novel biological marker system for the human male reproductive system are also considered

Application of environmental DNA to detect an endangered marine skate species in the wild.

Science.gov (United States)

Weltz, Kay; Lyle, Jeremy M; Ovenden, Jennifer; Morgan, Jessica A T; Moreno, David A; Semmens, Jayson M

2017-01-01

Environmental DNA (eDNA) techniques have only recently been applied in the marine environment to detect the presence of marine species. Species-specific primers and probes were designed to detect the eDNA of the endangered Maugean skate (Zearaja maugeana) from as little as 1 L of water collected at depth (10-15 m) in Macquarie Harbour (MH), Tasmania. The identity of the eDNA was confirmed as Z. maugeana by sequencing the qPCR products and aligning these with the target sequence for a 100% match. This result has validated the use of this eDNA technique for detecting a rare species, Z. maugeana, in the wild. Being able to investigate the presence, and possibly the abundance, of Z. maugeana in MH and Bathurst harbour (BH), would be addressing a conservation imperative for the endangered Z. maugeana. For future application of this technique in the field, the rate of decay was determined for Z. maugeana eDNA under ambient dissolved oxygen (DO) levels (55% saturation) and lower DO (20% saturation) levels, revealing that the eDNA can be detected for 4 and 16 hours respectively, after which eDNA concentration drops below the detection threshold of the assay. With the rate of decay being influenced by starting eDNA concentrations, it is recommended that samples be filtered as soon as possible after collection to minimize further loss of eDNA prior to and during sample processing.

Application of environmental DNA to detect an endangered marine skate species in the wild.

Directory of Open Access Journals (Sweden)

Kay Weltz

Full Text Available Environmental DNA (eDNA techniques have only recently been applied in the marine environment to detect the presence of marine species. Species-specific primers and probes were designed to detect the eDNA of the endangered Maugean skate (Zearaja maugeana from as little as 1 L of water collected at depth (10-15 m in Macquarie Harbour (MH, Tasmania. The identity of the eDNA was confirmed as Z. maugeana by sequencing the qPCR products and aligning these with the target sequence for a 100% match. This result has validated the use of this eDNA technique for detecting a rare species, Z. maugeana, in the wild. Being able to investigate the presence, and possibly the abundance, of Z. maugeana in MH and Bathurst harbour (BH, would be addressing a conservation imperative for the endangered Z. maugeana. For future application of this technique in the field, the rate of decay was determined for Z. maugeana eDNA under ambient dissolved oxygen (DO levels (55% saturation and lower DO (20% saturation levels, revealing that the eDNA can be detected for 4 and 16 hours respectively, after which eDNA concentration drops below the detection threshold of the assay. With the rate of decay being influenced by starting eDNA concentrations, it is recommended that samples be filtered as soon as possible after collection to minimize further loss of eDNA prior to and during sample processing.

Putting prey and predator into the CO2 equation--qualitative and quantitative effects of ocean acidification on predator-prey interactions.

Science.gov (United States)

Ferrari, Maud C O; McCormick, Mark I; Munday, Philip L; Meekan, Mark G; Dixson, Danielle L; Lonnstedt, Öona; Chivers, Douglas P

2011-11-01

Little is known about the impact of ocean acidification on predator-prey dynamics. Herein, we examined the effect of carbon dioxide (CO(2)) on both prey and predator by letting one predatory reef fish interact for 24 h with eight small or large juvenile damselfishes from four congeneric species. Both prey and predator were exposed to control or elevated levels of CO(2). Mortality rate and predator selectivity were compared across CO(2) treatments, prey size and species. Small juveniles of all species sustained greater mortality at high CO(2) levels, while large recruits were not affected. For large prey, the pattern of prey selectivity by predators was reversed under elevated CO(2). Our results demonstrate both quantitative and qualitative consumptive effects of CO(2) on small and larger damselfish recruits respectively, resulting from CO(2)-induced behavioural changes likely mediated by impaired neurological function. This study highlights the complexity of predicting the effects of climate change on coral reef ecosystems. © 2011 Blackwell Publishing Ltd/CNRS.

Wild North Island Robins (Petroica longipes respond to Prey Animacy

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Alexis Garland

2014-08-01

Full Text Available North Island robins of New Zealand are a food hoarding species, which is unique in that they almost exclusively cache highly perishable hunted insects for later retrieval. In order to do so, they either kill and dismember or paralyze their prey for caching, depending on the prey size and kind. The present study comprises two experiments, using a Violation of Expectancy (VoE paradigm to examine variation in search behavior response to different prey conditions. The first experiment presents three different types of prey (mealworms, earthworms and locusts in expected (present and unexpected (absent conditions. The second experiment presents prey in varying states of animacy (alive and whole, dead and whole, dead and halved, and an inanimate stick and reveals prey in expected (same state or unexpected (differing state conditions. While robins did not respond with differential search times to different types of unexpectedly missing prey in Experiment 1, in Experiment 2 robins searched longer in conditions where prey was found in a differing state of animacy than initially shown. Robins also searched longer for prey when immediately consuming retrieved prey than when caching retrieved prey. Results indicate that North Island robins may be sensitive to prey animacy upon storage and retrieval of insect prey; such information could play a role in storage, pilfering and retrieval strategies of such a perishable food source.

An improved method for detecting genetic variation in DNA using denaturing gradient gel electrophoresis

International Nuclear Information System (INIS)

Takahashi, Norio; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

1990-05-01

We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32 P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)

Detection of anthrax lef with DNA-based photonic crystal sensors

Science.gov (United States)

Zhang, Bailin; Dallo, Shatha; Peterson, Ralph; Hussain, Syed; Weitao, Tao; Ye, Jing Yong

2011-12-01

Bacillus anthracis has posed a threat of becoming biological weapons of mass destruction due to its virulence factors encoded by the plasmid-borne genes, such as lef for lethal factor. We report the development of a fast and sensitive anthrax DNA biosensor based on a photonic crystal structure used in a total-internal-reflection configuration. For the detection of the lef gene, a single-stranded DNA lef probe was biotinylated and immobilized onto the sensor via biotin-streptavidin interactions. A positive control, lef-com, was the complementary strand of the probe, while a negative control was an unrelated single-stranded DNA fragment from the 16S rRNA gene of Acinetobacter baumannii. After addition of the biotinylated lef probe onto the sensor, significant changes in the resonance wavelength of the sensor were observed, resulting from binding of the probe to streptavidin on the sensor. The addition of lef-com led to another significant increase as a result of hybridization between the two DNA strands. The detection sensitivity for the target DNA reached as low as 0.1 nM. In contrast, adding the unrelated DNAs did not cause an obvious shift in the resonant wavelength. These results demonstrate that detection of the anthrax lef by the photonic crystal structure in a total-internal-reflection sensor is highly specific and sensitive.

Detection of circular telomeric DNA without 2D gel electrophoresis.

Science.gov (United States)

Dlaska, Margit; Anderl, Conrad; Eisterer, Wolfgang; Bechter, Oliver E

2008-09-01

The end of linear chromosomes forms a lasso-like structure called the t-loop. Such t-loops resemble a DNA recombination intermediate, where the single-stranded 3' overhang is arrested in a stretch of duplex DNA. Presumably, such a t-loop can also be deleted via a recombination process. This would result in the occurrence of circular extrachromosomal telomeric DNA (t-circles), which are known to be abundantly present in immortal cells engaging the recombination-based alternative lengthening of telomeres pathway (ALT pathway). Little is known about the basic mechanism of telomeric recombination in these cells and what ultimately causes the generation of such t-circles. Current standard procedures for detecting these molecules involve 2D gel electrophoresis or electron microscopy. However, both methods are labor intense and sophisticated to perform. Here, we present a simpler, faster, and equally sensitive method for detecting t-circles. Our approach is a telomere restriction fragment assay that involves the enzymatic preservation of circular DNA with Klenow enzyme followed by Bal31 degradation of the remaining linear DNA molecules. We show that with this approach t-circles can be detected in ALT cell lines, whereas no t-circles are present in telomerase-positive cell lines. We consider our approach a valid method in which t-circle generation is the experimental readout.

A multiplex microplatform for the detection of multiple DNA methylation events using gold-DNA affinity.

Science.gov (United States)

Sina, Abu Ali Ibn; Foster, Matthew Thomas; Korbie, Darren; Carrascosa, Laura G; Shiddiky, Muhammad J A; Gao, Jing; Dey, Shuvashis; Trau, Matt

2017-10-07

We report a new multiplexed strategy for the electrochemical detection of regional DNA methylation across multiple regions. Using the sequence dependent affinity of bisulfite treated DNA towards gold surfaces, the method integrates the high sensitivity of a micro-fabricated multiplex device comprising a microarray of gold electrodes, with the powerful multiplexing capability of multiplex-PCR. The synergy of this combination enables the monitoring of the methylation changes across several genomic regions simultaneously from as low as 500 pg μl -1 of DNA with no sequencing requirement.

Label-Free Ag+ Detection by Enhancing DNA Sensitized Tb3+ Luminescence

Directory of Open Access Journals (Sweden)

Kimberly Kleinke

2016-08-01

Full Text Available In this work, the effect of Ag+ on DNA sensitized Tb3+ luminescence was studied initially using the Ag+-specific RNA-cleaving DNAzyme, Ag10c. While we expected to observe luminescence quenching by Ag+, a significant enhancement was produced. Based on this observation, simple DNA oligonucleotide homopolymers were used with systematically varied sequence and length. We discovered that both poly-G and poly-T DNA have a significant emission enhancement by Ag+, while the absolute intensity is stronger with the poly-G DNA, indicating that a G-quadruplex DNA is not required for this enhancement. Using the optimized length of the G7 DNA (an oligo constituted with seven guanines, Ag+ was measured with a detection limit of 57.6 nM. The signaling kinetics, G7 DNA conformation, and the binding affinity of Tb3+ to the DNA in the presence or absence of Ag+ are also studied to reveal the mechanism of emission enhancement. This observation is useful not only for label-free detection of Ag+, but also interesting for the rational design of new biosensors using Tb3+ luminescence.

Assassin bug uses aggressive mimicry to lure spider prey.

Science.gov (United States)

Wignall, Anne E; Taylor, Phillip W

2011-05-07

Assassin bugs (Stenolemus bituberus) hunt web-building spiders by invading the web and plucking the silk to generate vibrations that lure the resident spider into striking range. To test whether vibrations generated by bugs aggressively mimic the vibrations generated by insect prey, we compared the responses of spiders to bugs with how they responded to prey, courting male spiders and leaves falling into the web. We also analysed the associated vibrations. Similar spider orientation and approach behaviours were observed in response to vibrations from bugs and prey, whereas different behaviours were observed in response to vibrations from male spiders and leaves. Peak frequency and duration of vibrations generated by bugs were similar to those generated by prey and courting males. Further, vibrations from bugs had a temporal structure and amplitude that were similar to vibrations generated by leg and body movements of prey and distinctly different to vibrations from courting males or leaves, or prey beating their wings. To be an effective predator, bugs do not need to mimic the full range of prey vibrations. Instead bugs are general mimics of a subset of prey vibrations that fall within the range of vibrations classified by spiders as 'prey'.

An alkaline separation method for detection of small amount of DNA damage

International Nuclear Information System (INIS)

Sakai, Kazuo; Okada, Shigefumi

1981-01-01

An alkaline separation technique originally established by Ahnstroem is modified to detect small amount of DNA damage in X-irradiated mouse leukemic L5178Y cells. It is made quantitative by calibration with an alkaline sucrose gradient centrifugation. The present method would make it possible to study DNA damage and its repair within a dose range of X-rays where cell survival and mutation are usually investigated. It is also useful for detecting DNA damage caused by chemicals. (author)

Predatory mites avoid ovipositing near counter-attacking prey

NARCIS (Netherlands)

Faraji, F.; Janssen, A.; Sabelis, M.W.

2001-01-01

Attacking prey is not without risk; predators may endure counterattackby the prey. Here, we study the oviposition behaviour of a predatory mite(Iphiseius degenerans) in relation to its prey, thewesternflower thrips (Frankliniella occidentalis). This thrips iscapable of killing the eggs of the

Thermodynamic framework to assess low abundance DNA mutation detection by hybridization

Science.gov (United States)

Willems, Hanny; Jacobs, An; Hadiwikarta, Wahyu Wijaya; Venken, Tom; Valkenborg, Dirk; Van Roy, Nadine; Vandesompele, Jo; Hooyberghs, Jef

2017-01-01

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine. PMID:28542229

Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores.

Science.gov (United States)

Singer, Alon; Kuhn, Heiko; Frank-Kamenetskii, Maxim; Meller, Amit

2010-11-17

The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.

Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores

International Nuclear Information System (INIS)

Singer, Alon; Kuhn, Heiko; Frank-Kamenetskii, Maxim; Meller, Amit

2010-01-01

The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.

Development of laser-induced fluorescence detection to assay DNA damage

International Nuclear Information System (INIS)

Sharma, M.; Freund, H.G.

1991-01-01

A precolumn derivation method has been developed for high performance liquid chromatographic (HPLC) analysis of DNA damage using fluorescence detection. The modified nucleotide, having excised enzymatically from the exposed DNA, is enriched from the normal nucleotides and labeled with a fluorescent reagent. The labeling procedure involves phosphoramidation of the nucleotide with ethylenediamine (EDA) followed by conjugation of the free amino end of the phosphoramidate with 5-dimethylaminonaphthalene 1-sulfonyl chloride, commonly known as Dansyl chloride. The dansylated nucleotide can be analyzed with a sub-picomole limit of detection (LOD) by conventional HPLC using a conventional fluorescence detector. By combining microbore HPLC with laser-induced fluorescence (LIF) detection, the authors present the development of an analytical system that has sub-femtomole LOD for real-time analysis of the dansylated nucleotide. In this paper the application of the developed system in fluorescence postlabeling assay of a small alkyl-modified nucleotide (5-methyl CMP) in calf-thymus DNA is discussed

Plant DNA detection from grasshopper guts: A step-by-step protocol, from tissue preparation to obtaining plant DNA sequences1

Science.gov (United States)

Avanesyan, Alina

2014-01-01

• Premise of the study: A PCR-based method of identifying ingested plant DNA in gut contents of Melanoplus grasshoppers was developed. Although previous investigations have focused on a variety of insects, there are no protocols available for plant DNA detection developed for grasshoppers, agricultural pests that significantly influence plant community composition. • Methods and Results: The developed protocol successfully used the noncoding region of the chloroplast trnL (UAA) gene and was tested in several feeding experiments. Plant DNA was obtained at seven time points post-ingestion from whole guts and separate gut sections, and was detectable up to 12 h post-ingestion in nymphs and 22 h post-ingestion in adult grasshoppers. • Conclusions: The proposed protocol is an effective, relatively quick, and low-cost method of detecting plant DNA from the grasshopper gut and its different sections. This has important applications, from exploring plant “movement” during food consumption, to detecting plant–insect interactions. PMID:25202604

Complexes of DNA with fluorescent dyes are effective reagents for detection of autoimmune antibodies

DEFF Research Database (Denmark)

Domljanovic, Ivana; Carstens, Annika; Okholm, Anders

2017-01-01

as targets for these antibodies. This is done in a simple, rapid and specific immunofluorescence assay. Specifically, employing 3D nanostructures (DNA origami), we present a new approach in the detection and study of human antibodies to DNA. We demonstrate the detection of anti-DNA antibodies...

Jaguar interactions with pumas and prey at the northern edge of jaguars’ range

Directory of Open Access Journals (Sweden)

Carmina E. Gutiérrez-González

2017-01-01

Full Text Available We present the first study that evaluates jaguar-puma interactions in the arid lands of northern Mexico, where jaguars have their northernmost breeding population and both predators are persecuted for livestock depredation. We tested whether jaguars are the dominant species in this unique ecosystem, where: (1 pumas outnumber jaguars, (2 pumas are better adapted to arid environments, and (3 jaguars and pumas are of similar size. We analyzed four years of data with two approaches; a two species conditional occupancy model and an activity patterns analysis. We used camera location and prey presence as covariates for jaguar and puma detection and presence probabilities. We also explored overlap in activities of predators and prey. Where both species were detected, peccary presence was positively correlated with both jaguar and puma presence, whereas in areas where jaguars were detected but pumas were not, deer presence explained the probability of jaguar presence. We found that both predators were more likely to co-occur together than to be found independently, and so we rejected the hypothesis that jaguars were the dominant species in our study area. Predators were mainly nocturnal and their activity patterns overlapped by 60%. Jaguar, as compared with puma, overlapped more with deer and calves; puma overlapped with calves more than with other prey, suggesting a preference. We believe exploring predator relationships at different scales may help elucidate mechanisms that regulate their coexistence.

Bio-Physical Coupling of Seabirds and Prey with a Dynamic River Plume

Science.gov (United States)

Phillips, E. M.; Horne, J. K.; Zamon, J. E.; Adams, J.

2016-02-01

Freshwater plumes and plume density fronts are important regions of bio-physical coupling. On the west coast of North America, discharge from the Columbia River into the northern California Current creates a large, dynamic plume and multiple plume fronts. These nutrient-rich, productive waters fuel primary and secondary production, supporting a wide variety of small pelagic prey fish, large populations of Pacific salmon, seabirds, and marine mammals. To determine the influence of the Columbia River plume on marine predators, we analyzed at-sea seabird counts, in situ environmental data, surface trawl densities of prey fish, and acoustic backscatter measurements collected from research vessels in May and June 2010-2012. Concurrent distribution patterns of satellite-tagged sooty shearwaters (Puffinus griseus) and common murres (Uria aalge) were compared with seabird counts from ship surveys. To evaluate plume use by satellite-tagged birds, daily surface salinity values from SELFE hindcast models were extracted at each tag location. Both seabird species occurred in plume waters disproportionate to the total surveyed area, concentrating in the river plume when river flow and plume volume decreased. Murres were consistently within 20 km of the geographic mean center of the river plume. In contrast, shearwaters consistently occurred 100 km to the north of the plume center, where high densities of prey fish occur. Although acoustically detected prey also occurred in greater densities within the plume when volume decreased, surface catches of prey in the plume did not vary with changing plume conditions. Geographic indices of colocation (GIC) were low between murres and prey species caught in surface trawls, whereas GICs were >0.5 between shearwaters and prey species including squid (Loligo opalescens), juvenile Chinook salmon (Oncorhynchus tshawytscha), and coho (O. kisutch) salmon. We conclude that the river plume and associated fronts are identifiable, predictable, and

Fear on the move: predator hunting mode predicts variation in prey mortality and plasticity in prey spatial response.

Science.gov (United States)

Miller, Jennifer R B; Ament, Judith M; Schmitz, Oswald J

2014-01-01

Ecologists have long searched for a framework of a priori species traits to help predict predator-prey interactions in food webs. Empirical evidence has shown that predator hunting mode and predator and prey habitat domain are useful traits for explaining predator-prey interactions. Yet, individual experiments have yet to replicate predator hunting mode, calling into question whether predator impacts can be attributed to hunting mode or merely species identity. We tested the effects of spider predators with sit-and-wait, sit-and-pursue and active hunting modes on grasshopper habitat domain, activity and mortality in a grassland system. We replicated hunting mode by testing two spider predator species of each hunting mode on the same grasshopper prey species. We observed grasshoppers with and without each spider species in behavioural cages and measured their mortality rates, movements and habitat domains. We likewise measured the movements and habitat domains of spiders to characterize hunting modes. We found that predator hunting mode explained grasshopper mortality and spider and grasshopper movement activity and habitat domain size. Sit-and-wait spider predators covered small distances over a narrow domain space and killed fewer grasshoppers than sit-and-pursue and active predators, which ranged farther distances across broader domains and killed more grasshoppers, respectively. Prey adjusted their activity levels and horizontal habitat domains in response to predator presence and hunting mode: sedentary sit-and-wait predators with narrow domains caused grasshoppers to reduce activity in the same-sized domain space; more mobile sit-and-pursue predators with broader domains caused prey to reduce their activity within a contracted horizontal (but not vertical) domain space; and highly mobile active spiders led grasshoppers to increase their activity across the same domain area. All predators impacted prey activity, and sit-and-pursue predators generated strong

Detection of influenza A virus using carbon nanotubes field effect transistor based DNA sensor

Science.gov (United States)

Tran, Thi Luyen; Nguyen, Thi Thuy; Huyen Tran, Thi Thu; Chu, Van Tuan; Thinh Tran, Quang; Tuan Mai, Anh

2017-09-01

The carbon nanotubes field effect transistor (CNTFET) based DNA sensor was developed, in this paper, for detection of influenza A virus DNA. Number of factors that influence the output signal and analytical results were investigated. The initial probe DNA, decides the available DNA strands on CNTs, was 10 μM. The hybridization time for defined single helix was 120 min. The hybridization temperature was set at 30 °C to get a net change in drain current of the DNA sensor without altering properties of any biological compounds. The response time of the DNA sensor was less than one minute with a high reproducibility. In addition, the DNA sensor has a wide linear detection range from 1 pM to 10 nM, and a very low detection limit of 1 pM. Finally, after 7-month storage in 7.4 pH buffer, the output signal of DNA sensor recovered 97%.

Presence of Native Prey Does Not Divert Predation on Exotic Pests by Harmonia axyridis in Its Indigenous Range

Science.gov (United States)

Zhang, Gui Fen; Lövei, Gábor L; Wu, Xia; Wan, Fang Hao

2016-01-01

In China, two invasive pests, Bemisia tabaci MEAM1 (Gennadius) and Frankliniella occidentalis (Pergande), often co-occur with the native pest, Aphis gossypii (Glover), on plants of Malvaceae and Cucurbitaceae. All three are preyed on by the native ladybird, Harmonia axyridis (Pallas); however, the native predator might be expected to prefer native prey to the exotic ones due to a shared evolutionary past. In order to clarify whether the presence of native prey affected the consumption of these two invasive species by the native predator, field-cage experiments were conducted. A duplex qPCR was used to simultaneously detect both non-native pests within the gut of the predator. H. axyridis readily accepted both invasive prey species, but preferred B. tabaci. With all three prey species available, H. axyridis consumption of B. tabaci was 39.3±2.2% greater than consumption of F. occidentalis. The presence of A. gossypii reduced (by 59.9% on B. tabaci, and by 60.6% on F. occidentalis), but did not stop predation on the two exotic prey when all three were present. The consumption of B. tabaci was similar whether it was alone or together with A. gossypii. However, the presence of aphids reduced predation on the invasive thrips. Thus, some invasive prey may be incorporated into the prey range of a native generalist predator even in the presence of preferred native prey. PMID:27391468

Environmental DNA (eDNA From the Wake of the Whales: Droplet Digital PCR for Detection and Species Identification

Directory of Open Access Journals (Sweden)

C. Scott Baker

2018-04-01

Full Text Available Genetic sampling for identification of species, subspecies or stock of whales, dolphins and porpoises at sea remains challenging. Most samples have been collected with some form of a biopsy dart requiring a close approach of a vessel while the individual is at the surface. Here we have adopted droplet digital (ddPCR technology for detection and species identification of cetaceans using environmental (eDNA collected from seawater. We conducted a series of eDNA sampling experiments during 25 encounters with killer whales, Orcinus orca, in Puget Sound (the Salish Sea. The regular habits of killer whales in these inshore waters allowed us to locate pods and collect seawater, at an initial distance of 200 m and at 15-min intervals, for up to 2 h after the passage of the whales. To optimize detection, we designed a set of oligonucleotide primers and probes to target short fragments of the mitochondrial (mtDNA control region, with a focus on identification of known killer whale ecotypes. We confirmed the potential to detect eDNA in the wake of the whales for up to 2 h, despite movement of the water mass by several kilometers due to tidal currents. Re-amplification and sequencing of the eDNA barcode confirmed that the ddPCR detection included the “southern resident community” of killer whales, consistent with the calls from hydrophone recordings and visual observations.

Detection of DNA of genetically modified maize by a silicon nanowire field-effect transistor

International Nuclear Information System (INIS)

Pham, Van Binh; Tung Pham, Xuan Thanh; Duong Dang, Ngoc Thuy; Tuyen Le, Thi Thanh; Tran, Phu Duy; Nguyen, Thanh Chien; Nguyen, Van Quoc; Dang, Mau Chien; Tong, Duy Hien; Van Rijn, Cees J M

2011-01-01

A silicon nanowire field-effect transistor based sensor (SiNW-FET) has been proved to be the most sensitive and powerful device for bio-detection applications. In this paper, SiNWs were first fabricated by using our recently developed deposition and etching under angle technique (DEA), then used to build up the complete SiNW device based biosensor. The fabricated SiNW biosensor was used to detect DNA of genetically modified maize. As the DNA of the genetically modified maize has particular DNA sequences of 35S promoter, we therefore designed 21 mer DNA oligonucleotides, which are used as a receptor to capture the transferred DNA of maize. In our work, the SiNW biosensor could detect DNA of genetically modified maize with concentrations down to about 200 pM

Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay.

Directory of Open Access Journals (Sweden)

Yong Huang

Full Text Available Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus and PCV2 (DNA virus from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29% and TGEV (11.7% preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility.

Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay

Science.gov (United States)

Wang, Zengguo; Zhang, Xiujuan; Zhao, Xiaomin; Du, Qian; Chang, Lingling; Tong, Dewen

2015-01-01

Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility. PMID:26544710

Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay.

Science.gov (United States)

Huang, Yong; Xing, Na; Wang, Zengguo; Zhang, Xiujuan; Zhao, Xiaomin; Du, Qian; Chang, Lingling; Tong, Dewen

2015-01-01

Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility.

Prey size selection and cannibalistic behaviour of juvenile barramundi Lates calcarifer.

Science.gov (United States)

Ribeiro, F F; Qin, J G

2015-05-01

This study assessed the cannibalistic behaviour of juvenile barramundi Lates calcarifer and examined the relationship between prey size selection and energy gain of cannibals. Prey handling time and capture success by cannibals were used to estimate the ratio of energy gain to energy cost in prey selection. Cannibals selected smaller prey despite its capability of ingesting larger prey individuals. In behavioural analysis, prey handling time significantly increased with prey size, but it was not significantly affected by cannibal size. Conversely, capture success significantly decreased with the increase of both prey and cannibal sizes. The profitability indices showed that the smaller prey provides the most energy return for cannibals of all size classes. These results indicate that L. calcarifer cannibals select smaller prey for more profitable return. The behavioural analysis, however, indicates that L. calcarifer cannibals attack prey of all size at a similar rate but ingest smaller prey more often, suggesting that prey size selection is passively orientated rather than at the predator's choice. The increase of prey escape ability and morphological constraint contribute to the reduction of intracohort cannibalism as fish grow larger. This study contributes to the understanding of intracohort cannibalism and development of strategies to reduce fish cannibalistic mortalities. © 2015 The Fisheries Society of the British Isles.

Rapid detection of DNA-interstrand and DNA-protein cross-links in mammalian cells by gravity-flow alkaline elution

International Nuclear Information System (INIS)

Hincks, J.R.; Coulombe, R.A. Jr.

1989-01-01

Alkaline elution is a sensitive and commonly used technique to detect cellular DNA damage in the form of DNA strand breaks and DNA cross-links. Conventional alkaline elution procedures have extensive equipment requirements and are tedious to perform. Our laboratory recently presented a rapid, simplified, and sensitive modification of the alkaline elution technique to detect carcinogen-induced DNA strand breaks. In the present study, we have further modified this technique to enable the rapid characterization of chemically induced DNA-interstrand and DNA-protein associated cross-links in cultured epithelial cells. Cells were exposed to three known DNA cross-linking agents, nitrogen mustard (HN 2 ), mitomycin C (MMC), or ultraviolet irradiation (UV). One hour exposures of HN 2 at 0.25, 1.0, and 4.0 microM or of MMC at 20, 40, and 60 microM produced a dose-dependent induction of total DNA cross-links by these agents. Digestion with proteinase K revealed that HN 2 and MMC induced both DNA-protein cross-links and DNA-interstrand cross-links. Ultraviolet irradiation induced both DNA cross-links and DNA strand breaks, the latter of which were either protein and nonprotein associated. The results demonstrate that gravity-flow alkaline elution is a sensitive and accurate method to characterize the molecular events of DNA cross-linking. Using this procedure, elution of DNA from treated cells is completed in 1 hr, and only three fractions per sample are analyzed. This method may be useful as a rapid screening assay for genotoxicity and/or as an adjunct to other predictive assays for potential mutagenic or carcinogenic agents

Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

Science.gov (United States)

Taylor M. Wilcox; Kevin S. McKelvey; Michael K. Young; Adam J. Sepulveda; Bradley B. Shepard; Stephen F. Jane; Andrew R. Whiteley; Winsor H. Lowe; Michael K. Schwartz

2016-01-01

Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive...

Is the red spotted green frog Hypsiboas punctatus (Anura: Hylidae) selecting its preys? The importance of prey availability.

Science.gov (United States)

López, Javier A; Scarabotti, Pablo A; Medrano, María C; Ghirardi, Romina

2009-09-01

The study of the feeding ecology of amphibians is an old issue in herpetology. Notwithstanding, the lack of food resources data in many studies of amphibians feeding has lead to partial understanding of frog feeding strategies. In this study we evaluate the trophic selectivity of a red spotted green frog (Hypsiboas punctatus) population from a Middle Paraná River floodplain pond in Argentina, and discuss the importance of prey availability data when interpreting results from diet analysis. We analyzed the gut contents of 47 H. punctatus adults and compared frog's diet with the environmental food resources. Prey availability was estimated by systematically seep-netting the microhabitat where anurans were localized foraging. We identified 33 taxonomic categories from gastrointestinal contents. Numerically, the most important prey categories were dipterans, followed by hemipterans, homopterans and coleopterans. The diet similarity between males and females was high and no statistical differences in diet composition were found. The most abundant food resources in the environment were dipterans, coleopterans, homopterans and collembolans. In order to assess whether frogs were selecting their preys, we calculated Pianka's niche overlap index and Jacobs' electivity index comparing gut contents to prey availability data. Trophic niche overlap was medium but significantly higher than expected by chance. The electivity index indicated that H. punctatus foraged dipterans slightly above their environmental abundance. Among the secondary preys, hemipterans were foraged selectively, homopterans were consumed in the same proportion to their occurrence in the environment, coleopterans were foraged quite under their availability and collembolans were practically ignored by frogs. Without food resources data, H. punctatus could be classified as a specialist feeder, but dipterans also were quite abundant in the environment. Our results show that H. punctatus fit better as a

Invasive lionfish had no measurable effect on prey fish community structure across the Belizean Barrier Reef.

Science.gov (United States)

Hackerott, Serena; Valdivia, Abel; Cox, Courtney E; Silbiger, Nyssa J; Bruno, John F

2017-01-01

Invasive lionfish are assumed to significantly affect Caribbean reef fish communities. However, evidence of lionfish effects on native reef fishes is based on uncontrolled observational studies or small-scale, unrepresentative experiments, with findings ranging from no effect to large effects on prey density and richness. Moreover, whether lionfish affect populations and communities of native reef fishes at larger, management-relevant scales is unknown. The purpose of this study was to assess the effects of lionfish on coral reef prey fish communities in a natural complex reef system. We quantified lionfish and the density, richness, and composition of native prey fishes (0-10 cm total length) at sixteen reefs along ∼250 km of the Belize Barrier Reef from 2009 to 2013. Lionfish invaded our study sites during this four-year longitudinal study, thus our sampling included fish community structure before and after our sites were invaded, i.e., we employed a modified BACI design. We found no evidence that lionfish measurably affected the density, richness, or composition of prey fishes. It is possible that higher lionfish densities are necessary to detect an effect of lionfish on prey populations at this relatively large spatial scale. Alternatively, negative effects of lionfish on prey could be small, essentially undetectable, and ecologically insignificant at our study sites. Other factors that influence the dynamics of reef fish populations including reef complexity, resource availability, recruitment, predation, and fishing could swamp any effects of lionfish on prey populations.

Invasive lionfish had no measurable effect on prey fish community structure across the Belizean Barrier Reef

Directory of Open Access Journals (Sweden)

Serena Hackerott

2017-05-01

Full Text Available Invasive lionfish are assumed to significantly affect Caribbean reef fish communities. However, evidence of lionfish effects on native reef fishes is based on uncontrolled observational studies or small-scale, unrepresentative experiments, with findings ranging from no effect to large effects on prey density and richness. Moreover, whether lionfish affect populations and communities of native reef fishes at larger, management-relevant scales is unknown. The purpose of this study was to assess the effects of lionfish on coral reef prey fish communities in a natural complex reef system. We quantified lionfish and the density, richness, and composition of native prey fishes (0–10 cm total length at sixteen reefs along ∼250 km of the Belize Barrier Reef from 2009 to 2013. Lionfish invaded our study sites during this four-year longitudinal study, thus our sampling included fish community structure before and after our sites were invaded, i.e., we employed a modified BACI design. We found no evidence that lionfish measurably affected the density, richness, or composition of prey fishes. It is possible that higher lionfish densities are necessary to detect an effect of lionfish on prey populations at this relatively large spatial scale. Alternatively, negative effects of lionfish on prey could be small, essentially undetectable, and ecologically insignificant at our study sites. Other factors that influence the dynamics of reef fish populations including reef complexity, resource availability, recruitment, predation, and fishing could swamp any effects of lionfish on prey populations.

DNA detection on ultrahigh-density optical fiber-based nanoarrays.

Science.gov (United States)

Tam, Jenny M; Song, Linan; Walt, David R

2009-04-15

Nanoarrays for DNA detection were fabricated on etched nanofiber bundles based on recently developed techniques for microscale arrays. Two different-sized nanoarrays were created: one with 700 nm feature sizes and a 1 microm center-to-center pitch (approximately 1x10(6) array elements/mm(2)) and one with 300 nm feature sizes and a 500 nm center-to-center pitch (4.6x10(6) array elements/mm(2)). A random, multiplexed array composed of oligonucleotide-functionalized nanospheres was constructed and used for parallel detection and analysis of fluorescently labeled DNA targets. We have used these arrays to detect a variety of target sequences including Bacillus thuringiensis kurstaki and vaccina virus sequences, two potential biowarfare agents, as well as interleukin-2 sequences, an immune system modulator that has been used for the diagnosis of HIV.

Microfabricated electrochemical sensor for the detection of radiation-induced DNA damage

Energy Technology Data Exchange (ETDEWEB)

Wang, J.; Rivas, G.; Ozsoz, M.; Grant, D.H.; Cai, X.; Parrado, C. [New Mexico State Univ., Las Cruces, NM (United States)

1997-04-01

An electrochemical biosensor protocol for the detection of radiation-induced DNA damage is described. The procedure employs a dsDNA-coated screen-printed electrode and relies on changes in the guanine-DNA oxidation signal upon exposure to ultraviolet radiation. The decreased signal is ascribed primarily to conformational changes in the DNA and to the photoconversion of the guanine-DNA moiety to a nonelectroactive monomeric base product. Factors influencing the response of these microfabricated DNA sensors, such as irradiation time, wavelength, and distance, are explored, and future prospects are discussed. Similar results are given for the use of bare strip electrodes in connection with irradiated DNA solutions. 8 refs., 4 figs.

Polypyrrole–gold nanoparticle composites for highly sensitive DNA detection

International Nuclear Information System (INIS)

Spain, Elaine; Keyes, Tia E.; Forster, Robert J.

2013-01-01

DNA capture surfaces represent a powerful approach to developing highly sensitive sensors for identifying the cause of infection. Electrochemically deposited polypyrrole, PPy, films have been functionalized with electrodeposited gold nanoparticles to give a nanocomposite material, PPy–AuNP. Thiolated capture strand DNA, that is complementary to the sequence from the pathogen Staphylococcus aureus that causes mammary gland inflammation, was then immobilized onto the gold nanoparticles and any of the underlying gold electrode that is exposed. A probe strand, labelled with horse radish peroxidase, HRP, was then hybridized to the target. The concentration of the target was determined by measuring the current generated by reducing benzoquinone produced by the HRP label. Semi-log plots of the pathogen DNA concentration vs. faradaic current are linear from 150 pM to 1 μM and pM concentrations can be detected without the need for molecular, e.g., PCR or NASBA, amplification. The nanocomposite also exhibits excellent selectivity and single base mismatches in a 30 mer sequence can be detected

Immunological detection of O6-methylguanine in alkylated DNA

International Nuclear Information System (INIS)

Briscoe, W.T.; Spizizen, J.; Tan, E.M.

1978-01-01

Antibodies to O 6 -methyldeoxyguanosine were produced in rabbits and utilized in a radioimmunoassay to detect this nucleoside at picomole levels. The specificity of the antibodies was demonstrated by the use of nucleoside analogues as inhibitors in the radioimmunoassay. The antibodies cross-reacted with O 6 -methylguanosine, O 6 -methylguanine, and O 6 -ethylguanosine. There was 10 4 to 10 6 times less sensitivity to inhibition by deoxyadenosine, deoxyguanosine, and guanosine than by O 6 -methyldeoxyguanosine. The radioimmunoassay also detected O 6 -methylguanine in DNA alkylated by agents known to produce O 6 -methylguanine, such as N'-methyl-N-nitrosourea. DNA alkylated with dimethyl sulfate, which does not produce O 6 -methylguanine in DNA, cross-reacted with the antibodies to a very limited extent. Such an assay system for modified nucleic acid components would be very useful in following the production, persistence, and repair of these lesions in a variety of cells and tissues treated with a broad spectrum of carcinogens and suspected carcinogens

Detection of Adriamycin-DNA adducts by accelerator mass spectrometry at clinically relevant Adriamycin concentrations.

Science.gov (United States)

Coldwell, Kate E; Cutts, Suzanne M; Ognibene, Ted J; Henderson, Paul T; Phillips, Don R

2008-09-01

Limited sensitivity of existing assays has prevented investigation of whether Adriamycin-DNA adducts are involved in the anti-tumour potential of Adriamycin. Previous detection has achieved a sensitivity of a few Adriamycin-DNA adducts/10(4) bp DNA, but has required the use of supra-clinical drug concentrations. This work sought to measure Adriamycin-DNA adducts at sub-micromolar doses using accelerator mass spectrometry (AMS), a technique with origins in geochemistry for radiocarbon dating. We have used conditions previously validated (by less sensitive decay counting) to extract [(14)C]Adriamycin-DNA adducts from cells and adapted the methodology to AMS detection. Here we show the first direct evidence of Adriamycin-DNA adducts at clinically-relevant Adriamycin concentrations. [(14)C]Adriamycin treatment (25 nM) resulted in 4.4 +/- 1.0 adducts/10(7) bp ( approximately 1300 adducts/cell) in MCF-7 breast cancer cells, representing the best sensitivity and precision reported to date for the covalent binding of Adriamycin to DNA. The exceedingly sensitive nature of AMS has enabled over three orders of magnitude increased sensitivity of Adriamycin-DNA adduct detection and revealed adduct formation within an hour of drug treatment. This method has been shown to be highly reproducible for the measurement of Adriamycin-DNA adducts in tumour cells in culture and can now be applied to the detection of these adducts in human tissues.

DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem.

Directory of Open Access Journals (Sweden)

Eglė Jakubavičiūtė

Full Text Available The three-spined stickleback (Gasterosteus aculeatus L., hereafter 'stickleback' is a common mesopredatory fish in marine, coastal and freshwater areas. In large parts of the Baltic Sea, stickleback densities have increased >10-fold during the last decades, and it is now one of the dominating fish species both in terms of biomass and effects on lower trophic levels. Still, relatively little is known about its diet-knowledge which is essential to understand the increasing role sticklebacks play in the ecosystem. Fish diet analyses typically rely on visual identification of stomach contents, a labour-intensive method that is made difficult by prey digestion and requires expert taxonomic knowledge. However, advances in DNA-based metabarcoding methods promise a simultaneous identification of most prey items, even from semi-digested tissue. Here, we studied the diet of stickleback from the western Baltic Sea coast using both DNA metabarcoding and visual analysis of stomach contents. Using the cytochrome oxidase (CO1 marker we identified 120 prey taxa in the diet, belonging to 15 phyla, 83 genera and 84 species. Compared to previous studies, this is an unusually high prey diversity. Chironomids, cladocerans and harpacticoids were dominating prey items. Large sticklebacks were found to feed more on benthic prey, such as amphipods, gastropods and isopods. DNA metabarcoding gave much higher taxonomic resolution (median rank genus than visual analysis (median rank order, and many taxa identified using barcoding could not have been identified visually. However, a few taxa identified by visual inspection were not revealed by barcoding. In summary, our results suggest that the three-spined stickleback feeds on a wide variety of both pelagic and benthic organisms, indicating that the strong increase in stickleback populations may affect many parts of the Baltic Sea coastal ecosystem.

Behavior of prey links midwater and demersal piscivorous reef fishes

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Peter J. Auster

Full Text Available Pelagic and demersal guilds of piscivorous fishes are linked by a variety of biological and physical processes that mediate interactions with common prey species. Understanding the behaviors of predators and prey can provide insight into the conditions that make such linkages possible. Here we report on the behaviors of mid-water piscivorous fishes and the responses of prey that produce feeding opportunities for demersal piscivorous fishes associated with "live bottom" ledge habitats off the coast of Georgia (northwest Atlantic Ocean. Prey taxa reduced nearest neighbor distances and retreated towards the seafloor during predatory attacks by mid-water fishes. Demersal fishes subsequently attacked and consumed prey in these ephemeral high density patches. No predation by demersal fishes was observed when prey species were at background densities. If the predator-prey interactions of demersal piscivorous fishes are commonly mediated by the predatory behavior of midwater piscivorous fishes and their prey, such indirect facilitative behaviors may be important in terms of the population processes (e.g., prey consumption and growth rates of these demersal fishes.

Microfluidic Arrayed Lab-On-A-Chip for Electrochemical Capacitive Detection of DNA Hybridization Events.

Science.gov (United States)

Ben-Yoav, Hadar; Dykstra, Peter H; Bentley, William E; Ghodssi, Reza

2017-01-01

A microfluidic electrochemical lab-on-a-chip (LOC) device for DNA hybridization detection has been developed. The device comprises a 3 × 3 array of microelectrodes integrated with a dual layer microfluidic valved manipulation system that provides controlled and automated capabilities for high throughput analysis of microliter volume samples. The surface of the microelectrodes is functionalized with single-stranded DNA (ssDNA) probes which enable specific detection of complementary ssDNA targets. These targets are detected by a capacitive technique which measures dielectric variation at the microelectrode-electrolyte interface due to DNA hybridization events. A quantitative analysis of the hybridization events is carried out based on a sensing modeling that includes detailed analysis of energy storage and dissipation components. By calculating these components during hybridization events the device is able to demonstrate specific and dose response sensing characteristics. The developed microfluidic LOC for DNA hybridization detection offers a technology for real-time and label-free assessment of genetic markers outside of laboratory settings, such as at the point-of-care or in-field environmental monitoring.

Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique

International Nuclear Information System (INIS)

Noll, W.W.; Collins, M.

1987-01-01

Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. The authors have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and the reaction mixture is electrophoresed on a denaturing gradient gel. Only the genomic DNA probe hybrids migrate into the gel. Differences in hybrid mobility on the gel indicate base pair changes in the genomic DNA. They have used this technique to identify two polymorphic sites within a 1.2-kilobase region of human chromosome 20. This approach should greatly facilitate the identification of DNA polymorphisms useful for gene linkage studies and the diagnosis of genetic diseases

Comparison between Mt-DNA D-Loop and Cyt B primers for porcine DNA detection in meat products

Science.gov (United States)

Hamzah, Azhana; Mutalib, Sahilah Abd.; Babji, Abdul Salam

2013-11-01

This study was conducted to detect the presence of porcine DNA in meat products in the market using conventional polymerase chain reaction (PCR) and commercial PCR-southern hybridization analysis. Porcine DNA detection in meat products was tested due to some issues associated with the adulteration of food products in Malaysia. This is an important issue especially for Halal authentication which is required for some religious practices such as in Islam and Hinduisms. Many techniques have been developed for determining the Halal status of food products. In this paper, mt-DNA D-loop primer and cytochrome (cyt) b were used to detect the presence of porcine DNA in meat products. Positive and negative controls were always present for each batch of extraction. DNA of raw pork meat was used as a positive control while nucleus free water is used as negative control. A pair of oligonucleotide primer was used namely Pork1 and Pork2 which produced amplicon of 531 base pair (bp) in size. While, PCR-southern hybridization was conducted using primers readily supplied by commercial PCR-Southern hybridization and produced amplicon with 276 bp in size. In the present study, demonstrated that none of the samples were contaminated with porcine residuals but selected samples with pork meat were positive. The species-specific PCR amplification yielded excellent results for identification of pork derivatives in food products and it is a potentially reliable and suitable technique in routine food analysis for Halal certification.

Ultrasensitive norovirus detection using DNA aptasensor technology.

Directory of Open Access Journals (Sweden)

Amanda Giamberardino

Full Text Available DNA aptamers were developed against murine norovirus (MNV using SELEX (Systematic Evolution of Ligands by EXponential enrichment. Nine rounds of SELEX led to the discovery of AG3, a promising aptamer with very high affinity for MNV as well as for lab-synthesized capsids of a common human norovirus (HuNoV outbreak strain (GII.3. Using fluorescence anisotropy, AG3 was found to bind with MNV with affinity in the low picomolar range. The aptamer could cross-react with HuNoV though it was selected against MNV. As compared to a non-specific DNA control sequence, the norovirus-binding affinity of AG3 was about a million-fold higher. In further tests, the aptamer also showed nearly a million-fold higher affinity for the noroviruses than for the feline calicivirus (FCV, a virus similar in size and structure to noroviruses. AG3 was incorporated into a simple electrochemical sensor using a gold nanoparticle-modified screen-printed carbon electrode (GNPs-SPCE. The aptasensor could detect MNV with a limit of detection of approximately 180 virus particles, for possible on-site applications. The lead aptamer candidate and the aptasensor platform show promise for the rapid detection and identification of noroviruses in environmental and clinical samples.

Multicolor fluorescent biosensor for multiplexed detection of DNA.

Science.gov (United States)

Hu, Rong; Liu, Tao; Zhang, Xiao-Bing; Huan, Shuang-Yan; Wu, Cuichen; Fu, Ting; Tan, Weihong

2014-05-20

Development of efficient methods for highly sensitive and rapid screening of specific oligonucleotide sequences is essential to the early diagnosis of serious diseases. In this work, an aggregated cationic perylene diimide (PDI) derivative was found to efficiently quench the fluorescence emission of a variety of anionic oligonucleotide-labeled fluorophores that emit at wavelengths from the visible to NIR region. This broad-spectrum quencher was then adopted to develop a multicolor biosensor via a label-free approach for multiplexed fluorescent detection of DNA. The aggregated perylene derivative exhibits a very high quenching efficiency on all ssDNA-labeled dyes associated with biosensor detection, having efficiency values of 98.3 ± 0.9%, 97 ± 1.1%, and 98.2 ± 0.6% for FAM, TAMRA, and Cy5, respectively. An exonuclease-assisted autocatalytic target recycling amplification was also integrated into the sensing system. High quenching efficiency combined with autocatalytic target recycling amplification afforded the biosensor with high sensitivity toward target DNA, resulting in a detection limit of 20 pM, which is about 50-fold lower than that of traditional unamplified homogeneous fluorescent assay methods. The quencher did not interfere with the catalytic activity of nuclease, and the biosensor could be manipulated in either preaddition or postaddition manner with similar sensitivity. Moreover, the proposed sensing system allows for simultaneous and multicolor analysis of several oligonucleotides in homogeneous solution, demonstrating its potential application in the rapid screening of multiple biotargets.

Detection of Methylated Circulating DNA as Noninvasive Biomarkers for Breast Cancer Diagnosis

Science.gov (United States)

Cheuk, Isabella Wai Yin; Shin, Vivian Yvonne

2017-01-01

Internationally, breast cancer is the most common female cancer, and is induced by a combination of environmental, genetic, and epigenetic risk factors. Despite the advancement of imaging techniques, invasive sampling of breast epithelial cells is the only definitive diagnostic procedure for patients with breast cancer. To date, molecular biomarkers with high sensitivity and specificity for the screening and early detection of breast cancer are lacking. Recent evidence suggests that the detection of methylated circulating cell-free DNA in the peripheral blood of patients with cancer may be a promising quantitative and noninvasive method for cancer diagnosis. Methylation detection based on a multi-gene panel, rather than on the methylation status of a single gene, may be used to increase the sensitivity and specificity of breast cancer screening. In this review, the results of 14 relevant studies, investigating the efficacy of cell-free DNA methylation screening for breast cancer diagnosis, have been summarized. The genetic risk factors for breast cancer, the methods used for breast cancer detection, and the techniques and limitations related to the detection of cell-free DNA methylation status, have also been reviewed and discussed. From this review, we conclude that the analysis of peripheral blood or other samples to detect differentially methylated cell-free DNA is a promising technique for use in clinical settings, and may improve the sensitivity of screening for both, early detection and disease relapse, and thus improve the future prognosis of patients with breast cancer. PMID:28382090

Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum)

Science.gov (United States)

Goldberg, Caren S.; Sepulveda, Adam; Ray, Andrew; Baumgardt, Jeremy A.; Waits, Lisette P.

2013-01-01

Early detection of aquatic invasive species is a critical task for management of aquatic ecosystems. This task is hindered by the difficulty and cost of surveying aquatic systems thoroughly. The New Zealand mudsnail (Potamopyrgus antipodarum) is a small, invasive parthenogenic mollusk that can reach very high population densities and severely affects ecosystem functioning. To assist in the early detection of this invasive species, we developed and validated a highly sensitive environmental deoxyribonucleic acid (eDNA) assay. We used a dose–response laboratory experiment to investigate the relationship between New Zealand mudsnail density and eDNA detected through time. We documented that as few as 1 individual in 1.5 L of water for 2 d could be detected with this method, and that eDNA from this species may remain detectable for 21 to 44 d after mudsnail removal. We used the eDNA method to confirm the presence of New Zealand mudsnail eDNA at densities as low as 11 to 144 snails/m2 in a eutrophic 5th-order river. Combined, these results demonstrate the high potential for eDNA surveys to assist with early detection of a widely distributed invasive aquatic invertebrate.

A specialized araneophagic predator's short-term nutrient utilization depends on the macronutrient content of prey rather than on prey taxonomic affiliation

DEFF Research Database (Denmark)

Toft, Søren; Li, Daiqin; Mayntz, David

2010-01-01

rate of high-protein flies than of high-lipid flies and spiders but, after 5 days of feeding, there is no significant difference in growth between treatments, and the diets lead to significant changes in the macronutrient composition of P. quei as a result of variable extraction and utilization...... of the prey. The short-term utilization of spider prey is similar to that of high-lipid flies and both differ in several respects from the utilization of high-protein flies. Thus, the short-term nutrient utilization is better explained by prey macronutrient content than by whether the prey is a spider or not....... The results suggest that spider prey may have a more optimal macronutrient composition for P. quei and that P. quei does not depend on spider-specific substances....

Detection of DNA hybridization based on SnO2 nanomaterial enhanced fluorescence

International Nuclear Information System (INIS)

Gu Cuiping; Huang Jiarui; Ni Ning; Li Minqiang; Liu Jinhuai

2008-01-01

In this paper, enhanced fluorescence emissions were firstly investigated based on SnO 2 nanomaterial, and its application in the detection of DNA hybridization was also demonstrated. The microarray of SnO 2 nanomaterial was fabricated by the vapour phase transport method catalyzed by patterned Au nanoparticles on a silicon substrate. A probe DNA was immobilized on the substrate with patterned SnO 2 nanomaterial, respectively, by covalent and non-covalent linking schemes. When a fluorophore labelled target DNA was hybridized with a probe DNA on the substrate, fluorescence emissions were only observed on the surface of SnO 2 nanomaterial, which indicated the property of enhancing fluorescence signals from the SnO 2 nanomaterial. By comparing the different fluorescence images from covalent and non-covalent linking schemes, the covalent method was confirmed to be more effective for immobilizing a probe DNA. With the combined use of SnO 2 nanomaterial and the covalent linking scheme, the target DNA could be detected at a very low concentration of 10 fM. And the stability of SnO 2 nanomaterial under the experimental conditions was also compared with silicon nanowires. The findings strongly suggested that SnO 2 nanomaterial could be extensively applied in detections of biological samples with enhancing fluorescence property and high stability

Environmental DNA (eDNA metabarcoding assays to detect invasive invertebrate species in the Great Lakes.

Directory of Open Access Journals (Sweden)

Katy E Klymus

Full Text Available Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring. We employed careful primer design and in vitro testing with mock communities to assess ability of the markers to amplify and sequence targeted species DNA, while retaining rank abundance information. In our mock communities, read abundances reflected the initial input abundance, with regressions having significant slopes (p<0.05 and high coefficients of determination (R2 for all comparisons. Tests on field environmental samples revealed similar ability of our markers to measure relative abundance. Due to the limited reference sequence data available for these invertebrate species, care must be taken when analyzing results and identifying sequence reads to species level. These markers extend eDNA metabarcoding research for molluscs and appear relevant to other invertebrate taxa, such as rotifers and bryozoans. Furthermore, the sphaeriid mussel assay is group-specific, exclusively amplifying bivalves in the Sphaeridae family and providing species-level identification. Our assays provide useful tools for managers and conservation scientists, facilitating early detection of invasive species as well as improving resolution of mollusc diversity.

Application of DNA Machineries for the Barcode Patterned Detection of Genes or Proteins.

Science.gov (United States)

Zhou, Zhixin; Luo, Guofeng; Wulf, Verena; Willner, Itamar

2018-06-05

The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes. Mixtures of DNA machineries that yield, upon sensing of different genes (or aptamer ligands), one-, two-, or three-band barcode patterns are described. The combination of nucleic acid scaffolds acting, in the presence of polymerase/nicking enzyme and nucleotide mixture, as DNA machineries, that generate multiband barcode patterns provide an analytical platform for the detection of an individual gene out of many possible genes. The diversity of genes (or other analytes) that can be analyzed by the DNA machineries and the barcode patterned imaging is given by the Pascal's triangle. As a proof-of-concept, the detection of one of six genes, that is, TP53, Werner syndrome, Tay-Sachs normal gene, BRCA1, Tay-Sachs mutant gene, and cystic fibrosis disorder gene by six two-band barcode patterns is demonstrated. The advantages and limitations of the detection of analytes by polymerase/nicking DNA machineries that yield barcode patterns as imaging readout signals are discussed.

Detection of dietary DNA, protein, and glyphosate in meat, milk, and eggs.

Science.gov (United States)

Van Eenennaam, A L; Young, A E

2017-07-01

Products such as meat, milk, and eggs from animals that have consumed genetically engineered (GE) feed are not currently subject to mandatory GE labeling requirements. Some voluntary "non-genetically modified organism" labeling has been associated with such products, indicating that the animals were not fed GE crops, as there are no commercialized GE food animals. This review summarizes the available scientific literature on the detection of dietary DNA and protein in animal products and briefly discusses the implications of mandatory GE labeling for products from animals that have consumed GE feed. Because glyphosate is used on some GE crops, the available studies on glyphosate residues in animal products are also reviewed. In GE crops, recombinant DNA (rDNA) makes up a small percentage of the plant's total DNA. The final amount of DNA in food/feed depends on many factors including the variable number and density of cells in the edible parts, the DNA-containing matrix, environmental conditions, and the specific transgenic event. Processing treatments and animals' digestive systems degrade DNA into small fragments. Available reports conclude that endogenous DNA and rDNA are processed in exactly the same way in the gastrointestinal tract and that they account for a very small proportion of food intake by weight. Small pieces of high copy number endogenous plant genes have occasionally been detected in meat and milk. Similarly sized pieces of rDNA have also been identified in meat, primarily fish, although detection is inconsistent. Dietary rDNA fragments have not been detected in chicken or quail eggs or in fresh milk from cows or goats. Collectively, studies have failed to identify full-length endogenous or rDNA transcripts or recombinant proteins in meat, milk, or eggs. Similarly, because mammals do not bioaccumulate glyphosate and it is rapidly excreted, negligible levels of glyphosate in cattle, pig and poultry meat, milk, and eggs have been reported. Despite

AFFINITY BIOSENSOR BASED ON SCREEN-PRINTED ELECTRODE MODIFIED WITH DNA FOR GENOTOXIC COMPOUNDS DETECTION

Directory of Open Access Journals (Sweden)

Bambang Kuswandi

2010-06-01

Full Text Available An electrochemical method for the detection of the genotoxic compounds using a DNA-modified electrode was developed. This electrode was successfully used for the electrochemical detection of genotoxic compounds in water samples. The electrochemical results clearly demonstrated that, the development is related to the molecular interaction between the surface-linked DNA obtained from calf thymus and the target compounds, such as pollutants, in order to develop a simple device for rapid screening of genotoxic compounds in environmental samples. The detection of such compounds was measured by their effect on the oxidation signal of the guanine peak of the DNA immobilised on the surface of carbon based Screen-Printed Electrode (SPE in disposable mode, and monitored by square-wave voltametric analysis. The DNA biosensor is able to detect known intercalating and groove-binding genotoxic compounds such as Dioxin, Bisphenol A, PCBs, and Phtalates. Application to real water samples is discussed and reported.   Keywords: electrochemical, screen-printed electrode, DNA biosensor, genotoxic compounds

Diet choice of a predator in the wild: overabundance of prey and missed opportunities along the prey capture sequence

OpenAIRE

Brechbühl, Rolf; Casas, Jérôme; Bacher, Sven

2012-01-01

Optimal diet theory (ODT) postulates that predators adjust their foraging decisions by calculating a prey value from the potential biomass gain, handling time, prey vulnerability and encounter rate. Tests of ODT have however so far mainly been restricted to laboratory settings. By video surveillance, we gathered a large data set of more than 2000 field observations of crab spider (Misumena vatia) encounters with potential prey. We then tested whether the complex ODT or two simpler models (pre...

Orthopteran insects as potential and preferred preys of the Red-footed Falcon (Falco vespertinus in Hungary

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Szövényi Gergely

2015-06-01

Full Text Available Orthopterans play an important role in Red-footed Falcon diet, however, most studies focus only on its qualitative food composition, and less on quantitative composition and preferences of the taxa identified as prey. During the present research, an extensive orthopterological investigation was carried out in the Red-footed Falcon study area, Vásárhelyi Plain (SE-Hungary between 2006 and 2008. Grasshoppers were sampled in their main habitats by sweep netting and pitfall trapping, and orthopterans were identified in the food remnants collected from the nests, both artificial and natural ones. 26 species were detected during the field works, 18 species from the food remnants. Altogether 32 species were identified. Prey preference values for all species for each year were calculated. More than two thirds of the identified preys were Decticus verrucivorus, and nearly 20% were Tettigonia viridissima. Other common prey species were Melanogryllus desertus, Platycleis affinis, Gryllotalpa gryllotalpa, Calliptamus italicus and Gryllus campestris. Based on the prey preference analysis, the most preferred species was Decticus verrucivorus with extreme high values, and the other preferred ones, overlapping with the previous list, were Platycleis affinis, Bicolorana bicolor, Tettigonia viridissima, Calliptamus italicus and Roeseliana roeselii. These results may help in the development of Red-footed Falcon-friendly habitats through the application of habitat management favourable for the preferred prey species.

Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA.

Science.gov (United States)

Piaggio, Antoinette J; Engeman, Richard M; Hopken, Matthew W; Humphrey, John S; Keacher, Kandy L; Bruce, William E; Avery, Michael L

2014-03-01

Recent studies have demonstrated that detection of environmental DNA (eDNA) from aquatic vertebrates in water bodies is possible. The Burmese python, Python bivittatus, is a semi-aquatic, invasive species in Florida where its elusive nature and cryptic coloration make its detection difficult. Our goal was to develop a diagnostic PCR to detect P. bivittatus from water-borne eDNA, which could assist managers in monitoring this invasive species. First, we used captive P. bivittatus to determine whether reptilian DNA could be isolated and amplified from water samples. We also evaluated the efficacy of two DNA isolation methods and two DNA extraction kits commonly used in eDNA preparation. A fragment of the mitochondrial cytochrome b gene from P. bivittatus was detected in all water samples isolated with the sodium acetate precipitate and the QIAamp DNA Micro Kit. Next, we designed P. bivittatus-specific primers and assessed the degradation rate of eDNA in water. Our primers did not amplify DNA from closely related species, and we found that P. bivittatus DNA was consistently detectable up to 96 h. Finally, we sampled water from six field sites in south Florida. Samples from five sites, where P. bivittatus has been observed, tested positive for eDNA. The final site was negative and had no prior documented evidence of P. bivittatus. This study shows P. bivittatus eDNA can be isolated from water samples; thus, this method is a new and promising technique for the management of invasive reptiles. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

Using CdTe/ZnSe core/shell quantum dots to detect DNA and damage to DNA

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Moulick A

2017-02-01

Full Text Available Amitava Moulick,1,2 Vedran Milosavljevic,1,2 Jana Vlachova,1,2 Robert Podgajny,3 David Hynek,1,2 Pavel Kopel,1,2 Vojtech Adam1,2 1Department of Chemistry and Biochemistry, Mendel University, 2Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic; 3Faculty of Chemistry, Jagiellonian University, Krakow, Poland Abstract: CdTe/ZnSe core/shell quantum dot (QD, one of the strongest and most highly luminescent nanoparticles, was directly synthesized in an aqueous medium to study its individual interactions with important nucleobases (adenine, guanine, cytosine, and thymine in detail. The results obtained from the optical analyses indicated that the interactions of the QDs with different nucleobases were different, which reflected in different fluorescent emission maxima and intensities. The difference in the interaction was found due to the different chemical behavior and different sizes of the formed nanoconjugates. An electrochemical study also confirmed that the purines and pyrimidines show different interactions with the core/shell QDs. Based on these phenomena, a novel QD-based method is developed to detect the presence of the DNA, damage to DNA, and mutation. The QDs were successfully applied very easily to detect any change in the sequence (mutation of DNA. The QDs also showed their ability to detect DNAs directly from the extracts of human cancer (PC3 and normal (PNT1A cells (detection limit of 500 pM of DNA, which indicates the possibilities to use this easy assay technique to confirm the presence of living organisms in extreme environments. Keywords: nanoparticles, nucleobases, biosensor, fluorescence, mutation

Detection of DNA and poly-l-lysine using CVD graphene-channel FET biosensors

International Nuclear Information System (INIS)

Kakatkar, Aniket; Craighead, H G; Abhilash, T S; Alba, R De; Parpia, J M

2015-01-01

A graphene channel field-effect biosensor is demonstrated for detecting the binding of double-stranded DNA and poly-l-lysine. Sensors consist of chemical vapor deposition graphene transferred using a clean, etchant-free transfer method. The presence of DNA and poly-l-lysine are detected by the conductance change of the graphene transistor. A readily measured shift in the Dirac voltage (the voltage at which the graphene’s resistance peaks) is observed after the graphene channel is exposed to solutions containing DNA or poly-l-lysine. The ‘Dirac voltage shift’ is attributed to the binding/unbinding of charged molecules on the graphene surface. The polarity of the response changes to positive direction with poly-l-lysine and negative direction with DNA. This response results in detection limits of 8 pM for 48.5 kbp DNA and 11 pM for poly-l-lysine. The biosensors are easy to fabricate, reusable and are promising as sensors of a wide variety of charged biomolecules. (paper)

Prey selectivity affects reproductive success of a corallivorous reef fish.

Science.gov (United States)

Brooker, Rohan M; Jones, Geoffrey P; Munday, Philip L

2013-06-01

Most animals consume a narrower range of food resources than is potentially available in the environment, but the underlying basis for these preferences is often poorly understood. Foraging theory predicts that prey selection should represent a trade-off between prey preferences based on nutritional value and prey availability. That is, species should consume preferred prey when available, but select less preferred prey when preferred prey is rare. We employed both field observation and laboratory experiments to examine the relationship between prey selection and preferences in the obligate coral-feeding filefish, Oxymonacanthus longirostris. To determine the drivers of prey selection, we experimentally established prey preferences in choice arenas and tested the consequences of prey preferences for key fitness-related parameters. Field studies showed that individuals fed almost exclusively on live corals from the genus Acropora. While diet was dominated by the most abundant species, Acropora nobilis, fish appeared to preferentially select rarer acroporids, such as A. millepora and A. hyacinthus. Prey choice experiments confirmed strong preferences for these corals, suggesting that field consumption is constrained by availability. In a longer-term feeding experiment, reproductive pairs fed on non-preferred corals exhibited dramatic reductions to body weight, and in hepatic and gonad condition, compared with those fed preferred corals. The majority of pairs fed preferred corals spawned frequently, while no spawning was observed for any pairs fed a non-preferred species of coral. These experiments suggest that fish distinguish between available corals based on their intrinsic value as prey, that reproductive success is dependent on the presence of particular coral species, and that differential loss of preferred corals could have serious consequences for the population success of these dietary specialists.

Prey Selection of Scandinavian Wolves: Single Large or Several Small?

Science.gov (United States)

Sand, Håkan; Eklund, Ann; Zimmermann, Barbara; Wikenros, Camilla; Wabakken, Petter

2016-01-01

Research on large predator-prey interactions are often limited to the predators' primary prey, with the potential for prey switching in systems with multiple ungulate species rarely investigated. We evaluated wolf (Canis lupus) prey selection at two different spatial scales, i.e., inter- and intra-territorial, using data from 409 ungulate wolf-kills in an expanding wolf population in Scandinavia. This expansion includes a change from a one-prey into a two-prey system with variable densities of one large-sized ungulate; moose (Alces alces) and one small-sized ungulate; roe deer (Capreolus capreolus). Among wolf territories, the proportion of roe deer in wolf kills was related to both pack size and roe deer density, but not to moose density. Pairs of wolves killed a higher proportion of roe deer than did packs, and wolves switched to kill more roe deer as their density increased above a 1:1 ratio in relation to the availability of the two species. At the intra-territorial level, wolves again responded to changes in roe deer density in their prey selection whereas we found no effect of snow depth, time during winter, or other predator-related factors on the wolves' choice to kill moose or roe deer. Moose population density was only weakly related to intra-territorial prey selection. Our results show that the functional response of wolves on moose, the species hitherto considered as the main prey, was strongly dependent on the density of a smaller, alternative, ungulate prey. The impact of wolf predation on the prey species community is therefore likely to change with the composition of the multi-prey species community along with the geographical expansion of the wolf population.

New approaches to detect 8-hydroxyguanine in γ-irradiated cellular DNA

International Nuclear Information System (INIS)

Mei, Nan; Tamae, Kazuyoshi; Hirano, Takeshi; Kasai, Hiroshi; Kunugita, Naoki

2003-01-01

This report describes an assay to detect 8-hydroxydeoxyguanosine 5'-monophosphate (8-OH-dGMP) in cellular DNA by modification of enzyme treatment after DNA extraction, using a high-performance liquid chromatography system equipped with an electrochemical detector (HPLC-ECD). This modification greatly reduces the measured background level of 8-hydroxyguanine (8-OH-Gua) in DNA, and improves the HPLC-ECD sensitivity to measure oxidative DNA damage. The 8-OH-Gua value in the DNA was expressed by the ratio of 8-OH-dGMP to deoxycytidine 5'-monophosphate (dCMP). Background level of 8-OH-Gua in DNA under our conditions was several times lower than that by a previous method. The human lung carcinoma cells (A549) were exposed to γ-rays of 20-100 Gy. A dose-dependent increase in oxidative DNA damage of 8-OH-Gua was observed. Furthermore, using commercial FITC-kit of an immunohistochemical type procedure, 8-OH-Gua was clearly detected in A549 cells and the fluorescence intensity of cells with oxidative DNA damage increased with the doses of γ-irradiation. Using an 8-OH-Gua repair activity assay, we also found that γ-rays decreased the repair enzyme activity. We conclude that the 8-OH-Gua level in human cellular DNA increases partly by the generation of reactive oxygen species (ROS) and partly by the inhibition of repair activity for 8-OH-Gua. (author)

Does small mammal prey guild affect the exposure of predators to anticoagulant rodenticides?

International Nuclear Information System (INIS)

Tosh, D.G.; McDonald, R.A.; Bearhop, S.; Lllewellyn, N.R.; Fee, S.; Sharp, E.A.; Barnett, E.A.; Shore, R.F.

2011-01-01

Ireland has a restricted small mammal prey guild but still includes species most likely to consume anticoagulant rodenticide (AR) baits. This may enhance secondary exposure of predators to ARs. We compared liver AR residues in foxes (Vulpes vulpes) in Northern Ireland (NI) with those in foxes from Great Britain which has a more diverse prey guild but similar agricultural use of ARs. Liver ARs were detected in 84% of NI foxes, more than in a comparable sample of foxes from Scotland and similar to that of suspected AR poisoned animals from England and Wales. High exposure in NI foxes is probably due to greater predation of commensal rodents and non-target species most likely to take AR baits, and may also partly reflect greater exposure to highly persistent brodifacoum and flocoumafen. High exposure is likely to enhance risk and Ireland may be a sentinel for potential effects on predator populations. - Highlights: → Exposure of a predator to anticoagulant rodenticides was compared in Britain and Ireland. → Exposure was higher in Ireland. → Differences driven by small mammal prey guilds. → Ireland a potential sentinel for predator exposure to anticoagulants. - Restriction of the small mammal prey guild is associated with enhanced exposure of predators to anticoagulant rodenticides.

Release from prey preservation behavior via prey switch allowed diversification of cuticular hydrocarbon profiles in digger wasps.

Science.gov (United States)

Wurdack, Mareike; Polidori, Carlo; Keller, Alexander; Feldhaar, Heike; Schmitt, Thomas

2017-11-01

The cuticle of insects is covered by a layer of hydrocarbons (CHC), whose original function is the protection from desiccation and pathogens. However, in most insects CHC profiles are species specific. While this variability among species was largely linked to communication and recognition functions, additional selective forces may shape insect CHC profiles. Here, we show that in Philanthinae digger wasps (Crabronidae) the CHC profile coevolved with a peculiar brood-care strategy. In particular, we found that the behavior to embalm prey stored in the nest with hydrocarbons is adaptive to protect larval food from fungi in those species hunting for Hymenoptera. The prey embalming secretion is identical in composition to the alkene-dominated CHC profile in these species, suggesting that their profile is adaptively conserved for this purpose. In contrast, prey embalming is not required in those species that switched to Coleoptera as prey. Released from this chemical brood-care strategy, Coleoptera-hunting species considerably diversified their CHC profiles. Differential needs to successfully protect prey types used as larval food have thus driven the diversification of CHCs profiles of female Philanthinae wasps. To the best of our knowledge, this is the first evidence of a direct link between selection pressure for food preservation and CHC diversity. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Perch, Perca fluviatilis show a directional preference for, but do not increase attacks toward, prey in response to water-borne cortisol

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Lindsay J. Henderson

2017-10-01

Full Text Available In freshwater environments, chemosensory cues play an important role in predator-prey interactions. Prey use a variety of chemosensory cues to detect and avoid predators. However, whether predators use the chemical cues released by disturbed or stressed prey has received less attention. Here we tested the hypothesis that the disturbance cue cortisol, in conjunction with visual cues of prey, elevates predatory behavior. We presented predators (perch, Perca fluviatilis with three chemosensory choice tests and recorded their location, orientation, and aggressive behavior. We compared the responses of predators when provided with (i visual cues of prey only (two adjacent tanks containing sticklebacks; (ii visual and natural chemical cues of prey vs. visual cues only; and (iii visual cues of prey with cortisol vs. visual cues only. Perch spent a significantly higher proportion of time in proximity to prey, and orientated toward prey more, when presented with a cortisol stimulus plus visual cues, relative to presentations of visual and natural chemical cues of prey, or visual cues of prey only. There was a trend that perch directed a higher proportion of predatory behaviors (number of lunges toward sticklebacks when presented with a cortisol stimulus plus visual cues, relative to the other chemosensory conditions. But they did not show a significant increase in total predatory behavior in response to cortisol. Therefore, it is not clear whether water-borne cortisol, in conjunction with visual cues of prey, affects predatory behavior. Our results provide evidence that cortisol could be a source of public information about prey state and/or disturbance, but further work is required to confirm this.

Detection of tyrosine hydroxylase in dopaminergic neuron cell using gold nanoparticles-based barcode DNA.

Science.gov (United States)

An, Jeung Hee; Oh, Byung-Keun; Choi, Jeong Woo

2013-04-01

Tyrosine hydroxylase, the rate-limiting enzyme of catecholamine biosysthesis, is predominantly expressed in several cell groups within the brain, including the dopaminergic neurons of the substantia nigra and ventral tegmental area. We evaluated the efficacy of this protein-detection method in detecting tyrosine hydroxylase in normal and oxidative stress damaged dopaminergic cells. In this study, a coupling of DNA barcode and bead-based immnunoassay for detecting tyrosine hydroxylaser with PCR-like sensitivity is reported. The method relies on magnetic nanoparticles with antibodies and nanoparticles that are encoded with DNA and antibodies that can sandwich the target protein captured by the nanoparticle-bound antibodies. The aggregate sandwich structures are magnetically separated from solution, and treated to remove the conjugated barcode DNA. The DNA barcodes were identified by PCR analysis. The concentration of tyrosine hydroxylase in dopaminergic cell can be easily and rapidly detected using bio-barcode assay. The bio-barcode assay is a rapid and high-throughput screening tool to detect of neurotransmitter such as dopamine.

Myxobacteria Are Able to Prey Broadly upon Clinically-Relevant Pathogens, Exhibiting a Prey Range Which Cannot Be Explained by Phylogeny

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Paul G. Livingstone

2017-08-01

Full Text Available Myxobacteria are natural predators of microorganisms and the subjects of concerted efforts to identify novel antimicrobial compounds. Myxobacterial predatory activity seems to require more than just the possession of specific antimicrobial metabolites. Thus a holistic approach to studying predation promises novel insights into antimicrobial action. Here, we report the isolation of 113 myxobacteria from samples of soil taken from a range of habitats in mid Wales. Predatory activity of each isolate was quantified against a panel of clinically important prey organisms, including Klebsiella pneumoniae, Proteus mirabilis, Candida albicans, Enterococcus faecalis, and three species of Staphylococcus. Myxobacterial isolates exhibited a wide range of predation activity profiles against the panel of prey. Efficient predation of all prey by isolates within the collection was observed, with K. pneumoniae and C. albicans proving particularly susceptible to myxobacterial predation. Notably efficient predators tended to be proficient at predating multiple prey organisms, suggesting they possess gene(s encoding a broad range killing activity. However, predatory activity was not congruent with phylogeny, suggesting prey range is subject to relatively rapid specialization, potentially involving lateral gene transfer. The broad but patchy prey ranges observed for natural myxobacterial isolates also implies multiple (potentially overlapping genetic determinants are responsible for dictating predatory activity.

Molecular Markers Detect Cryptic Predation on Coffee Berry Borer (Coleoptera: Curculionidae) by Silvanid and Laemophloeid Flat Bark Beetles (Coleoptera: Silvanidae, Laemophloeidae) in Coffee Beans.

Science.gov (United States)

Sim, Sheina B; Yoneishi, Nicole M; Brill, Eva; Geib, Scott M; Follett, Peter A

2016-02-01

The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae), is a serious pest of coffee worldwide. It was first detected in Hawai'i in 2010. Two predatory beetles, Cathartus quadricollis (Coleoptera: Silvanidae) and Leptophloeus sp. (Coleoptera: Laemophloeidae), have been observed in H. hampei-infested coffee. Under laboratory conditions, colony-reared C. quadricollis and Leptophloeus sp. prey upon all life stages of H. hampei. However, the H. hampei life cycle occurs almost exclusively within a coffee bean obscured from direct observation. Thus, it is unknown if C. quadricollis and Leptophloeus sp. consume H. hampei as prey in the wild. To demonstrate predation of H. hampei by C. quadricollis and Leptophloeus sp., a molecular assay was developed utilizing species-specific primers targeting short regions of the mitochondrial COI gene to determine species presence. Using these primers, wild C. quadricollis and Leptophloeus sp. were collected and screened for the presence of H. hampei DNA using PCR. Analysis of collections from five coffee farms revealed predation of C. quadricollis and Leptophloeus sp. on H. hampei. Further laboratory testing showed that H. hampei DNA could be detected in predators for as long as 48 h after feeding, indicating the farm-caught predators had preyed on H. hampei within 2 d of sampling. This study demonstrates the utility of molecular markers for the study of the ecology of predators and prey with cryptic behavior, and suggests C. quadricollis and Leptophloeus sp. might be useful biocontrol agents against H. hampei. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

Prey Selection of Scandinavian Wolves: Single Large or Several Small?

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Håkan Sand

Full Text Available Research on large predator-prey interactions are often limited to the predators' primary prey, with the potential for prey switching in systems with multiple ungulate species rarely investigated. We evaluated wolf (Canis lupus prey selection at two different spatial scales, i.e., inter- and intra-territorial, using data from 409 ungulate wolf-kills in an expanding wolf population in Scandinavia. This expansion includes a change from a one-prey into a two-prey system with variable densities of one large-sized ungulate; moose (Alces alces and one small-sized ungulate; roe deer (Capreolus capreolus. Among wolf territories, the proportion of roe deer in wolf kills was related to both pack size and roe deer density, but not to moose density. Pairs of wolves killed a higher proportion of roe deer than did packs, and wolves switched to kill more roe deer as their density increased above a 1:1 ratio in relation to the availability of the two species. At the intra-territorial level, wolves again responded to changes in roe deer density in their prey selection whereas we found no effect of snow depth, time during winter, or other predator-related factors on the wolves' choice to kill moose or roe deer. Moose population density was only weakly related to intra-territorial prey selection. Our results show that the functional response of wolves on moose, the species hitherto considered as the main prey, was strongly dependent on the density of a smaller, alternative, ungulate prey. The impact of wolf predation on the prey species community is therefore likely to change with the composition of the multi-prey species community along with the geographical expansion of the wolf population.

Prey Selection of Scandinavian Wolves: Single Large or Several Small?

Science.gov (United States)

Eklund, Ann; Zimmermann, Barbara; Wikenros, Camilla; Wabakken, Petter

2016-01-01

Research on large predator-prey interactions are often limited to the predators’ primary prey, with the potential for prey switching in systems with multiple ungulate species rarely investigated. We evaluated wolf (Canis lupus) prey selection at two different spatial scales, i.e., inter- and intra-territorial, using data from 409 ungulate wolf-kills in an expanding wolf population in Scandinavia. This expansion includes a change from a one-prey into a two-prey system with variable densities of one large-sized ungulate; moose (Alces alces) and one small-sized ungulate; roe deer (Capreolus capreolus). Among wolf territories, the proportion of roe deer in wolf kills was related to both pack size and roe deer density, but not to moose density. Pairs of wolves killed a higher proportion of roe deer than did packs, and wolves switched to kill more roe deer as their density increased above a 1:1 ratio in relation to the availability of the two species. At the intra-territorial level, wolves again responded to changes in roe deer density in their prey selection whereas we found no effect of snow depth, time during winter, or other predator-related factors on the wolves’ choice to kill moose or roe deer. Moose population density was only weakly related to intra-territorial prey selection. Our results show that the functional response of wolves on moose, the species hitherto considered as the main prey, was strongly dependent on the density of a smaller, alternative, ungulate prey. The impact of wolf predation on the prey species community is therefore likely to change with the composition of the multi-prey species community along with the geographical expansion of the wolf population. PMID:28030549

Feeding behaviour of the nauplii of the marine calanoid copepod Paracartia grani Sars: Functional response, prey size spectrum, and effects of the presence of alternative prey.

Directory of Open Access Journals (Sweden)

Laura K Helenius

Full Text Available Laboratory feeding experiments were conducted to study the functional response and prey size spectrum of the young naupliar stages of the calanoid copepod Paracartia grani Sars. Experiments were conducted on a range of microalgal prey of varying sizes and motility patterns. Significant feeding was found in all prey of a size range of 4.5-19.8 μm, with Holling type III functional responses observed for most prey types. The highest clearance rates occurred when nauplii fed on the dinoflagellate Heterocapsa sp. and the diatom Thalassiosira weissflogii (respectively, 0.61 and 0.70 mL ind-1 d-1, suggesting an optimal prey:predator ratio of 0.09. Additional experiments were conducted to examine the effects of the presence of alternative prey (either Heterocapsa sp. or Gymnodinium litoralis on the functional response to the haptophyte Isochrysis galbana. In the bialgal mixtures, clearance and ingestion rates of I. galbana along the range of the functional response were significantly reduced as a result of selectivity towards the larger, alternative prey. Paradoxically, relatively large prey trigger a perception response in the nauplii, but most likely such prey cannot be completely ingested and a certain degree of sloppy feeding may occur. Our results are further evidence of the complex prey-specific feeding interactions that are likely to occur in natural assemblages with several available prey types.

Red fox prey demands and implications to prairie duck production

Science.gov (United States)

Sargeant, A.B.

1978-01-01

Experiments were conducted during spring and summer with 33 red foxes (Vulpes vulpes) to determine prey demands, feeding characteristics, and growth rates using natural foods. Pups began eating prey the 4th week after birth. Then, prey consumption averaged 1.38 and 1.90 kg/pup/week for weeks 5-8 and 9-12 of the denning season respectively, and 2.54 kg/pup/week for the postdenning period. Feeding by adults averaged 2.25 kg/adult/week. Free water was not needed by either pups or adults. About 90 percent of the prey offered to pups on simulated natural diets was consumed, remains varied with prey availability and prey type. Prey biomass required by a typical fox family was estimated at 18.5 kg/km2 for the 12-week denning season and 2.4 kg/km2/week for the postdenning period. Because of the large prey demands, ducks could represent a small part of the foxes' diet and yet be of consequence to the productivity of particular species. An example is provided for the mallard (Anas platyrhynchos).

Intermolecular G-quadruplex structure-based fluorescent DNA detection system.

Science.gov (United States)

Zhou, Hui; Wu, Zai-Sheng; Shen, Guo-Li; Yu, Ru-Qin

2013-03-15

Adopting multi-donors to pair with one acceptor could improve the performance of fluorogenic detection probes. However, common dyes (e.g., fluorescein) in close proximity to each other would self-quench the fluorescence, and the fluorescence is difficult to restore. In this contribution, we constructed a novel "multi-donors-to-one acceptor" fluorescent DNA detection system by means of the intermolecular G-quadruplex (IGQ) structure-based fluorescence signal enhancement combined with the hairpin oligonucleotide. The novel IGQ-hairpin system was characterized using the p53 gene as the model target DNA. The proposed system showed an improved assay performance due to the introduction of IGQ-structure into fluorescent signaling probes, which could inhibit the background fluorescence and increase fluorescence restoration amplitude of fluoresceins upon target DNA hybridization. The proof-of-concept scheme is expected to provide new insight into the potential of G-quadruplex structure and promote the application of fluorescent oligonucleotide probes in fundamental research, diagnosis, and treatment of genetic diseases. Copyright © 2012 Elsevier B.V. All rights reserved.

Statistical guidelines for detecting past population shifts using ancient DNA

DEFF Research Database (Denmark)

Mourier, Tobias; Ho, Simon Y. W.; Gilbert, Tom

2012-01-01

Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both...... quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast...... results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when...

DNA Nucleotides Detection via capacitance properties of Graphene

Science.gov (United States)

Khadempar, Nahid; Berahman, Masoud; Yazdanpanah, Arash

2016-05-01

In the present paper a new method is suggested to detect the DNA nucleotides on a first-principles calculation of the electronic features of DNA bases which chemisorbed to a graphene sheet placed between two gold electrodes in a contact-channel-contact system. The capacitance properties of graphene in the channel are surveyed using non-equilibrium Green's function coupled with the Density Functional Theory. Thus, the capacitance properties of graphene are theoretically investigated in a biological environment, and, using a novel method, the effect of the chemisorbed DNA nucleotides on electrical charges on the surface of graphene is deciphered. Several parameters in this method are also extracted including Electrostatic energy, Induced density, induced electrostatic potential, Electron difference potential and Electron difference density. The qualitative and quantitative differences among these parameters can be used to identify DNA nucleotides. Some of the advantages of this approach include its ease and high accuracy. What distinguishes the current research is that it is the first experiment to investigate the capacitance properties of gaphene changes in the biological environment and the effect of chemisorbed DNA nucleotides on the surface of graphene on the charge.

Rapid colorimetric assay for detection of Listeria monocytogenes in food samples using LAMP formation of DNA concatemers and gold nanoparticle-DNA probe complex

Science.gov (United States)

Wachiralurpan, Sirirat; Sriyapai, Thayat; Areekit, Supatra; Sriyapai, Pichapak; Augkarawaritsawong, Suphitcha; Santiwatanakul, Somchai; Chansiri, Kosum

2018-04-01

ABSTRACT Listeria monocytogenes is a major foodborne pathogen of global health concern. Herein, the rapid diagnosis of L. monocytogenes has been achieved using loop-mediated isothermal amplification (LAMP) based on the phosphatidylcholine-phospholipase C gene (plcB). Colorimetric detection was then performed through the formation of DNA concatemers and a gold nanoparticle/DNA probe complex (GNP/DNA probe). The overall detection process was accomplished within approximately 1 h with no need for complicated equipment. The limits of detection for L. monocytogenes in the forms of purified genomic DNA and pure culture were 800 fg and 2.82 CFU mL-1, respectively. No cross reactions were observed from closely related bacteria species. The LAMP-GNP/DNA probe assay was applied to the detection of 200 raw chicken meat samples and compared to routine standard methods. The data revealed that the specificity, sensitivity and accuracy were 100%, 90.20% and 97.50%, respectively. The present assay was 100% in conformity with LAMP-agarose gel electrophoresis assay. Five samples that were negative by both assays appeared to have the pathogen at below the level of detection. The assay can be applied as a rapid direct screening method for L. monocytogenes.

Selective detection of labeled DNA using an air-clad photonic crystal fiber

DEFF Research Database (Denmark)

Jensen, Jesper Bo Damm; Hoiby, P.E.; Pedersen, L.H.

2004-01-01

Demonstration of selective detection of fluorophore labeled DNA by hybridization inside the air holes of a photonic crystal fiber A laser exposes the fiber from the side and the emitted fluorescence tunnels into the core.......Demonstration of selective detection of fluorophore labeled DNA by hybridization inside the air holes of a photonic crystal fiber A laser exposes the fiber from the side and the emitted fluorescence tunnels into the core....

Quenching the chemiluminescence of acridinium ester by graphene oxide for label-free and homogeneous DNA detection.

Science.gov (United States)

He, Yi; Huang, Guangming; Cui, Hua

2013-11-13

It was found that graphene oxide (GO) could effectively quench the chemiluminescence (CL) emission from a acridinium ester (AE)-hydrogen peroxide system. By taking advantage of this quenching effect, as a proof of concept, a label-free and homogeneous DNA assay was developed for the detection of Mycobacterium tuberculosis DNA. In the absence of target DNA, both probe DNA and AE were absorbed on the surface of GO, producing a weak CL emission owing to the CL quenching effect of GO. However, in the presence of target DNA, a double-stranded structure of DNA was generated, leading to the release of the oligonucleotide from the GO surface. AE favors binding with double-stranded DNA, which will be released from the GO surface; thus, the quenching effect of GO will be no longer effective and a strong CL signal can be observed. This assay can detect M. tuberculosis DNA with a detection limit of 0.65 nM. This sensitivity is lower than that of previously reported electrochemical detection.

Revealing the role of predator interference in a predator-prey system with disease in prey population

DEFF Research Database (Denmark)

Chakraborty, Subhendu; Kooi, B.W.; Biswas, B.

2015-01-01

Predation on a species subjected to an infectious disease can affect both the infection level and the population dynamics. There is an ongoing debate about the act of managing disease in natural populations through predation. Recent theoretical and empirical evidence shows that predation...... on infected populations can have both positive and negative influences on disease in prey populations. Here, we present a predator-prey system where the prey population is subjected to an infectious disease to explore the impact of predator on disease dynamics. Specifically, we investigate how...... on the strength of interference among predators, predators enhance or control disease outbreaks and population persistence. Moreover, the presence of multistable regimes makes the system very sensitive to perturbations and facilitates a number of regime shifts. Since, the habitat structure and the choice...

Detection of mitochondrial DNA with the compact bead array sensor system (cBASS)

Science.gov (United States)

Mulvaney, Shawn P.; Ibe, Carol N.; Caldwell, Jane M.; Levine, Jay F.; Whitman, Lloyd J.; Tamanaha, Cy R.

2009-02-01

Enteric pathogens are a significant contaminant in surface waters used for recreation, fish and shellfish harvesting, crop irrigation, and human consumption. The need for water monitoring becomes more pronounced when industrial, agricultural, and residential lands are found in close proximity. Fecal contamination is particularly problematic and identification of the pollution source essential to remediation efforts. Standard monitoring for fecal contamination relies on indicator organisms, but the technique is too broad to identify the source of contamination. Instead, real-time PCR of mitochondrial DNA (mtDNA) is an emerging method for identification of the contamination source. Presented herein, we evaluate an alternative technology, the compact Bead Array Sensor System (cBASS®) and its assay approach Fluidic Force Discrimination (FFD), for the detection of mtDNA. Previously, we achieved multiplexed, attomolar detection of toxins and femtomolar detection of nucleic acids in minutes with FFD assays. More importantly, FFD assays are compatible with a variety of complex matrices and therefore potentially applicable for samples where the matrix would interfere with PCR amplification. We have designed a triplex assay for the NADH gene found in human, swine, and bovine mtDNA and demonstrated the specific detection of human mtDNA spiked into a waste water sample.

The use of gold nanoparticle aggregation for DNA computing and logic-based biomolecular detection

International Nuclear Information System (INIS)

Lee, In-Hee; Yang, Kyung-Ae; Zhang, Byoung-Tak; Lee, Ji-Hoon; Park, Ji-Yoon; Chai, Young Gyu; Lee, Jae-Hoon

2008-01-01

The use of DNA molecules as a physical computational material has attracted much interest, especially in the area of DNA computing. DNAs are also useful for logical control and analysis of biological systems if efficient visualization methods are available. Here we present a quick and simple visualization technique that displays the results of the DNA computing process based on a colorimetric change induced by gold nanoparticle aggregation, and we apply it to the logic-based detection of biomolecules. Our results demonstrate its effectiveness in both DNA-based logical computation and logic-based biomolecular detection

Ratiometric FRET-based detection of DNA and micro-RNA in solution

International Nuclear Information System (INIS)

Matveeva, Evgenia G.; Gryczynski, Zygmunt; Stewart, Donald R.; Gryczynski, Ignacy

2009-01-01

A ratiometric method for detecting DNA oligomers in bulk solution based on Foerster resonance energy transfer (FRET) is described. The two fluorescence signals (green and red), originating from Cy3 (donor, green) and Cy5 (acceptor, red) labels, are simultaneously detected from the pre-hybridized Cy3oligomerY:Cy5oligomerX system. The ratio of red to green intensities is sensitive to the presence of the single-stranded complimentary oligomer, which replaces single-stranded Cy3oligomerY in the donor:acceptor complex and perturbs the FRET. The detection scheme is generally applicable to the detection of DNA and RNA, and particularly micro-RNA. The proposed method is applicable to various double-stranded various lengths targets (manipulation of the sample preparation conditions, such as temperature, incubation time, denaturizing agent, may be needed).

Enhanced sensing of dengue virus DNA detection using O_2 plasma treated-silicon nanowire based electrical biosensor

International Nuclear Information System (INIS)

Rahman, S.F.A.; Yusof, N.A.; Hashim, U.; Hushiarian, R.; Nuzaihan, M.N.M.; Hamidon, M.N.; Zawawi, R.M.; Fathil, M.F.M.

2016-01-01

Dengue Virus (DENV) has become one of the most serious arthropod-borne viral diseases, causing death globally. The existing methods for DENV detection suffer from the late stage treatment due to antibodies-based detection which is feasible only after five days following the onset of the illness. Here, we demonstrated the highly effective molecular electronic based detection utilizing silicon nanowire (SiNW) integrated with standard complementary metal-oxide-semiconductor (CMOS) process as a sensing device for detecting deoxyribonucleic acid (DNA) related to DENV in an early stage diagnosis. To transform the fabricated devices as a functional sensing element, three-step procedure consist of SiNW surface modification, DNA immobilization and DNA hybridization were employed. The detection principle works by detecting the changes in current of SiNW which bridge the source and drain terminal to sense the immobilization of probe DNA and their hybridization with target DNA. The oxygen (O_2) plasma was proposed as an effective strategy for increasing the binding amounts of target DNA by modified the SiNW surface. It was found that the detection limit of the optimized O_2 plasma treated-SiNW device could be reduced to 1.985 × 10"−"1"4 M with a linear detection range of the sequence-specific DNA from 1.0 × 10"−"9 M to 1.0 × 10"−"1"3 M. In addition, the developed biosensor device was able to discriminate between complementary, single mismatch and non-complementary DNA sequences. This highly sensitive assay was then applied to the detection of reverse transcription-polymerase chain reaction (RT-PCR) product of DENV-DNA, making it as a potential method for disease diagnosis through electrical biosensor. - Highlights: • Molecular electronic detection of Dengue Virus (DENV) DNA using SiNW biosensor is presented. • Oxygen plasma surface treatment as an enhancer technique for device sensitivity is highlighted. • The limit of detection (LoD) as low as 1.985�

DNA of Dientamoeba fragilis detected within surface-sterilized eggs of Enterobius vermicularis.

Science.gov (United States)

Röser, Dennis; Nejsum, Peter; Carlsgart, Anne Josefine; Nielsen, Henrik Vedel; Stensvold, Christen Rune

2013-01-01

With no evidence of a cyst stage, the mode of transmission of Dientamoeba fragilis, an intestinal protozoon of common occurrence and suggested pathogenicity, is incompletely known. Numerous studies have suggested that eggs of intestinal nematodes, primarily Enterobius vermicularis (pinworm), can serve as vectors for D. fragilis, although attempts to culture D. fragilis from pinworm eggs have been unsuccessful and data from epidemiological studies on D. fragilis/pinworm co-infection have been conflicting. The aim of this study was to investigate whether we could detect D. fragilis DNA from pinworm eggs collected from routine diagnostic samples (cellophane tape) and surface-sterilised by hypochlorite. DNA was extracted from individual eggs and tested by PCR using D. fragilis- and E. vermicularis-specific primers; amplicons were sequenced for confirmation. In cellophane tape samples from 64 patients with unknown D. fragilis status we detected D. fragilis DNA in 12/238 (5%) eggs, and in a patient known to harbour D. fragilis we detected D. fragilis DNA in 39/99 (39%) eggs. The finding of D. fragilis DNA within eggs of E. vermicularis strongly supports the hypothesis of D. fragilis-transmission by pinworm and has implications for antimicrobial intervention as well as control and public health measures. Copyright © 2012 Elsevier Inc. All rights reserved.

Echolocating bats use a nearly time-optimal strategy to intercept prey.

Directory of Open Access Journals (Sweden)

Kaushik Ghose

2006-05-01

Full Text Available Acquisition of food in many animal species depends on the pursuit and capture of moving prey. Among modern humans, the pursuit and interception of moving targets plays a central role in a variety of sports, such as tennis, football, Frisbee, and baseball. Studies of target pursuit in animals, ranging from dragonflies to fish and dogs to humans, have suggested that they all use a constant bearing (CB strategy to pursue prey or other moving targets. CB is best known as the interception strategy employed by baseball outfielders to catch ballistic fly balls. CB is a time-optimal solution to catch targets moving along a straight line, or in a predictable fashion--such as a ballistic baseball, or a piece of food sinking in water. Many animals, however, have to capture prey that may make evasive and unpredictable maneuvers. Is CB an optimum solution to pursuing erratically moving targets? Do animals faced with such erratic prey also use CB? In this paper, we address these questions by studying prey capture in an insectivorous echolocating bat. Echolocating bats rely on sonar to pursue and capture flying insects. The bat's prey may emerge from foliage for a brief time, fly in erratic three-dimensional paths before returning to cover. Bats typically take less than one second to detect, localize and capture such insects. We used high speed stereo infra-red videography to study the three dimensional flight paths of the big brown bat, Eptesicus fuscus, as it chased erratically moving insects in a dark laboratory flight room. We quantified the bat's complex pursuit trajectories using a simple delay differential equation. Our analysis of the pursuit trajectories suggests that bats use a constant absolute target direction strategy during pursuit. We show mathematically that, unlike CB, this approach minimizes the time it takes for a pursuer to intercept an unpredictably moving target. Interestingly, the bat's behavior is similar to the interception strategy

Echolocating bats use a nearly time-optimal strategy to intercept prey.

Science.gov (United States)

Ghose, Kaushik; Horiuchi, Timothy K; Krishnaprasad, P S; Moss, Cynthia F

2006-05-01

Acquisition of food in many animal species depends on the pursuit and capture of moving prey. Among modern humans, the pursuit and interception of moving targets plays a central role in a variety of sports, such as tennis, football, Frisbee, and baseball. Studies of target pursuit in animals, ranging from dragonflies to fish and dogs to humans, have suggested that they all use a constant bearing (CB) strategy to pursue prey or other moving targets. CB is best known as the interception strategy employed by baseball outfielders to catch ballistic fly balls. CB is a time-optimal solution to catch targets moving along a straight line, or in a predictable fashion--such as a ballistic baseball, or a piece of food sinking in water. Many animals, however, have to capture prey that may make evasive and unpredictable maneuvers. Is CB an optimum solution to pursuing erratically moving targets? Do animals faced with such erratic prey also use CB? In this paper, we address these questions by studying prey capture in an insectivorous echolocating bat. Echolocating bats rely on sonar to pursue and capture flying insects. The bat's prey may emerge from foliage for a brief time, fly in erratic three-dimensional paths before returning to cover. Bats typically take less than one second to detect, localize and capture such insects. We used high speed stereo infra-red videography to study the three dimensional flight paths of the big brown bat, Eptesicus fuscus, as it chased erratically moving insects in a dark laboratory flight room. We quantified the bat's complex pursuit trajectories using a simple delay differential equation. Our analysis of the pursuit trajectories suggests that bats use a constant absolute target direction strategy during pursuit. We show mathematically that, unlike CB, this approach minimizes the time it takes for a pursuer to intercept an unpredictably moving target. Interestingly, the bat's behavior is similar to the interception strategy implemented in some

DNA-mediated strand displacement facilitates sensitive electronic detection of antibodies in human serums.

Science.gov (United States)

Dou, Baoting; Yang, Jianmei; Shi, Kai; Yuan, Ruo; Xiang, Yun

2016-09-15

We describe here the development of a sensitive and convenient electronic sensor for the detection of antibodies in human serums. The sensor is constructed by self-assembly formation of a mixed monolayer containing the small molecule epitope conjugated double stranded DNA probes on gold electrode. The target antibody binds the epitope on the dsDNA probe and lowers the melting temperature of the duplex, which facilitates the displacement of the antibody-linked strand of the duplex probe by an invading methylene blue-tagged single stranded DNA (MB-ssDNA) through the strand displacement reaction and leads to the capture of many MB-ssDNA on the sensor surface. Subsequent electrochemical oxidation of the methylene blue labels results in amplified current response for sensitive monitoring of the antibodies. The antibody assay conditions are optimized and the sensor exhibits a linear range between 1.0 and 25.0nM with a detection limit of 0.67nM for the target antibody. The sensor is also selective and can be employed to detect the target antibodies in human serum samples. With the advantages of using small molecule epitope as the antibody recognition element over traditional antigen, the versatile manipulability of the DNA probes and the unique properties of the electrochemical transduction technique, the developed sensor thus hold great potential for simple and sensitive detection of different antibodies and other proteins in real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

AN IMAGE-ANALYSIS TECHNIQUE FOR DETECTION OF RADIATION-INDUCED DNA FRAGMENTATION AFTER CHEF ELECTROPHORESIS

NARCIS (Netherlands)

ROSEMANN, M; KANON, B; KONINGS, AWT; KAMPINGA, HH

CHEF-electrophoresis was used as a technique to detect radiation-induced DNA breakage with special emphasis to biological relevant X-ray doses (0-10 Gy). Fluorescence detection of DNA-fragments using a sensitive image analysis system was directly compared with conventional scintillation counting of

Phosphorescent quantum dots/doxorubicin nanohybrids based on photoinduced electron transfer for detection of DNA.

Science.gov (United States)

Miao, Yanming; Zhang, Zhifeng; Gong, Yan; Yan, Guiqin

2014-09-15

MPA-capped Mn-doped ZnS QDs/DXR nanohybrids (MPA: 3-mercaptopropionic acid; QDs: quantum dots; DXR: cetyltrimethyl ammonium bromide) were constructed via photoinduced electron transfer (PIET) and then used as a room-temperature phosphorescence (RTP) probe for detection of DNA. DXR as a quencher will quench the RTP of Mn-doped ZnS QDs via PIET, thereby forming Mn-doped ZnS QDs/DXR nanohybrids and storing RTP. With the addition of DNA, it will be inserted into DXR and thus DXR will be competitively desorbed from the surface of Mn-doped ZnS QDs, thereby releasing the RTP of Mn-doped ZnS QDs. Based on this, a new method for DNA detection was built. The sensor for DNA has a detection limit of 0.039 mg L(-1) and a linear range from 0.1 to 14 mg L(-1). The present QDs-based RTP method does not need deoxidants or other inducers as required by conventional RTP detection methods, and avoids interference from autofluorescence and the scattering light of the matrix that are encountered in spectrofluorometry. Therefore, this method can be used to detect the DNA content in body fluid. Copyright © 2014 Elsevier B.V. All rights reserved.

Branched-DNA signal amplification combined with paper chromatography hybridization assay and used in hepatitis B virus DNA detection

International Nuclear Information System (INIS)

Fu, F.Z.; Liu, L.X.; Wang, W.Q.; Sun, S. H.; Liu, L.B.

2002-01-01

Nucleic acids detection method is vital to the clinical pathogen diagnosis. The established method can be classified into target direct amplification and signal amplification format according to the target DNA or RNA being directly amplified or not. Those methods have advantages and disadvantages respectively in the clinical application. In the United States of American, branched-DNA as a strong signal amplifier is broadly used in the quantification of the nucleic acids. To gain satisfied sensitivity, some expensive label molecular and instruments should be adopted. Personnel should be special trained to perform. Hence, those can't be widely carried out in the Third World. To avoid those disadvantages, we used the branched-DNA amplifier in the paper chromatography hybridization assay. Methods: Branched DNA signal amplifier and series of probes complementary to the nucleic acid sequence of hepatitis B virus (HBV) have been synthesized. HBV-DNA or it's capture probe were immobilized on the high flow nitrocellulose strip. Having loaded at one end of the strip in turn, probes or HBV-DNA in the hybridization solution migrate to the opposite end of the strip by capillary forces and hybridizes to the immobilized DNA. The branched-DNA signal amplifier and probe labeled with biotin or 32P were then loaded. Through streptavidin-alkaline phosphatase (SA-AP) conjugate and NBT/BCIP ( the specific chromogenic substrate of AP) or autoradiography, the result can be visualized by color reaction or image production on the X-ray film. Results: The sensitivity of this HBV-DNA detection method used probe labeled with biotin and 32P are 1ng and 10pg. The method using the probe labeled with biotin is simple and rapid (2h) without depending on special instruments, it also avoids the pollution of EtBr which can lead to tumor. And the method using the probe labeled with 32P is simple and sensitive, with the exception of long time autoradiography and the inconvenient isotopic disposal

Rapid Detection of Cell-Free Mycobacterium tuberculosis DNA in Tuberculous Pleural Effusion.

Science.gov (United States)

Che, Nanying; Yang, Xinting; Liu, Zichen; Li, Kun; Chen, Xiaoyou

2017-05-01

Tuberculous pleurisy is one of the most common types of extrapulmonary tuberculosis, but its diagnosis remains difficult. In this study, we report for the first time on the detection of cell-free Mycobacterium tuberculosis DNA in pleural effusion and an evaluation of a newly developed molecular assay for the detection of cell-free Mycobacterium tuberculosis DNA. A total of 78 patients with pleural effusion, 60 patients with tuberculous pleurisy, and 18 patients with alternative diseases were included in this study. Mycobacterial culture, the Xpert MTB/RIF assay, the adenosine deaminase assay, the T-SPOT.TB assay, and the cell-free Mycobacterium tuberculosis DNA assay were performed on all the pleural effusion samples. The cell-free Mycobacterium tuberculosis DNA assay and adenosine deaminase assay showed significantly higher sensitivities of 75.0% and 68.3%, respectively, than mycobacterial culture and the Xpert MTB/RIF assay, which had sensitivities of 26.7% and 20.0%, respectively ( P pleural effusion showed the highest sensitivity of 95.0% but the lowest specificity of 38.9%. The cell-free Mycobacterium tuberculosis DNA assay detected as few as 1.25 copies of IS 6110 per ml of pleural effusion and showed good accordance of the results between repeated tests ( r = 0.978, P = 2.84 × 10 -10 ). These data suggest that the cell-free Mycobacterium tuberculosis DNA assay is a rapid and accurate molecular test which provides direct evidence of Mycobacterium tuberculosis etiology. Copyright © 2017 American Society for Microbiology.

Improving Probe Immobilization for Label-Free Capacitive Detection of DNA Hybridization on Microfabricated Gold Electrodes

Directory of Open Access Journals (Sweden)

Sandro Carrara

2008-02-01

Full Text Available Alternative approaches to labeled optical detection for DNA arrays are actively investigated for low-cost point-of-care applications. In this domain, label-free capacitive detection is one of the most intensely studied techniques. It is based on the idea to detect the Helmholtz ion layer displacements when molecular recognition occurs at the electrodes/solution interface. The sensing layer is usually prepared by using thiols terminated DNA single-strength oligonucleotide probes on top of the sensor electrodes. However, published data shows evident time drift, which greatly complicates signal conditioning and processing and ultimately increases the uncertainty in DNA recognition sensing. The aim of this work is to show that newly developed ethylene-glycol functionalized alkanethiols greatly reduce time drift, thereby significantly improving capacitance based label-free detection of DNA.

Detection of DNA damage in cells exposed to ionizing radiation by use of antisingle-stranded-DNA monoclonal antibody

International Nuclear Information System (INIS)

Schans, G.P. van der; Loon, A.A.W.M. van; Groenendijk, R.H.; Baan, R.A.

1989-03-01

An immunochemical method has been developed for quantitative detection of DNA damage in mammalian cells. The method is based on the binding of a monoclonal antibody to single-stranded DNA. The clone producing this antibody, D1B, was obtained as a by-product from fusion of mouse myeloma cells with spleen cells isolated from a mouse immunized with chemically modified DNA. The technique is based upon the determination of the percentage single-strandedness resulting from the partial umwinding of cellular DNA under alkaline conditions, a time-dependent process. Single-strand and double-strand DNA breaks, or lesions converted into such breaks in alkaline medium, form initiation points for the unwinding. The extent of unwinding under controlled conditions is a measure, therefore, of the amount of such sites. The method is rapid, does not require radioactive labelling of DNA or physical separation of single- from double-stranded molecules, is sufficiently sensitive to detect damage induced by 1 Gu of ionizing radiation and needs only small amounts of cells. The usefulness of the technique was demonstrated in a study on the induction of damage and its repair in unlabelled cultured Chinese hamster cells and in DNA-containing cells of human blood, both after exposure to 60 Co-γ-rays, and in white blood cells and bone marrow cells of X-irradiated mice. A dose-related degree of unwinding was observed and repair could be observed up to 60 min after irradiation. (author). 19 refs.; 3 figs.; 1 tab

DNA based methods used for characterization and detection of food ...

African Journals Online (AJOL)

Detection of food borne pathogen is of outmost importance in the food industries and related agencies. For the last few decades conventional methods were used to detect food borne pathogens based on phenotypic characters. At the advent of complementary base pairing and amplification of DNA, the diagnosis of food ...

A novel input-parasitic compensation technique for a nanopore-based CMOS DNA detection sensor

Science.gov (United States)

Kim, Jungsuk

2016-12-01

This paper presents a novel input-parasitic compensation (IPC) technique for a nanopore-based complementary metal-oxide-semiconductor (CMOS) DNA detection sensor. A resistive-feedback transimpedance amplifier is typically adopted as the headstage of a DNA detection sensor to amplify the minute ionic currents generated from a nanopore and convert them to a readable voltage range for digitization. But, parasitic capacitances arising from the headstage input and the nanopore often cause headstage saturation during nanopore sensing, thereby resulting in significant DNA data loss. To compensate for the unwanted saturation, in this work, we propose an area-efficient and automated IPC technique, customized for a low-noise DNA detection sensor, fabricated using a 0.35- μm CMOS process; we demonstrated this prototype in a benchtop test using an α-hemolysin ( α-HL) protein nanopore.

Loggerhead turtles (Caretta caretta use vision to forage on gelatinous prey in mid-water.

Directory of Open Access Journals (Sweden)

Tomoko Narazaki

Full Text Available Identifying characteristics of foraging activity is fundamental to understanding an animals' lifestyle and foraging ecology. Despite its importance, monitoring the foraging activities of marine animals is difficult because direct observation is rarely possible. In this study, we use an animal-borne imaging system and three-dimensional data logger simultaneously to observe the foraging behaviour of large juvenile and adult sized loggerhead turtles (Caretta caretta in their natural environment. Video recordings showed that the turtles foraged on gelatinous prey while swimming in mid-water (i.e., defined as epipelagic water column deeper than 1 m in this study. By linking video and 3D data, we found that mid-water foraging events share the common feature of a marked deceleration phase associated with the capture and handling of the sluggish prey. Analysis of high-resolution 3D movements during mid-water foraging events, including presumptive events extracted from 3D data using deceleration in swim speed as a proxy for foraging (detection rate = 0.67, showed that turtles swam straight toward prey in 171 events (i.e., turning point absent but made a single turn toward the prey an average of 5.7±6.0 m before reaching the prey in 229 events (i.e., turning point present. Foraging events with a turning point tended to occur during the daytime, suggesting that turtles primarily used visual cues to locate prey. In addition, an incident of a turtle encountering a plastic bag while swimming in mid-water was recorded. The fact that the turtle's movements while approaching the plastic bag were analogous to those of a true foraging event, having a turning point and deceleration phase, also support the use of vision in mid-water foraging. Our study shows that integrated video and high-resolution 3D data analysis provides unique opportunities to understand foraging behaviours in the context of the sensory ecology involved in prey location.

DNA extraction methods for detecting genetically modified foods: A comparative study.

Science.gov (United States)

Elsanhoty, Rafaat M; Ramadan, Mohamed Fawzy; Jany, Klaus Dieter

2011-06-15

The work presented in this manuscript was achieved to compare six different methods for extracting DNA from raw maize and its derived products. The methods that gave higher yield and quality of DNA were chosen to detect the genetic modification in the samples collected from the Egyptian market. The different methods used were evaluated for extracting DNA from maize kernels (without treatment), maize flour (mechanical treatment), canned maize (sweet corn), frozen maize (sweet corn), maize starch, extruded maize, popcorn, corn flacks, maize snacks, and bread made from corn flour (mechanical and thermal treatments). The quality and quantity of the DNA extracted from the standards, containing known percentages of GMO material and from the different food products were evaluated. For qualitative detection of the GMO varieties in foods, the GMOScreen 35S/NOS test kit was used, to screen the genetic modification in the samples. The positive samples for the 35S promoter and/or the NOS terminator were identified by the standard methods adopted by EU. All of the used methods extracted yielded good DNA quality. However, we noted that the purest DNA extract were obtained using the DNA extraction kit (Roche) and this generally was the best method for extracting DNA from most of the maize-derived foods. We have noted that the yield of DNA extracted from maize-derived foods was generally lower in the processed products. The results indicated that 17 samples were positive for the presence of 35S promoter, while 34% from the samples were positive for the genetically modified maize line Bt-176. Copyright © 2010 Elsevier Ltd. All rights reserved.

Phosphorescent quantum dots/ethidium bromide nanohybrids based on photoinduced electron transfer for DNA detection.

Science.gov (United States)

Bi, Lin; Yu, Yuan-Hua

2015-04-05

Mercaptopropionic acid-capped Mn-doped ZnS quantum dots/ethidium bromide (EB) nanohybrids were constructed for photoinduced electron transfer (PIET) and then used as a room-temperature phosphorescence (RTP) probe for DNA detection. EB could quench the RTP of Mn-doped ZnS QDs by PIET, thereby forming Mn-doped ZnS QDs/EB nanohybrids and storing RTP. Meanwhile, EB could be inserted into DNA and EB could be competitively desorbed from the surface of Mn-doped ZnS QDs by DNA, thereby releasing the RTP of Mn-doped ZnS QDs. Based on this mechanism, a RTP sensor for DNA detection was developed. Under optimal conditions, the detection limit for DNA was 0.045 mg L(-1), the relative standard deviation was 1.7%, and the method linear ranged from 0.2 to 20 mg L(-1). The proposed method was applied to biological fluids, in which satisfactory results were obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

Lévy flight and Brownian search patterns of a free-ranging predator reflect different prey field characteristics.

Science.gov (United States)

Sims, David W; Humphries, Nicolas E; Bradford, Russell W; Bruce, Barry D

2012-03-01

1. Search processes play an important role in physical, chemical and biological systems. In animal foraging, the search strategy predators should use to search optimally for prey is an enduring question. Some models demonstrate that when prey is sparsely distributed, an optimal search pattern is a specialised random walk known as a Lévy flight, whereas when prey is abundant, simple Brownian motion is sufficiently efficient. These predictions form part of what has been termed the Lévy flight foraging hypothesis (LFF) which states that as Lévy flights optimise random searches, movements approximated by optimal Lévy flights may have naturally evolved in organisms to enhance encounters with targets (e.g. prey) when knowledge of their locations is incomplete. 2. Whether free-ranging predators exhibit the movement patterns predicted in the LFF hypothesis in response to known prey types and distributions, however, has not been determined. We tested this using vertical and horizontal movement data from electronic tagging of an apex predator, the great white shark Carcharodon carcharias, across widely differing habitats reflecting different prey types. 3. Individual white sharks exhibited movement patterns that predicted well the prey types expected under the LFF hypothesis. Shark movements were best approximated by Brownian motion when hunting near abundant, predictable sources of prey (e.g. seal colonies, fish aggregations), whereas movements approximating truncated Lévy flights were present when searching for sparsely distributed or potentially difficult-to-detect prey in oceanic or shelf environments, respectively. 4. That movement patterns approximated by truncated Lévy flights and Brownian behaviour were present in the predicted prey fields indicates search strategies adopted by white sharks appear to be the most efficient ones for encountering prey in the habitats where such patterns are observed. This suggests that C. carcharias appears capable of exhibiting

Comparative growth and development of spiders reared on live and dead prey.

Science.gov (United States)

Peng, Yu; Zhang, Fan; Gui, Shaolan; Qiao, Huping; Hose, Grant C

2013-01-01

Scavenging (feeding on dead prey) has been demonstrated across a number of spider families, yet the implications of feeding on dead prey for the growth and development of individuals and population is unknown. In this study we compare the growth, development, and predatory activity of two species of spiders that were fed on live and dead prey. Pardosa astrigera (Lycosidae) and Hylyphantes graminicola (Lyniphiidae) were fed live or dead fruit flies, Drosophila melanogaster. The survival of P. astrigera and H. graminicola was not affected by prey type. The duration of late instars of P. astrigera fed dead prey were longer and mature spiders had less protein content than those fed live prey, whereas there were no differences in the rate of H. graminicola development, but the mass of mature spiders fed dead prey was greater than those fed live prey. Predation rates by P. astrigera did not differ between the two prey types, but H. graminicola had a higher rate of predation on dead than alive prey, presumably because the dead flies were easier to catch and handle. Overall, the growth, development and reproduction of H. graminicola reared with dead flies was better than those reared on live flies, yet for the larger P. astrigera, dead prey may suit smaller instars but mature spiders may be best maintained with live prey. We have clearly demonstrated that dead prey may be suitable for rearing spiders, although the success of the spiders fed such prey appears size- and species specific.

The hydrodynamics of predator-prey interactions in zebrafish

Science.gov (United States)

McHenry, Matthew; Soto, Alberto; Carrillo, Andres; Byron, Margaret

2017-11-01

Hydrodynamics govern the behavior of fishes when they operate as predators or prey. In addition to the role of fluid forces in propulsion, fishes relay on flow stimuli to sense a predatory threat and to localize palatable prey. We have performed a series of experiments on zebrafish (Danio rerio) that aim to resolve the major factors that determine whether prey survive an encounter with a predator. Zebrafish serve as a model system in this pursuit because the adults prey on larvae of the same species and the larvae are often successful in evading the attacks of the adults. We use a combination of theoretical and experimental approaches to resolve the behavioral algorithms and kinematics that determined the outcome of these interactions. In this context, the hydrodynamics of intermediate Reynolds numbers largely determines the range of flow stimuli and the limits to locomotor performance at dictate prey survival. These principles have the potential to apply to a broad diversity of fishes and other aquatic animals. ONR: N00014-15-1-2249.

One-pot synthesis of strongly fluorescent DNA-CuInS2 quantum dots for label-free and ultrasensitive detection of anthrax lethal factor DNA

International Nuclear Information System (INIS)

Liu, Ziping; Su, Xingguang

2016-01-01

Herein, high quality DNA-CuInS 2 QDs are facilely synthesized through a one-pot hydrothermal method with fluorescence quantum yield as high as 23.4%, and the strongly fluorescent DNA-CuInS 2 QDs have been utilized as a novel fluorescent biosensor for label-free and ultrasensitive detection of anthrax lethal factor DNA. L-Cysteine (L-Cys) and a specific-sequence DNA are used as co-ligands to stabilize the CuInS 2 QDs. The specific-sequence DNA consists of two domains: phosphorothiolates domain (sulfur-containing variants of the usual phosphodiester backbone) controls the nanocrystal passivation and serves as a ligand, and the functional domain (non-phosphorothioates) controls the biorecognition. The as-prepared DNA-CuInS 2 QDs have high stability, good water-solubility and low toxicity. Under the optimized conditions, a linear correlation was established between the fluorescence intensity ratio I/I 0 (I 0 is the original fluorescence intensity of DNA-CuInS 2 QDs, and I is the fluorescence intensity of DNA-CuInS 2 QDs/GO with the addition of various concentrations of anthrax lethal factor DNA) and the concentration of anthrax lethal factor DNA in the range of 0.029–0.733 nmol L −1 with a detection limit of 0.013 nmol L −1 . The proposed method has been successfully applied to the determination of anthrax lethal factor DNA sequence in human serum samples with satisfactory results. Because of low toxicity and fine biocompatibility, DNA-CuInS 2 QDs also hold potential applications in bioimaging. - Highlights: • Strongly fluorescent DNA-QDs were successfully prepared by a one-pot hydrothermal method with quantum yield up to 23.4%. • A biosensor for label-free detection of anthrax lethal factor DNA was established based on the as-prepared DNA-QDs. • The DNA sensor took advantage of the feature that ssDNA binds to GO with significantly higher affinity than dsDNA. • Good sensitivity and selectivity were obtained. • This method was utilized to detect

Label-free, electrochemical detection of methicillin-resistant staphylococcus aureus DNA with reduced graphene oxide-modified electrodes

KAUST Repository

Wang, Zhijuan

2011-05-01

Reduced graphene oxide (rGO)-modified glassy carbon electrode is used to detect the methicillin-resistant Staphylococcus aureus (MRSA) DNA by using electrochemical impedance spectroscopy. Our experiments confirm that ssDNA, before and after hybridization with target DNA, are successfully anchored on the rGO surface. After the probe DNA, pre-adsorbed on rGO electrode, hybridizes with target DNA, the measured impedance increases dramatically. It provides a new method to detect DNA with high sensitivity (10-13M, i.e., 100 fM) and selectivity. © 2011 Elsevier B.V.

DNA-Based Nanobiosensors as an Emerging Platform for Detection of Disease

Directory of Open Access Journals (Sweden)

Khalid M. Abu-Salah

2015-06-01

Full Text Available Detection of disease at an early stage is one of the biggest challenges in medicine. Different disciplines of science are working together in this regard. The goal of nanodiagnostics is to provide more accurate tools for earlier diagnosis, to reduce cost and to simplify healthcare delivery of effective and personalized medicine, especially with regard to chronic diseases (e.g., diabetes and cardiovascular diseases that have high healthcare costs. Up-to-date results suggest that DNA-based nanobiosensors could be used effectively to provide simple, fast, cost-effective, sensitive and specific detection of some genetic, cancer, and infectious diseases. In addition, they could potentially be used as a platform to detect immunodeficiency, and neurological and other diseases. This review examines different types of DNA-based nanobiosensors, the basic principles upon which they are based and their advantages and potential in diagnosis of acute and chronic diseases. We discuss recent trends and applications of new strategies for DNA-based nanobiosensors, and emphasize the challenges in translating basic research to the clinical laboratory.

Ehrlichia canis morulae and DNA detection in whole blood and spleen aspiration samples.

Science.gov (United States)

Faria, Joice Lara Maia; Dagnone, Ana Sílvia; Munhoz, Thiago Demarchi; João, Carolina Franchi; Pereira, Wanderson Adriano Biscola; Machado, Rosângela Zacarias; Tinucci-Costa, Mirela

2010-01-01

The aim of this study was to compare the detection of Ehrlichia canis morulae and DNA by nPCR in whole blood and spleen aspiration. The sample included 40 dogs showing thrombocytopenia associated to clinical signs suggestive of canine ehrlichiosis. Morulae detection showed that in 35 of the dogs studied, 17 had morulae in spleen tissue, and two in buffy coat smears. E. canis DNA was detected in 29/40 blood samples. We verified that morulae detection is more efficient in cytological preparations from spleen aspiration. On the other hand, nPCR on spleen and blood samples were equally efficient for disease diagnosis.

Molecular beacon-based real-time PCR method for detection of porcine DNA in gelatin and gelatin capsules.

Science.gov (United States)

Mohamad, Nurhidayatul Asma; Mustafa, Shuhaimi; Khairil Mokhtar, Nur Fadhilah; El Sheikha, Aly Farag

2018-03-05

The pharmaceutical industry has boosted gelatin consumption worldwide. This is supported by the availability of cost-effective gelatin production from porcine by-products. However, cross-contamination of gelatin materials, where porcine gelatin was unintentionally included in the other animal sources of gelatin, has caused significant concerns about halal authenticity. The real-time polymerase chain reaction (PCR) has enabled a highly specific and sensitive animal species detection method in various food products. Hence, such a technique was employed in the present study to detect and quantify porcine DNA in gelatin using a molecular beacon probe, with differences in performance between mitochondrial (cytochrome b gene) and chromosomal DNA-(MPRE42 repetitive element) based porcine-specific PCR assays being compared. A higher sensitivity was observed in chromosomal DNA (MPRE-PCR assay), where this assay allows the detection of gelatin DNA at amounts as as low as 1 pg, whereas mitochondrial DNA (CBH-PCR assay) can only detect at levels down to 10 pg of gelatin DNA. When an analysis with commercial gelatin and gelatin capsule samples was conducted, the same result was observed, with a significantly more sensitive detection being provided by the repetitive element of chromosomal DNA. The present study has established highly sensitive DNA-based porcine detection systems derived from chromosomal DNA that are feasible for highly processed products such as gelatin and gelatin capsules containing a minute amount of DNA. This sensitive detection method can also be implemented to assist the halal authentication process of various food products available on the market. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.