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Sample records for dna-based diet analysis

  1. Simultaneous DNA-based diet analysis of breeding, non-breeding and chick Adélie penguins.

    PubMed

    McInnes, Julie C; Emmerson, Louise; Southwell, Colin; Faux, Cassandra; Jarman, Simon N

    2016-01-01

    As central place foragers, breeding penguins are restricted in foraging range by the need to return to the colony to feed chicks. Furthermore, breeding birds must balance energetic gain from self-feeding with the costs of returning to provision young. Non-breeding birds, however, are likely to be less restricted in foraging range and lack the high energy demands of provisioning, therefore may consume different prey to breeders. We used DNA dietary analysis to determine whether there was a difference in provisioning and self-feeding diet by identifying prey DNA in scat samples from breeding and chick Adélie penguins at two locations in East Antarctica. We also investigated diet differences between breeders and non-breeders at one site. Although previous work shows changing foraging behaviour between chick provisioning and self-feeding, our results suggest no significant differences in the main prey groups consumed by chicks and breeders at either site or between breeding stages. This may reflect the inability of penguins to selectively forage when provisioning, or resources were sufficient for all foraging needs. Conversely, non-breeders were found to consume different prey groups to breeders, which may reflect less restricted foraging ranges, breeders actively selecting particular prey during breeding or reduced foraging experience of non-breeders. PMID:26909171

  2. Simultaneous DNA-based diet analysis of breeding, non-breeding and chick Adélie penguins

    PubMed Central

    McInnes, Julie C.; Emmerson, Louise; Southwell, Colin; Faux, Cassandra; Jarman, Simon N.

    2016-01-01

    As central place foragers, breeding penguins are restricted in foraging range by the need to return to the colony to feed chicks. Furthermore, breeding birds must balance energetic gain from self-feeding with the costs of returning to provision young. Non-breeding birds, however, are likely to be less restricted in foraging range and lack the high energy demands of provisioning, therefore may consume different prey to breeders. We used DNA dietary analysis to determine whether there was a difference in provisioning and self-feeding diet by identifying prey DNA in scat samples from breeding and chick Adélie penguins at two locations in East Antarctica. We also investigated diet differences between breeders and non-breeders at one site. Although previous work shows changing foraging behaviour between chick provisioning and self-feeding, our results suggest no significant differences in the main prey groups consumed by chicks and breeders at either site or between breeding stages. This may reflect the inability of penguins to selectively forage when provisioning, or resources were sufficient for all foraging needs. Conversely, non-breeders were found to consume different prey groups to breeders, which may reflect less restricted foraging ranges, breeders actively selecting particular prey during breeding or reduced foraging experience of non-breeders. PMID:26909171

  3. Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and DNA-based diet analyses.

    PubMed

    Egeter, Bastian; Bishop, Phillip J; Robertson, Bruce C

    2015-03-01

    Amphibians are currently the most threatened group of vertebrates worldwide, and introduced fauna play a major role in their decline. The control of introduced predators to protect endangered species is often based on predation rates derived from diet studies of predators, but prey detection probabilities using different techniques are variable. We measured the detectability of frogs as prey, using morphological and DNA-based diet analyses, in the stomachs and faeces of four mammal species that have been introduced to many areas of the world. Frogs (Litoria raniformis) were fed to rats (Rattus norvegicus and R. rattus), mice (Mus musculus) and hedgehogs (Erinaceus europaeus). DNA-based analysis outperformed morphological analysis, increasing the prey detection rate from 2% to 70% in stomachs and from 0% to 53% in faeces. In most cases, utilizing either stomachs or faeces did not affect the success of prey DNA detection; however, using faeces extended the detectability half-life from 7 to 21 h. This study is the first to measure prey DNA detection periods in mammalian stomachs, and the first to compare prey DNA detection periods in the stomachs and faeces of vertebrates. The results indicate that DNA-based diet analysis provides a more reliable approach for detecting amphibians as prey and has the potential to be used to estimate the rate of predation by introduced mammals on endangered amphibians. PMID:25052066

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

    USGS Publications Warehouse

    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.

  5. Traditional Mold Analysis Compared to a DNA-based Method of Mold Analysis with Applications in Asthmatics' Homes

    EPA Science Inventory

    Traditional environmental mold analysis is based-on microscopic observations and counting of mold structures collected from the air on a sticky surface or culturing of molds on growth media for identification and quantification. A DNA-based method of mold analysis called mol...

  6. Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis

    PubMed Central

    Ng, Chun Kiat; Miller, Dana; Cao, Bin

    2015-01-01

    Introduction As bioaerosol research attracts increasing attention, there is a need for additional efforts that focus on method development to deal with different environmental samples. Bioaerosol environmental samples typically have very low biomass concentrations in the air, which often leaves researchers with limited options in choosing the downstream analysis steps, especially when culture-independent methods are intended. Objectives This study investigates the impacts of three important factors that can influence the performance of culture-independent DNA-based analysis in dealing with bioaerosol environmental samples engaged in this study. The factors are: 1) enhanced high temperature sonication during DNA extraction; 2) effect of sampling duration on DNA recoverability; and 3) an alternative method for concentrating composite samples. In this study, DNA extracted from samples was analysed using the Qubit fluorometer (for direct total DNA measurement) and quantitative polymerase chain reaction (qPCR). Results and Findings The findings suggest that additional lysis from high temperature sonication is crucial: DNA yields from both high and low biomass samples increased up to 600% when the protocol included 30-min sonication at 65°C. Long air sampling duration on a filter media was shown to have a negative impact on DNA recoverability with up to 98% of DNA lost over a 20-h sampling period. Pooling DNA from separate samples during extraction was proven to be feasible with margins of error below 30%. PMID:26619279

  7. Selective enzymatic cleavage and labeling for sensitive capillary electrophoresis laser-induced fluorescence analysis of oxidized DNA bases.

    PubMed

    Li, Cuiping; Wang, Hailin

    2015-08-01

    Oxidatively generated DNA damage is considered to be a significant contributing factor to cancer, aging, and age-related human diseases. It is important to detect oxidatively generated DNA damage to understand and clinically diagnosis diseases caused by oxidative damage. In this study, using selective enzymatic cleavage and quantum dot (QD) labeling, we developed a novel capillary electrophoresis-laser induced fluorescence method for the sensitive detection of oxidized DNA bases. First, oxidized DNA bases are recognized and removed by one DNA base excision repair glycosylase, leaving apurinic and apyrimidinic sites (AP sites) at the oxidized positions. The AP sites are further excised by the AP nicking activity of the chosen glycosylase, generating a nucleotide gap with 5'- and 3'- phosphate groups. After dephosphorylation with one alkaline phosphatase, a biotinylated ddNTP is introduced into the nucleotide space within the DNA strand by DNA polymerase I. The biotin-tagged DNA is further labeled with a QD-streptavidin conjugate via non-covalent interactions. The DNA-bound QD is well-separated from excess DNA-unbound QD by highly efficient capillary electrophoresis and is sensitively detected by online coupled laser-induced fluorescence analysis. Using this method, we can assess the trace levels of oxidized DNA bases induced by the Fenton reaction and UV irradiation. Interestingly, the use of the formamidopyrimidine glycosylase (FPG) protein and endonuclease VIII enables the detection of oxidized purine and pyrimidine bases, respectively. Using the synthesized standard DNA, the approach has low limits of detection of 1.1×10(-19)mol in mass and 2.9pM in concentration. PMID:26105778

  8. Detection of Human Sewage in Urban Stormwater Using DNA Based Methods and Stable Isotope Analysis

    NASA Astrophysics Data System (ADS)

    McLellan, S. L.; Malet, N.; Sauer, E.; Mueller-Spitz, S.; Borchardt, M.

    2008-12-01

    related to the mixed organic matter sources in polluted stormwater runoff, and that this signal will distinct from untreated sanitary sewage. Stable isotope signatures of stormwater and untreated sewage were determined and compared with the rivers. Isotopic values of stormwater was delta 15N = 1.1 ± 2 %; delta 13C = -25.5 ± 3 % and sewage was delta 15N = -1.9 ± 0.2 %; delta 13C = -23.6 ± 0.3. Suspended particular organic matter (SPOM) of Milwaukee River showed depleted delta 13C (-28.6 ± 1.6 %) and enriched delta 15N (7.7 ± 1.9 %) values. SPOM of the KK River exhibited the most depleted delta 15N (0.2 ± 1.6 %) and enriched delta 13C (-24.8 ± 1.8 %) isotopic values. Menomonee River SPOM showed intermediate isotopic values. The delta 13C values of each river and the estuary enriched significantly throughout the summer storm periods. The isotope signals in the KK and Menomonee were indicative of stormwater runoff and sewage contamination. These results suggest that unrecognized sewage inputs are chronically present and may be delivered through urban stormwater systems. DNA based methods combined with isotope analysis may provide a useful tool for urban watershed assessments and to identify sewage inputs. Delineating the relative contribution of stormwater and sewage to overall degraded water quality might give the first indication of the impact of these sources on the Michigan Lake waters.

  9. From Puffins to Plankton: A DNA-Based Analysis of a Seabird Food Chain in the Northern Gulf of Maine

    PubMed Central

    Bowser, A. Kirsten; Diamond, Antony W.; Addison, Jason A.

    2013-01-01

    The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis. PMID:24358258

  10. From puffins to plankton: a DNA-based analysis of a seabird food chain in the northern Gulf of Maine.

    PubMed

    Bowser, A Kirsten; Diamond, Antony W; Addison, Jason A

    2013-01-01

    The predator-prey interactions within food chains are used to both characterize and understand ecosystems. Conventional methods of constructing food chains from visual identification of prey in predator diet can suffer from poor taxonomic resolution, misidentification, and bias against small or completely digestible prey. Next-generation sequencing (NGS) technology has become a powerful tool for diet reconstruction through barcoding of DNA in stomach content or fecal samples. Here we use multi-locus (16S and CO1) next-generation sequencing of DNA barcodes on the feces of Atlantic puffin (Fratercula arctica) chicks (n=65) and adults (n=64) and the stomach contents of their main prey, Atlantic herring (Clupea harengus, n=44) to investigate a previously studied food chain. We compared conventional and molecular-derived chick diet, tested the similarity between the diets of puffin adults and chicks, and determined whether herring prey can be detected in puffin diet samples. There was high variability in the coverage of prey groups between 16S and CO1 markers. We identified more unique prey with our 16S compared to CO1 barcoding markers (51 and 39 taxa respectively) with only 12 taxa identified by both genes. We found no significant difference between the 16S-identified diets of puffin adults (n=17) and chicks (n=41). Our molecular method is more taxonomically resolved and detected chick prey at higher frequencies than conventional field observations. Many likely planktonic prey of herring were detected in feces from puffin adults and chicks, highlighting the impact secondary consumption may have on the interpretation of molecular dietary analysis. This study represents the first simultaneous molecular investigation into the diet of multiple components of a food chain and highlights the utility of a multi-locus approach to diet reconstruction that is broadly applicable to food web analysis. PMID:24358258

  11. Phylogenetic Analysis and DNA-based Species Confirmation in Anopheles (Nyssorhynchus)

    PubMed Central

    Foster, Peter G.; Bergo, Eduardo S.; Bourke, Brian P.; Oliveira, Tatiane M. P.; Nagaki, Sandra S.; Sant’Ana, Denise C.; Sallum, Maria Anice M.

    2013-01-01

    Specimens of neotropical Anopheles (Nyssorhynchus) were collected and identified morphologically. We amplified three genes for phylogenetic analysis–the single copy nuclear white and CAD genes, and the COI barcode region. Since we had multiple specimens for most species we were able to test how well the single or combined genes were able to corroborate morphologically defined species by placing the species into exclusive groups. We found that single genes, including the COI barcode region, were poor at confirming species, but that the three genes combined were able to do so much better. This has implications for species identification, species delimitation, and species discovery, and we caution that single genes are not enough. Higher level groupings were partially resolved with some well-supported groupings, whereas others were found to be either polyphyletic or paraphyletic. There were examples of known groups, such as the Myzorhynchella Section, which were poorly supported with single genes but were well supported with combined genes. From this we can infer that more sequence data will be needed in order to show more higher-level groupings with good support. We got unambiguously good support (0.94–1.0 Bayesian posterior probability) from all DNA-based analyses for a grouping of An. dunhami with An. nuneztovari and An. goeldii, and because of this and because of morphological similarities we propose that An. dunhami be included in the Nuneztovari Complex. We obtained phylogenetic corroboration for new species which had been recognised by morphological differences; these will need to be formally described and named. PMID:23390494

  12. Adélie Penguin Population Diet Monitoring by Analysis of Food DNA in Scats

    PubMed Central

    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. PMID:24358158

  13. A DNA-based method for identification of krill species and its application to analysing the diet of marine vertebrate predators.

    PubMed

    Jarman, S N; Gales, N J; Tierney, M; Gill, P C; Elliott, N G

    2002-12-01

    Accurate identification of species that are consumed by vertebrate predators is necessary for understanding marine food webs. Morphological methods for identifying prey components after consumption often fail to make accurate identifications of invertebrates because prey morphology becomes damaged during capture, ingestion and digestion. Another disadvantage of morphological methods for prey identification is that they often involve sampling procedures that are disruptive for the predator, such as stomach flushing or lethal collection. We have developed a DNA-based method for identifying species of krill (Crustacea: Malacostraca), an enormously abundant group of invertebrates that are directly consumed by many groups of marine vertebrates. The DNA-based approach allows identification of krill species present in samples of vertebrate stomach contents, vomit, and, more importantly, faeces. Utilizing samples of faeces from vertebrate predators minimizes the impact of dietary studies on the subject animals. We demonstrate our method first on samples of Adelie penguin (Pygoscelis adeliae) stomach contents, where DNA-based species identification can be confirmed by prey morphology. We then apply the method to faeces of Adelie penguins and to faeces of the endangered pygmy blue whale (Balaenoptera musculus brevicauda). In each of these cases, krill species consumed by the predators could be identified from their DNA present in faeces or stomach contents. PMID:12453250

  14. High-throughput enantiopurity analysis using enantiomeric DNA-based sensors.

    PubMed

    Feagin, Trevor A; Olsen, David P V; Headman, Zachary C; Heemstra, Jennifer M

    2015-04-01

    Distinguishing between the two enantiomers of a molecule is a challenging task due to their nearly identical physical properties. Time-consuming chromatography methods are typically required for this task, which greatly limits the throughput of analysis. Here we describe a fluorescence-based method for the rapid and high-throughput analysis of both small-molecule enantiopurity and concentration. Our approach relies on selective molecular recognition of one enantiomer of the target molecule using a DNA aptamer, and the ability of aptamer-based biosensors to transduce the presence of a target molecule into a dose-dependent fluorescence signal. The key novel aspect of our approach is the implementation of enantiomeric DNA biosensors, which are synthesized from D- and L-DNA, but labeled with orthogonal fluorophores. According to the principle of reciprocal chiral substrate specificity, these biosensors will bind to opposite enantiomers of the target with equal affinity and selectivity, enabling simultaneous quantification of both enantiomers of the target. Using the previously reported DNA biosensor for L-tyrosinamide (L-Tym), we demonstrate the ability to rapidly and accurately measure both enantiopurity and concentration for mixtures of L- and D-Tym. We also apply our enantiomeric biosensors to the optimization of reaction conditions for the synthesis of D-Tym and provide mathematical modeling to suggest that DNA biosensors having only modest binding selectivity can also be used for fluorescence-based enantiopurity measurement. This research provides a generalizable method for high-throughput analysis of reaction mixtures, which is anticipated to significantly accelerate reaction optimization for the synthesis of high-value chiral small molecules. PMID:25747268

  15. Control of origin of sesame oil from various countries by stable isotope analysis and DNA based markers--a pilot study.

    PubMed

    Horacek, Micha; Hansel-Hohl, Karin; Burg, Kornel; Soja, Gerhard; Okello-Anyanga, Walter; Fluch, Silvia

    2015-01-01

    The indication of origin of sesame seeds and sesame oil is one of the important factors influencing its price, as it is produced in many regions worldwide and certain provenances are especially sought after. We joined stable carbon and hydrogen isotope analysis with DNA based molecular marker analysis to study their combined potential for the discrimination of different origins of sesame seeds. For the stable carbon and hydrogen isotope data a positive correlation between both isotope parameters was observed, indicating a dominant combined influence of climate and water availability. This enabled discrimination between sesame samples from tropical and subtropical/moderate climatic provenances. Carbon isotope values also showed differences between oil from black and white sesame seeds from identical locations, indicating higher water use efficiency of plants producing black seeds. DNA based markers gave independent evidence for geographic variation as well as provided information on the genetic relatedness of the investigated samples. Depending on the differences in ambient environmental conditions and in the genotypic fingerprint, a combination of both analytical methods is a very powerful tool to assess the declared geographic origin. To our knowledge this is the first paper on food authenticity combining the stable isotope analysis of bio-elements with DNA based markers and their combined statistical analysis. PMID:25831054

  16. Control of Origin of Sesame Oil from Various Countries by Stable Isotope Analysis and DNA Based Markers—A Pilot Study

    PubMed Central

    Horacek, Micha; Hansel-Hohl, Karin; Burg, Kornel; Soja, Gerhard; Okello-Anyanga, Walter; Fluch, Silvia

    2015-01-01

    The indication of origin of sesame seeds and sesame oil is one of the important factors influencing its price, as it is produced in many regions worldwide and certain provenances are especially sought after. We joined stable carbon and hydrogen isotope analysis with DNA based molecular marker analysis to study their combined potential for the discrimination of different origins of sesame seeds. For the stable carbon and hydrogen isotope data a positive correlation between both isotope parameters was observed, indicating a dominant combined influence of climate and water availability. This enabled discrimination between sesame samples from tropical and subtropical/moderate climatic provenances. Carbon isotope values also showed differences between oil from black and white sesame seeds from identical locations, indicating higher water use efficiency of plants producing black seeds. DNA based markers gave independent evidence for geographic variation as well as provided information on the genetic relatedness of the investigated samples. Depending on the differences in ambient environmental conditions and in the genotypic fingerprint, a combination of both analytical methods is a very powerful tool to assess the declared geographic origin. To our knowledge this is the first paper on food authenticity combining the stable isotope analysis of bio-elements with DNA based markers and their combined statistical analysis. PMID:25831054

  17. Diets

    MedlinePlus

    Your diet is made up of what you eat. A healthy diet May include fruits, vegetables, whole grains, and fat- ... added sugars There are many different types of diets. Some, like a vegetarian diet, don't include ...

  18. DNA-based machines.

    PubMed

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications. PMID:24647836

  19. Karnyothrips flavipes, a previously unreported predatory thrips of the coffee berry borer: DNA-based gut content analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new predator of the coffee berry borer, Hypothenemus hampei, was found in the coffee growing area of Kisii in Western Kenya. Field observations, laboratory trials and gut content analysis using molecular tools have confirmed the role of the predatory thrips Karnyothrips flavipes Jones (Phlaeothrip...

  20. The DNA-based human karyotype.

    PubMed

    Mayall, B H; Carrano, A V; Moore, D H; Ashworth, L K; Bennett, D E; Mendelsohn, M L

    1984-07-01

    Image cytometry and computer analysis are used to determine the relative DNA content and the DNA-based centromeric index of the 24 chromosomes of the human karyotype. A two-step procedure is used. Chromosomes of cells in metaphase first are stained with quinacrine and identified visually by their fluorescent Q-band patterns. They then are stained for DNA using gallocyanin-chrome alum. The chromosome images are scanned and recorded as digital values of optical density by an CYDAC image cytometric microscope system, CYDAC. The digital images are processed by computer to measure for each chromosome the relative DNA stain contents of the whole chromosome and of the p and q arms and the DNA-based centromeric index. About ten cells are analyzed for each of the donors, who are phenotypically normal men and women. The chromosome measurements are pooled by chromosome type for each donor and are compared among donors. The means of the chromosome measurements give the DNA-based human karyotype. Analysis of the DNA-based data shows that some chromosomes or portions of chromosomes vary significantly among donors. These variants do not correlate with detectable morphologic polymorphisms, such as Q- or C-band variants; thus they represent new and otherwise undetectable chromosome polymorphisms whose genetic basis and clinical significance are yet to be determined. PMID:6205836

  1. DNA-based identification of Peucedanum ostruthium specimens and detection of common adulterants by high-resolution melting curve analysis.

    PubMed

    Schmiderer, Corinna; Ruzicka, Joana; Novak, Johannes

    2015-12-01

    Masterwort (Peucedanum ostruthium, syn. Imperatoria ostruthium, Apiaceae) is an old economic plant in Alpine countries cultivated as ornamental plant and used for spirits and in folk medicine. P. ostruthium is a species that has often been confused with related Apiaceae species or morphologically similar roots or tubers resulting in products of minor quality. Masterwort can be distinguished from other Apiaceae species by nrDNA (ITS1 and ITS2). The analysed chloroplast markers (trnK 5' intron, trnT-trnL, and psbA-trnH), however, showed no species-specific mutations. With the application of two primer pairs amplifying parts of ITS and developed for high-resolution melting curve analysis (HRM) the target species was distinguishable from the other Peucedanum and Apiaceae species of our reference set. A multiplex PCR/HRM was developed to detect adulterations with Gentiana spp., Aconitum napellus and Veratrum album. PMID:26493217

  2. 16S rDNA-based analysis of dominant bacterial populations associated with early life stages of coho salmon (Oncorhynchus kisutch).

    PubMed

    Romero, Jaime; Navarrete, Paola

    2006-05-01

    In this study, we used a 16S rDNA-based approach to determine bacterial populations associated with coho salmon (Oncorhynchus kisutch) in its early life stages, highlighting dominant bacteria in the gastrointestinal tract during growth in freshwater. The present article is the first molecular analysis of bacterial communities of coho salmon. Cultivability of the salmon gastrointestinal microbiota was estimated by comparison of direct microscopic counts (using acridine orange) with colony counts (in tryptone soy agar). In general, a low fraction (about 1%) of the microbiota could be recovered as cultivable bacteria. Using DNA extracted directly from individuals belonging to the same lot, bacterial communities present in eggs and gastrointestinal tract of first-feeding fries and juveniles were monitored by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The DGGE profiles revealed simple communities in all stages and exposed changes in bacterial community during growth. Sequencing and phylogenetic analysis of excised DGGE bands revealed the nature of the main bacteria found in each stage. In eggs, the dominant bacteria belonged to beta-Proteobacteria (Janthinobacterium and Rhodoferax). During the first feeding stage, the most abundant bacteria in the gastrointestinal tract clustered with gamma-Proteobacteria (Shewanella and Aeromonas). In juveniles ranging from 2 to 15 g, prevailing bacteria were Pseudomonas and Aeromonas. To determine the putative origin of dominant Pseudomonas and Aeromonas found in juvenile gastrointestinal tracts, primers for these groups were designed based on sequences retrieved from DGGE gel. Subsequently, samples of the water influent, pelletized feed, and eggs were analyzed by PCR amplification. Only those amplicons obtained from samples of eggs and the water influent presented identical sequences to the dominant bands of DGGE. Overall, our results suggest that a stable microbiota is established after the first

  3. Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn.

    PubMed

    Woodruff, S P; Johnson, T R; Waits, L P

    2015-07-01

    Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark-recapture analyses. Deposition data were collected at five watering holes using sampling intervals of 1-7 days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We evaluated the efficiency of different sampling intervals (1-10 days) by estimating the number of successful samples, success rate of individual identification and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation and demographic monitoring of Sonoran pronghorn. We recommend collecting samples <7 days old and estimate that a sampling interval of four to seven days in summer conditions (i.e., extreme heat and exposure to UV light) will achieve desired sample sizes for mark-recapture analysis while also maximizing efficiency [Corrected]. PMID:25522240

  4. Communication: Electron ionization of DNA bases

    NASA Astrophysics Data System (ADS)

    Rahman, M. A.; Krishnakumar, E.

    2016-04-01

    No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve the existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space.

  5. Communication: Electron ionization of DNA bases.

    PubMed

    Rahman, M A; Krishnakumar, E

    2016-04-28

    No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve the existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space. PMID:27131520

  6. A computerized diet analysis system for the research nutritionist.

    PubMed

    Dare, D; Al-Bander, S Y

    1987-05-01

    A computerized diet analysis system can assist in the many dietary computations performed daily by the research nutritionist. When selecting a computerized diet analysis system, the research nutritionist must consider present and future needs and select a system that is accurate, efficient, and cost-effective. The purpose of this article is to review the computer needs of the research nutritionist, identify areas to be considered when selecting a diet analysis system, and describe a system that functions easily in research or clinical settings. The diet analysis system described here is interactive and easy to use and provides flexible programming to accommodate changing research or clinical needs. The nutrient data base is accurate, verified, and periodically updated by the company that provides the system. Data entry is easy, and new foods or recipes can readily be added to the nutrient data base. The system's programs and special features provide efficient, accurate methods for creating and analyzing complex research diets, analyzing nutrient intake, and reporting nutrient data. PMID:3106451

  7. [Forced Oscillations of DNA Bases].

    PubMed

    Yakushevich, L V; Krasnobaeva, L A

    2016-01-01

    This paper presents the results of the studying of forced angular oscillations of the DNA bases with the help of the mathematical model consisting of two coupled nonlinear differential equations that take into account the effects of dissipation and the influence of an external periodic field. The calculation results are illustrated for sequence of gene encoding interferon alpha 17 (IFNA 17). PMID:27192830

  8. Validity of electronic diet recording nutrient estimates compared to dietitian analysis of diet records: A randomized controlled trial

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Dietary intake assessment with diet records (DR) is a standard research and practice tool in nutrition. Manual entry and analysis of DR is time-consuming and expensive. New electronic tools for diet entry by clients and research participants may reduce the cost and effort of nutrient int...

  9. Dark States in Single DNA Bases and DNA Base Polymers

    NASA Astrophysics Data System (ADS)

    Kohler, Bern; Hare, Patrick M.; Middleton, Chris T.

    2009-06-01

    DNA is vulnerable to photochemical modification by UV light. The excited electronic states that initiate DNA damage have been difficult to characterize due to their ultrashort lifetimes, and most excitations in single DNA bases decay to the electronic ground state in hundreds of femtoseconds. Although many workers have now located conical intersections between various electronic states of the nucleobases, there is still confusion over the precise dynamics that lead to deactivation. This is especially true for the pyrimidine bases where the initial Franck-Condon population bifurcates with some molecules decaying to the ground state and others relaxing to a relatively long-lived ^1nπ* state. Results from UV/UV and UV/mid-IR transient absorption experiments will be presented that illustrate these dual decay pathways. Evidence suggests that the ^1nπ* state mediates intersystem crossing to the triplet state. Finally, current understanding of how these single-base decay pathways are modified by interactions in DNA polymers will be discussed.

  10. Validity of electronic assessment methods compared to RD analysis of diet records

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Assessment of dietary intake by diet records (DR) is a standard research and practice tool. However, manual entry and analysis of DR is time-consuming. New electronic tools for diet entry by clients and research participants may reduce the RD effort spent in diet entry. In order to determine the ...

  11. Characterization of the tunneling conductance across DNA bases

    SciTech Connect

    Zikic, Radomir; Krstic, Predrag S; Zhang, Xiaoguang; Fuentes-Cabrera, Miguel A; Wells, Jack C; Zhao, Xiongce

    2006-01-01

    Characterization of the electrical properties of the DNA bases, Adenine, Cytosine, Guanine and Thymine, besides building the basic knowledge on these fundamental constituents of a DNA, is a crucial step in developing a DNA sequencing technology. We present a first-principles study of the current-voltage characteristics of nucleotide-like molecules of the DNA bases, placed in a 1.5 nm gap formed between gold nanoelectrodes. The quantum transport calculations in the tunneling regime are shown to vary strongly with the electrode-molecule geometry and the choice of the DFT exchangecorrelation functionals. Analysis of the results in the zero-bias limit indicates that distinguishable current-voltage characteristics of different DNA bases are dominated by the geometrical conformations of the bases and nanoelectrodes.

  12. Analysis of energy expenditure in diet-induced obese rats

    PubMed Central

    Assaad, Houssein; Yao, Kang; Tekwe, Carmen D.; Feng, Shuo; Bazer, Fuller W.; Zhou, Lan; Carroll, Raymond J.; Meininger, Cynthia J.; Wu, Guoyao

    2014-01-01

    Development of obesity in animals is affected by energy intake, dietary composition, and metabolism. Useful models for studying this metabolic problem are Sprague-Dawley rats fed low-fat (LF) or high-fat (HF) diets beginning at 28 days of age. Through experimental design, their dietary intakes of energy, protein, vitamins, and minerals per kg body weight (BW) do not differ in order to eliminate confounding factors in data interpretation. The 24-h energy expenditure of rats is measured using indirect calorimetry. A regression model is constructed to accurately predict BW gain based on diet, initial BW gain, and the principal component scores of respiratory quotient and heat production. Time-course data on metabolism (including energy expenditure) are analyzed using a mixed effect model that fits both fixed and random effects. Cluster analysis is employed to classify rats as normal-weight or obese. HF-fed rats are heavier than LF-fed rats, but rates of their heat production per kg non-fat mass do not differ. We conclude that metabolic conversion of dietary lipids into body fat primarily contributes to obesity in HF-fed rats. PMID:24896330

  13. Effects of diet and diet-plus-exercise programs on resting metabolic rate: a meta-analysis.

    PubMed

    Thompson, J L; Manore, M M; Thomas, J R

    1996-03-01

    Studies examining the effects of diet (D) and diet-plus-exercise (DE) programs on resting metabolic rate (RMR) report equivocal results. The purpose of this study was to use meta-analysis to determine if exercise prevents the decrease in RMR observed with dieting. Results from the 22 studies included in this analysis revealed that the majority of studies used female subjects ages 31-45 years, who were fed a relatively low-fat, high-carbohydrate diet of less than 5,023 kJ.day-1. The predominant prescribed exercise was aerobic in nature, 31-60 min in duration, performed 4-5 days per week, and of moderate intensity (51-70% of VO2max). Contrary to what is reported in narrative reviews, RMR decreased significantly with both D and DE programs, and the drop with D was significantly greater than that with DE. In conclusion, the addition of exercise to dietary restriction appears to prevent some of the decrease in RMR observed in premenopausal women. PMID:8653104

  14. A High Phosphorus Diet Affects Lipid Metabolism in Rat Liver: A DNA Microarray Analysis

    PubMed Central

    Chun, Sunwoo; Bamba, Takeshi; Suyama, Tatsuya; Ishijima, Tomoko; Fukusaki, Eiichiro; Abe, Keiko; Nakai, Yuji

    2016-01-01

    A high phosphorus (HP) diet causes disorders of renal function, bone metabolism, and vascular function. We previously demonstrated that DNA microarray analysis is an appropriate method to comprehensively evaluate the effects of a HP diet on kidney dysfunction such as calcification, fibrillization, and inflammation. We reported that type IIb sodium-dependent phosphate transporter is significantly up-regulated in this context. In the present study, we performed DNA microarray analysis to investigate the effects of a HP diet on the liver, which plays a pivotal role in energy metabolism. DNA microarray analysis was performed with total RNA isolated from the livers of rats fed a control diet (containing 0.3% phosphorus) or a HP diet (containing 1.2% phosphorus). Gene Ontology analysis of differentially expressed genes (DEGs) revealed that the HP diet induced down-regulation of genes involved in hepatic amino acid catabolism and lipogenesis, while genes related to fatty acid β-oxidation process were up-regulated. Although genes related to fatty acid biosynthesis were down-regulated in HP diet-fed rats, genes important for the elongation and desaturation reactions of omega-3 and -6 fatty acids were up-regulated. Concentrations of hepatic arachidonic acid and eicosapentaenoic acid were increased in HP diet-fed rats. These essential fatty acids activate peroxisome proliferator-activated receptor alpha (PPARα), a transcription factor for fatty acid β-oxidation. Evaluation of the upstream regulators of DEGs using Ingenuity Pathway Analysis indicated that PPARα was activated in the livers of HP diet-fed rats. Furthermore, the serum concentration of fibroblast growth factor 21, a hormone secreted from the liver that promotes fatty acid utilization in adipose tissue as a PPARα target gene, was higher (p = 0.054) in HP diet-fed rats than in control diet-fed rats. These data suggest that a HP diet enhances energy expenditure through the utilization of free fatty acids

  15. Mucus: a new tissue fraction for rapid determination of fish diet switching using stable isotope analysis.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stable isotope analysis of diet switching by fishes is often hampered by slow turnover rates of the tissues analyzed (usually muscle or fins). We examined epidermal mucus as a potentially faster turnover “tissue” that might provide a more rapid assessment of diet switching. In a controlled hatchery...

  16. Mucus: A new tissue fraction for rapid determination of fish diet switching using stable isotope analysis

    EPA Science Inventory

    Stable isotope analysis of diet switching by fishes often is hampered by slow turnover rates of the tissues analyzed (usually muscle or fins). We examined epidermal mucus as a potentially faster turnover “tissue” that might provide a more rapid assessment of diet switching. In a ...

  17. Determining the efficacy of microsatellite DNA-based mixed-stock analysis of Lake Michigan’s lake whitefish commercial fishery

    USGS Publications Warehouse

    VanDeHey, Justin A.; Sloss, Brian L.; Peeters, Paul J.; Sutton, Trent M.

    2009-01-01

    Management of commercially exploited fish should be conducted at the stock level. If a mixed stock fishery exists, a comprehensive mixed stock analysis is required for stock-based management. The lake whitefish Coregonus clupeaformis comprises the primary commercial fishery across the Great Lakes. Recent research resolved that six genetic stocks of lake whitefish were present in Lake Michigan, and long-term tagging data indicate that Lake Michigan's lake whitefish commercial fishery is a mixed stock fishery. The objective of this research was to determine the usefulness of microsatellite data for conducting comprehensive mixed stock analyses of the Lake Michigan lake whitefish commercial fishery. We used the individual assignment method as implemented in the program ONCOR to determine the accuracy level at which microsatellite data can reliably identify component populations or stocks. Self-assignment of lake whitefish to their population and stock of origin ranged from > 96% to 100%. Evaluation of genetic stock discreteness indicated a moderately high degree of correct assignment (average = 75%); simulations indicated supplementing baseline data by ∼ 50 to 100 individuals could increase accuracy by up to 4.5%. Simulated mixed stock commercial harvests with known stock composition showed a high degree of correct proportional assignment between observed and predicted harvest values. These data suggest that a comprehensive mixed stock analysis of Lake Michigan's lake whitefish commercial fishery is viable and would provide valuable information for improving management.

  18. DNA-based diagnosis of lymphatic filariasis.

    PubMed

    Nuchprayoon, Surang

    2009-09-01

    Lymphatic filariasis (LF) is still a major public health problem. The disease is ranked by the World Health Organization (WHO) as the second leading cause of permanent and long-term disability, and has been targeted for elimination by 2020. Effective diagnosis LF is required for treatment of infected individuals, for epidemiological assessment and for monitoring of the control program. Conventional diagnosis of LF depends on detection of microfilariae (Mf) in blood specimens, which has low sensitivity and specificity. Detection of specific circulating filarial antigens is regarded by WHO as the 'gold standard' for diagnosis of LF. However, the limitations of the antigen tests are cost and inconsistent availability. Although anti-filarial IgG4 antibody levels are associated with active LF infections, however, cross-reactivity with other filarial parasites is common. Not as sensitive as antigen tests, DNA-based techniques have been developed to diagnose and differentiate filarial parasites in humans, animal reservoir hosts, and mosquito vectors. These include DNA hybridization, polymerase chain reaction (PCR) amplification using specific primers (eg Ssp I repeat, pWb12 repeat, pWb-35 repeat, and LDR repeat for Wuchereria bancrofti and Hha I repeat, glutathione peroxidase gene, mitochondrial DNA for Brugia malayi), and universal primers, multiplex-PCR, PCR-restriction fragment length polymorphism (PCR-RFLP), PCR-enzyme linked immunosorbent assay (PCR-ELISA), as well as quantitative PCR. Furthermore, because bancroftian filariasis is endemic on the Thai-Myanmar border, the potential now exists for a re-emergence of bancroftian filariasis in Thailand, and random amplified polymorphic DNA (RAPD) analysis has proved effective to differentiate Thai and Myanmar strains of W. bancrofti. PMID:19842372

  19. Direct Detection and Sequencing of Damaged DNA Bases

    PubMed Central

    2011-01-01

    Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications. PMID:22185597

  20. Validity of Electronic Diet Recording Nutrient Estimates Compared to Dietitian Analysis of Diet Records: Randomized Controlled Trial

    PubMed Central

    Scheett, Angela J; Johnson, LuAnn K; Jahns, Lisa

    2015-01-01

    Background Dietary intake assessment with diet records (DR) is a standard research and practice tool in nutrition. Manual entry and analysis of DR is time-consuming and expensive. New electronic tools for diet entry by clients and research participants may reduce the cost and effort of nutrient intake estimation. Objective To determine the validity of electronic diet recording, we compared responses to 3-day DR kept by Tap & Track software for the Apple iPod Touch and records kept on the Nutrihand website to DR coded and analyzed by a research dietitian into a customized US Department of Agriculture (USDA) nutrient analysis program, entitled GRAND (Grand Forks Research Analysis of Nutrient Data). Methods Adult participants (n=19) enrolled in a crossover-designed clinical trial. During each of two washout periods, participants kept a written 3-day DR. In addition, they were randomly assigned to enter their DR in a Web-based dietary analysis program (Nutrihand) or a handheld electronic device (Tap & Track). They completed an additional 3-day DR and the alternate electronic diet recording methods during the second washout. Entries resulted in 228 daily diet records or 12 for each of 19 participants. Means of nutrient intake were calculated for each method. Concordance of the intake estimates were determined by Bland-Altman plots. Coefficients of determination (R 2) were calculated for each comparison to assess the strength of the linear relationship between methods. Results No significant differences were observed between the mean nutrient values for energy, carbohydrate, protein, fat, saturated fatty acids, total fiber, or sodium between the recorded DR analyzed in GRAND and either Nutrihand or Tap & Track, or for total sugars comparing GRAND and Tap & Track. Reported values for total sugars were significantly reduced (P<.05) comparing Nutrihand to GRAND. Coefficients of determination (R 2) for Nutrihand and Tap & Track compared to DR entries into GRAND, respectively

  1. The effect of low calorie diet on adiponectin concentration: a systematic review and meta-analysis.

    PubMed

    Salehi-Abargouei, A; Izadi, V; Azadbakht, L

    2015-07-01

    Adiponectin secreted from adipose tissue is proposed to be inversely related to the body fat mass. However, the magnitude of the effect of low calorie diet on adiponectin concentrations remains unknown. The present study was aimed to conduct a systematic review and meta-analysis on clinical trials that access the effect of low calorie diet on adiponectin concentration. We searched PubMed, SCOPUS, ISI web of science, and Google scholar for RCTs until January 2015. Totally, 13 trials were found, which examined the effect of low calorie diet on adiponectin concentration compared control group without low calorie diet.Our meta-analysis showed that weight loss diet can substantially increase the adiponectin concentration in overall (Hedges' g=0.34, 95% CI:0.17-0.50, p<0.001). Subgroup analysis also revealed that the low calorie diet can substantially enhance adiponectin concentrations when prescribed for ≤16 weeks (Hedges' g=0.48, 95% CI: 0.12-0.83, p=0.01) compared to >16 weeks (Hedges' g=0.30, 95% CI: 0.11-0.48, p=0.002). Weight loss diet beneficially affects blood adiponectin concentrations. More clinical trials are recommended to clear this effect among different genders and nationalities, and assess the magnitude of the effect based on changes in fat mass. PMID:25985324

  2. Evaluating gull diets: A comparison of conventional methods and stable isotope analysis

    USGS Publications Warehouse

    Weiser, E.L.; Powell, A.N.

    2011-01-01

    Samples such as regurgitated pellets and food remains have traditionally been used in studies of bird diets, but these can produce biased estimates depending on the digestibility of different foods. Stable isotope analysis has been developed as a method for assessing bird diets that is not biased by digestibility. These two methods may provide complementary or conflicting information on diets of birds, but are rarely compared directly. We analyzed carbon and nitrogen stable isotope ratios of feathers of Glaucous Gull (Larus hyperboreus) chicks from eight breeding colonies in northern Alaska, and used a Bayesian mixing model to generate a probability distribution for the contribution of each food group to diets. We compared these model results with probability distributions from conventional diet samples (pellets and food remains) from the same colonies and time periods. Relative to the stable isotope estimates, conventional analysis often overestimated the contributions of birds and small mammals to gull diets and often underestimated the contributions of fish and zooplankton. Both methods gave similar estimates for the contributions of scavenged caribou, miscellaneous marine foods, and garbage to diets. Pellets and food remains therefore may be useful for assessing the importance of garbage relative to certain other foods in diets of gulls and similar birds, but are clearly inappropriate for estimating the potential impact of gulls on birds, small mammals, or fish. However, conventional samples provide more species-level information than stable isotope analysis, so a combined approach would be most useful for diet analysis and assessing a predator's impact on particular prey groups. ?? 2011 Association of Field Ornithologists.

  3. DNA-Based Applications in Nanobiotechnology

    PubMed Central

    Abu-Salah, Khalid M.; Ansari, Anees A.; Alrokayan, Salman A.

    2010-01-01

    Biological molecules such as deoxyribonucleic acid (DNA) have shown great potential in fabrication and construction of nanostructures and devices. The very properties that make DNA so effective as genetic material also make it a very suitable molecule for programmed self-assembly. The use of DNA to assemble metals or semiconducting particles has been extended to construct metallic nanowires and functionalized nanotubes. This paper highlights some important aspects of conjugating the unique physical properties of dots or wires with the remarkable recognition capabilities of DNA which could lead to miniaturizing biological electronics and optical devices, including biosensors and probes. Attempts to use DNA-based nanocarriers for gene delivery are discussed. In addition, the ecological advantages and risks of nanotechnology including DNA-based nanobiotechnology are evaluated. PMID:20652049

  4. Multiphoton excitation of fluorescent DNA base analogs

    NASA Astrophysics Data System (ADS)

    Katilius, Evaldas; Woodbury, Neal W.

    2006-07-01

    Multiphoton excitation was used to investigate properties of the fluorescent DNA base analogs, 2-aminopurine (2AP) and 6-methylisoxanthopterin (6MI). 2-aminopurine, a fluorescent analog of adenine, was excited by three-photon absorption. Fluorescence correlation measurements were attempted to evaluate the feasibility of using three-photon excitation of 2AP for DNA-protein interaction studies. However, high excitation power and long integration times needed to acquire high signal-to-noise fluorescence correlation curves render three-photon excitation FCS of 2AP not very useful for studying DNA base dynamics. The fluorescence properties of 6-methylisoxanthopterin, a guanine analog, were investigated using two-photon excitation. The two-photon absorption cross-section of 6MI was estimated to be about 2.5×10-50 cm4s (2.5 GM units) at 700 nm. The two-photon excitation spectrum was measured in the spectral region from 700 to 780 nm; in this region the shape of the two-photon excitation spectrum is very similar to the shape of single-photon excitation spectrum in the near-UV spectral region. Two-photon excitation of 6MI is suitable for fluorescence correlation measurements. Such measurements can be used to study DNA base dynamics and DNA-protein interactions over a broad range of time scales.

  5. Does early-life diet affect longevity? A meta-analysis across experimental studies.

    PubMed

    English, Sinead; Uller, Tobias

    2016-09-01

    Life-history theory predicts that nutrition influences lifespan owing to trade-offs between allocating resources to reproduction, growth and repair. Despite occasional reports that early diet has strong effects on lifespan, it is unclear whether this prediction is generally supported by empirical studies. We conducted a meta-analysis across experimental studies manipulating pre- or post-natal diet and measuring longevity. We found no overall effect of early diet on lifespan. We used meta-regression, considering moderator variables based on experimental and life-history traits, to test predictions regarding the strength and direction of effects that could lead to positive or negative effects. Pre-natal diet manipulations reduced lifespan, but there were no effects of later diet, manipulation type, development mode, or sex. The results are consistent with the prediction that early diet restriction disrupts growth and results in increased somatic damage, which incurs lifespan costs. Our findings raise a cautionary note, however, for placing too strong an emphasis on early diet effects on lifespan and highlight limitations of measuring these effects under laboratory conditions. PMID:27601722

  6. Do ketogenic diets really suppress appetite? A systematic review and meta-analysis.

    PubMed

    Gibson, A A; Seimon, R V; Lee, C M Y; Ayre, J; Franklin, J; Markovic, T P; Caterson, I D; Sainsbury, A

    2015-01-01

    Very-low-energy diets (VLEDs) and ketogenic low-carbohydrate diets (KLCDs) are two dietary strategies that have been associated with a suppression of appetite. However, the results of clinical trials investigating the effect of ketogenic diets on appetite are inconsistent. To evaluate quantitatively the effect of ketogenic diets on subjective appetite ratings, we conducted a systematic literature search and meta-analysis of studies that assessed appetite with visual analogue scales before (in energy balance) and during (while in ketosis) adherence to VLED or KLCD. Individuals were less hungry and exhibited greater fullness/satiety while adhering to VLED, and individuals adhering to KLCD were less hungry and had a reduced desire to eat. Although these absolute changes in appetite were small, they occurred within the context of energy restriction, which is known to increase appetite in obese people. Thus, the clinical benefit of a ketogenic diet is in preventing an increase in appetite, despite weight loss, although individuals may indeed feel slightly less hungry (or more full or satisfied). Ketosis appears to provide a plausible explanation for this suppression of appetite. Future studies should investigate the minimum level of ketosis required to achieve appetite suppression during ketogenic weight loss diets, as this could enable inclusion of a greater variety of healthy carbohydrate-containing foods into the diet. PMID:25402637

  7. Kirtland's warbler diet as determined through fecal analysis

    USGS Publications Warehouse

    Deloria-Sheffield, C.M.; Millenbah, Kelly F.; Bocetti, C.I.; Sykes, P.W., Jr.; Kepler, C.B.

    2001-01-01

    The endangered Kirtland's Warbler (Dendroica kirtlandii) nests primarily in large (>32 ha) stands of young (5- to 25-yr-old) jack pine (Pinus banksiana) which grow on Grayling sand soil. These specific habitat requirements restrict the Kirtland's Warbler breeding range to only 13-16 counties in the northern lower peninsula of Michigan. Although the nature of the species' affinity for this habitat is poorly understood, one theory suggests that higher prey abundance in young jack pine may play a role. To explore further the hypothesis that Kirtland's Warblers choose nesting habitat due to prey abundance, a more thorough knowledge of the warblers' diet is needed. To better understand the diet, we identified arthropod and plant fragments found in 202 Kirtland's Warbler fecal samples, collected from June to September, 1995-1997. The major food items recorded were spittlebugs and aphids (Homoptera; found in 61% of all samples), ants and wasps (Hymenoptera; 45%), blueberry (Vaccinium augustifolium; 42%), beetles (Coleoptera; 25%), and moth larvae (Lepidoptera; 22%).

  8. Excess Electron Localization in Solvated DNA Bases

    SciTech Connect

    Smyth, Maeve; Kohanoff, Jorge

    2011-06-10

    We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

  9. Effects of low-carbohydrate diets v. low-fat diets on body weight and cardiovascular risk factors: a meta-analysis of randomised controlled trials.

    PubMed

    Mansoor, Nadia; Vinknes, Kathrine J; Veierød, Marit B; Retterstøl, Kjetil

    2016-02-14

    The effects of low-carbohydrate (LC) diets on body weight and cardiovascular risk are unclear, and previous studies have found varying results. Our aim was to conduct a meta-analysis of randomised controlled trials (RCT), assessing the effects of LC diets v. low-fat (LF) diets on weight loss and risk factors of CVD. Studies were identified by searching MEDLINE, Embase and Cochrane Trials. Studies had to fulfil the following criteria: a RCT; the LC diet was defined in accordance with the Atkins diet, or carbohydrate intake of <20% of total energy intake; twenty subjects or more per group; the subjects were previously healthy; and the dietary intervention had a duration of 6 months or longer. Results from individual studies were pooled as weighted mean difference (WMD) using a random effect model. In all, eleven RCT with 1369 participants met all the set eligibility criteria. Compared with participants on LF diets, participants on LC diets experienced a greater reduction in body weight (WMD -2·17 kg; 95% CI -3·36, -0·99) and TAG (WMD -0·26 mmol/l; 95% CI -0·37, -0·15), but a greater increase in HDL-cholesterol (WMD 0·14 mmol/l; 95% CI 0·09, 0·19) and LDL-cholesterol (WMD 0·16 mmol/l; 95% CI 0·003, 0·33). This meta-analysis demonstrates opposite change in two important cardiovascular risk factors on LC diets--greater weight loss and increased LDL-cholesterol. Our findings suggest that the beneficial changes of LC diets must be weighed against the possible detrimental effects of increased LDL-cholesterol. PMID:26768850

  10. Diet of spotted bats (Euderma maculatum) in Arizona as indicated by fecal analysis and stable isotopes

    EPA Science Inventory

    We assessed diet of spotted bats (Euderma maculatum (J.A. Allen, 1891)) by visual analysis of bat feces and stable carbon (δ13C) and nitrogen (δ15N) isotope analysis of bat feces, wing, hair, and insect prey. We collected 33 fecal samples from spotted bats and trapped 3755 insect...

  11. Understanding sustainable diets: a descriptive analysis of the determinants and processes that influence diets and their impact on health, food security, and environmental sustainability.

    PubMed

    Johnston, Jessica L; Fanzo, Jessica C; Cogill, Bruce

    2014-07-01

    The confluence of population, economic development, and environmental pressures resulting from increased globalization and industrialization reveal an increasingly resource-constrained world in which predictions point to the need to do more with less and in a "better" way. The concept of sustainable diets presents an opportunity to successfully advance commitments to sustainable development and the elimination of poverty, food and nutrition insecurity, and poor health outcomes. This study examines the determinants of sustainable diets, offers a descriptive analysis of these areas, and presents a causal model and framework from which to build. The major determinants of sustainable diets fall into 5 categories: 1) agriculture, 2) health, 3) sociocultural, 4) environmental, and 5) socioeconomic. When factors or processes are changed in 1 determinant category, such changes affect other determinant categories and, in turn, the level of "sustainability" of a diet. The complex web of determinants of sustainable diets makes it challenging for policymakers to understand the benefits and considerations for promoting, processing, and consuming such diets. To advance this work, better measurements and indicators must be developed to assess the impact of the various determinants on the sustainability of a diet and the tradeoffs associated with any recommendations aimed at increasing the sustainability of our food system. PMID:25022991

  12. Understanding Sustainable Diets: A Descriptive Analysis of the Determinants and Processes That Influence Diets and Their Impact on Health, Food Security, and Environmental Sustainability123

    PubMed Central

    Johnston, Jessica L.; Fanzo, Jessica C.; Cogill, Bruce

    2014-01-01

    The confluence of population, economic development, and environmental pressures resulting from increased globalization and industrialization reveal an increasingly resource-constrained world in which predictions point to the need to do more with less and in a “better” way. The concept of sustainable diets presents an opportunity to successfully advance commitments to sustainable development and the elimination of poverty, food and nutrition insecurity, and poor health outcomes. This study examines the determinants of sustainable diets, offers a descriptive analysis of these areas, and presents a causal model and framework from which to build. The major determinants of sustainable diets fall into 5 categories: 1) agriculture, 2) health, 3) sociocultural, 4) environmental, and 5) socioeconomic. When factors or processes are changed in 1 determinant category, such changes affect other determinant categories and, in turn, the level of “sustainability” of a diet. The complex web of determinants of sustainable diets makes it challenging for policymakers to understand the benefits and considerations for promoting, processing, and consuming such diets. To advance this work, better measurements and indicators must be developed to assess the impact of the various determinants on the sustainability of a diet and the tradeoffs associated with any recommendations aimed at increasing the sustainability of our food system. PMID:25022991

  13. DNA-based control of protein activity.

    PubMed

    Engelen, W; Janssen, B M G; Merkx, M

    2016-03-01

    DNA has emerged as a highly versatile construction material for nanometer-sized structures and sophisticated molecular machines and circuits. The successful application of nucleic acid based systems greatly relies on their ability to autonomously sense and act on their environment. In this feature article, the development of DNA-based strategies to dynamically control protein activity via oligonucleotide triggers is discussed. Depending on the desired application, protein activity can be controlled by directly conjugating them to an oligonucleotide handle, or expressing them as a fusion protein with DNA binding motifs. To control proteins without modifying them chemically or genetically, multivalent ligands and aptamers that reversibly inhibit their function provide valuable tools to regulate proteins in a noncovalent manner. The goal of this feature article is to give an overview of strategies developed to control protein activity via oligonucleotide-based triggers, as well as hurdles yet to be taken to obtain fully autonomous systems that interrogate, process and act on their environments by means of DNA-based protein control. PMID:26812623

  14. DNA-based control of protein activity

    PubMed Central

    Engelen, W.; Janssen, B. M. G.

    2016-01-01

    DNA has emerged as a highly versatile construction material for nanometer-sized structures and sophisticated molecular machines and circuits. The successful application of nucleic acid based systems greatly relies on their ability to autonomously sense and act on their environment. In this feature article, the development of DNA-based strategies to dynamically control protein activity via oligonucleotide triggers is discussed. Depending on the desired application, protein activity can be controlled by directly conjugating them to an oligonucleotide handle, or expressing them as a fusion protein with DNA binding motifs. To control proteins without modifying them chemically or genetically, multivalent ligands and aptamers that reversibly inhibit their function provide valuable tools to regulate proteins in a noncovalent manner. The goal of this feature article is to give an overview of strategies developed to control protein activity via oligonucleotide-based triggers, as well as hurdles yet to be taken to obtain fully autonomous systems that interrogate, process and act on their environments by means of DNA-based protein control. PMID:26812623

  15. Estimation of a Killer Whale (Orcinus orca) Population's Diet Using Sequencing Analysis of DNA from Feces.

    PubMed

    Ford, Michael J; Hempelmann, Jennifer; Hanson, M Bradley; Ayres, Katherine L; Baird, Robin W; Emmons, Candice K; Lundin, Jessica I; Schorr, Gregory S; Wasser, Samuel K; Park, Linda K

    2016-01-01

    Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%). Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population's summer diet. PMID:26735849

  16. Diet of upper paleolithic modern humans: evidence from microwear texture analysis.

    PubMed

    El Zaatari, Sireen; Hublin, Jean-Jacques

    2014-04-01

    This article presents the results of the occlusal molar microwear texture analysis of 32 adult Upper Paleolithic modern humans from a total of 21 European sites dating to marine isotope stages 3 and 2. The occlusal molar microwear textures of these specimens were analyzed with the aim of examining the effects of the climatic, as well as the cultural, changes on the diets of the Upper Paleolithic modern humans. The results of this analysis do not reveal any environmentally driven dietary shifts for the Upper Paleolithic hominins indicating that the climatic and their associated paleoecological changes did not force these humans to significantly alter their diets in order to survive. However, the microwear texture analysis does detect culturally related changes in the Upper Paleolithic humans' diets. Specifically, significant differences in diet were found between the earlier Upper Paleolithic individuals, i.e., those belonging to the Aurignacian and Gravettian contexts, and the later Magdalenian ones, such that the diet of the latter group was more varied and included more abrasive foods compared with those of the former. PMID:24449141

  17. Contribution of food prices and diet cost to socioeconomic disparities in diet quality and health: a systematic review and analysis

    PubMed Central

    Drewnowski, Adam

    2015-01-01

    Context: It is well established in the literature that healthier diets cost more than unhealthy diets. Objective: The aim of this review was to examine the contribution of food prices and diet cost to socioeconomic inequalities in diet quality. Data Sources: A systematic literature search of the PubMed, Google Scholar, and Web of Science databases was performed. Study Selection: Publications linking food prices, dietary quality, and socioeconomic status were selected. Data Extraction: Where possible, review conclusions were illustrated using a French national database of commonly consumed foods and their mean retail prices. Data Synthesis: Foods of lower nutritional value and lower-quality diets generally cost less per calorie and tended to be selected by groups of lower socioeconomic status. A number of nutrient-dense foods were available at low cost but were not always palatable or culturally acceptable to the low-income consumer. Acceptable healthier diets were uniformly associated with higher costs. Food budgets in poverty were insufficient to ensure optimum diets. Conclusions: Socioeconomic disparities in diet quality may be explained by the higher cost of healthy diets. Identifying food patterns that are nutrient rich, affordable, and appealing should be a priority to fight social inequalities in nutrition and health. PMID:26307238

  18. Effects of Low Glycemic Index Diets on Gestational Diabetes Mellitus: A Meta-Analysis of Randomized Controlled Clinical Trials.

    PubMed

    Wei, Jinhua; Heng, Weijun; Gao, Jianbo

    2016-05-01

    Studies of the effects of low glycemic index (LGI) diets on gestational diabetes mellitus (GDM) have reported conflicting findings.The aim of the study was to evaluate the results of randomized controlled trials (RCTs) that investigated the effects of LGI diets with and without added dietary fiber (DF) on maternal and neonatal outcomes in GDM patients.We searched the MEDLINE, EMBASE, EBSCO, Springer, Ovid, and Cochrane Library databases for studies of the effects of LGI diets in GDM patients. We performed a meta-analysis of the effects of the LGI diets with and without added dietary fiber (DF) on GDM outcomes. Risk ratios (RR) and 95% confidence intervals (CIs) were calculated using random- and fixed-effects models.Five RCTs involving 302 participants were included in our meta-analysis. No statistically significant differences in the risks of cesarean section delivery, large for gestational age, and small for gestational age were observed. The risk of macrosomia in the LGI groups was significantly lower (RR = 0.27; 95% CI: 0.10-0.71; P = 0.008) than that in the control groups. Our subgroup analysis of the effects of DF showed that LGI diets with an increased level of DF, relative to the control diet, reduced the risk of macrosomia beyond that of the LGI diets alone (RR: 0.17 vs 0.47, respectively). The subgroup analysis also showed that LGI diets in which the level of DF was approximately equivalent to that in the control diets significantly reduced the risk of insulin usage (RR = 0.69; 95% CI: 0.52-0.92; P = 0.01).The LGI diets reduced the risk of macrosomia in GDM patients, and LGI diets with added DF reduced the risk of macrosomia further. The LGI diets with levels of DF approximately equivalent to that in the control diets reduced the risk of insulin usage in GDM patients. PMID:27258511

  19. Automated DNA Base Pair Calling Algorithm

    Energy Science and Technology Software Center (ESTSC)

    1999-07-07

    The procedure solves the problem of calling the DNA base pair sequence from two channel electropherogram separations in an automated fashion. The core of the program involves a peak picking algorithm based upon first, second, and third derivative spectra for each electropherogram channel, signal levels as a function of time, peak spacing, base pair signal to noise sequence patterns, frequency vs ratio of the two channel histograms, and confidence levels generated during the run. Themore » ratios of the two channels at peak centers can be used to accurately and reproducibly determine the base pair sequence. A further enhancement is a novel Gaussian deconvolution used to determine the peak heights used in generating the ratio.« less

  20. The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

    PubMed Central

    Turnbaugh, Peter J.; Ridaura, Vanessa K.; Faith, Jeremiah J.; Rey, Federico E.; Knight, Rob; Gordon, Jeffrey I.

    2010-01-01

    Diet and nutritional status are among the most important, modifiable determinants of human health. The nutritional value of food is influenced in part by a person’s gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelationships between diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent, metagenomic analysis of the temporal, spatial and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized, and reproduced much of the bacterial diversity of the donor’s microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a high-fat/high-sugar “Western” diet shifted the structure of the microbiota within a single day, changed the representation of metabolic pathways in the microbiome, and altered microbiome gene expression. Reciprocal transplants involving various combinations of donor and recipient diets revealed that colonization history influences the initial structure of the microbial community, but that these effects can be rapidly altered by diet. Humanized mice fed the Western diet have increased adiposity; this trait is transmissible via microbiota transplantation. Humanized gnotobiotic mice will be useful for conducting proof-of-principle “clinical trials” that test the effects of environmental and genetic factors on the gut microbiota and host physiology. PMID:20368178

  1. Content Analysis of Diet-Related Mobile Apps: A Self-Regulation Perspective.

    PubMed

    Zahry, Nagwan R; Cheng, Ying; Peng, Wei

    2016-10-01

    Diet-related mobile apps hold promise in helping individuals self-regulate their eating behaviors. Nevertheless, little is known about the extent to which diet-related mobile apps incorporate the established behavior change theories and evidence-based practices that promote dietary self-regulation. Guided by the self-regulation aspect of Bandura's social cognitive theory and the Dietary Guidelines for Americans 2010 of the U.S. Department of Agriculture, this study conducts a content analysis of diet-related mobile apps for iPhone (N = 400). In terms of the adherence to the self-regulation aspect of the social cognitive theory, results show that although 72.5% of the apps incorporate at least one theoretical construct, few apps tap all three processes of self-regulation (i.e., self-observation/monitoring, judgment process, and self-reaction). Additionally, outcome expectation is manifested in a majority of the diet-related apps. In terms of the Dietary Guidelines for Americans 2010, while the diet-related apps equally emphasize setting goals for calorie intake or nutrient consumption, more apps feature nutrient tracking than calorie tracking. Implications and limitations are discussed. PMID:26940817

  2. Diet-Induced Alterations in Total and Metabolically Active Microbes within the Rumen of Dairy Cows

    PubMed Central

    Lettat, Abderzak; Benchaar, Chaouki

    2013-01-01

    DNA-based techniques are widely used to study microbial populations; however, this approach is not specific to active microbes, because DNA may originate from inactive and/or dead cells. Using cDNA and DNA, respectively, we aimed to discriminate the active microbes from the total microbial community within the rumen of dairy cows fed diets with increasing proportions of corn silage (CS). Nine multiparous lactating Holstein cows fitted with ruminal cannulas were used in a replicated 3×3 Latin square (32-d period; 21-d adaptation) design to investigate diet-induced shifts in microbial populations by targeting the rDNA gene. Cows were fed a total mixed ration with the forage portion being either barley silage (0% CS), a 50∶50 mixture of barley silage and corn silage (50% CS), or corn silage (100% CS). No differences were found for total microbes analyzed by quantitative PCR, but changes were observed within the active ones. Feeding more CS to dairy cows was accompanied by an increase in Prevotella rRNA transcripts (P = 0.10) and a decrease in the protozoal rRNA transcripts (P<0.05). Although they were distributed differently among diets, 78% of the amplicons detected in DNA- and cDNA-based fingerprints were common to total and active bacterial communities. These may represent a bacterial core of abundant and active cells that drive the fermentation processes. In contrast, 10% of amplicons were specific to total bacteria and may represent inactive or dead cells, whereas 12% were only found within the active bacterial community and may constitute slow-growing bacteria with high metabolic activity. It appears that cDNA-based analysis is more discriminative to identify diet-induced shifts within the microbial community. This approach allows the detection of diet-induced changes in the microbial populations as well as particular bacterial amplicons that remained undetected using DNA-based methods. PMID:23593365

  3. DNA based computing for understanding complex shapes.

    PubMed

    Ullah, A M M Sharif; D'Addona, Doriana; Arai, Nobuyuki

    2014-03-01

    This study deals with a computing method called DNA based computing (DBC) that takes inspiration from the Central Dogma of Molecular Biology. The proposed DBC uses a set of user-defined rules to create a DNA-like sequence from a given piece of problem-relevant information (e.g., image data) in a dry-media (i.e., in an ordinary computer). It then uses another set of user-defined rules to create an mRNA-like sequence from the DNA. Finally, it uses the genetic code to translate the mRNA (or directly the DNA) to a protein-like sequence (a sequence of amino acids). The informational characteristics of the protein (entropy, absence, presence, abundance of some selected amino acids, and relationships among their likelihoods) can be used to solve problems (e.g., to understand complex shapes from their image data). Two case studies ((1) fractal geometry generated shape of a fern-leaf and (2) machining experiment generated shape of the worn-zones of a cutting tool) are presented elucidating the shape understanding ability of the proposed DBC in the presence of a great deal of variability in the image data of the respective shapes. The implication of the proposed DBC from the context of Internet-aided manufacturing system is also described. Further study can be carried out in solving other complex computational problems by using the proposed DBC and its derivatives. PMID:24447435

  4. Magnetic Propulsion of Microswimmers with DNA-Based Flagellar Bundles

    PubMed Central

    2016-01-01

    We show that DNA-based self-assembly can serve as a general and flexible tool to construct artificial flagella of several micrometers in length and only tens of nanometers in diameter. By attaching the DNA flagella to biocompatible magnetic microparticles, we provide a proof of concept demonstration of hybrid structures that, when rotated in an external magnetic field, propel by means of a flagellar bundle, similar to self-propelling peritrichous bacteria. Our theoretical analysis predicts that flagellar bundles that possess a length-dependent bending stiffness should exhibit a superior swimming speed compared to swimmers with a single appendage. The DNA self-assembly method permits the realization of these improved flagellar bundles in good agreement with our quantitative model. DNA flagella with well-controlled shape could fundamentally increase the functionality of fully biocompatible nanorobots and extend the scope and complexity of active materials. PMID:26821214

  5. Magnetic Propulsion of Microswimmers with DNA-Based Flagellar Bundles.

    PubMed

    Maier, Alexander M; Weig, Cornelius; Oswald, Peter; Frey, Erwin; Fischer, Peer; Liedl, Tim

    2016-02-10

    We show that DNA-based self-assembly can serve as a general and flexible tool to construct artificial flagella of several micrometers in length and only tens of nanometers in diameter. By attaching the DNA flagella to biocompatible magnetic microparticles, we provide a proof of concept demonstration of hybrid structures that, when rotated in an external magnetic field, propel by means of a flagellar bundle, similar to self-propelling peritrichous bacteria. Our theoretical analysis predicts that flagellar bundles that possess a length-dependent bending stiffness should exhibit a superior swimming speed compared to swimmers with a single appendage. The DNA self-assembly method permits the realization of these improved flagellar bundles in good agreement with our quantitative model. DNA flagella with well-controlled shape could fundamentally increase the functionality of fully biocompatible nanorobots and extend the scope and complexity of active materials. PMID:26821214

  6. Effects of a Gluten-Free Diet on Rate of Achievement in Autistic Children in an Applied Behavioral Analysis Program.

    ERIC Educational Resources Information Center

    Gemmell, Melissa; Chambliss, Catherine

    This study used both between-subjects and within-subjects analyses to examine the effects of a gluten-free diet on the academic achievement of autistic children. The between-subjects analysis included data from eight autistic children (ages 5 to 7) with four on a gluten-free diet and four serving as controls. The number of attempts needed before…

  7. Vegetarian diets and glycemic control in diabetes: a systematic review and meta-analysis

    PubMed Central

    Barnard, Neal D.; Levin, Susan M.; Watanabe, Mitsuhiro

    2014-01-01

    Introduction Previous studies have suggested an association between vegetarian diets and improvements in glycemic control in diabetes, although this relationship is not well established. No meta-analysis of these studies has been performed. Methods To conduct a systematic review and meta-analysis of controlled clinical trials examining the association between vegetarian diets and glycemic control in type 2 diabetes. Data source: The electronic databases Medline, Web of Science, Excerpta Medica Database (EMBASE), and Cochrane Central Register of Controlled Trials were searched for articles published in any language through December 9, 2013. Study selection: The following criteria were used for study inclusion: (I) age of participants >20 years; (II) vegetarian diet as intervention; (III) mean difference in hemoglobin A1c (HbA1c) and/or fasting blood glucose levels used as outcomes; and (IV) controlled trials, duration ≥4 weeks. Exclusion criteria were: (I) not an original investigation; (II) duplicate samples; (III) diabetes other than type 2; (IV) multiple interventions; and (V) uncontrolled studies. Data extraction and synthesis: The data collected included study design, baseline population characteristics, dietary data, and outcomes. Data were pooled using a random-effects model. Main outcomes and measures: Differences in HbA1c and fasting blood glucose levels associated with vegetarian diets were assessed. Results Of 477 studies identified, six met the inclusion criteria (n=255, mean age 42.5 years). Consumption of vegetarian diets was associated with a significant reduction in HbA1c [−0.39 percentage point; 95% confidence interval (CI), −0.62 to −0.15; P=0.001; I2=3.0; P for heterogeneity =0.389], and a non-significant reduction in fasting blood glucose concentration (−0.36 mmol/L; 95% CI, −1.04 to 0.32; P=0.301; I2=0; P for heterogeneity =0.710), compared with consumption of comparator diets. Conclusions Consumption of vegetarian diets is

  8. Unhealthy diets, obesity and time discounting: a systematic literature review and network analysis

    PubMed Central

    Reeves, Aaron; McKee, Martin; Galea, Gauden; Stuckler, David

    2016-01-01

    Summary There is an increasing policy commitment to address the avoidable burdens of unhealthy diet, overweight and obesity. However, to design effective policies, it is important to understand why people make unhealthy dietary choices. Research from behavioural economics suggests a critical role for time discounting, which describes how people's value of a reward, such as better health, decreases with delay to its receipt. We systematically reviewed the literature on the relationship of time discounting with unhealthy diets, overweight and obesity in Web of Science and PubMed. We identified 41 studies that met our inclusion criteria as they examined the association between time discount rates and (i) unhealthy food consumption; (ii) overweight and (iii) response to dietary and weight loss interventions. Nineteen out of 25 cross‐sectional studies found time discount rates positively associated with overweight, obesity and unhealthy diets. Experimental studies indicated that lower time discounting was associated with greater weight loss. Findings varied by how time discount rates were measured; stronger results were observed for food than monetary‐based measurements. Network co‐citation analysis revealed a concentration of research in nutrition journals. Overall, there is moderate evidence that high time discounting is a significant risk factor for unhealthy diets, overweight and obesity and may serve as an important target for intervention. © 2016 The Authors Obesity Reviews published by John Wiley & Sons Ltd on behalf of International Association for the Study of Obesity (IASO) PMID:27256685

  9. Unhealthy diets, obesity and time discounting: a systematic literature review and network analysis.

    PubMed

    Barlow, Pepita; Reeves, Aaron; McKee, Martin; Galea, Gauden; Stuckler, David

    2016-09-01

    There is an increasing policy commitment to address the avoidable burdens of unhealthy diet, overweight and obesity. However, to design effective policies, it is important to understand why people make unhealthy dietary choices. Research from behavioural economics suggests a critical role for time discounting, which describes how people's value of a reward, such as better health, decreases with delay to its receipt. We systematically reviewed the literature on the relationship of time discounting with unhealthy diets, overweight and obesity in Web of Science and PubMed. We identified 41 studies that met our inclusion criteria as they examined the association between time discount rates and (i) unhealthy food consumption; (ii) overweight and (iii) response to dietary and weight loss interventions. Nineteen out of 25 cross-sectional studies found time discount rates positively associated with overweight, obesity and unhealthy diets. Experimental studies indicated that lower time discounting was associated with greater weight loss. Findings varied by how time discount rates were measured; stronger results were observed for food than monetary-based measurements. Network co-citation analysis revealed a concentration of research in nutrition journals. Overall, there is moderate evidence that high time discounting is a significant risk factor for unhealthy diets, overweight and obesity and may serve as an important target for intervention. © 2016 The Authors Obesity Reviews published by John Wiley & Sons Ltd on behalf of International Association for the Study of Obesity (IASO). PMID:27256685

  10. Rarity and Incomplete Sampling in DNA-Based Species Delimitation.

    PubMed

    Ahrens, Dirk; Fujisawa, Tomochika; Krammer, Hans-Joachim; Eberle, Jonas; Fabrizi, Silvia; Vogler, Alfried P

    2016-05-01

    DNA-based species delimitation may be compromised by limited sampling effort and species rarity, including "singleton" representatives of species, which hampers estimates of intra- versus interspecies evolutionary processes. In a case study of southern African chafers (beetles in the family Scarabaeidae), many species and subclades were poorly represented and 48.5% of species were singletons. Using cox1 sequences from >500 specimens and ∼100 species, the Generalized Mixed Yule Coalescent (GMYC) analysis as well as various other approaches for DNA-based species delimitation (Automatic Barcode Gap Discovery (ABGD), Poisson tree processes (PTP), Species Identifier, Statistical Parsimony), frequently produced poor results if analyzing a narrow target group only, but the performance improved when several subclades were combined. Hence, low sampling may be compensated for by "clade addition" of lineages outside of the focal group. Similar findings were obtained in reanalysis of published data sets of taxonomically poorly known species assemblages of insects from Madagascar. The low performance of undersampled trees is not due to high proportions of singletons per se, as shown in simulations (with 13%, 40% and 52% singletons). However, the GMYC method was highly sensitive to variable effective population size ([Formula: see text]), which was exacerbated by variable species abundances in the simulations. Hence, low sampling success and rarity of species affect the power of the GMYC method only if they reflect great differences in [Formula: see text] among species. Potential negative effects of skewed species abundances and prevalence of singletons are ultimately an issue about the variation in [Formula: see text] and the degree to which this is correlated with the census population size and sampling success. Clade addition beyond a limited study group can overcome poor sampling for the GMYC method in particular under variable [Formula: see text] This effect was less

  11. Documenting the diet in ancient human populations through stable isotope analysis of hair.

    PubMed Central

    Macko, S A; Engel, M H; Andrusevich, V; Lubec, G; O'Connell, T C; Hedges, R E

    1999-01-01

    Fundamental to the understanding of human history is the ability to make interpretations based on artefacts and other remains which are used to gather information about an ancient population. Sequestered in the organic matrices of these remains can be information, for example, concerning incidence of disease, genetic defects and diet. Stable isotopic compositions, especially those made on isolates of collagen from bones, have been used to help suggest principal dietary components. A significant problem in the use of collagen is its long-term stability, and the possibility of isotopic alteration during early diagenesis, or through contaminating condensation reactions. In this study, we suggest that a commonly overlooked material, human hair, may represent an ideal material to be used in addressing human diets of ancient civilizations. Through the analysis of the amino-acid composition of modern hair, as well as samples that were subjected to radiation (thus simulating ageing of the hair) and hair from humans that is up to 5200 years old, we have observed little in the way of chemical change. The principal amino acids observed in all of these samples are essentially identical in relative abundances and content. Dominating the compositions are serine, glutamic acid, threonine, glycine and leucine, respectively accounting for approximately 15%, 17%, 10%, 8% and 8% of the total hydrolysable amino acids. Even minor components (for example, alanine, valine, isoleucine) show similar constancy between the samples of different ages. This constancy clearly indicates minimal alteration of the amino-acid composition of the hair. Further, it would indicate that hair is well preserved and is amenable to isotopic analysis as a tool for distinguishing sources of nutrition. Based on this observation, we have isotopically characterized modern individuals for whom the diet has been documented. Both stable nitrogen and carbon isotope compositions were assessed, and together provide an

  12. Molecular analysis of the human laminin alpha3a chain gene (LAMA3a): a strategy for mutation identification and DNA-based prenatal diagnosis in Herlitz junctional epidermolysis bullosa.

    PubMed

    Pulkkinen, L; Cserhalmi-Friedman, P B; Tang, M; Ryan, M C; Uitto, J; Christiano, A M

    1998-09-01

    Mutations in the genes (LAMA3, LAMB3, and LAMC2) encoding the subunit polypeptides of the cutaneous basement membrane zone protein laminin 5 have been reported in different forms of junctional epidermolysis bullosa (JEB), an inherited blistering skin disease. In this study, we present the complete exon-intron organization of the "a" transcript of the laminin alpha3 chain gene, LAMA3a, which is expressed primarily in the skin. We have performed fine-resolution mapping of this gene on chromosome 18q11.2 using a human-hamster radiation hybrid panel. We have also developed a mutation-detection strategy based on the exon-intron structure of LAMA3a. This strategy, based on PCR amplification of genomic sequences, followed by heteroduplex scanning and automated nucleotide sequencing, was used for successful mutation screening in a family with the lethal (Herlitz) type of JEB, and two novel LAMA3 mutations were identified in the proband. The mutations consisted of a single-base pair deletion in LAMA3a exon A11 on the paternal allele, designated 1239delC, and a two-base pair deletion in LAMA3a exon A23 on the maternal allele, designated 2959delGG. This information was also used for DNA-based prenatal testing in a subsequent pregnancy in this family. Collectively, these results attest to our expanding capability to elucidate the genetic basis of various forms of epidermolysis bullosa using molecular techniques. PMID:9759651

  13. Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet.

    PubMed

    Leray, Matthieu; Meyer, Christopher P; Mills, Suzanne C

    2015-01-01

    Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach

  14. Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet

    PubMed Central

    Meyer, Christopher P.; Mills, Suzanne C.

    2015-01-01

    Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators’ diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach

  15. New insights into the diets of harbor seals in the Salish Sea revealed by quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.; Lance, Monique M.; Elliott, Elizabeth W.; Jeffries, Steven J.; Acevedo-Gutiérrez, Alejandro; Kennish, John M.

    2012-01-01

    Harbor seals (Phoca vitulina) are an abundant predator along the west coast of North America, and there is considerable interest in their diet composition, especially in regard to predation on valued fish stocks. Available information on harbor seal diets, primarily derived from scat analysis, suggests that adult salmon (Oncorhynchus spp.), Pacific Herring (Clupea pallasii), and gadids predominate. Because diet assessments based on scat analysis may be biased, we investigated diet composition through quantitative analysis of fatty acid signatures. Blubber samples from 49 harbor seals captured in western North America from haul-outs within the area of the San Juan Islands and southern Strait of Georgia in the Salish Sea were analyzed for fatty acid composition, along with 269 fish and squid specimens representing 27 potential prey classes. Diet estimates varied spatially, demographically, and among individual harbor seals. Findings confirmed the prevalence of previously identified prey species in harbor seal diets, but other species also contributed significantly. In particular, Black (Sebastes melanops) and Yellowtail (S. flavidus) Rockfish were estimated to compose up to 50% of some individual seal diets. Specialization and high predation rates on Black and Yellowtail Rockfish by a subset of harbor seals may play a role in the population dynamics of these regional rockfish stocks that is greater than previously realized.

  16. Molecular diet analysis of two african free-tailed bats (molossidae) using high throughput sequencing.

    PubMed

    Bohmann, Kristine; Monadjem, Ara; Lehmkuhl Noer, Christina; Rasmussen, Morten; Zeale, Matt R K; Clare, Elizabeth; Jones, Gareth; Willerslev, Eske; Gilbert, M Thomas P

    2011-01-01

    Given the diversity of prey consumed by insectivorous bats, it is difficult to discern the composition of their diet using morphological or conventional PCR-based analyses of their faeces. We demonstrate the use of a powerful alternate tool, the use of the Roche FLX sequencing platform to deep-sequence uniquely 5' tagged insect-generic barcode cytochrome c oxidase I (COI) fragments, that were PCR amplified from faecal pellets of two free-tailed bat species Chaerephon pumilus and Mops condylurus (family: Molossidae). Although the analyses were challenged by the paucity of southern African insect COI sequences in the GenBank and BOLD databases, similarity to existing collections allowed the preliminary identification of 25 prey families from six orders of insects within the diet of C. pumilus, and 24 families from seven orders within the diet of M. condylurus. Insects identified to families within the orders Lepidoptera and Diptera were widely present among the faecal samples analysed. The two families that were observed most frequently were Noctuidae and Nymphalidae (Lepidoptera). Species-level analysis of the data was accomplished using novel bioinformatics techniques for the identification of molecular operational taxonomic units (MOTU). Based on these analyses, our data provide little evidence of resource partitioning between sympatric M. condylurus and C. pumilus in the Simunye region of Swaziland at the time of year when the samples were collected, although as more complete databases against which to compare the sequences are generated this may have to be re-evaluated. PMID:21731749

  17. The First New Zealanders: Patterns of Diet and Mobility Revealed through Isotope Analysis

    PubMed Central

    Kinaston, Rebecca L.; Walter, Richard K.; Jacomb, Chris; Brooks, Emma; Tayles, Nancy; Halcrow, Sian E.; Stirling, Claudine; Reid, Malcolm; Gray, Andrew R.; Spinks, Jean; Shaw, Ben; Fyfe, Roger; Buckley, Hallie R.

    2013-01-01

    Direct evidence of the environmental impact of human colonization and subsequent human adaptational responses to new environments is extremely rare anywhere in the world. New Zealand was the last Polynesian island group to be settled by humans, who arrived around the end of the 13th century AD. Little is known about the nature of human adaptation and mobility during the initial phase of colonization. We report the results of the isotopic analysis (carbon, nitrogen and strontium) of the oldest prehistoric skeletons discovered in New Zealand to assess diet and migration patterns. The isotope data show that the culturally distinctive burials, Group 1, had similar diets and childhood origins, supporting the assertion that this group was distinct from Group 2/3 and may have been part of the initial colonizing population at the site. The Group 2/3 individuals displayed highly variable diets and likely lived in different regions of the country before their burial at Wairau Bar, supporting the archaeological evidence that people were highly mobile in New Zealand since the initial phase of human settlement. PMID:23691250

  18. Analysis of rumen methanogen diversity in water buffaloes (Bubalus bubalis) under three different diets.

    PubMed

    Franzolin, Raul; St-Pierre, Benoit; Northwood, Korinne; Wright, André-Denis G

    2012-07-01

    The water buffalo (Bubalus bubalis) is a prominent livestock species for the production of milk and meat in many countries. We investigated the diversity of rumen methanogens in Mediterranean water buffaloes maintained in Brazil under different diets: corn silage, grazing pasture, or sugar cane. A total of 467 clones were isolated from three methanogen 16S rRNA gene clone libraries that each represented a distinct feed type. The 467 clones were assigned to 19 species-level operational taxonomic units (OTUs). Four OTUs were represented in all three libraries, eight OTUs were library-specific, six OTUs were found in only the corn silage and pasture grazing libraries, and one OTU was shared only between pasture grazing and sugar cane libraries. We found that Methanobrevibacter-related sequences were the most abundant in the water buffaloes sampled for our analysis, in contrast to previously reported studies showing that Methanomicrobium mobile-like methanogens were the most abundant methanogens in water buffaloes of Murrah and Surti breeds sampled in India. Considering the worldwide distribution of water buffaloes and the likely wide variety of diets provided, our results combined with studies from other groups support that larger scope analyses of microbiomes for this livestock species would provide great insight into the contribution of geographical location, breed, and diet in determining the population structure of rumen microorganisms. PMID:22286379

  19. Popular Mobile Phone Apps for Diet and Weight Loss: A Content Analysis

    PubMed Central

    Roehrer, Erin

    2016-01-01

    Background A review of the literature has revealed that the rates of overweight and obesity have been increasing in Australia over the last two decades and that wellness mobile phone apps play a significant role in monitoring and managing individuals’ weight. Although mobile phone app markets (iTunes and Google Play) list thousands of mobile phone health apps, it is not always clear whether those apps are supported by credible sources. Likewise, despite the prevailing use of mobile phone apps to aid with weight management, the usability features of these apps are not well characterized. Objective The research explored how usability taxonomy could inform the popularity of downloaded, socially focused wellness mobile phone apps, in particular weight loss and diet apps. The aim of the study was to investigate the Australian mobile phone app stores (iTunes and Google Play) in order to examine the usability features of the most popular (ie, most downloaded) wellness apps. Methods The design of this study comprises 3 main stages: stage 1, identifying apps; stage 2, development of weight loss and diet evaluation framework; and stage 3, application of the evaluation framework. Each stage includes specific data collection, analysis tools, and techniques. Results The study has resulted in the development of a justified evaluation framework for weight loss and diet mobile phone apps. Applying the evaluation framework to the identified apps has shown that the most downloaded iTunes and Google Play apps are not necessarily the most usable or effective. In addition, the research found that search algorithms for iTunes and Google Play are biased toward apps’ titles and keywords that do not accurately define the real functionality of the app. Moreover, the study has also analyzed the apps’ user reviews, which served as justification for the developed evaluation framework. Conclusions The analysis has shown that ease of use, reminder, bar code scanning, motivation, usable for

  20. Toward DNA-based facial composites: preliminary results and validation.

    PubMed

    Claes, Peter; Hill, Harold; Shriver, Mark D

    2014-11-01

    The potential of constructing useful DNA-based facial composites is forensically of great interest. Given the significant identity information coded in the human face these predictions could help investigations out of an impasse. Although, there is substantial evidence that much of the total variation in facial features is genetically mediated, the discovery of which genes and gene variants underlie normal facial variation has been hampered primarily by the multipartite nature of facial variation. Traditionally, such physical complexity is simplified by simple scalar measurements defined a priori, such as nose or mouth width or alternatively using dimensionality reduction techniques such as principal component analysis where each principal coordinate is then treated as a scalar trait. However, as shown in previous and related work, a more impartial and systematic approach to modeling facial morphology is available and can facilitate both the gene discovery steps, as we recently showed, and DNA-based facial composite construction, as we show here. We first use genomic ancestry and sex to create a base-face, which is simply an average sex and ancestry matched face. Subsequently, the effects of 24 individual SNPs that have been shown to have significant effects on facial variation are overlaid on the base-face forming the predicted-face in a process akin to a photomontage or image blending. We next evaluate the accuracy of predicted faces using cross-validation. Physical accuracy of the facial predictions either locally in particular parts of the face or in terms of overall similarity is mainly determined by sex and genomic ancestry. The SNP-effects maintain the physical accuracy while significantly increasing the distinctiveness of the facial predictions, which would be expected to reduce false positives in perceptual identification tasks. To the best of our knowledge this is the first effort at generating facial composites from DNA and the results are preliminary

  1. DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents

    PubMed Central

    Lopes, C M; De Barba, M; Boyer, F; Mercier, C; da Silva Filho, P J S; Heidtmann, L M; Galiano, D; Kubiak, B B; Langone, P; Garcias, F M; Gielly, L; Coissac, E; de Freitas, T R O; Taberlet, P

    2015-01-01

    Closely related sympatric species commonly develop different ecological strategies to avoid competition. Ctenomys minutus and C. flamarioni are subterranean rodents parapatrically distributed in the southern Brazilian coastal plain, showing a narrow sympatric zone. To gain understanding on food preferences and possible competition for food resources, we evaluated their diet composition performing DNA metabarcoding analyzes of 67 C. minutus and 100 C. flamarioni scat samples, collected along the species geographical ranges. Thirteen plant families, mainly represented by Poaceae, Araliaceae, Asteraceae and Fabaceae, were identified in the diet of C. minutus. For C. flamarioni, 10 families were recovered, with a predominance of Poaceae, Araliaceae and Asteraceae. A significant correlation between diet composition and geographical distance was detected in C. minutus, whereas the diet of C. flamarioni was quite homogeneous throughout its geographical distribution. No significant differences were observed between males and females of each species. However, differences in diet composition between species were evident according to multivariate analysis. Our results suggest some level of diet partitioning between C. flamarioni and C. minutus in the sympatric region. While the first species is more specialized on few plant items, the second showed a more varied and heterogeneous diet pattern among individuals. These differences might have been developed to avoid competition in the region of co-occurrence. Resource availability in the environment also seems to influence food choices. Our data indicate that C. minutus and C. flamarioni are generalist species, but that some preference for Poaceae, Asteraceae and Araliaceae families can be suggested for both rodents. PMID:25649502

  2. A Qualitative Analysis of User Experiences With a Self-Tracker for Activity, Sleep, and Diet

    PubMed Central

    2014-01-01

    Background The recent increase in chronic diseases and an aging population warrant the necessity of health self-management. As small electronic devices that track one’s activity, sleep, and diet, called self-trackers, are being widely distributed, it is prudent to investigate the user experience and the effectiveness of these devices, and use the information toward engineering better devices that would result in increased efficiency and usability. Objective The aim of this study was to abstract the constructs that constitute the user experiences of the self-tracker for activity, sleep, and diet. Additionally, we aimed to develop and verify the Health Information Technology Acceptance Model-II (HITAM-II) through a qualitative data analysis approach. Methods The study group consisted of 18 female college students who participated in an in-depth interview after completing a 3-month study of utilizing a self-tracker designed to monitor activity, sleep, and diet. The steps followed in the analysis were: (1) extraction of constructs from theoretical frameworks, (2) extraction of constructs from interview data using a qualitative methodology, and (3) abstraction of constructs and modeling of the HITAM-II. Results The constructs that constitute the HITAM-II are information technology factors, personal factors, social factors, attitude, behavioral intention, and behavior. These constructs are further divided into subconstructs to additionally support the HITAM-II. Conclusions The HITAM-II was found to successfully describe the health consumer’s attitude, behavioral intention, and behavior from another perspective. The result serves as the basis for a unique understanding of the user experiences of HIT. PMID:24594898

  3. Macronutrient Optimization and Seasonal Diet Mixing in a Large Omnivore, the Grizzly Bear: A Geometric Analysis

    PubMed Central

    Coogan, Sean C. P.; Raubenheimer, David; Stenhouse, Gordon B.; Nielsen, Scott E.

    2014-01-01

    Nutrient balance is a strong determinant of animal fitness and demography. It is therefore important to understand how the compositions of available foods relate to required balance of nutrients and habitat suitability for animals in the wild. These relationships are, however, complex, particularly for omnivores that often need to compose balanced diets by combining their intake from diverse nutritionally complementary foods. Here we apply geometric models to understand how the nutritional compositions of foods available to an omnivorous member of the order Carnivora, the grizzly bear (Ursus arctos L.), relate to optimal macronutrient intake, and assess the seasonal nutritional constraints on the study population in west-central Alberta, Canada. The models examined the proportion of macronutrients that bears could consume by mixing their diet from food available in each season, and assessed the extent to which bears could consume the ratio of protein to non-protein energy previously demonstrated using captive bears to optimize mass gain. We found that non-selective feeding on ungulate carcasses provided a non-optimal macronutrient balance with surplus protein relative to fat and carbohydrate, reflecting adaptation to an omnivorous lifestyle, and that optimization through feeding selectively on different tissues of ungulate carcasses is unlikely. Bears were, however, able to dilute protein intake to an optimal ratio by mixing their otherwise high-protein diet with carbohydrate-rich fruit. Some individual food items were close to optimally balanced in protein to non-protein energy (e.g. Hedysarum alpinum roots), which may help explain their dietary prevalence. Ants may be consumed particularly as a source of lipids. Overall, our analysis showed that most food available to bears in the study area were high in protein relative to lipid or carbohydrate, suggesting the lack of non-protein energy limits the fitness (e.g. body size and reproduction) and population density

  4. Macronutrient optimization and seasonal diet mixing in a large omnivore, the grizzly bear: a geometric analysis.

    PubMed

    Coogan, Sean C P; Raubenheimer, David; Stenhouse, Gordon B; Nielsen, Scott E

    2014-01-01

    Nutrient balance is a strong determinant of animal fitness and demography. It is therefore important to understand how the compositions of available foods relate to required balance of nutrients and habitat suitability for animals in the wild. These relationships are, however, complex, particularly for omnivores that often need to compose balanced diets by combining their intake from diverse nutritionally complementary foods. Here we apply geometric models to understand how the nutritional compositions of foods available to an omnivorous member of the order Carnivora, the grizzly bear (Ursus arctos L.), relate to optimal macronutrient intake, and assess the seasonal nutritional constraints on the study population in west-central Alberta, Canada. The models examined the proportion of macronutrients that bears could consume by mixing their diet from food available in each season, and assessed the extent to which bears could consume the ratio of protein to non-protein energy previously demonstrated using captive bears to optimize mass gain. We found that non-selective feeding on ungulate carcasses provided a non-optimal macronutrient balance with surplus protein relative to fat and carbohydrate, reflecting adaptation to an omnivorous lifestyle, and that optimization through feeding selectively on different tissues of ungulate carcasses is unlikely. Bears were, however, able to dilute protein intake to an optimal ratio by mixing their otherwise high-protein diet with carbohydrate-rich fruit. Some individual food items were close to optimally balanced in protein to non-protein energy (e.g. Hedysarum alpinum roots), which may help explain their dietary prevalence. Ants may be consumed particularly as a source of lipids. Overall, our analysis showed that most food available to bears in the study area were high in protein relative to lipid or carbohydrate, suggesting the lack of non-protein energy limits the fitness (e.g. body size and reproduction) and population density

  5. Transcriptomic Analysis of the Effects of a Fish Oil Enriched Diet on Murine Brains

    PubMed Central

    Gautam, Aarti; Miller, Stacy-Ann; Muhie, Seid; Meyerhoff, James; Jett, Marti

    2014-01-01

    The health benefits of fish oil enriched with high omega-3 polyunsaturated fatty acids (n-3 PUFA) are widely documented. Fish oil as dietary supplements, however, show moderate clinical efficacy, highlighting an immediate scope of systematic in vitro feedback. Our transcriptomic study was designed to investigate the genomic shift of murine brains fed on fish oil enriched diets. A customized fish oil enriched diet (FD) and standard lab diet (SD) were separately administered to two randomly chosen populations of C57BL/6J mice from their weaning age until late adolescence. Statistical analysis mined 1,142 genes of interest (GOI) differentially altered in the hemibrains collected from the FD- and SD-fed mice at the age of five months. The majority of identified GOI (∼40%) encodes proteins located in the plasma membrane, suggesting that fish oil primarily facilitated the membrane-oriented biofunctions. FD potentially augmented the nervous system's development and functions by selectively stimulating the Src-mediated calcium-induced growth cascade and the downstream PI3K-AKT-PKC pathways. FD reduced the amyloidal burden, attenuated oxidative stress, and assisted in somatostatin activation—the signatures of attenuation of Alzheimer's disease, Parkinson's disease, and affective disorder. FD induced elevation of FKBP5 and suppression of BDNF, which are often linked with the improvement of anxiety disorder, depression, and post-traumatic stress disorder. Hence we anticipate efficacy of FD in treating illnesses such as depression that are typically triggered by the hypoactivities of dopaminergic, adrenergic, cholinergic, and GABAergic networks. Contrastingly, FD's efficacy could be compromised in treating illnesses such as bipolar disorder and schizophrenia, which are triggered by hyperactivities of the same set of neuromodulators. A more comprehensive investigation is recommended to elucidate the implications of fish oil on disease pathomechanisms, and the result

  6. The cell as the smallest DNA-based molecular computer.

    PubMed

    Ji, S

    1999-10-01

    The pioneering work of Adleman (1994) demonstrated that DNA molecules in test tubes can be manipulated to perform a certain type of mathematical computation. This has stimulated a theoretical interest in the possibility of constructing DNA-based molecular computers. To gauge the practicality of realizing such microscopic computers, it was thought necessary to learn as much as possible from the biology of the living cell--presently the only known DNA-based molecular computer in existence. Here the recently developed theoretical model of the living cell (the Bhopalator) and its associated theories (e.g. cell language), principles, laws and concepts (e.g. conformons, IDS's) are briefly reviewed and summarized in the form of a set of five laws of 'molecular semiotics' (synonyms include 'microsemiotics', 'cellular semiotics', or 'cytosemiotics') the study of signs mediating measurement, computation, and communication on the cellular and molecular levels. Hopefully, these laws will find practical applications in designing DNA-based computing systems. PMID:10636037

  7. Impact of low-carbohydrate diet on body composition: meta-analysis of randomized controlled studies.

    PubMed

    Hashimoto, Y; Fukuda, T; Oyabu, C; Tanaka, M; Asano, M; Yamazaki, M; Fukui, M

    2016-06-01

    The effect of low-carbohydrate diet (LCD) on body composition, especially fat mass, in obese individuals remains to be elucidated. We performed a meta-analysis to provide quantitative summary estimates of the mean change of body weight (kg) and fat mass (kg) in LCD comparing to those in control diet. Literature searches were performed using EMBASE, MEDLINE and Cochrane Library until Dec 2014. Fourteen randomized controlled studies were included in this meta-analysis. Eight studies including very LCD (50 g carbohydrate or 10% calorie from carbohydrate) and seven studies including mild LCD (about 40% calorie from carbohydrate). Meta-analysis carried out on data of 1416 obese individuals, showed that LCD was associated with decrease in body weight (-0.70 kg [95% CI -1.07/-0.33]) or fat mass (-0.77 kg [-1.55/-0.32]). Subgroup meta-analysis of studies in over 12 months suggested that LCD was not associated with decrease in body weight (-0.44 kg [-0.94/0.07]), but LCD was associated with decrease in fat mass (-0.57 kg [-1.05/-0.09]). In addition, very LCD was associated with decrease in fat mass (-0.97 kg [-1.50/-0.44]), but mild LCD was not associated with decrease in fat mass (-0.43 kg [-1.15/0.33]). LCD, especially very LCD, might be effective for decrease in fat mass in obese individuals. © 2016 World Obesity. PMID:27059106

  8. DNA-based methods of geochemical prospecting

    DOEpatents

    Ashby, Matthew

    2011-12-06

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  9. Reconstructing diet and behaviour of Neanderthals from Central Italy through dental macrowear analysis.

    PubMed

    Fiorenza, Luca

    2015-07-20

    Neanderthals have been traditionally considered at the top of the food chain with a diet mostly consisting of animal proteins. New findings challenged this view and suggested that Neanderthals living in areas with more favourable climatic conditions exploited various food sources, including plant materials. In this study, the attention is focused on dental macrowear of Neanderthals from Central Italy, whose diet has been largely unexplored. Three-dimensional digital models of teeth have been examined through occlusal fingerprint analysis (OFA), a method used to understand how wear facets are formed. The results show a close similarity between the specimens of Saccopastore 1 and 2, with a wear pattern that indicates the use of diverse sources of food, but with a predominance of animal proteins. On the other hand, the specimens of Guattari 2 and 3 display a slightly different dental wear from each other, which probably reflects the chronological sequence of the Guattari Cave. It appears that at the end of the marine isotope stage (MIS)5 the occupants of this cave consumed marginally more plant foods, while during MIS 3 they relied more on animal proteins. Finally, a close look at the Saccopastore maxillary molars reveals the presence of a distinct type of wear that has been previously described in some Neanderthals and early Homo sapiens from Near East, and it provides additional information about the culture and lifestyle of these Pleistocene human populations. PMID:25324463

  10. Effect of mycotoxin-containing diets on epigenetic modifications of mouse oocytes by fluorescence microscopy analysis.

    PubMed

    Zhu, Cheng-Cheng; Hou, Yan-Jun; Han, Jun; Liu, Hong-Lin; Cui, Xiang-Shun; Kim, Nam-Hyung; Sun, Shao-Chen

    2014-08-01

    Mycotoxins, such as aflatoxin (AF), fumonisin B1, zearalenone (ZEA), and deoxynivalenol (DON), are commonly found in many food commodities. Mycotoxins have been shown to increase DNA methylation levels in a human intestinal cell line. We previously showed that the developmental competence of oocytes was affected in mice that had been fed a mycotoxin-containing diet. In this study, we explored possible mechanisms of low mouse oocyte developmental competence after mycotoxin treatment in an epigenetic modification perspective. Mycotoxin-contaminated maize (DON at 3,875 μg/kg, ZEA at 1,897 μg/kg, and AF at 806 μg/kg) was included in diets at three different doses (mass percentage: 0, 15, and 30%) and fed to mice for 4 weeks. The fluorescence intensity analysis showed that the general DNA methylation levels increased in oocytes from high dose mycotoxin-fed mice. Mouse oocyte histone methylation was also altered. H3K9me3 and H4K20me3 level increased in oocytes from mycotoxin-fed mice, whereas H3K27me3 and H4K20me2 level decreased in oocytes from mycotoxin-fed mice. Thus, our results indicate that naturally occurring mycotoxins have effects on epigenetic modifications in mouse oocytes, which may be one of the reasons for reduced oocyte developmental competence. PMID:24810297

  11. Reliability and Efficiency of a DNA-Based Computation

    NASA Astrophysics Data System (ADS)

    Deaton, R.; Garzon, M.; Murphy, R. C.; Rose, J. A.; Franceschetti, D. R.; Stevens, S. E., Jr.

    1998-01-01

    DNA-based computing uses the tendency of nucleotide bases to bind (hybridize) in preferred combinations to do computation. Depending on reaction conditions, oligonucleotides can bind despite noncomplementary base pairs. These mismatched hybridizations are a source of false positives and negatives, which limit the efficiency and scalability of DNA-based computing. The ability of specific base sequences to support error-tolerant Adleman-style computation is analyzed, and criteria are proposed to increase reliability and efficiency. A method is given to calculate reaction conditions from estimates of DNA melting.

  12. Operation of a DNA-Based Autocatalytic Network in Serum

    NASA Astrophysics Data System (ADS)

    Graugnard, Elton; Cox, Amber; Lee, Jeunghoon; Jorcyk, Cheryl; Yurke, Bernard; Hughes, William L.

    The potential for inferring the presence of cancer by the detection of miRNA in human blood has motivated research into the design and operation of DNA-based chemical amplifiers that can operate in bodily fluids. As a first step toward this goal, we have tested the operation of a DNA-based autocatalytic network in human serum and mouse serum. With the addition of sodium dodecyl sulfate to prevent degradation by nuclease activity, the network was found to operate successfully with both DNA and RNA catalysts.

  13. Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces

    PubMed Central

    Ford, Michael J.; Hempelmann, Jennifer; Hanson, M. Bradley; Ayres, Katherine L.; Baird, Robin W.; Emmons, Candice K.; Lundin, Jessica I.; Schorr, Gregory S.; Wasser, Samuel K.; Park, Linda K.

    2016-01-01

    Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%). Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population’s summer diet. PMID:26735849

  14. Very-low-carbohydrate ketogenic diet v. low-fat diet for long-term weight loss: a meta-analysis of randomised controlled trials.

    PubMed

    Bueno, Nassib Bezerra; de Melo, Ingrid Sofia Vieira; de Oliveira, Suzana Lima; da Rocha Ataide, Terezinha

    2013-10-01

    The role of very-low-carbohydrate ketogenic diets (VLCKD) in the long-term management of obesity is not well established. The present meta-analysis aimed to investigate whether individuals assigned to a VLCKD (i.e. a diet with no more than 50 g carbohydrates/d) achieve better long-term body weight and cardiovascular risk factor management when compared with individuals assigned to a conventional low-fat diet (LFD; i.e. a restricted-energy diet with less than 30% of energy from fat). Through August 2012, MEDLINE, CENTRAL, ScienceDirect,Scopus, LILACS, SciELO, ClinicalTrials.gov and grey literature databases were searched, using no date or language restrictions, for randomised controlled trials that assigned adults to a VLCKD or a LFD, with 12 months or more of follow-up. The primary outcome was bodyweight. The secondary outcomes were TAG, HDL-cholesterol (HDL-C), LDL-cholesterol (LDL-C), systolic and diastolic blood pressure,glucose, insulin, HbA1c and C-reactive protein levels. A total of thirteen studies met the inclusion/exclusion criteria. In the overall analysis,five outcomes revealed significant results. Individuals assigned to a VLCKD showed decreased body weight (weighted mean difference 20·91 (95% CI 21·65, 20·17) kg, 1415 patients), TAG (weighted mean difference 20·18 (95% CI 20·27, 20·08) mmol/l, 1258 patients)and diastolic blood pressure (weighted mean difference 21·43 (95% CI 22·49, 20·37) mmHg, 1298 patients) while increased HDL-C(weighted mean difference 0·09 (95% CI 0·06, 0·12) mmol/l, 1257 patients) and LDL-C (weighted mean difference 0·12 (95% CI 0·04,0·2) mmol/l, 1255 patients). Individuals assigned to a VLCKD achieve a greater weight loss than those assigned to a LFD in the longterm; hence, a VLCKD may be an alternative tool against obesity. PMID:23651522

  15. Artifacts associated with the measurement of oxidized DNA bases.

    PubMed Central

    Cadet, J; Douki, T; Ravanat, J L

    1997-01-01

    In this paper we review recent aspects of the measurement of oxidized DNA bases, currently a matter of debate. There has long been an interest in the determination of the level of oxidized bases in cellular DNA under both normal and oxidative stress conditions. In this respect, the situation is confusing because variations that may be as large as two orders of magnitude have been reported for the yield of the formation of 8-oxo-7,8-dihydroguanine (8-oxoGua) in similar DNA samples. However, recent findings clearly show that application of several assays like gas chromatography-mass spectrometry (GC-MS) and -32P--postlabeling may lead to a significant overestimation of the level of oxidized bases in cellular DNA. In particular, the silylation step, which is required to make the samples volatile for the GC-MS analysis, has been shown to induce oxidation of normal bases at the level of about one oxidized base per 10(4) normal bases. This has been found to be a general process that applies in particular to 8-oxoGua, 8-oxo-7, 8-dihydroadenine,5-hydroxycytosine, 5-(hydroxymethyl)uracil, and 5-formyluracil. Interestingly, prepurification of the oxidized bases from DNA hydrolysate prior to the derivatization reaction prevents artefactual oxidation. Under these conditions, the level of oxidized bases measured by GC-MS is similar to that obtained by HPLC associated with electrochemical detection (HPLC-EC). It should be added that the level of 8-oxo-7,8-dihydro-2;-deoxyguanosine in control cellular DNA has been found to be about fivefold lower than in earlier HPLC-EC measurements by using appropriate conditions of extraction and enzymatic digestion of DNA. Similar conclusions were reached by measuring formamidopyrimidine-DNA glycosylase sensitive sites as revealed by the single cell gel electrophoresis (comet) assay. Images Figure 1. PMID:9349826

  16. Hydrogen bond disruption in DNA base pairs from (14)C transmutation.

    PubMed

    Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Christopher R; Mancera, Ricardo L; Marks, Nigel A

    2014-09-01

    Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that (14)C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these (14)C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication. PMID:25127298

  17. Microwave acid digestion and preconcentration neutron activation analysis of biological and diet samples for iodine.

    PubMed

    Rao, R R; Chatt, A

    1991-07-01

    A simple preconcentration neutron activation analysis (PNAA) method has been developed for the determination of low levels of iodine in biological and nutritional materials. The method involves dissolution of the samples by microwave digestion in the presence of acids in closed Teflon bombs and preconcentration of total iodine, after reduction to iodide with hydrazine sulfate, by coprecipitation with bismuth sulfide. The effects of different factors such as acidity, time for complete precipitation, and concentrations of bismuth, sulfide, and diverse ions on the quantitative recovery of iodide have been studied. The absolute detection limit of the PNAA method is 5 ng of iodine. Precision of measurement, expressed in terms of relative standard deviation, is about 5% at 100 ppb and 10% at 20 ppb levels of iodine. The PNAA method has been applied to several biological reference materials and total diet samples. PMID:1897721

  18. Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases

    NASA Astrophysics Data System (ADS)

    Ahmed, Towfiq; Haraldsen, Jason T.; Rehr, John J.; Di Ventra, Massimiliano; Schuller, Ivan; Balatsky, Alexander V.

    2014-03-01

    Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new ‘multi-point cross-correlation’ technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology.

  19. Oxidation of DNA bases, deoxyribonucleosides and homopolymers by peroxyl radicals.

    PubMed Central

    Simandan, T; Sun, J; Dix, T A

    1998-01-01

    DNA base oxidation is considered to be a key event associated with disease initiation and progression in humans. Peroxyl radicals (ROO. ) are important oxidants found in cells whose ability to react with the DNA bases has not been characterized extensively. In this paper, the products resulting from ROO. oxidation of the DNA bases are determined by gas chromatography/MS in comparison with authentic standards. ROO. radicals oxidize adenine and guanine to their 8-hydroxy derivatives, which are considered biomarkers of hydroxyl radical (HO.) oxidations in cells. ROO. radicals also oxidize adenine to its hydroxylamine, a previously unidentified product. ROO. radicals oxidize cytosine and thymine to the monohydroxy and dihydroxy derivatives that are formed by oxidative damage in cells. Identical ROO. oxidation profiles are observed for each base when exposed as deoxyribonucleosides, monohomopolymers and base-paired dihomopolymers. These results have significance for the development, utilization and interpretation of DNA base-derived biomarkers of oxidative damage associated with disease initiation and propagation, and support the idea that the mutagenic potential of N-oxidized bases, when generated in cellular DNA, will require careful evaluation. Adenine hydroxylamine is proposed as a specific molecular probe for the activity of ROO. in cellular systems. PMID:9761719

  20. Quantitative analysis of ruminal methanogenic microbial populations in beef cattle divergent in phenotypic residual feed intake (RFI) offered contrasting diets

    PubMed Central

    2014-01-01

    Background Methane (CH4) emissions in cattle are an undesirable end product of rumen methanogenic fermentative activity as they are associated not only with negative environmental impacts but also with reduced host feed efficiency. The aim of this study was to quantify total and specific rumen microbial methanogenic populations in beef cattle divergently selected for residual feed intake (RFI) while offered (i) a low energy high forage (HF) diet followed by (ii) a high energy low forage (LF) diet. Ruminal fluid was collected from 14 high (H) and 14 low (L) RFI animals across both dietary periods. Quantitative real time PCR (qRT-PCR) analysis was conducted to quantify the abundance of total and specific rumen methanogenic microbes. Spearman correlation analysis was used to investigate the association between the relative abundance of methanogens and animal performance, rumen fermentation variables and diet digestibility. Results Abundance of methanogens, did not differ between RFI phenotypes. However, relative abundance of total and specific methanogen species was affected (P < 0.05) by diet type, with greater abundance observed while animals were offered the LF compared to the HF diet. Conclusions These findings suggest that differences in abundance of specific rumen methanogen species may not contribute to variation in CH4 emissions between efficient and inefficient animals, however dietary manipulation can influence the abundance of total and specific methanogen species. PMID:25276350

  1. [Analysis of diet composition and overlap in four species of the genus Diplectrum (Perciformes: Serranidae) in the Mexican Central Pacific].

    PubMed

    Aguilar Palomino, Bernabé; González Sansón, Gaspar

    2010-12-01

    Analysis of diet composition and overlap in four species of the genus Diplectrum (Perciformes: Serranidae) in the Mexican Central Pacific. The information of trophic interactions among species is essential to understand ecosystem function. To assess this in four Diplectrum species, we analyzed the stomach contents of 397 individuals caught using shrimp trawling nets off the coasts of Jalisco and Colima, Mexico. Main food component of D. eumelum were fish of the Order Pleuronectiformes, followed by shrimps (Metapenaeopsis spp). D. euryplectrum feeds mainly on crustaceans, with stomatopods (Squilla mantoidea) as main food items followed by shrimps and brachyurans. Fish and polychaetes had a low representation in the diet of this species. D. labarum feeds mainly on crustaceans, mollusks and fish. The stomatopod Eurysquilla veleronis contributed to with a high diet percentage by weight, followed by shrimps (mostly Solenoceraflorae) and brachyurans, as well as the squid Lolliguncula diomedae. Fishes (Ophidion spp.) were also an important component of the diet of this species. The most common preys of D. rostrum were crustaceans, mollusks, polychaetes and fish. The squid Lolliguncula diomedae and fishes of genus Ophidion were also well represented in the diet. Diet breadth index yielded significant differences between species. The number of diet items varied from 16 in D. euryplectrum to 6 in D. eumelum. The average value of overlap (0.247) was not significantly different (p = 0.118) from the expected one for a null model (0.174). The observed variance of the overlap index (0.071) was significantly higher (V = 0.025, p = 0.0004) than the value expected for a null model. PMID:21250475

  2. Anti-Tumor Effects of Ketogenic Diets in Mice: A Meta-Analysis

    PubMed Central

    Klement, Rainer J.; Champ, Colin E.; Otto, Christoph; Kämmerer, Ulrike

    2016-01-01

    Background Currently ketogenic diets (KDs) are hyped as an anti-tumor intervention aimed at exploiting the metabolic abnormalities of cancer cells. However, while data in humans is sparse, translation of murine tumor models to the clinic is further hampered by small sample sizes, heterogeneous settings and mixed results concerning tumor growth retardation. The aim was therefore to synthesize the evidence for a growth inhibiting effect of KDs when used as a monotherapy in mice. Methods We conducted a Bayesian random effects meta-analysis on all studies assessing the survival (defined as the time to reach a pre-defined endpoint such as tumor volume) of mice on an unrestricted KD compared to a high carbohydrate standard diet (SD). For 12 studies meeting the inclusion criteria either a mean survival time ratio (MR) or hazard ratio (HR) between the KD and SD groups could be obtained. The posterior estimates for the MR and HR averaged over four priors on the between-study heterogeneity τ2 were MR = 0.85 (95% highest posterior density interval (HPDI) = [0.73, 0.97]) and HR = 0.55 (95% HPDI = [0.26, 0.87]), indicating a significant overall benefit of the KD in terms of prolonged mean survival times and reduced hazard rate. All studies that used a brain tumor model also chose a late starting point for the KD (at least one day after tumor initiation) which accounted for 26% of the heterogeneity. In this subgroup the KD was less effective (MR = 0.89, 95% HPDI = [0.76, 1.04]). Conclusions There was an overall tumor growth delaying effect of unrestricted KDs in mice. Future experiments should aim at differentiating the effects of KD timing versus tumor location, since external evidence is currently consistent with an influence of both of these factors. PMID:27159218

  3. Macronutrient contributions of insects to the diets of hunter-gatherers: a geometric analysis.

    PubMed

    Raubenheimer, David; Rothman, Jessica M; Pontzer, Herman; Simpson, Stephen J

    2014-06-01

    We present a geometric model for examining the macronutrient contributions of insects in the diets of pre-agricultural humans, and relate the findings to some contemporary societies that regularly eat insects. The model integrates published data on the macronutrient composition of insects and other foods in the diets of humans, recommended human macronutrient intakes, and estimated macronutrient intakes to examine the assumption that insects provided to pre-agricultural humans an invertebrate equivalent of vertebrate-derived meats, serving primarily as a source of protein. Our analysis suggests that insects vary more widely in their macronutrient content than is likely to be the case for most wild vertebrate meats, spanning a broad range of protein, fat and carbohydrate concentrations. Potentially, therefore, in terms of their proportional macronutrient composition, insects could serve as equivalents not only of wild meat, but of a range of other foods including some shellfish, nuts, pulses, vegetables and even fruits. Furthermore, humans might systematically manipulate the composition of edible insects to meet specific needs through pre-ingestive processing, such as cooking and selective removal of body parts. We present data suggesting that in modern societies for which protein is the more limiting macronutrient, pre-ingestive processing of edible insects might serve to concentrate protein. It is likely, however, that the dietary significance of insects was different for Paleolithic hunter-gatherers who were more limited in non-protein energy. Our conclusions are constrained by available data, but highlight the need for further studies, and suggest that our model provides an integrative framework for conceiving these studies. PMID:24630913

  4. Inclusion of sorghum, millet and cottonseed meal in broiler diets: a meta-analysis of effects on performance.

    PubMed

    Batonon-Alavo, D I; Umar Faruk, M; Lescoat, P; Weber, G M; Bastianelli, D

    2015-07-01

    A meta-analysis was conducted (i) to evaluate broiler response to partial or total substitution of corn by sorghum and millet and (ii) to determine the effect of soybean meal replacement by cottonseed meal in broiler diet. The database included 190 treatments from 29 experiments published from 1990 to 2013. Bird responses to an experimental diet were calculated relative to the control (Experimental-Control), and were submitted to mixed-effect models. Results showed that diets containing millet led to similar performance as the corn-based ones for all parameters, whereas sorghum-based diets decreased growth performance. No major effect of the level of substitution was observed with millet or cottonseed meal. No effect of the level of substitution of sorghum on feed intake was found; however, growth performance decreased when the level of substitution of corn by sorghum increased. Cottonseed meal was substituted to soybean meal up to 40% and found to increase feed intake while reducing growth performance. Young birds were not more sensitive to these ingredients than older birds since there was no negative effect of these ingredients on performance in the starter phase. Results obtained for sorghum pointed out the necessity to find technological improvements that will increase the utilization of these feedstuffs in broiler diet. An additional work is scheduled to validate these statistical results in vivo and to evaluate the interactions induced with the simultaneous inclusions of sorghum, millet and cottonseed meal in broiler feeding. PMID:25735210

  5. A comparative analysis of double-crested cormorant diets from stomachs and pellets from two Lake Ontario colonies

    USGS Publications Warehouse

    Johnson, James H.; Ross, Robert M.; McCullough, Russell D.; Mathers, Alastair

    2010-01-01

    Double-crested cormorant (Phalacrocorax auritus) diets were compared with evidence from the stomachs of shot birds and from regurgitated pellets at High Bluff Island and Little Galloo Island, Lake Ontario. The highest similarity in diets determined by stomach and pellet analyses occurred when both samples were collected on the same day. Diet overlap dropped substantially between the two methods when collection periods were seven to ten days apart, which suggested differences in prey availability between the two periods. Since the average number of fish recovered in pellets was significantly higher than that in stomachs, use of pellets to determine fish consumption of double-crested cormorants may be more valid than stomach analysis because pellet content represent an integrated sampling of food consumed over approximately 24 hours.

  6. High-Moisture Diet for Laboratory Rats: Nutrient Analysis, Growth, and Organ Weights

    NASA Technical Reports Server (NTRS)

    Battles, August H.; Knapka, Joseph T.; Lewis, Laura; Lang, Marie T.; Gruendel, Douglas J.

    1991-01-01

    A diet (KSC-25) to be sterilized by irradiation was formulated to contain 66% moisture and to provide the required nutrients for growing rats. Analyses of the irradiated dry diet provided data to evaluate its nutrient content. The diet was evaluated for its ability to supply all nutrients, including water, required by immature rats. Sixteen Sprague-Dawley rats were fed the high-moisture diet with or without access to a water bottle. Rats (n = 16) fed an irradiated purified diet in a meal form with access to a water bottle were the control animals. Feed efficiency, food and water consumption, and growth rate data were collected during the 28-day study. Organ weights were collected on day 28. The test diet met or exceeded the National Research Council (NRC) estimated nutritional requirements for immature laboratory rats. The 66% moisture KSC-25 diet provided all nutrients, including water, required by weanling male Sprague-Dawley rats for growth equivalent to the established purified diet.

  7. Composition of horse diets on cool-season grass pastures using microhistological analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grazing patterns and diet composition can be difficult to determine with horses, but are important when pastures contain species that have the potential to cause animal toxicity. The objective of this study was to determine the composition of domesticated horse diets when grazing mixed cool-season p...

  8. IsoWeb: A Bayesian Isotope Mixing Model for Diet Analysis of the Whole Food Web

    PubMed Central

    Kadoya, Taku; Osada, Yutaka; Takimoto, Gaku

    2012-01-01

    Quantitative description of food webs provides fundamental information for the understanding of population, community, and ecosystem dynamics. Recently, stable isotope mixing models have been widely used to quantify dietary proportions of different food resources to a focal consumer. Here we propose a novel mixing model (IsoWeb) that estimates diet proportions of all consumers in a food web based on stable isotope information. IsoWeb requires a topological description of a food web, and stable isotope signatures of all consumers and resources in the web. A merit of IsoWeb is that it takes into account variation in trophic enrichment factors among different consumer-resource links. Sensitivity analysis using realistic hypothetical food webs suggests that IsoWeb is applicable to a wide variety of food webs differing in the number of species, connectance, sample size, and data variability. Sensitivity analysis based on real topological webs showed that IsoWeb can allow for a certain level of topological uncertainty in target food webs, including erroneously assuming false links, omission of existent links and species, and trophic aggregation into trophospecies. Moreover, using an illustrative application to a real food web, we demonstrated that IsoWeb can compare the plausibility of different candidate topologies for a focal web. These results suggest that IsoWeb provides a powerful tool to analyze food-web structure from stable isotope data. We provide R and BUGS codes to aid efficient applications of IsoWeb. PMID:22848427

  9. Trial watch: Naked and vectored DNA-based anticancer vaccines

    PubMed Central

    Bloy, Norma; Buqué, Aitziber; Aranda, Fernando; Castoldi, Francesca; Eggermont, Alexander; Cremer, Isabelle; Sautès-Fridman, Catherine; Fucikova, Jitka; Galon, Jérôme; Spisek, Radek; Tartour, Eric; Zitvogel, Laurence; Kroemer, Guido; Galluzzi, Lorenzo

    2015-01-01

    One type of anticancer vaccine relies on the administration of DNA constructs encoding one or multiple tumor-associated antigens (TAAs). The ultimate objective of these preparations, which can be naked or vectored by non-pathogenic viruses, bacteria or yeast cells, is to drive the synthesis of TAAs in the context of an immunostimulatory milieu, resulting in the (re-)elicitation of a tumor-targeting immune response. In spite of encouraging preclinical results, the clinical efficacy of DNA-based vaccines employed as standalone immunotherapeutic interventions in cancer patients appears to be limited. Thus, efforts are currently being devoted to the development of combinatorial regimens that allow DNA-based anticancer vaccines to elicit clinically relevant immune responses. Here, we discuss recent advances in the preclinical and clinical development of this therapeutic paradigm. PMID:26155408

  10. Charge Transport across DNA-Based Three-Way Junctions.

    PubMed

    Young, Ryan M; Singh, Arunoday P N; Thazhathveetil, Arun K; Cho, Vincent Y; Zhang, Yuqi; Renaud, Nicolas; Grozema, Ferdinand C; Beratan, David N; Ratner, Mark A; Schatz, George C; Berlin, Yuri A; Lewis, Frederick D; Wasielewski, Michael R

    2015-04-22

    DNA-based molecular electronics will require charges to be transported from one site within a 2D or 3D architecture to another. While this has been shown previously in linear, π-stacked DNA sequences, the dynamics and efficiency of charge transport across DNA three-way junction (3WJ) have yet to be determined. Here, we present an investigation of hole transport and trapping across a DNA-based three-way junction systems by a combination of femtosecond transient absorption spectroscopy and molecular dynamics simulations. Hole transport across the junction is proposed to be gated by conformational fluctuations in the ground state which bring the transiently populated hole carrier nucleobases into better aligned geometries on the nanosecond time scale, thus modulating the π-π electronic coupling along the base pair sequence. PMID:25822073

  11. Effects of a Gluten-Free Diet on Rate of Learning in Autistic Children in an Applied Behavioral Analysis Program: Summary Analysis.

    ERIC Educational Resources Information Center

    Pontino, Jamie Lyn; Schaal, Kelly; Chambliss, Catherine

    This summary analysis discusses a series of studies that used both between-subjects and within-subjects analyses to examine the effects of a gluten-free diet on the academic achievement of children with autism. In the first study, the between-subjects analysis included data from eight children with autism (ages 5-7), with four on a gluten-free…

  12. Vertical stratification of fatty acids in the blubber of southern elephant seals (Mirounga leonina): implications for diet analysis.

    PubMed

    Best, Narelle J; Bradshaw, Corey J A; Hindell, Mark A; Nichols, Peter D

    2003-02-01

    Fatty acid signature analysis (FASA) is a powerful ecological tool that uses essential fatty acids (FA) from the tissues of animals to indicate aspects of diet. However, the presence of vertical stratification in FA distribution throughout blubber complicates the application of FASA to marine mammals. Blubber biopsy samples were collected from adult female southern elephant seals (Mirounga leonina) from Macquarie Island (n=11), and blubber cores were divided into inner and outer sections to determine the degree to which the blubber layer was stratified in FA composition, we found 19 FA from both blubber layers in greater than trace amounts (>0.5%). The inner and outer blubber layers could be separated using principal components analysis based on the relative proportion of FA in each layer. Dietary polyunsaturated fatty acids (PUFA) were also observed in significantly higher proportions in the inner blubber layer. Due to the degree of FA stratification in southern elephant seals, we concur with other marine mammal studies that sampling only the outer blubber layer will result in a loss of recently accumulated information regarding diet structure (as indicated by 'surplus' PUFA from the diet). This finding suggests that differential mobilization/deposition of certain FA may result in a modified signature from prey to predator. Thus, sampling animals to recover the inner blubber layer is important for studies attempting to describe aspects of marine mammal diet. This can be achieved in animals such as pinnipeds where the whole blubber layer can be readily sampled. PMID:12568803

  13. A systematic review and meta-analysis on the effects of exercise training versus hypocaloric diet: distinct effects on body weight and visceral adipose tissue.

    PubMed

    Verheggen, R J H M; Maessen, M F H; Green, D J; Hermus, A R M M; Hopman, M T E; Thijssen, D H T

    2016-08-01

    Exercise training ('exercise') and hypocaloric diet ('diet') are frequently prescribed for weight loss in obesity. Whilst body weight changes are commonly used to evaluate lifestyle interventions, visceral adiposity (VAT) is a more relevant and stronger predictor for morbidity and mortality. A meta-analysis was performed to assess the effects of exercise or diet on VAT (quantified by radiographic imaging). Relevant databases were searched through May 2014. One hundred seventeen studies (n = 4,815) were included. We found that both exercise and diet cause VAT loss (P < 0.0001). When comparing diet versus training, diet caused a larger weight loss (P = 0.04). In contrast, a trend was observed towards a larger VAT decrease in exercise (P = 0.08). Changes in weight and VAT showed a strong correlation after diet (R(2)  = 0.737, P < 0.001), and a modest correlation after exercise (R(2)  = 0.451, P < 0.001). In the absence of weight loss, exercise is related to 6.1% decrease in VAT, whilst diet showed virtually no change (1.1%). In conclusion, both exercise and diet reduce VAT. Despite a larger effect of diet on total body weight loss, exercise tends to have superior effects in reducing VAT. Finally, total body weight loss does not necessarily reflect changes in VAT and may represent a poor marker when evaluating benefits of lifestyle-interventions. PMID:27213481

  14. Ma-Pi 2 macrobiotic diet and type 2 diabetes mellitus: pooled analysis of short-term intervention studies.

    PubMed

    Porrata-Maury, C; Hernández-Triana, M; Ruiz-Álvarez, V; Díaz-Sánchez, M E; Fallucca, F; Bin, W; Baba-Abubakari, B; Pianesi, M

    2014-03-01

    The macrobiotic, Ma-Pi 2 diet (12% protein, 18% fat and 70% carbohydrate), has shown benefit in adults with type 2 diabetes mellitus (T2DM). This pooled analysis aims to confirm results from four, 21-day intervention studies with the Ma-Pi 2 diet, carried out in Cuba, China, Ghana and Italy. Baseline and end of study biochemical, body composition and blood pressure data, were compared using multivariate statistical methods and assessment of the Cohen effect size (d). Results showed that all measured indicators demonstrated significant changes (p < 0.001); most of them with a very high (d ≥ 1.30), or high (d = 0.80-1.29) effect size. The global effect size of the diet was Italy (1.96), China (1.79), Cuba (1.38) and Ghana (0.98). The magnitude of the individual effect on each variable by country, and the global effect by country, was independent of the sample size (p > 0.05). Similarly, glycemia and glycemic profiles in all four studies were independent of the sample size (p = 0.237). The Ma-Pi diet 2 significantly reduced glycemia, serum lipids, uremia and cardiovascular risk in adults with T2DM. These results suggest that the Ma-Pi 2 diet could be a valid alternative treatment for patients with T2DM and point to the need for further clinical studies. Mechanisms related to its benefits as a functional diet are discussed. PMID:24532293

  15. Diet analysis of small mammal pests: A comparison of molecular and microhistological methods.

    PubMed

    Khanam, Surrya; Howitt, Robyn; Mushtaq, Muhammad; Russell, James C

    2016-03-01

    Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly. In this study, we investigated the food habits of 2 rodents, Rattus rattus (ship rat) and Mus musculus castaneus (house mouse) as well as an insectivore, Suncus murinus (shrew), present in human dwellings. Both a microhistological approach and a DNA barcoding approach were used in the present study. Following DNA extraction, amplification was performed using group-specific primers targeting birds, plants and invertebrates. Resulting polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut contents. The findings from the application of both techniques were in agreement, but the detection of prey type with each technique was different. The DNA barcoding approach gave greater species-level identification when compared to the microhistological method, especially for the invertebrate and avian prey. Overall, with both techniques, 23 prey taxa were identified in the gut contents of the 3 species, including 15 plants, 7 insects and a single bird species. We conclude that with a selection of suitable "barcode genes" and optimization of polymerase chain reaction protocols, DNA barcoding can provide more accurate and faster results. Prey detection from either technique alone can bias the dietary information. Hence, combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet, especially if the pest is an omnivore or insectivore species. PMID:27001489

  16. Stable isotope ratio analysis to differentiate temporal diets of a free-ranging herbivore.

    PubMed

    Walter, W D; Leslie, D M

    2009-07-01

    Stable isotope ratio analysis (SIRA) of carbon (delta13C) and nitrogen (delta15N) in tissue samples of herbivores can identify photosynthetic pathways (C3 vs. C4) of plants consumed. We present results from free-ranging Rocky Mountain elk (Cervus elaphus) that highlight the ability to differentiate diets using tissue delta13C and delta15N. The signatures of delta13C and delta15N differed in tissues of varying metabolic activity: muscle, a short-term dietary indicator (i.e., 1-2 months) and hoof, a long-term dietary indicator (i.e., 3-12 months). We also documented that delta13C and delta15N values along elk hooves (proximal, middle, distal sections) elucidated temporal shifts in dietary selection. The carbon isotopes of the composite hoof were similar to those of the middle section, but the composite hoof differed in delta(13)C from the distal and proximal sections. The delta13C and delta15N signatures also differed among elk populations, indicating temporal dietary shifts of individuals occupying disparate native range and human-derived agricultural landscapes. Analyses of stable isotopes in various tissues highlighted carbon and nitrogen assimilation through time and differences in the foraging ecology of a rangeland herbivore. PMID:19530151

  17. Fatty acids in serum and diet--a canonical correlation analysis among toddlers.

    PubMed

    Uusitalo, Liisa; Nevalainen, Jaakko; Salminen, Irma; Ovaskainen, Marja-Leena; Kronberg-Kippilä, Carina; Ahonen, Suvi; Niinistö, Sari; Alfthan, Georg; Simell, Olli; Ilonen, Jorma; Veijola, Riitta; Knip, Mikael; Virtanen, Suvi M

    2013-07-01

    Fatty acid concentrations in blood are potential biomarkers of dietary fat intake, but methodological studies among children are scarce. The large number of fatty acids and their complex interrelationships pose a special challenge in research on fatty acids. Our target was to assess the interrelationships between the total fatty acid profiles in diet and serum of young children. The study subjects were healthy control children from the birth cohort of the Type 1 Diabetes Prediction and Prevention Study. A 3-day food record and a frozen serum sample were available from 135 children at the age of 1 year, from 133 at 2 years, and from 92 at 3 years. The relationship between dietary and serum fatty acid profiles was analysed using canonical correlation analysis. The consumption of fatty milk correlated positively with serum fatty acids, pentadecanoic acid, palmitic acid and conjugated linoleic acid (CLA) at all ages. Correlations between dietary and serum eicosapentaenoic and/or docosahexaenoic acid were observed at 2 and 3 years of age. Serum linoleic acid was positively associated with the consumption of infant formula at the age of 1 year, and with the consumption of vegetable margarine at 2 and 3 years. The results indicate a high quality of the 3-day food records kept by parents and other caretakers of the children, and suitability of non-fasting, un-fractioned serum samples for total fatty acid analyses. The correlation between intake of milk fat and serum proportion of CLA is a novel finding. PMID:22066932

  18. Determination of multielements in a typical Japanese diet certified reference material by instrumental neutron activation analysis.

    PubMed

    Suzuki, Shogo; Okada, Yukiko; Hirai, Shoji

    2003-08-01

    Multielements in a typical Japanese diet certified reference material prepared at the National Institute for Environmental Studies (NIES) of Japan, in collaboration with the National Institute of Radiological Sciences (NIRS) of Japan were determined by instrumental neutron activation analysis (INAA). Five samples (ca. 510-1000 mg) and comparative standards were irradiated for a short time (10 s) at a thermal neutron flux of 1.5 x 10(12) n cm(-2) s(-1) (pneumatic transfer) and for a long time (6 h) at a thermal neutron flux of 3.7 x 10(12) n cm(-2) s(-1) (central thimble) in the Rikkyo University Research Reactor (TRIGA Mark-II, 100 kW). The irradiated samples were measured by conventional gama-ray spectrometry using a coaxial Ge detector, and by anti-coincidence and coincidence gamma-ray spectrometry with a coaxial Ge detector and a well-type NaI(Tl) detector. The concentrations of 38 elements were determined by these methods. PMID:12945682

  19. Analysis of Health Consumers' Behavior Using Self-Tracker for Activity, Sleep, and Diet

    PubMed Central

    2014-01-01

    Abstract Background: With the ever-increasing availability of health information technology (HIT) enabling health consumers to measure, store, and manage their health data (e.g., self-tracking devices), more people are logging and managing their own health data for the purpose of promoting general well-being. To develop and implement effective and efficient strategies for improving personal monitoring devices, a rigorous theoretical framework to explain the health consumer's attitude, intention, and behavior needs to be established. The aim of this study is to verify the HIT acceptance model (HITAM) in the context of the health consumer's attitude, behavioral intention, and behavior of utilizing self-trackers. Furthermore, the study aims to gain better understanding of self-tracking behavior in the context of logging daily activity level, sleep patterns, and dietary habits. Subjects and Methods: Forty-four female college students were selected as voluntary study participants. They used self-trackers for activity, sleep, and diet monitoring for 90 or more consecutive days. The logged data were analyzed and fitted to the HITAM to verify whether the model was suitable for capturing the various behavioral and intention-related characteristics observed. Results: The overall fitness indices for the HITAM using the field data yielded an acceptable fitness to the model, with all path coefficients being statistically significant. The model accounts for 66.8% of the variance in perceived usefulness, 43.9% of the variance in perceived ease of use, 83.1% of the variance in attitude, and 48.4% of the variance in behavioral intention. The compliance ranking of self-tracking behavior, in order of decreasing compliance, was activity, sleep, and diet. This ranking was consistent with that of ease of use of the personal monitoring device used in the study. Conclusions: The HITAM was verified for its ability to describe the health consumer's attitude, behavioral intention, and

  20. Transcriptome analysis of age-, gender- and diet-associated changes in murine thymus ☆

    PubMed Central

    Lustig, Ana; Weeraratna, Ashani T.; Wood, William W.; Teichberg, Diane; Bertak, Dorothy; Carter, Arnell; Poosala, Suresh; Firman, Jeffrey; Becker, Kevin G.; Zonderman, Alan B.; Longo, Dan L.; Taub, Dennis D.

    2008-01-01

    The loss of thymic function with age may be due to diminished numbers of T-cell progenitors and the loss of critical mediators within the thymic microenvironment. To assess the molecular changes associated with this loss, we examined transcriptomes of progressively aging mouse thymi, of different sexes and on caloric-restricted (CR) vs. ad libitum (AL) diets. Genes involved in various biological and molecular processes including transcriptional regulators, stress response, inflammation and immune function significantly changed during thymic aging. These differences depended on variables such as sex and diet. Interestingly, many changes associated with thymic aging are either muted or almost completely reversed in mice on caloric-restricted diets. These studies provide valuable insight into the molecular mechanisms associated with thymic aging and emphasize the need to account for biological variables such as sex and diet when elucidating the genomic correlates that influence the molecular pathways responsible for thymic involution. PMID:17499630

  1. Transcriptome analysis of grass carp (Ctenopharyngodon idella) fed with animal and plant diets.

    PubMed

    Li, Ling; Liang, Xu-Fang; He, Shan; Sun, Jian; Wen, Zheng-Yong; He, Yu-Hui; Cai, Wen-Jing; Wang, Ya-Ping; Tao, Ya-Xiong

    2015-12-15

    Numerous studies have been focused on the replacement of fish meal by other alternative protein sources. However, little is currently known about the molecular mechanism of utilization of diets with different protein sources in fish. Grass carp is a typical herbivorous fish. To elucidate the relationship between gene expression and utilization of animal and plant diets, transcriptome sequencing was performed in grass carp fed with chironomid larvae and duckweed. Grass carp fed with duckweed had significantly higher relative length of gut than those fed with chironomid larvae. 4435 differentially expressed genes were identified between grass carp fed with chironomid larvae and duckweed in brain, liver and gut, involved in cell proliferation and differentiation, appetite control, circadian rhythm, digestion and metabolism pathways. These pathways might play important roles in utilization of diets with different protein sources in grass carp. And the findings could provide a new insight into the replacement of fish meal in artificial diets. PMID:26283148

  2. Stable isotope analysis of temporal variation in the diets of pre-fledged Laughing Gulls

    USGS Publications Warehouse

    Knoff, A.J.; Macko, S.A.; Erwin, R.M.; Brown, K.M.

    2002-01-01

    The *13C, *15N, and *34S stable isotopic values of feathers from pre-fledged Laughing Gulls (Larus atricilla) in coastal Virginia and Jamaica Bay, New York were used to examine dietary variation during the nestling period. The tip portions of the feathers were used to indicate diet during the initiation of primary feather growth, whereas the base portions indicated diet during the period immediately prior to fledging. The results indicate that diets of the nestlings in Virginia moved to a higher trophic level during the period prior to fledging, however the New York nestlings did not appear to undergo any appreciable dietary change during this period. Overall, nestlings from both colonies consumed proportionately more foods of marine origin than freshwater or terrestrial. Therefore, the results do not support those of earlier studies that suggested that partially developed salt glands in young gulls might restrict the diet to more terrestrial or freshwater prey in the early stages of nestling growth.

  3. Morphoquantitative analysis of the Ileum of C57BL/6 mice (Mus musculus) fed with a high-fat diet

    PubMed Central

    Navarrete, Javiera; Vásquez, Bélgica; del Sol, Mariano

    2015-01-01

    Due to the increase in overweight and obesity in humans, various studies have been conducted in recent years that demonstrate the detrimental effects on tissues and organs. The aim of this study was to assess the morphoquantitative changes produced in the ileum of mice, associated with high-fat diets. Fourteen male C57BL/6 mice, 5 months old, were fed two types of diets for 14 weeks. The control group (C) was fed a standard diet (10% fat, AIN-93M) and the experimental group (E) was fed a high-fat diet (42% fat, AIN-93M-AG). The assessments included: body weight, calorie consumption, food efficiency, biochemical analysis of plasma lipids, diameter, total wall thickness, thickness of the tunica mucosa and tunica muscularis, length and width of the intestinal villi, depth of the intestinal crypts and number of goblet cells per mm-2 (NA). For the statistical analysis the Student’s t-test was used, considering a P value less than 0.05. The mice in the E group presented greater weight gain (P = 0.028), higher levels of total and LDL cholesterol (P = 0.03 and P = 0.01, respectively), and length of the intestinal villi (P = 0.000). The width of the intestinal villi and the NA of PAS-positive goblet cells presented significantly lower values (P = 0.037 and P = 0.039, respectively) than the C group. The observed changes could be related to the higher demand for fat absorption and to possible alterations in the intestinal microflora and inflammation by action of high-fat diets. PMID:26823788

  4. Do healthier foods and diet patterns cost more than less healthy options? A systematic review and meta-analysis

    PubMed Central

    Rao, Mayuree; Afshin, Ashkan; Singh, Gitanjali; Mozaffarian, Dariush

    2013-01-01

    Objective To conduct a systematic review and meta-analysis of prices of healthier versus less healthy foods/diet patterns while accounting for key sources of heterogeneity. Data sources MEDLINE (2000–2011), supplemented with expert consultations and hand reviews of reference lists and related citations. Design Studies reviewed independently and in duplicate were included if reporting mean retail price of foods or diet patterns stratified by healthfulness. We extracted, in duplicate, mean prices and their uncertainties of healthier and less healthy foods/diet patterns and rated the intensity of health differences for each comparison (range 1–10). Prices were adjusted for inflation and the World Bank purchasing power parity, and standardised to the international dollar (defined as US$1) in 2011. Using random effects models, we quantified price differences of healthier versus less healthy options for specific food types, diet patterns and units of price (serving, day and calorie). Statistical heterogeneity was quantified using I2 statistics. Results 27 studies from 10 countries met the inclusion criteria. Among food groups, meats/protein had largest price differences: healthier options cost $0.29/serving (95% CI $0.19 to $0.40) and $0.47/200 kcal ($0.42 to $0.53) more than less healthy options. Price differences per serving for healthier versus less healthy foods were smaller among grains ($0.03), dairy (−$0.004), snacks/sweets ($0.12) and fats/oils ($0.02; p<0.05 each) and not significant for soda/juice ($0.11, p=0.64). Comparing extremes (top vs bottom quantile) of food-based diet patterns, healthier diets cost $1.48/day ($1.01 to $1.95) and $1.54/2000 kcal ($1.15 to $1.94) more. Comparing nutrient-based patterns, price per day was not significantly different (top vs bottom quantile: $0.04; p=0.916), whereas price per 2000 kcal was $1.56 ($0.61 to $2.51) more. Adjustment for intensity of differences in healthfulness yielded similar results. Conclusions

  5. Economical and financial analysis of lamb finishing fed with diets formulated according to the NRC (1985) and the NRC (2007).

    PubMed

    Rogério, Marcos Cláudio Pinheiro; de Castro, Eliane Minervina; Martins, Espedito Cezário; Monteiro, Jomar Patrício; Silva, Kleibe de Moraes; Cândido, Magno José Duarte; Gomes, Tereza Cristina Lacerda; Bloc, Antoine Francis Roux; de Vasconcelos, Angela Maria; Leite, Eneas Reis; Costa, Hélio Henrique Araújo

    2013-01-01

    This study compares both versions of the nutritional requirement system determined by the National Research Council (NRC) version 1985 (NRC85) and NRC version 2007 (NRC07), for finishing lambs in feedlots. Nineteen crossbred lambs were divided in four groups representing four experimental treatments: one diet according to NRC85 and three diets according to NRC07. The diets recommended by NRC07 considers crude protein intake relative to ruminal undegradable protein at 20, 40, and 60 % levels (NRC07/20, NRC07/40, and NRC07/60). Diets were composed of Brazilian semi-arid native grass silage, soybean meal, corn, annatto byproduct, and limestone. Purchases and sales of lambs were done according to average market prices in Brazil. The economic indicators considered pointed that all treatments were viable but NRC07/20 and NRC07/60 were more profitable with similar net present values (NPVs) and internal return rates (IRRs). NRC07/20 was the best option showing an IRR of 17.20 % and a payback period (PP) of 5.07 considering a fixed annual interest rate of 6 %. Sensitivity analysis considering a 10 % raise in variable costs showed negative NPVs, IRRs inferior to the opportunity cost rates adopted and PPs that exceeded the planning horizon of 7 years for both NRC85 and NRC07/40. PMID:22760727

  6. New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces

    PubMed Central

    Sistiaga, Ainara; Wrangham, Richard; Rothman, Jessica M.; Summons, Roger E.

    2015-01-01

    Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes) and mountain gorilla (Gorilla beringei). Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets. PMID:26061730

  7. New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces.

    PubMed

    Sistiaga, Ainara; Wrangham, Richard; Rothman, Jessica M; Summons, Roger E

    2015-01-01

    Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes) and mountain gorilla (Gorilla beringei). Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets. PMID:26061730

  8. Diet History Questionnaire: Suggested Citations

    Cancer.gov

    Use of the Diet History Questionnaire and Diet*Calc Analysis Software for publication purposes should contain a citation which includes version information for the software, questionnaire, and nutrient database.

  9. Magnetophoresis of flexible DNA-based dumbbell structures

    NASA Astrophysics Data System (ADS)

    Babić, B.; Ghai, R.; Dimitrov, K.

    2008-02-01

    Controlled movement and manipulation of magnetic micro- and nanostructures using magnetic forces can give rise to important applications in biomedecine, diagnostics, and immunology. We report controlled magnetophoresis and stretching, in aqueous solution, of a DNA-based dumbbell structure containing magnetic and diamagnetic microspheres. The velocity and stretching of the dumbbell were experimentally measured and correlated with a theoretical model based on the forces acting on individual magnetic beads or the entire dumbbell structures. The results show that precise and predictable manipulation of dumbbell structures is achievable and can potentially be applied to immunomagnetic cell separators.

  10. The effect of macrobiotic Ma-Pi 2 diet on systemic inflammation in patients with type 2 diabetes: a post hoc analysis of the MADIAB trial

    PubMed Central

    Soare, Andreea; Del Toro, Rossella; Roncella, Elena; Khazrai, Yeganeh Manon; Angeletti, Silvia; Dugo, Laura; Fallucca, Sara; Fontana, Lucia; Altomare, Maria; Formisano, Valeria; Capata, Francesca; Gesuita, Rosaria; Manfrini, Silvia; Fallucca, Francesco; Pianesi, Mario; Pozzilli, Paolo

    2015-01-01

    Introduction Current guidelines for the management of type 2 diabetes (T2D) emphasize diet as essential therapy. However, the effect of diet on systemic inflammation remains unclear. We investigated the effects of consuming a macrobiotic Ma-Pi 2 diet versus a standard recommended diet (control diet) on markers of inflammation in patients with T2D. Methods This was a post hoc analysis of the MADIAB trial, a 21-day randomized controlled trial conducted in 51 patients (25 males and 26 females) with T2D. Patients were randomized 1:1 to the Ma-Pi 2 macrobiotic diet or a control diet based on dietary guidelines for T2D. Biological antioxidant potential of plasma and circulating levels of high-sensitivity C reactive protein, interleukin-6, tumor necrosis factor-α, and insulin-like growth factor-1 were assessed. Results After 21 days on the Ma-Pi 2 or control diet, markers of inflammation were reduced in both groups. The antioxidant potential of plasma improved significantly in the Ma-Pi group. A significant reduction in insulin growth factor-1 was observed in the Ma-Pi group versus control group (p<0.001). Conclusions Findings of this post hoc analysis demonstrated that the Ma-Pi 2 diet is a safe dietary strategy to reduce levels of the markers of insulin resistance and inflammation, compared with baseline values, in the short term. Furthermore, the Ma-Pi 2 diet was superior to the control diet in reducing insulin growth factor-1 and may be beneficial for patients with T2D. Trial registration number Current Controlled Trials ISRCTN10467793. PMID:25852946

  11. Evaluation of protein supplementation for growing cattle fed grass silage-based diets: a meta-analysis.

    PubMed

    Huuskonen, A; Huhtanen, P; Joki-Tokola, E

    2014-10-01

    The objective of this meta-analysis was to develop empirical equations predicting growth responses of growing cattle to protein intake. Overall, the data set comprised 199 diets in 80 studies. The diets were mainly based on grass silage or grass silage partly or completely replaced by whole-crop silages or straw. The concentrate feeds consisted of cereal grains, fibrous by-products and protein supplements. The analyses were conducted both comprehensively for all studies and also separately for studies in which soybean meal (SBM; n=71 diets/28 studies), fish meal (FM; 27/12) and rapeseed meal (RSM; 74/35) were used as a protein supplement. Increasing dietary CP concentration increased (P<0.01) BW gain (BWG), but the responses were quantitatively small (1.4 g per 1 g/kg dry matter (DM) increase in dietary CP concentration). The BWG responses were not different for bulls v. steers and heifers (1.4 v. 1.3 g per 1 g/kg DM increase in dietary CP concentration) and for dairy v. beef breeds (1.2 v. 1.7 g per 1 g/kg, respectively). The effect of increased CP concentration declined (P<0.01) with increasing mean BW of the animals and with improved BWG of the control animals (the lowest CP diet in each study). The BWG responses to protein supplementation were not related to the CP concentration in the control diet. The BWG responses increased (P<0.05) with increased ammonia N concentration in silage N and declined marginally (P>0.10) with increasing proportion of concentrate in the diet. All protein supplements had a significant effect on BWG, but the effects were greater for RSM (P<0.01) and FM (P<0.05) than for SBM. Increasing dietary CP concentration improved (P<0.01) feed efficiency when expressed as BWG/kg DM intake, but decreased markedly when expressed as BWG/kg CP intake. Assuming CP concentration of 170 g/kg BW marginal efficiency of the utilisation of incremental CP intake was only 0.05. Increasing dietary CP concentration had no effects on carcass weight, dressing

  12. Pleiotropy and genotype by diet interaction: A multivariate genetic analysis of HDL-C subfractions

    SciTech Connect

    Mahaney, M.C.; Blangero, J.; Comuzzie, A.G.

    1994-09-01

    Reduced high density lipoprotein cholesterol (HDL-C) is a risk factor for cardiovascular disease in humans. Both major genes and major genotype by diet interaction have been reported for HDL-C, but the genetics of the HDL-C subfractions are less well known. In a baboon model for human atherosclerosis, we investigated the pleiotropic effects of genes on normal quantitative variation in three HDL-C subfractions (HDL{sub 1}-C, HDL{sub 2}-C, and HDL{sub 3}-C) in two dietary environments -- a basal diet and a 7 week high cholesterol, saturated fat (HCSF) diet. We analyzed data on serum HDL-C subfraction levels, quantified by gradient gel eletrophoresis, for 942 baboons (Papo hamadryas, sensu lato) from 17 pedigrees. We used multivariate maximum likelihood methods to simultaneously estimate phenotypic means, standard deviations, and heritabilities (h{sup 2}); effects of sex, age-by-sex, age{sup 2}-by-sex, percent subspecies admixture, and infant feeding modality; plus estimated significant h{sup 2} values for all three subfractions on both diets. When tested within dietary environments, we obtained significant genetic correlations between all three subfractions [i.e., P({rho}{sub G} = 0) < 0.001] and evidence of complete pleiotropy [i.e., P({vert_bar}{rho}{sub G}{vert_bar} = 1.0) > 0.1] between HDL{sub 1}-C and HDL{sub 3}-C ({rho}{sub G} = 0.81) on the basal diet. On the HCSF diet, only the genetic correlation between HDL{sub 1}-C and HDL{sub 3}-C ({rho}{sub g} = 0.61) was significant (p > 0.1). Complete pleiotropy was observed for each of the three subfractions between both diets. Given these results, we reject genotype by diet interaction for HDL{sub 1}-C, HDL{sub 2}-C or HDL{sub 3}-C; i.e., the same genes influence variation in each subfraction to the same degree on either diet. However, the apparent disruption of pleiotropy between HDL{sub 2}-C and the other two subfractions needs to be investigated further.

  13. Comparison of ITS, RAPD and ISSR from DNA-based genetic diversity techniques.

    PubMed

    Poyraz, Ismail

    2016-01-01

    ITS, RAPD-PCR and ISSR-PCR are most popular DNA-based techniques that are extensively applied in the determination of the genetic diversity of species among populations. However, especially for organisms having high genetic polymorphism, phylogenetic trees drawn from the results of these techniques may be different. For finding a meaningful phylogenetic tree, it should be compared phylogenetic trees obtained from these different techniques with geographic locations of populations. Lichens have a high genetic polymorphism and tolerance against different environmental conditions. In this study, these three DNA-based genetic diversity techniques were compared, using different populations of a lichen species (Xanthoria parietina). X. parietina was especially chosen because of its high genetic diversity in narrow zones. Lichen samples were collected from ten different locations in a narrow transition climate zone Bilecik (Turkey). Statistical analyses of all results were calculated using UPGMA analysis. Phylogenic trees for each technique were drawn and transferred to the Bilecik map for comparative analysis. The results of three techniques allowed us to verify that populations of X. parietina have high genetic variety in a narrow zone. But phylogenetic trees obtained from these results were found to be very different. Our comparative analysis demonstrated that the results of these techniques are not similar and have critical differences. We observed that the ITS method provides more clear data and is more successful in genetic diversity analyses of more asunder populations, in contrast to ISSR-PCR and RAPD-PCR methods. PMID:27156497

  14. The Conflict between Cheetahs and Humans on Namibian Farmland Elucidated by Stable Isotope Diet Analysis

    PubMed Central

    Voigt, Christian C.; Thalwitzer, Susanne; Melzheimer, Jörg; Blanc, Anne-Sophie; Jago, Mark; Wachter, Bettina

    2014-01-01

    Large areas of Namibia are covered by farmland, which is also used by game and predator species. Because it can cause conflicts with farmers when predators, such as cheetahs (Acinonyx jubatus), hunt livestock, we assessed whether livestock constitutes a significant part of the cheetah diet by analysing the stable isotope composition of blood and tissue samples of cheetahs and their potential prey species. According to isotopic similarities, we defined three isotopic categories of potential prey: members of a C4 food web with high δ15N values (gemsbok, cattle, springhare and guinea fowl) and those with low δ15N values (hartebeest, warthog), and members of a C3 food web, namely browsers (eland, kudu, springbok, steenbok and scrub hare). We quantified the trophic discrimination of heavy isotopes in cheetah muscle in 9 captive individuals and measured an enrichment for 15N (3.2‰) but not for 13C in relation to food. We captured 53 free-ranging cheetahs of which 23 were members of groups. Cheetahs of the same group were isotopically distinct from members of other groups, indicating that group members shared their prey. Solitary males (n = 21) and males in a bachelor groups (n = 11) fed mostly on hartebeest and warthogs, followed by browsers in case of solitary males, and by grazers with high δ15N values in case of bachelor groups. Female cheetahs (n = 9) predominantly fed on browsers and used also hartebeest and warthogs. Mixing models suggested that the isotopic prey category that included cattle was only important, if at all, for males living in bachelor groups. Stable isotope analysis of fur, muscle, red blood cells and blood plasma in 9 free-ranging cheetahs identified most individuals as isotopic specialists, focussing on isotopically distinct prey categories as their food. PMID:25162403

  15. Data set for diet specific differential gene expression analysis in three Spodoptera moths.

    PubMed

    Roy, A; Walker, W B; Vogel, H; Kushwaha, S K; Chattington, S; Larsson, M C; Anderson, P; Heckel, D G; Schlyter, F

    2016-09-01

    Examination of closely related species pairs is suggested for evolutionary comparisons of different degrees of polyphagy, which we did here with three taxa of lepidopteran herbivores, Spodoptera spp (S. littoralis, S. frugiperda maize (C) and rice (R) strains) for a RNAseq analysis of the midguts from the 3rd instar insect larvae for differential metabolic responses after feeding on pinto bean based artificial diet vs maize leaves. Paired-end (2×100 bp) Illumina HiSeq2500 sequencing resulted in a total of 24, 23, 24, and 21 million reads for the SF-C-Maize, SF-C-Pinto, SF-R-Maize, SF-R Pinto, and a total of 35 and 36 million reads for the SL-Maize and SL-Pinto samples, respectively. After quality control measures, a total of 62.2 million reads from SL and 71.7 million reads from SF were used for transcriptome assembly (TA). The resulting final de novo reference TA (backbone) for the SF taxa contained 37,985 contigs with a N50 contig size of 1030 bp and a maximum contig length of 17,093 bp, while for SL, 28,329 contigs were generated with a N50 contig size of 1980 bp and a maximum contig length of 18,267 bp. The data presented herein contains supporting information related to our research article Roy et al. (2016) http://dx.doi.org/10.1016/j.ibmb.2016.02.006[1]. PMID:27366783

  16. The conflict between cheetahs and humans on Namibian farmland elucidated by stable isotope diet analysis.

    PubMed

    Voigt, Christian C; Thalwitzer, Susanne; Melzheimer, Jörg; Blanc, Anne-Sophie; Jago, Mark; Wachter, Bettina

    2014-01-01

    Large areas of Namibia are covered by farmland, which is also used by game and predator species. Because it can cause conflicts with farmers when predators, such as cheetahs (Acinonyx jubatus), hunt livestock, we assessed whether livestock constitutes a significant part of the cheetah diet by analysing the stable isotope composition of blood and tissue samples of cheetahs and their potential prey species. According to isotopic similarities, we defined three isotopic categories of potential prey: members of a C4 food web with high δ15N values (gemsbok, cattle, springhare and guinea fowl) and those with low δ15N values (hartebeest, warthog), and members of a C3 food web, namely browsers (eland, kudu, springbok, steenbok and scrub hare). We quantified the trophic discrimination of heavy isotopes in cheetah muscle in 9 captive individuals and measured an enrichment for 15N (3.2‰) but not for 13C in relation to food. We captured 53 free-ranging cheetahs of which 23 were members of groups. Cheetahs of the same group were isotopically distinct from members of other groups, indicating that group members shared their prey. Solitary males (n = 21) and males in a bachelor groups (n = 11) fed mostly on hartebeest and warthogs, followed by browsers in case of solitary males, and by grazers with high δ15N values in case of bachelor groups. Female cheetahs (n = 9) predominantly fed on browsers and used also hartebeest and warthogs. Mixing models suggested that the isotopic prey category that included cattle was only important, if at all, for males living in bachelor groups. Stable isotope analysis of fur, muscle, red blood cells and blood plasma in 9 free-ranging cheetahs identified most individuals as isotopic specialists, focussing on isotopically distinct prey categories as their food. PMID:25162403

  17. Vegetarian Diet

    MedlinePlus

    A vegetarian diet focuses on plants for food. These include fruits, vegetables, dried beans and peas, grains, seeds and nuts. There is no single type of vegetarian diet. Instead, vegetarian eating patterns usually fall into the ...

  18. Vegetarian Diet

    MedlinePlus

    A vegetarian diet focuses on plants for food. These include fruits, vegetables, dried beans and peas, grains, seeds and nuts. There is no single type of vegetarian diet. Instead, vegetarian eating patterns usually fall into the following ...

  19. A systematic review and meta-analysis of changes in body weight in clinical trials of vegetarian diets.

    PubMed

    Barnard, Neal D; Levin, Susan M; Yokoyama, Yoko

    2015-06-01

    In observational studies, vegetarians generally have lower body weights compared with omnivores. However, weight changes that occur when vegetarian diets are prescribed have not been well quantified. We estimated the effect on body weight when vegetarian diets are prescribed. We searched PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials for articles through December 31, 2013. Additional articles were identified from reference lists. We included intervention trials in which participants were adults, interventions included vegetarian diets of ≥4 weeks' duration without energy intake limitations, and effects on body weight were reported. Two investigators independently extracted data using predetermined fields. Estimates of body weight change, comparing intervention groups to untreated control groups, were derived using a random effects model to estimate the weighted mean difference. To quantify effects on body weight of baseline weight, sex, age, study duration, study goals, type of diet, and study authorship, additional analyses examined within-group changes for all studies reporting variance data. We identified 15 trials (17 intervention groups), of which 4 included untreated controls. Prescription of vegetarian diets was associated with a mean weight change of -3.4 kg (95% CI -4.4 to -2.4; P<0.001) in an intention-to-treat analysis and -4.6 kg (95% CI -5.4 to -3.8; P<0.001) in a completer analysis (omitting missing post-intervention values). Greater weight loss was reported in studies with higher baseline weights, smaller proportions of female participants, older participants, or longer durations, and in studies in which weight loss was a goal. Using baseline data for missing values, I(2) equaled 52.3 (P=0.10), indicating moderate heterogeneity. When missing data were omitted, I(2) equaled 0 (P=0.65), indicating low heterogeneity. Studies are relatively few, with variable quality. The prescription of vegetarian diets reduces mean body

  20. The current state of eukaryotic DNA base damage and repair.

    PubMed

    Bauer, Nicholas C; Corbett, Anita H; Doetsch, Paul W

    2015-12-01

    DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair. PMID:26519467

  1. The current state of eukaryotic DNA base damage and repair

    PubMed Central

    Bauer, Nicholas C.; Corbett, Anita H.; Doetsch, Paul W.

    2015-01-01

    DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair. PMID:26519467

  2. Network analysis reveals contrasting effects of intraspecific competition on individual vs. population diets.

    PubMed

    Araújo, Márcio S; Guimarães, Paulo R; Svanbäck, Richard; Pinheiro, Aluisio; Guimarães, Paulo; Dos Reis, Sérgio F; Bolnick, Daniel I

    2008-07-01

    Optimal foraging theory predicts that individuals should become more opportunistic when intraspecific competition is high and preferred resources are scarce. This density-dependent diet shift should result in increased diet breadth for individuals as they add previously unused prey to their repertoire. As a result, the niche breadth of the population as a whole should increase. In a recent study, R. Svanbäck and D. I. Bolnick confirmed that intraspecific competition led to increased population diet breadth in threespine stickleback (Gasterosteus aculeatus). However, individual diet breadth did not expand as resource levels declined. Here, we present a new method based on complex network theory that moves beyond a simple measure of diet breadth, and we use the method to reexamine the stickleback experiment. This method reveals that the population as a whole added new types of prey as stickleback density was increased. However, whereas foraging theory predicts that niche expansion is achieved by individuals accepting new prey in addition to previously preferred prey, we found that a subset of individuals ceased to use their previously preferred prey, even though other members of their population continued to specialize on the original prey types. As a result, populations were subdivided into groups of ecologically similar individuals, with diet variation among groups reflecting phenotype-dependent changes in foraging behavior as prey density declined. These results are consistent with foraging theory if we assume that quantitative trait variation among consumers affects prey preferences, and if cognitive constraints prevent individuals from continuing to use their formerly preferred prey while adding new prey. PMID:18705384

  3. Diet of yellow-billed loons (Gavia adamsii) in Arctic lakes during the nesting season inferred from fatty acid analysis

    USGS Publications Warehouse

    Haynes, T B; Schmutz, Joel A.; Bromaghin, Jeffrey; Iverson, S J; Padula, V M; Rosenberger, A E

    2015-01-01

    Understanding the dietary habits of yellow-billed loons (Gavia adamsii) can give important insights into their ecology, however, studying the diet of loons is difficult when direct observation or specimen collection is impractical. We investigate the diet of yellow-billed loons nesting on the Arctic Coastal Plain of Alaska using quantitative fatty acid signature analysis. Tissue analysis from 26 yellow-billed loons and eleven prey groups (nine fish species and two invertebrate groups) from Arctic lakes suggests that yellow-billed loons are eating high proportions of Alaska blackfish (Dallia pectoralis), broad whitefish (Coregonus nasus) and three-spined stickleback (Gasterosteus aculeatus) during late spring and early summer. The prominence of blackfish in diets highlights the widespread availability of blackfish during the early stages of loon nesting, soon after spring thaw. The high proportions of broad whitefish and three-spined stickleback may reflect a residual signal from the coastal staging period prior to establishing nesting territories on lakes, when loons are more likely to encounter these species. Our analyses were sensitive to the choice of calibration coefficient based on data from three different species, indicating the need for development of loon-specific coefficients for future study and confirmation of our results. Regardless, fish that are coastally distributed and that successfully overwinter in lakes are likely key food items for yellow-billed loons early in the nesting season.

  4. Proteomic analysis of the dorsal and ventral hippocampus of rats maintained on a high fat and refined sugar diet.

    PubMed

    Francis, Heather M; Mirzaei, Mehdi; Pardey, Margery C; Haynes, Paul A; Cornish, Jennifer L

    2013-10-01

    The typical Western diet, rich in high saturated fat and refined sugar (HFS), has been shown to increase cognitive decline with aging and Alzheimer's disease, and to affect cognitive functions that are dependent on the hippocampus, including memory processes and reversal learning. To investigate neurophysiological changes underlying these impairments, we employed a proteomic approach to identify differentially expressed proteins in the rat dorsal and ventral hippocampus following maintenance on an HFS diet. Rats maintained on the HFS diet for 8 weeks were impaired on a novel object recognition task that assesses memory and on a Morris Water Maze task assessing reversal learning. Quantitative label-free shotgun proteomic analysis was conducted on biological triplicates for each group. For the dorsal hippocampus, 59 proteins were upregulated and 36 downregulated in the HFS group compared to controls. Pathway ana-lysis revealed changes to proteins involved in molecular transport and cellular and molecular signaling, and changes to signaling pathways including calcium signaling, citrate cycle, and oxidative phosphorylation. For the ventral hippocampus, 25 proteins were upregulated and 27 downregulated in HFS fed rats. Differentially expressed proteins were involved in cell-to-cell signaling and interaction, and cellular and molecular function. Changes to signaling pathways included protein ubiquitination, ubiquinone biosynthesis, oxidative phosphorylation, and mitochondrial dysfunction. This is the first shotgun proteomics study to examine protein changes in the hippocampus following long-term consumption of a HFS diet, identifying changes to a large number of proteins including those involved in synaptic plasticity and energy metabolism. All MS data have been deposited in the ProteomeXchange with identifier PXD000028. PMID:23963966

  5. A novel method for the analysis of clinical biomarkers to investigate the effect of diet on health in a rat model.

    PubMed

    Hopes, K; Cauchi, M; Walton, C; MacQueen, H; Wassif, W; Turner, C

    2015-05-01

    Experiments into the relationship between diet and health have been an area of high interest for a long time. In this study, we investigate the application of multivariate data analysis to differentiate between rat populations fed on two different diets: normal rat diet (control) and Western affluent diet (WAD). Two sets of data were acquired and analysed: one from a biochemical clinical analyser, taking measurements of blood-based biochemical markers; the other from the analysis of the volatile organic compounds (VOCs) emitted from faecal samples from the same animals using selected ion flow tube mass spectrometry (SIFT-MS). Five classes were considered: weanlings, 12 month controls, 12 month WADs, 18 month controls, and 18 month WADs. Data from the biochemical analyser, weanlings and 18 month WAD fed rats showed significant differences from the other measurement classes. This was shown in both the exploratory analysis and through multivariate classification. Classification of control diet versus WAD diets suggested there are differences between classes with 92% accuracy for the 12 month classes and 91% for the 18 month classes. Cholesterol markers, especially as low density lipoprotein-cholesterol (LDL), were the main factor in influencing WAD samples. The data from the SIFT-MS analysis also produced very good classification accuracies. Classification of control diet versus WAD diets using the H3O(+) precursor ion data suggested there are differences between classes with 71% accuracy for the 12 month classes and 100% for the 18 month classes. These findings confirm that total cholesterol and LDL-cholesterol are elevated in the 18 month WAD-fed rats. We therefore suggest that the analysis of VOCs from faecal samples in conjunction with multivariate data analysis may be a useful alternative to blood analysis for the detection of parameters of health. PMID:25747619

  6. Life History and Cost Analysis for Rearing Ceratitis Capitata (Diptera:Tephritidae) in a Liquid Diet

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A liquid diet for rearing Bactrocera dorsalis was developed. Three hydrolyzed yeast (LS65, FNI200, FNI210), a glutamine enriched yeast (G, Fermaid SuperRelax, GSH), RDA500 (R, an enriched high vitamins yeast), Korea yeast, and their yeast products (FNI200+G, FNI200+R, FNI200+G+R, LS65 +G, LS65+R, L...

  7. Analysis of stable isotopes in fish mucus during a controlled diet switch

    EPA Science Inventory

    We have used a controlled diet switch in steelhead trout (Oncorhynchus mykiss) at the Oregon Hatchery Research Center to study the time rates of changes in stable isotopes of carbon and nitrogen (13C and 15N) in epidermal mucus, a rapidly responding “tissue.” Because of the ra...

  8. Stable isotope analysis of fish mucus during a controlled diet switch

    EPA Science Inventory

    We have used a controlled diet switch in steelhead trout (Oncorhynchus mykiss) at the Oregon Hatchery Research Center to study the time rates of changes in stable isotopes of carbon and nitrogen (13C and 15N) in epidermal mucus, a rapidly responding “tissue.” Because of the ra...

  9. Relationship between diet and anticoagulant response to warfarin – A factor analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diet composition is one of the factors that may contribute to intraindividual variability in the anticoagulant response to warfarin. The aim of this study was to determine the associations between food pattern and anticoagulant response to warfarin in a group of Brazilian patients with vascular dis...

  10. Stable-isotope analysis of canvasback winter diet in upper Chesapeake Bay

    USGS Publications Warehouse

    Haramis, G.M.; Jorde, D.G.; Macko, S.A.; Walker, J.L.

    2001-01-01

    A major decline in submerged aquatic vegetation (SAV) in Chesapeake Bay has altered the diet of wintering Canvasbacks (Aythya valisineria) from historically plant to a combination of benthic animal foods, especially the ubiquitous Baltic clam (Macoma balthica), supplemented with anthropogenic corn (Zea mays). Because the isotopic signature of corn is readily discriminated from bay benthos, but not SAV, we used stable-isotope methodology to investigate the corn-SAV component of the winter diet of Canvasbacks. Feeding trials with penned Canvasbacks were conducted to establish turnover rates and fractionation end-point loci of *13C and *15N signatures of whole blood for individual ducks fed ad libitum diets of (1) Baltic clams, (2) Baltic clams and corn, and (3) tubers of wild celery (Vallisneria americana). Turnover time constants averaged 4.5 weeks, indicating that signatures of wild ducks would be representative of bay diets by late February. Isotopic signatures of wild Canvasbacks sampled in February fell on a continuum between end-point loci for the Baltic clam and the combination Baltic clam and corn diet. Although that finding verifies a clear dependence on corn-SAV for wintering Canvasbacks, it also reveals that not enough corn-SAV is available to establish ad libitum consumption for the 15,000+ Canvasbacks wintering in the upper bay. On the basis of mean *13C signature of bay Canvasbacks (n=59) and ingestion rates from feeding trials, we estimated that 258 kg corn per day would account for the observed *13C enrichment and supply 18% of daily energetic needs for 15,000 Canvasbacks. That level of corn availability is so realistic that we conclude that SAV is likely of little dietary importance to Canvasbacks in that portion of the bay.

  11. The Effect of Increasing Fruit and Vegetable Consumption on Overall Diet: A Systematic Review and Meta-analysis.

    PubMed

    Fulton, Sharon L; McKinley, Michelle C; Young, Ian S; Cardwell, Chris R; Woodside, Jayne V

    2016-04-01

    Increasing fruit and vegetable (FV) consumption is associated with reduced risk of major diseases. However, it is unclear if health benefits are related to increased micronutrient intake or to improvements in overall diet profile. This review aimed to assess if increasing FV consumption had an impact on diet profile. In the systematic review, 12 studies revealed increases in micronutrient intakes, whilst the meta-analysis confirmed macronutrient findings from the systematic review showing no significant difference between the intervention and control groups in energy (kcals) in seven studies (mean difference = 1 kcals [95% CI = -115, 117]; p = 0.98), significant decreases in total fat (% energy) in five studies (Mean difference = -4% [95% CI = -5, -3]; p = < 0.00001) and significant increases in fiber in six studies (Mean difference = 5.36 g [95% CI = 4, 7]; p = < 0.00001) and total carbohydrate (% energy) in four studies (Mean = 4% [95% CI= 2, 5]; p = < 0.00001). In conclusion, results indicate that increased FV consumption increases micronutrient, carbohydrate and fiber intakes and possibly reduces fat intake, with no overall effect on energy intake. Therefore health benefits may act through an improvement in overall diet profile alongside increased micronutrient intakes. PMID:25118067

  12. An holistic ecological analysis of the diet of Cory's shearwaters using prey morphological characters and DNA barcoding.

    PubMed

    Alonso, Hany; Granadeiro, José P; Waap, Silke; Xavier, José; Symondson, William O C; Ramos, Jaime A; Catry, Paulo

    2014-08-01

    Knowledge of the dietary choices and trophic niches of organisms is the key to understanding their roles in ecosystems. In seabird diet studies, prey identification is a difficult challenge, often yielding results with technique-specific biases. Additionally, sampling efforts are often not extensive enough to reveal intrapopulational variation. Immature animals, which may constitute up to 50% of a population, may occupy a significantly different trophic niche to more experienced birds, but this remains largely unexplored. We investigated the diet of Cory's shearwater (Calonectris diomedea) from Selvagem Grande, an island located off the northwest African coast, collecting a total of 698 regurgitate samples over three consecutive breeding seasons. The diet was assessed using two complementary approaches for prey identification: conventional morphological analysis (using fish vertebrae, otoliths and cephalopod beaks) and DNA barcoding of the 16S rRNA mitochondrial gene, in cases where a positive identification could not be retrieved. Species assignments employed BLAST and distance-based methods, as well as direct optimization of the tree length based on unaligned sequences in POY. This method resulted in robust tree estimates and species assignments, showing its potential for DNA barcoding of stomach contents using hypervariable markers such as the 16S. The molecular approach increased taxonomic resolution and revealed an additional 17 taxa. Diet differed significantly according to breeding status, sex, breeding phase (prelaying and chick rearing) and year. Such direct evidence of trophic segregation within the same population has rarely been shown in seabirds and highlights the importance of including such variables in ecosystem-based management approaches. PMID:24806079

  13. A Rewritable, Random-Access DNA-Based Storage System

    PubMed Central

    Tabatabaei Yazdi, S. M. Hossein; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

    2015-01-01

    We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications. PMID:26382652

  14. A Rewritable, Random-Access DNA-Based Storage System.

    PubMed

    Yazdi, S M Hossein Tabatabaei; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

    2015-01-01

    We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications. PMID:26382652

  15. A Rewritable, Random-Access DNA-Based Storage System

    NASA Astrophysics Data System (ADS)

    Tabatabaei Yazdi, S. M. Hossein; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

    2015-09-01

    We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.

  16. Multiphoton excitation fluorescence correlation spectroscopy of fluorescent DNA base analogs

    NASA Astrophysics Data System (ADS)

    Katilius, Evaldas; Woodbury, Neal W.

    2004-06-01

    Two- and three-photon excitation was used to investigate the properties of two fluorescent DNA base analogs: 2-aminopurine and 6-methylisoxanthopterin. 2-aminopurine is a widely used fluorescent analog of the DNA base adenine. Three-photon excitation of 2-aminopurine is achievable by using intense femtosecond laser pulses in 850-950 nm spectral region. Interestingly, the three-photon excitation spectrum is blue-shifted relative to the three-times-wavelength single-photon excitation spectrum. The maximum of the absorbance band in the UV is at 305 nm, while the three-photon excitation spectrum has a maximum at around 880 nm. Fluorescence correlation measurements were attempted to evaluate the feasibility of using three-photon excitation of 2-aminopurine for DNA-protein interaction studies. However, due to relatively small three-photon absorption cross-section, a good signal-to-noise fluorescence correlation curves take very long time to obtain. Fluorescence properties of 6-methylisoxanthopterin, the fluorescent analog of guanine, were investigated using two-photon excitation. This molecule has the lowest energy absorption band centered around 350 nm, thus, two-photon excitation is attainable using 700 to 760 nm output of Ti-sapphire laser. The excitation spectrum of this molecule in the infrared well matches the doubled-wavelength single-photon excitation spectrum in the UV. The high fluorescence quantum yield of 6-methylisoxanthopterin allows efficient fluorescence correlation measurements and makes this molecule a very good candidate for using in in vitro DNA-protein interaction studies.

  17. Comparative Proteomic and Bioinformatic Analysis of the Effects of a High-Grain Diet on the Hepatic Metabolism in Lactating Dairy Goats

    PubMed Central

    Jiang, Xueyuan; Zeng, Tao; Zhang, Shukun; Zhang, Yuanshu

    2013-01-01

    To gain insight on the impart of high-grain diets on liver metabolism in ruminants, we employed a comparative proteomic approach to investigate the proteome-wide effects of diet in lactating dairy goats by conducting a proteomic analysis of the liver extracts of 10 lactating goats fed either a control diet or a high-grain diet. More than 500 protein spots were detected per condition by two-dimensional electrophoresis (2-DE). In total, 52 differentially expressed spots (≥2.0-fold changed) were excised and analyzed using MALDI TOF/TOF. Fifty-one protein spots were successfully identified. Of these, 29 proteins were upregulated, while 22 were downregulated in the high-grain fed vs. control animals. Differential expressions of proteins including alpha enolase, elongation factor 2, calreticulin, cytochrome b5, apolipoprotein A-I, catalase, was verified by mRNA analysis and/or Western blotting. Database searches combined with Gene Ontology (GO) analysis and KEGG pathway analysis revealed that the high-grain diet resulted in altered expression of proteins related to amino acids metabolism. These results suggest new candidate proteins that may contribute to a better understanding of the signaling pathways and mechanisms that mediate liver adaptation to high-grain diet. PMID:24260456

  18. Proliferation, apoptosis, and fractal dimension analysis for the quantification of intestinal trophism in sole (Solea solea) fed mussel meal diets

    PubMed Central

    2014-01-01

    Background The evaluation of intestinal trophism, mainly the mucosal layer, is an important issue in various conditions associated with injury, atrophy, recovery, and healing of the gut. The aim of the present study was to evaluate the kinetics of the proliferation and apoptosis of enterocytes by immunohistochemistry and to assess the complexity of intestinal mucosa by fractal dimension (FD) analysis in Solea solea fed different experimental diets. Results Histomorphological evaluation of all intestinal segments did not show signs of degeneration or inflammation. Cell proliferation index and FD were significantly reduced with a diet high in mussel meal (MM; p = 0.0034 and p = 0.01063, respectively), while apoptotic index did not show any significant difference for the same comparison (p = 0.3859). Linear regression analysis between apoptotic index (independent variable) and FD (dependent variable) showed a statistically significant inverse relationship (p = 0.002528). Linear regression analysis between cell proliferation index (independent variable) and FD (dependent variable) did not show any significant correlation (p = 0.131582). Conclusions The results demonstrated that diets containing increasing levels of mussel meal in substitution of fishmeal did not incite a hyperplastic response of the intestinal mucosa. The mussel meal, which is derived from molluscs, could mimic the characteristics of the sole’s natural prey, being readily digestible, even without increasing the absorptive surface of intestinal mucosa. Interestingly, from this study emerged that FD could be used as a numeric indicator complementary to in situ quantification methods to measure intestinal trophism, in conjunction with functional parameters. PMID:24997003

  19. Finite Element Analysis of the Cingulata Jaw: An Ecomorphological Approach to Armadillo's Diets.

    PubMed

    Serrano-Fochs, Sílvia; De Esteban-Trivigno, Soledad; Marcé-Nogué, Jordi; Fortuny, Josep; Fariña, Richard A

    2014-01-01

    Finite element analyses (FEA) were applied to assess the lower jaw biomechanics of cingulate xenarthrans: 14 species of armadillos as well as one Pleistocene pampathere (11 extant taxa and the extinct forms Vassallia, Eutatus and Macroeuphractus). The principal goal of this work is to comparatively assess the biomechanical capabilities of the mandible based on FEA and to relate the obtained stress patterns with diet preferences and variability, in extant and extinct species through an ecomorphology approach. The results of FEA showed that omnivorous species have stronger mandibles than insectivorous species. Moreover, this latter group of species showed high variability, including some similar biomechanical features of the insectivorous Tolypeutes matacus and Chlamyphorus truncatus to those of omnivorous species, in agreement with reported diets that include items other than insects. It remains unclear the reasons behind the stronger than expected lower jaw of Dasypus kappleri. On the other hand, the very strong mandible of the fossil taxon Vassallia maxima agrees well with the proposed herbivorous diet. Moreover, Eutatus seguini yielded a stress pattern similar to Vassalia in the posterior part of the lower jaw, but resembling that of the stoutly built Macroeuphractus outesi in the anterior part. The results highlight the need for more detailed studies on the natural history of extant armadillos. FEA proved a powerful tool for biomechanical studies in a comparative framework. PMID:25919313

  20. Finite Element Analysis of the Cingulata Jaw: An Ecomorphological Approach to Armadillo’s Diets

    PubMed Central

    Serrano-Fochs, Sílvia; De Esteban-Trivigno, Soledad; Marcé-Nogué, Jordi; Fortuny, Josep; Fariña, Richard A.

    2015-01-01

    Finite element analyses (FEA) were applied to assess the lower jaw biomechanics of cingulate xenarthrans: 14 species of armadillos as well as one Pleistocene pampathere (11 extant taxa and the extinct forms Vassallia, Eutatus and Macroeuphractus). The principal goal of this work is to comparatively assess the biomechanical capabilities of the mandible based on FEA and to relate the obtained stress patterns with diet preferences and variability, in extant and extinct species through an ecomorphology approach. The results of FEA showed that omnivorous species have stronger mandibles than insectivorous species. Moreover, this latter group of species showed high variability, including some similar biomechanical features of the insectivorous Tolypeutes matacus and Chlamyphorus truncatus to those of omnivorous species, in agreement with reported diets that include items other than insects. It remains unclear the reasons behind the stronger than expected lower jaw of Dasypus kappleri. On the other hand, the very strong mandible of the fossil taxon Vassallia maxima agrees well with the proposed herbivorous diet. Moreover, Eutatus seguini yielded a stress pattern similar to Vassalia in the posterior part of the lower jaw, but resembling that of the stoutly built Macroeuphractus outesi in the anterior part. The results highlight the need for more detailed studies on the natural history of extant armadillos. FEA proved a powerful tool for biomechanical studies in a comparative framework. PMID:25919313

  1. Assessment of Helminth Biodiversity in Wild Rats Using 18S rDNA Based Metagenomics

    PubMed Central

    Tsai, Isheng J.; Palomares-Rius, Juan Emilio; Yoshida, Ayako; Ogura, Yoshitoshi; Hayashi, Tetsuya; Maruyama, Haruhiko; Kikuchi, Taisei

    2014-01-01

    Parasite diversity has important implications in several research fields including ecology, evolutionary biology and epidemiology. Wide-ranging analysis has been restricted because of the difficult, highly specialised and time-consuming processes involved in parasite identification. In this study, we assessed parasite diversity in wild rats using 18S rDNA-based metagenomics. 18S rDNA PCR products were sequenced using an Illumina MiSeq sequencer and the analysis of the sequences using the QIIME software successfully classified them into several parasite groups. The comparison of the results with those obtained using standard methods including microscopic observation of helminth parasites in the rat intestines and PCR amplification/sequencing of 18S rDNA from isolated single worms suggests that this new technique is reliable and useful to investigate parasite diversity. PMID:25340824

  2. Dietary Intervention for Overweight and Obese Adults: Comparison of Low-Carbohydrate and Low-Fat Diets. A Meta-Analysis

    PubMed Central

    Sackner-Bernstein, Jonathan; Kanter, David; Kaul, Sanjay

    2015-01-01

    Background Reduced calorie, low fat diet is currently recommended diet for overweight and obese adults. Prior data suggest that low carbohydrate diets may also be a viable option for those who are overweight and obese. Purpose Compare the effects of low carbohydrate versus low fats diet on weight and atherosclerotic cardiovascular disease risk in overweight and obese patients. Data Sources Systematic literature review via PubMed (1966–2014). Study Selection Randomized controlled trials with ≥8 weeks follow up, comparing low carbohydrate (≤120gm carbohydrates/day) and low fat diet (≤30% energy from fat/day). Data Extraction Data were extracted and prepared for analysis using double data entry. Prior to identification of candidate publications, the outcomes of change in weight and metabolic factors were selected as defined by Cochrane Collaboration. Assessment of the effects of diets on predicted risk of atherosclerotic cardiovascular disease risk was added during the data collection phase. Data Synthesis 1797 patients were included from 17 trials with <1 year follow up in 12. Compared with low fat diet, low carbohydrate was associated with significantly greater reduction in weight (Δ = -2.0 kg, 95% CI: -3.1, -0.9) and significantly lower predicted risk of atherosclerotic cardiovascular disease events (p<0.03). Frequentist and Bayesian results were concordant. The probability of greater weight loss associated with low carbohydrate was >99% while the reduction in predicted risk favoring low carbohydrate was >98%. Limitations Lack of patient-level data and heterogeneity in dropout rates and outcomes reported. Conclusions This trial-level meta-analysis of randomized controlled trials comparing LoCHO diets with LoFAT diets in strictly adherent populations demonstrates that each diet was associated with significant weight loss and reduction in predicted risk of ASCVD events. However, LoCHO diet was associated with modest but significantly greater improvements in

  3. Ileostomy and your diet

    MedlinePlus

    ... ileostomy - diet; Abdominal pouch - diet; End ileostomy - diet; Ostomy - diet ... odor: Eating parsley, yogurt, and buttermilk Keeping your ostomy devices clean Using special deodorants or adding vanilla ...

  4. Geographical patterns of human diet derived from stable-isotope analysis of fingernails

    USGS Publications Warehouse

    Nardoto, G.B.; Silva, S.; Kendall, C.; Ehleringer, J.R.; Chesson, L.A.; Ferraz, E.S.B.; Moreira, M.Z.; Ometto, J.P.H.B.; Martinelli, L.A.

    2006-01-01

    Carbon and nitrogen isotope ratios of human fingernails were measured in 490 individuals in the western US and 273 individuals in southeastern Brazil living in urban areas, and 53 individuals living in a moderately isolated area in the central Amazon region of Brazil and consuming mostly locally grown foods. In addition, we measured the carbon and nitrogen isotope ratios of common food items to assess the extent to which these isotopic signatures remain distinct for people eating both omnivorous and vegetarian diets and living in different parts of the world, and the extent to which dietary information can be interpreted from these analyses. Fingernail ??13C values (mean ?? standard deviation) were -15.4 ?? 1.0 and -18.8 ?? 0.8??? and ??15N values were 10.4 ?? 0.7 and 9.4 ?? 0.6??? for southeastern Brazil and western US populations, respectively. Despite opportunities for a "global supermarket" effect to swamp out carbon and nitrogen isotope ratios in these two urbanized regions of the world, differences in the fingernail isotope ratios between southeastern Brazil and western US populations persisted, and appeared to be more associated with regional agricultural and animal production practices. Omnivores and vegetarians from Brazil and the US were isotopically distinct, both within and between regions. In a comparison of fingernails of individuals from an urban city and isolated communities in the Amazonian region, the urban region was similar to southeastern Brazil, whereas individuals from isolated nonurban communities showed distinctive isotopic values consistent with their diets and with the isotopic values of local foods. Although there is a tendency for a "global supermarket" diet, carbon and nitrogen isotopes of human fingernails hold dietary information directly related to both food sources and dietary practices in a region. ?? 2006 Wiley-Liss, Inc.

  5. Effects of the Mediterranean Diet on Cardiovascular Outcomes—A Systematic Review and Meta-Analysis

    PubMed Central

    Liyanage, Thaminda; Ninomiya, Toshiharu; Wang, Amanda; Neal, Bruce; Jun, Min; Wong, Muh Geot; Jardine, Meg; Hillis, Graham S.; Perkovic, Vlado

    2016-01-01

    Background A Mediterranean dietary pattern is widely recommended for the prevention of chronic disease. We sought to define the most likely effects of the Mediterranean diet on vascular disease and mortality. Methods We searched MEDLINE, EMBASE and the Cochrane Central Register without language restriction for randomized controlled trials comparing Mediterranean to control diets. Data on study design, patient characteristics, interventions, follow-up duration, outcomes and adverse events were sought. Individual study relative risks (RR) were pooled to create summary estimates. Results Six studies with a total of 10950 participants were included. Effects on major vascular events (n = 477), death (n = 693) and vascular deaths (n = 315) were reported for 3, 5 and 4 studies respectively. For one large study (n = 1000) there were serious concerns about the integrity of the data. When data for all studies were combined there was evidence of protection against major vascular events (RR 0.63, 95% confidence interval 0.53–0.75), coronary events (0.65, 0.50–0.85), stroke (0.65, 0.48–0.88) and heart failure (0.30, 0.17–0.56) but not for all-cause mortality (1.00, 0.86–1.15) or cardiovascular mortality (0.90, 0.72–1.11). After the study of concern was excluded the benefit for vascular events (0.69, 0.55–0.86) and stroke (0.66, 0.48–0.92) persisted but apparently positive findings for coronary events (0.73, 0.51–1.05) and heart failure (0.25, 0.05–1.17) disappeared. Conclusion The Mediterranean diet may protect against vascular disease. However, both the quantity and quality of the available evidence is limited and highly variable. Results must be interpreted with caution. PMID:27509006

  6. Phosphoprotein network analysis of white adipose tissues unveils deregulated pathways in response to high-fat diet.

    PubMed

    Asfa, Alli Shaik; Qiu, Beiying; Wee, Sheena; Choi, Hyungwon; Gunaratne, Jayantha; Tergaonkar, Vinay

    2016-01-01

    Despite efforts in the last decade, signaling aberrations associated with obesity remain poorly understood. To dissect molecular mechanisms that define this complex metabolic disorder, we carried out global phosphoproteomic analysis of white adipose tissue (WAT) from mice fed on low-fat diet (LFD) and high-fat diet (HFD). We quantified phosphorylation levels on 7696 peptides, and found significant differential phosphorylation levels in 282 phosphosites from 191 proteins, including various insulin-responsive proteins and metabolic enzymes involved in lipid homeostasis in response to high-fat feeding. Kinase-substrate prediction and integrated network analysis of the altered phosphoproteins revealed underlying signaling modulations during HFD-induced obesity, and suggested deregulation of lipogenic and lipolytic pathways. Mutation of the differentially-regulated novel phosphosite on cytoplasmic acetyl-coA forming enzyme ACSS2 (S263A) upon HFD-induced obesity led to accumulation of serum triglycerides and reduced insulin-responsive AKT phosphorylation as compared to wild type ACSS2, thus highlighting its role in obesity. Altogether, our study presents a comprehensive map of adipose tissue phosphoproteome in obesity and reveals many previously unknown candidate phosphorylation sites for future functional investigation. PMID:27180971

  7. Phosphoprotein network analysis of white adipose tissues unveils deregulated pathways in response to high-fat diet

    PubMed Central

    Asfa, Alli Shaik; Qiu, Beiying; Wee, Sheena; Choi, Hyungwon; Gunaratne, Jayantha; Tergaonkar, Vinay

    2016-01-01

    Despite efforts in the last decade, signaling aberrations associated with obesity remain poorly understood. To dissect molecular mechanisms that define this complex metabolic disorder, we carried out global phosphoproteomic analysis of white adipose tissue (WAT) from mice fed on low-fat diet (LFD) and high-fat diet (HFD). We quantified phosphorylation levels on 7696 peptides, and found significant differential phosphorylation levels in 282 phosphosites from 191 proteins, including various insulin-responsive proteins and metabolic enzymes involved in lipid homeostasis in response to high-fat feeding. Kinase-substrate prediction and integrated network analysis of the altered phosphoproteins revealed underlying signaling modulations during HFD-induced obesity, and suggested deregulation of lipogenic and lipolytic pathways. Mutation of the differentially-regulated novel phosphosite on cytoplasmic acetyl-coA forming enzyme ACSS2 (S263A) upon HFD-induced obesity led to accumulation of serum triglycerides and reduced insulin-responsive AKT phosphorylation as compared to wild type ACSS2, thus highlighting its role in obesity. Altogether, our study presents a comprehensive map of adipose tissue phosphoproteome in obesity and reveals many previously unknown candidate phosphorylation sites for future functional investigation. PMID:27180971

  8. Associations between diet and disease activity in ulcerative colitis patients using a novel method of data analysis

    PubMed Central

    Magee, Elizabeth A; Edmond, Laurie M; Tasker, Shiona M; Kong, San Choon; Curno, Richard; Cummings, John H

    2005-01-01

    Background The relapsing nature and varying geographical prevalence of ulcerative colitis (UC) implicates environmental factors such as diet in its aetiology. Methods In order to determine which foods might be related to disease activity in UC a new method of dietary analysis was developed and applied. Eighty-one UC patients were recruited at all stages of the disease process. Following completion of a 7 d diet diary, clinical assessment including a sigmoidoscopic examination (scale 0 (normal mucosa) to 6 (very active disease)) was conducted. Food weights for each person were adjusted (divided) by the person's calorific intake for the week. Each food consumed was given a food sigmoidoscopy score (FSS) calculated by summing the products of the (adjusted) weight of food consumed and sigmoidoscopy score for each patient and occurrence of food and dividing by the total (adjusted) weight of the food consumed by all 81 patients. Thus, foods eaten in large quantities by patients with very active disease have high FSSs and vice versa. Foods consumed by <10 people or weighing <1 kg for the whole group were excluded, leaving 75 foods. Results High FSS foods were characterized by high levels of the anti-thiamin additive sulfite (Mann-Whitney, p < 0.001), i.e. bitter, white wine, burgers, soft drinks from concentrates, sausages, lager and red wine. Caffeine also has anti-thiamin properties and decaffeinated coffee was associated with a better clinical state than the caffeine containing version. Beneficial foods (average intake per week) included pork (210 g), breakfast cereals (200 g), lettuce (110 g), apples and pears (390 g), milk (1250 ml), melon (350 g), bananas (350 g), bacon (120 g), beef and beef products (500 g), tomatoes (240 g), soup (700 g), citrus fruits (300 g), fish (290 g), yogurt (410 g), cheese (110 g), potatoes (710 g) and legumes (120 g). Conclusions The dietary analysis method described provides a new tool for establishing relationships between diet and

  9. Responsive DNA-based hydrogels and their applications

    PubMed Central

    Xiong, Xiangling; Zhou, Cuisong; Wu, Cuichen; Zhu, Guizhi; Chen, Zhuo; Tan, Weihong

    2015-01-01

    The term hydrogel describes a type of soft and wet material formed by crosslinked hydrophilic polymers. The distinct feature of hydrogels is their ability to absorb a large amount of water and swell. The properties of a hydrogel are usually determined by the type of polymer and crosslinker, the degree of crosslinking, and the water content. However, a group of hydrogels, called “smart hydrogels”, changes properties in response to environmental changes or external stimuli. Recently, DNA or DNA-inspired responsive hydrogels have attracted considerable attention in construction of smart hydrogels because of the intrinsic advantages of DNA. As a biological polymer, DNA is hydrophilic, biocompatible, and highly programmable by Watson-Crick base pairing. DNA can form a hydrogel by itself under certain conditions, and it can also be incorporated into synthetic polymers to form DNA-hybrid hydrogels. Functional DNAs, such as aptamers and DNAzymes, provide additional molecular recognition capabilities and versatility. In this review, we discuss DNA-based hydrogels in terms of their stimulus response, as well as their applications. PMID:23857726

  10. Applications of nanoparticles for DNA based rabies vaccine.

    PubMed

    Shah, Muhammad Ali A; Khan, Sajid Umar; Ali, Zeeshan; Yang, Haowen; Liu, Keke; Mao, Lanlan

    2014-01-01

    Rabies is a fatal encephalomyelitis. Most cases occur in developing countries and are transmitted by dogs. The cell culture vaccines as associated with high cost; therefore, have not replaced the unsafe brain-derived vaccines. In the developing countries these brain-derived rabies vaccines still can be seen in action. Moreover, there will be a need for vaccines against rabies-related viruses against which classical vaccines are not always effective. The worldwide incidence of rabies and the inability of currently used vaccination strategies to provide highly potent and cost-effective therapy indicate the need for alternate control strategies. DNA vaccines have emerged as the safest vaccines and best remedy for complicated diseases like hepatitis, HIV, and rabies. A number of recombinant DNA vaccines are now being developed against several diseases such as AIDS and malaria. Therefore, it can be a valuable alternative for the production of cheaper rabies vaccines against its larger spectrum of viruses. In this review we report published data on DNA-based immunization with sequences encoding rabies with special reference to nanotechnology. PMID:24730305

  11. Electron accommodation dynamics in the DNA base thymine

    SciTech Connect

    King, Sarah B.; Yandell, Margaret A.; Kunin, Alice; Stephansen, Anne B.; Yokoi, Yuki; Takayanagi, Toshiyuki; Neumark, Daniel M.

    2015-07-14

    The dynamics of electron attachment to the DNA base thymine are investigated using femtosecond time-resolved photoelectron imaging of the gas phase iodide-thymine (I{sup −}T) complex. An ultraviolet pump pulse ejects an electron from the iodide and prepares an iodine-thymine temporary negative ion that is photodetached with a near-IR probe pulse. The resulting photoelectrons are analyzed with velocity-map imaging. At excitation energies ranging from −120 meV to +90 meV with respect to the vertical detachment energy (VDE) of 4.05 eV for I{sup −}T, both the dipole-bound and valence-bound negative ions of thymine are observed. A slightly longer rise time for the valence-bound state than the dipole-bound state suggests that some of the dipole-bound anions convert to valence-bound species. No evidence is seen for a dipole-bound anion of thymine at higher excitation energies, in the range of 0.6 eV above the I{sup −}T VDE, which suggests that if the dipole-bound anion acts as a “doorway” to the valence-bound anion, it only does so at excitation energies near the VDE of the complex.

  12. Hydroxyl radical mediated DNA base modification by manmade mineral fibres.

    PubMed Central

    Leanderson, P; Söderkvist, P; Tagesson, C

    1989-01-01

    Manmade mineral fibres (MMMFs) were examined for their ability to hydroxylate 2-deoxyguanosine (dG) to 8-hydroxydeoxyguanosine (8-OH-dG), a reaction that is mediated by hydroxyl radicals. It appeared that (1) catalase and the hydroxyl radical scavengers, dimethylsulphoxide and sodium benzoate, inhibited the hydroxylation, whereas Fe2+ and H2O2 potentiated it; (2) pretreatment of MMMFs with the iron chelator, deferoxamine, or with extensive heat (200-400 degrees C), attenuated the hydroxylation; (3) the hydroxylation obtained by various MMMFs varied considerably; (4) there was no apparent correlation between the hydroxylation and the surface area of different MMMFs, although increasing the surface area of a fibre by crushing it increased its hydroxylating capacity; and (5) there was good correlation between the hydroxylation of dG residues in DNA and the hydroxylation of pure dG in solution for the 16 different MMMFs investigated. These findings indicate that MMMFs cause a hydroxyl radical mediated DNA base modification in vitro and that there is considerable variation in the reactivity of different fibre species. The DNA modifying ability seems to depend on physical or chemical characteristics, or both, of the fibre. PMID:2765416

  13. Nanoinformatics and DNA-based computing: catalyzing nanomedicine.

    PubMed

    Maojo, Victor; Martin-Sanchez, Fernando; Kulikowski, Casimir; Rodriguez-Paton, Alfonso; Fritts, Martin

    2010-05-01

    Five decades of research and practical application of computers in biomedicine has given rise to the discipline of medical informatics, which has made many advances in genomic and translational medicine possible. Developments in nanotechnology are opening up the prospects for nanomedicine and regenerative medicine where informatics and DNA computing can become the catalysts enabling health care applications at sub-molecular or atomic scales. Although nanomedicine promises a new exciting frontier for clinical practice and biomedical research, issues involving cost-effectiveness studies, clinical trials and toxicity assays, drug delivery methods, and the implementation of new personalized therapies still remain challenging. Nanoinformatics can accelerate the introduction of nano-related research and applications into clinical practice, leading to an area that could be called "translational nanoinformatics." At the same time, DNA and RNA computing presents an entirely novel paradigm for computation. Nanoinformatics and DNA-based computing are together likely to completely change the way we model and process information in biomedicine and impact the emerging field of nanomedicine most strongly. In this article, we review work in nanoinformatics and DNA (and RNA)-based computing, including applications in nanopediatrics. We analyze their scientific foundations, current research and projects, envisioned applications and potential problems that might arise from them. PMID:20118825

  14. DNA-based nanoparticle composite materials for EMI shielding

    NASA Astrophysics Data System (ADS)

    Zang, De Yu; Grote, James

    2012-03-01

    Composite materials, such as polymer-matrix containing conductive fillers, are very attractive for shielding electromagnetic interference (EMI) due to their high shielding efficiency and seamlessness, processability, flexibility, light-weight and low-cost. Here, we report a development of novel, DNA-based EMI-shielding materials (DESM), consisting of DNA and metal nanoparticles. It has been shown that a thin DESM layer (typically ~30 - 50 μm) could block EMI radiations up to 60 dB effectively over an RF frequency range from KHz to tens GHz, exhibiting excellent EMI shielding efficiency. A wide selection of metal nanoparticle fillers for DESM has been tested for their performance in EMI shielding efficiency. Among them, silver and carbon-based nanoparticles have demonstrated the best performance and were selected for further investigation. The silver-doped DESM films could be also non-conductive while their EMI shielding efficiency is still well-preserved. The nonconductive DESM could have a great potential in the microelectronics industries for EMI shielding on electronic devices and circuit boards.

  15. Detection of Damaged DNA Bases by DNA Glycosylase Enzymes†

    PubMed Central

    Friedman, Joshua I.; Stivers, James T.

    2010-01-01

    A fundamental and shared process in all forms of life is the use of DNA glycosylase enzymes to excise rare damaged bases from genomic DNA. Without such enzymes, the highly-ordered primary sequences of genes would rapidly deteriorate. Recent structural and biophysical studies are beginning to reveal a fascinating multistep mechanism for damaged base detection that begins with short-range sliding of the glycosylase along the DNA chain in a distinct conformation we refer to as the search complex (SC). Sliding is frequently punctuated by the formation of a transient “interrogation” complex (IC) where the enzyme extrahelically inspects both normal and damaged bases in an exosite pocket that is distant from the active site. When normal bases are presented in the exosite, the IC rapidly collapses back to the SC, while a damaged base will efficiently partition forward into the active site to form the catalytically competent excision complex (EC). Here we review the unique problems associated with enzymatic detection of rare damaged DNA bases in the genome, and emphasize how each complex must have specific dynamic properties that are tuned to optimize the rate and efficiency of damage site location. PMID:20469926

  16. Stable isotope analysis of avian eggs: Determining diet, feeding source and role of endogenous reserves

    SciTech Connect

    Hobson, K.A.

    1995-12-31

    Contemporary and archived avian eggs have been used extensively as a means of assessing and monitoring contaminants in the environment. Eggs can also be analyzed for stable-isotope ratios to provide dietary information that may be used to link diet of laying females with contaminant levels in eggs. Various egg components can provide integrated dietary information based on periods ranging from about a day (e.g. albumen, shell carbonate) to a week (egg yolk). In addition, some species may mobilize stored proteins and lipids from endogenous reserves during egg formation and this needs to be considered when correlating contaminant levels in eggs with dietary patterns in adult females. The role of endogenous reserves in egg formation may be assessed if individuals move between food webs with distinct isotopic profiles. This approach is illustrated using isotopic investigations of captive quail, falcons and waterfowl raised on controlled diets and of wild birds (Phalacrocorax auritus, Larus argentatus, Stema caspia, Chen caerulescens) that migrate between marine and terrestrial biomes using a variety of isotopes ({sup 13}C, {sup 15}N, {sup 34}S and D) . Whereas {sup 15}N measurements may provide information primarily of trophic level, {sup 13}C, {sup 34}S and D measurements reveal important information on source of feeding and origin of endogenous reserves.

  17. A global transcriptional analysis of Megalobrama amblycephala revealing the molecular determinants of diet-induced hepatic steatosis.

    PubMed

    Zhang, Dingdong; Lu, Kangle; Jiang, Guangzhen; Liu, Wenbin; Dong, Zaijie; Tian, Hongyan; Li, Xiangfei

    2015-10-10

    Blunt snout bream (Megalobrama amblycephala), a prevalent species in China's intensive polyculture systems, is highly susceptible to hepatic steatosis, resulting in considerable losses to the fish farming industry. Due to a lack of genomic resources, the molecular mechanisms of lipid metabolism in M. amblycephala are poorly understood. Here, a hepatic cDNA library was generated from equal amounts of mRNAs isolated from M. amblycephala fed normal-fat and high-fat diets. Sequencing of this library using the Illumina/Solexa platform produced approximately 51.87 million clean reads, which were assembled into 48,439 unigenes with an average length of 596 bp and an N50 value of 800 bp. These unigenes were searched against the nucleotide (NT), non-redundant (NR), Swiss-Prot, Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases using the BLASTn or BLASTx algorithms (E-value ≤ 10(-5)). A total of 8602 unigenes and 22,155 unigenes were functionally classified into 25 COG categories and 259 KEGG pathways, respectively. Furthermore, 22,072 unigenes were grouped into 62 sub-categories belonging to three main Gene Ontology (GO) terms. Using a digital gene expression analysis and the M. amblycephala transcriptome as a reference, 477 genes (134 up-regulated and 343 down-regulated) were identified as differentially expressed in fish fed a high-fat diet versus a normal-fat diet. KEGG and GO functional enrichment analyses of the differentially expressed unigenes were performed and 12 candidate genes related to lipid metabolism were identified. This study provides a global survey of hepatic transcriptome profiles and identifies candidate genes that may be related to lipid metabolism in M. amblycephala. These findings will facilitate further investigations of the mechanisms underlying hepatic steatosis in M. amblycephala. PMID:26074088

  18. DNA-Based Nanostructures: Changes of Mechanical Properties of DNA upon Ligand Binding

    NASA Astrophysics Data System (ADS)

    Nechipurenko, Yury; Grokhovsky, Sergey; Gursky, Georgy; Nechipurenko, Dmitry; Polozov, Robert

    The formation of DNA-based nanostructures involves the binding of different kinds of ligands to DNA as well as the interaction of DNA molecules with each other. Complex formation between ligand and DNA can alter physicochemical properties of the DNA molecule. In the present work, the accessibility of DNA-ligand complexes to cleavage by DNase I are considered, and the exact algorithms for analysis of diagrams of DNase I footprinting for ligand-DNA complexes are obtained. Changes of mechanical properties of the DNA upon ligand binding are also demonstrated by the cleavage patterns generated upon ultrasound irradiation of cis-platin-DNA complexes. Propagation of the mechanical perturbations along DNA in the presence of bound ligands is considered in terms of a string model with a heterogeneity corresponding to the position of a bound ligand on DNA. This model can reproduce qualitatively the cleavage patterns obtained upon ultrasound irradiation of cis-platin-DNA complexes.

  19. Transcriptome analysis of anti-fatty liver action by Campari tomato using a zebrafish diet-induced obesity model

    PubMed Central

    2011-01-01

    Background High dietary intake of vegetable products is beneficial against obesity and its related diseases such as dyslipidemia, nonalcoholic fatty liver disease, and cancer. We previously developed a diet-induced obesity model of zebrafish (DIO-zebrafish) that develops visceral adiposity, dyslipidemia, and liver steatosis. Zebrafish is a polyphagous animal; thus we hypothesized that DIO-zebrafish could be used for transcriptome analysis of anti-obesity effects of vegetables. Results Each vegetable exhibited different effects against obesity. We focused on "Campari" tomato, which suppressed increase of body weight, plasma TG, and lipid droplets in livers of DIO-zebrafish. Campari tomato decreased srebf1 mRNA by increase of foxo1 gene expression, which may depend on high contents of β-carotene in this strain. Conclusions Campari tomato ameliorates diet-induced obesity, especially dyslipidemia and liver steatosis via downregulation of gene expression related to lipogenesis. DIO-zebrafish can discriminate the anti-obesity effects of different strains of vegetables, and will become a powerful tool to assess outcomes and find novel mechanisms of anti-obesity effects of natural products. PMID:22152339

  20. Breakfast and the diets of Australian adults: an analysis of data from the 1995 National Nutrition Survey.

    PubMed

    Williams, Peter

    2005-02-01

    The aim of this study was to describe the nutrients provided to Australian adults by the breakfast meal and to compare the food and nutrient intakes and health of regular breakfast eaters and breakfast skippers. The Australian Bureau of Statistics was commissioned to undertake additional analysis of data collected in the 1995 Australian National Nutrition Survey (NNS). The survey included 24-h recalls, physical measurements and a food habits questionnaire collected during the period February 1995-March 1996, with a nationally representative sample of 10,851 Australians aged 19 years and older. The median nutrient intakes at breakfast and the proportion of the daily total contributed by breakfast were calculated. Differences between regular breakfast eaters and breakfast skippers in terms of nutrient intake, body mass index and health status were compared using Student t-tests. The findings show the typical Australian breakfast was low in fat, high in carbohydrate and a good source of thiamin, riboflavin, niacin, calcium and magnesium. In the NNS regular breakfast eaters had more adequate diets overall, particularly those aged 65+ years. People who did not eat breakfast cereal were much more likely to have inadequate nutrient intakes, especially of thiamin, riboflavin, calcium, magnesium and iron. Regular breakfast eaters were more likely to rate their health as excellent or good than those who skip breakfast, but there was no difference between the fat intake or the body mass index of regular breakfast eaters compared with breakfast skippers. Regular breakfast consumption is associated with better diets for adults overall. PMID:16019316

  1. Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations

    PubMed Central

    Zarecki, Raphy; Oberhardt, Matthew; Ursell, Luke K.; Kupiec, Martin; Knight, Rob; Gophna, Uri; Ruppin, Eytan

    2014-01-01

    ABSTRACT Glycans form the primary nutritional source for microbes in the human gut, and understanding their metabolism is a critical yet understudied aspect of microbiome research. Here, we present a novel computational pipeline for modeling glycan degradation (GlyDeR) which predicts the glycan degradation potency of 10,000 reference glycans based on either genomic or metagenomic data. We first validated GlyDeR by comparing degradation profiles for genomes in the Human Microbiome Project against KEGG reaction annotations. Next, we applied GlyDeR to the analysis of human and mammalian gut microbial communities, which revealed that the glycan degradation potential of a community is strongly linked to host diet and can be used to predict diet with higher accuracy than sequence data alone. Finally, we show that a microbe’s glycan degradation potential is significantly correlated (R = 0.46) with its abundance, with even higher correlations for potential pathogens such as the class Clostridia (R = 0.76). GlyDeR therefore represents an important tool for advancing our understanding of bacterial metabolism in the gut and for the future development of more effective prebiotics for microbial community manipulation. PMID:25118239

  2. The Effect of the Traditional Mediterranean-Style Diet on Metabolic Risk Factors: A Meta-Analysis

    PubMed Central

    Garcia, Marissa; Bihuniak, Jessica D.; Shook, Julia; Kenny, Anne; Kerstetter, Jane; Huedo-Medina, Tania B.

    2016-01-01

    The Mediterranean-style diet (MedSD) has gained attention for its positive effects on health outcomes, including metabolic risk factors. However, it is unknown as to which components of MedSD interventions are most beneficial in reducing risk. The objective of this meta-analysis was to obtain effect sizes for metabolic risk factors and explain the variability across the current literature based on study design, sample, and diet characteristics. Six electronic databases were searched from inception until 9 February 2016. Data from 29 studies (N = 4133) were included. There were significant effects in favor of the MedSD for waist circumference, triglycerides, blood glucose, systolic blood pressure, and diastolic blood pressure (d+ = −0.54; d+ = −0.46; d+ = −0.50; d+ = −0.72; d+ = −0.94, respectively). The MedSD was significantly beneficial when the intervention was longer in duration, was conducted in Europe, used a behavioral technique, and was conducted using small groups. The traditional MedSD had significant beneficial effects on five of the six metabolic risk factors. Results from this study provide support for population specific dietary guideline for metabolic risk reduction. PMID:26999195

  3. Multi-isotopic analysis reveals individual mobility and diet at the Early Iron Age monumental tumulus of Magdalenenberg, Germany.

    PubMed

    Oelze, Vicky M; Koch, Julia K; Kupke, Katharina; Nehlich, Olaf; Zäuner, Steve; Wahl, Joachim; Weise, Stephan M; Rieckhoff, Sabine; Richards, Michael P

    2012-07-01

    For the Early Iron Age western Hallstatt culture, which includes the site of Magdalenenberg in southwest Germany, it has been proposed that people were mobile and maintained far reaching social and trading networks throughout Europe. We tested this hypothesis by analyzing multiple isotopes (strontium, oxygen, sulfur, carbon, and nitrogen) of the preserved skeletons from the Magdalenenberg elite cemetery to determine diets and to look for evidence of mobility. The analysis of carbon, nitrogen, and sulfur isotope ratios in collagen of humans (n = 50) and associated domestic fauna (n = 10) indicates a terrestrial-based diet. There was a heterogeneous range of isotope values in both strontium (0.70725 to 0.71923, n = 76) and oxygen (13.4‰ to 18.5‰, n = 78) measured in tooth enamel. Although many of the individuals had values consistent with being from Hallstatt culture sites within southwest Germany, some individuals likely originated from further afield. Possible areas include the Alps of Switzerland and Austria or even locations in Italy. Our study strongly supports the assumption of far reaching social and economic networks in the western Hallstatt culture. PMID:22553183

  4. An uncooked vegan diet shifts the profile of human fecal microflora: computerized analysis of direct stool sample gas-liquid chromatography profiles of bacterial cellular fatty acids.

    PubMed Central

    Peltonen, R; Ling, W H; Hänninen, O; Eerola, E

    1992-01-01

    The effect of an uncooked extreme vegan diet on fecal microflora was studied by direct stool sample gas-liquid chromatography (GLC) of bacterial cellular fatty acids and by quantitative bacterial culture by using classical microbiological techniques of isolation, identification, and enumeration of different bacterial species. Eighteen volunteers were divided randomly into two groups. The test group received an uncooked vegan diet for 1 month and a conventional diet of mixed Western type for the other month of the study. The control group consumed a conventional diet throughout the study period. Stool samples were collected. Bacterial cellular fatty acids were extracted directly from the stool samples and measured by GLC. Computerized analysis of the resulting fatty acid profiles was performed. Such a profile represents all bacterial cellular fatty acids in a sample and thus reflects its microflora and can be used to detect changes, differences, or similarities of bacterial flora between individual samples or sample groups. GLC profiles changed significantly in the test group after the induction and discontinuation of the vegan diet but not in the control group at any time, whereas quantitative bacterial culture did not detect any significant change in fecal bacteriology in either of the groups. The results suggest that an uncooked extreme vegan diet alters the fecal bacterial flora significantly when it is measured by direct stool sample GLC of bacterial fatty acids. PMID:1482187

  5. Meta-analysis investigating associations between healthy diet and fasting glucose and insulin levels and modification by loci associated with glucose homeostasis in data from 15 cohorts.

    PubMed

    Nettleton, Jennifer A; Hivert, Marie-France; Lemaitre, Rozenn N; McKeown, Nicola M; Mozaffarian, Dariush; Tanaka, Toshiko; Wojczynski, Mary K; Hruby, Adela; Djoussé, Luc; Ngwa, Julius S; Follis, Jack L; Dimitriou, Maria; Ganna, Andrea; Houston, Denise K; Kanoni, Stavroula; Mikkilä, Vera; Manichaikul, Ani; Ntalla, Ioanna; Renström, Frida; Sonestedt, Emily; van Rooij, Frank J A; Bandinelli, Stefania; de Koning, Lawrence; Ericson, Ulrika; Hassanali, Neelam; Kiefte-de Jong, Jessica C; Lohman, Kurt K; Raitakari, Olli; Papoutsakis, Constantina; Sjogren, Per; Stirrups, Kathleen; Ax, Erika; Deloukas, Panos; Groves, Christopher J; Jacques, Paul F; Johansson, Ingegerd; Liu, Yongmei; McCarthy, Mark I; North, Kari; Viikari, Jorma; Zillikens, M Carola; Dupuis, Josée; Hofman, Albert; Kolovou, Genovefa; Mukamal, Kenneth; Prokopenko, Inga; Rolandsson, Olov; Seppälä, Ilkka; Cupples, L Adrienne; Hu, Frank B; Kähönen, Mika; Uitterlinden, André G; Borecki, Ingrid B; Ferrucci, Luigi; Jacobs, David R; Kritchevsky, Stephen B; Orho-Melander, Marju; Pankow, James S; Lehtimäki, Terho; Witteman, Jacqueline C M; Ingelsson, Erik; Siscovick, David S; Dedoussis, George; Meigs, James B; Franks, Paul W

    2013-01-15

    Whether loci that influence fasting glucose (FG) and fasting insulin (FI) levels, as identified by genome-wide association studies, modify associations of diet with FG or FI is unknown. We utilized data from 15 U.S. and European cohort studies comprising 51,289 persons without diabetes to test whether genotype and diet interact to influence FG or FI concentration. We constructed a diet score using study-specific quartile rankings for intakes of whole grains, fish, fruits, vegetables, and nuts/seeds (favorable) and red/processed meats, sweets, sugared beverages, and fried potatoes (unfavorable). We used linear regression within studies, followed by inverse-variance-weighted meta-analysis, to quantify 1) associations of diet score with FG and FI levels and 2) interactions of diet score with 16 FG-associated loci and 2 FI-associated loci. Diet score (per unit increase) was inversely associated with FG (β = -0.004 mmol/L, 95% confidence interval: -0.005, -0.003) and FI (β = -0.008 ln-pmol/L, 95% confidence interval: -0.009, -0.007) levels after adjustment for demographic factors, lifestyle, and body mass index. Genotype variation at the studied loci did not modify these associations. Healthier diets were associated with lower FG and FI concentrations regardless of genotype at previously replicated FG- and FI-associated loci. Studies focusing on genomic regions that do not yield highly statistically significant associations from main-effect genome-wide association studies may be more fruitful in identifying diet-gene interactions. PMID:23255780

  6. DNA-based species detection capabilities using laser transmission spectroscopy

    PubMed Central

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

    2013-01-01

    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. PMID:23015524

  7. A DNA-Based Semantic Fusion Model for Remote Sensing Data

    PubMed Central

    Sun, Heng; Weng, Jian; Yu, Guangchuang; Massawe, Richard H.

    2013-01-01

    Semantic technology plays a key role in various domains, from conversation understanding to algorithm analysis. As the most efficient semantic tool, ontology can represent, process and manage the widespread knowledge. Nowadays, many researchers use ontology to collect and organize data's semantic information in order to maximize research productivity. In this paper, we firstly describe our work on the development of a remote sensing data ontology, with a primary focus on semantic fusion-driven research for big data. Our ontology is made up of 1,264 concepts and 2,030 semantic relationships. However, the growth of big data is straining the capacities of current semantic fusion and reasoning practices. Considering the massive parallelism of DNA strands, we propose a novel DNA-based semantic fusion model. In this model, a parallel strategy is developed to encode the semantic information in DNA for a large volume of remote sensing data. The semantic information is read in a parallel and bit-wise manner and an individual bit is converted to a base. By doing so, a considerable amount of conversion time can be saved, i.e., the cluster-based multi-processes program can reduce the conversion time from 81,536 seconds to 4,937 seconds for 4.34 GB source data files. Moreover, the size of result file recording DNA sequences is 54.51 GB for parallel C program compared with 57.89 GB for sequential Perl. This shows that our parallel method can also reduce the DNA synthesis cost. In addition, data types are encoded in our model, which is a basis for building type system in our future DNA computer. Finally, we describe theoretically an algorithm for DNA-based semantic fusion. This algorithm enables the process of integration of the knowledge from disparate remote sensing data sources into a consistent, accurate, and complete representation. This process depends solely on ligation reaction and screening operations instead of the ontology. PMID:24116207

  8. DNA-based eye colour prediction across Europe with the IrisPlex system.

    PubMed

    Walsh, Susan; Wollstein, Andreas; Liu, Fan; Chakravarthy, Usha; Rahu, Mati; Seland, Johan H; Soubrane, Gisele; Tomazzoli, Laura; Topouzis, Fotis; Vingerling, Johannes R; Vioque, Jesus; Fletcher, Astrid E; Ballantyne, Kaye N; Kayser, Manfred

    2012-05-01

    The ability to predict Externally Visible Characteristics (EVCs) from DNA, also referred to as Forensic DNA Phenotyping (FDP), is an exciting new chapter in forensic genetics holding great promise for tracing unknown individuals who are unidentifiable via standard forensic short tandem repeat (STR) profiling. For the purpose of DNA-based eye colour prediction, we previously developed the IrisPlex system consisting of a multiplex genotyping assay and a prediction model based on genotype and phenotype data from 3804 Dutch Europeans. Recently, we performed a forensic developmental validation study of the highly sensitive IrisPlex assay, which currently represents the only validated tool available for DNA-based prediction of eye colour in forensic applications. In the present study, we validate the IrisPlex prediction model by extending our initially described model towards genotype and phenotype data from multiple European populations. We performed IrisPlex analysis on 3840 individuals from seven sites across Europe as part of the European Eye (EUREYE) study for which DNA and high-resolution eye images were available. The accuracy rate of correctly predicting an individual's eye colour as being blue or brown, above the empirically established probability threshold of 0.7, was on average 94% across all seven European populations, ranging from 91% to 98%, despite the large variation in eye colour frequencies between the populations. The overall prediction accuracies expressed by the area under the receiver characteristic operating curves (AUC) were 0.96 for blue and 0.96 for brown eyes, which is considerably higher than those established before. The IrisPlex prediction model parameters generated from this multi-population European dataset, and thus its prediction capabilities, were highly comparable to those previously established. Therefore, the increased information regarding eye colour phenotype and genotype distributions across Europe, and the system's ability to

  9. IBS Diet

    MedlinePlus

    ... often conflicting advice is available, especially on the Internet. Much of it is associated with a considerable cost. Video with Peter Whorwell, MD Diet, Eating and IBS Symptoms There are a variety of ...

  10. DASH Diet

    MedlinePlus

    ... Diet Emphasizes vegetables, fruits, and fat-free or low-fat dairy products. Includes whole grains, fish, poultry, beans, seeds, nuts, and vegetable oils. Limits sodium, sweets, sugary beverages, ...

  11. Vegetarian diet

    MedlinePlus

    ... Fruits Whole grains Legumes Seeds Nuts May include eggs and milk A vegetarian diet contains no animal ... animal proteins or animal by-products such as eggs, milk, or honey. Lacto-vegetarian: includes plant foods ...

  12. Vegetarian diet

    MedlinePlus

    ... grains Legumes Seeds Nuts May include eggs and milk A vegetarian diet contains no animal proteins. A ... proteins or animal by-products such as eggs, milk, or honey. Lacto-vegetarian: includes plant foods plus ...

  13. Stable Isotope Analysis of Reindeer Diet in Northern Sweden and Norway

    NASA Astrophysics Data System (ADS)

    Zhao, L.; Hobbie, E. A.; Steele, K.; Lucas, R. W.; Varner, R. K.

    2012-12-01

    Shrub expansion in the Scandinavian Arctic has been recorded through ground observations and remote sensing techniques; however its effect on local mammalian ecology has yet to be fully understood. Warming in these subarctic ecosystems has been correlated with this increase in vascular plant production, which in turn has been correlated with a decline in lichen biomass. Our study examined δ13C and δ15N values in reindeer tissue to determine whether such biomass changes in northern Norway and Sweden have been substantial enough to affect the summer forage composition of reindeer. Hair and antler samples dating from 1909 to present day were collected from members of the Sámi community, museums, grazing areas near Abisko National Park, and Norwegian slaughterhouses. δ13C and δ15N values of hair and antler samples were compared to previously reported δ13C and δ15N values of potential reindeer forage species. This allowed for the prediction of the proportion of lichen versus graminoids, forbs, fungi and shrubs each reindeer consumed the summer before the sample was collected. Recent reindeer samples would be expected have lower δ13C and δ15N values, as compared to older specimens, if observed biomass changes had led to a decrease in reindeer summer lichen consumption in exchange for an increase in vascular plant consumption. After correcting δ13C data for the ongoing depletion of δ13C in the atmosphere due to combustion of fossil fuels (the Suess effect), no significant change of δ13C values in relation to age of sample was found. There was also no correlation between the age of the reindeer sample and δ15N values. These results indicate that summer diet composition of reindeer in northern Sweden and Norway has not notably changed since the early 1900s, regardless of potential vegetation changes. Further studies are needed to determine the extent to which reindeer will be able to selectively feed rather than change diet composition, where vascular plants

  14. Jatropha curcas leaves analysis, reveals it as mineral source for low sodium diets.

    PubMed

    Méndez, Lucero; Rojas, Janne; Izaguirre, César; Contreras, Billmary; Gómez, Rubén

    2014-12-15

    Jatropha curcas is a perennial herb, belonging to the family Euphorbiaceae, found in countries such as India, Mexico and Venezuela. In the present study, proximate composition and mineral content on the leaves of J. curcas was analysed and compared to spinach (Spinacia oleracea L.) using a ICP-AES. The bromatologic test (dry material) results for ashes, proteins, lipids and carbohydrates revealed 23.4%, 28.0%, 3.2% and 45.4% for J. curcas; whereas for S. oleracea values were 28.9%, 20.8%, 0.5% and 49.9%. Furthermore, minerals found in both species ashes were: calcium, potassium, magnesium, iron and phosphorus, resulting that leaves of J. curcas are composed by three times the iron and calcium amount comparing to spinach; while sodium was absent from the former species. In this study Cu and Zn were found only in spinach, while Pb and As were not detected in any of the studied species. These results indicate that J. curcas leaves might be considered as mineral source suitable for animal and human consumption, especially for people who requires a low sodium diet. PMID:25038714

  15. Stable isotope analysis of diet confirms niche separation of two sympatric species of Namib Desert lizard.

    PubMed

    Murray, Ian W; Lease, Hilary M; Hetem, Robyn S; Mitchell, Duncan; Fuller, Andrea; Woodborne, Stephan

    2016-01-01

    We used stable isotopes of carbon and nitrogen to study the trophic niche of two species of insectivorous lizards, the Husab sand lizard Pedioplanis husabensis and Bradfield's Namib day gecko living sympatrically in the Namib Desert. We measured the δ(13) C and δ(15) N ratios in lizard blood tissues with different turnover times (whole blood, red blood cells and plasma) to investigate lizard diet in different seasons. We also measured the δ(13) C and δ(15) N ratios in available arthropod prey and plant tissues on the site, to identify the avenues of nutrient movement between lizards and their prey. Through the use of stable isotope mixing models, we found that the two lizard species relied on a largely non-overlapping but seasonally variable array of arthropods: P. husabensis primarily fed on termites, beetles and wasps, while R. bradfieldi fed mainly on ants, wasps and hemipterans. Nutrients originating from C3 plants were proportionally higher for R. bradfieldi than for P. husabensis during autumn and late autumn/early winter, although not summer. Contrary to the few available data estimating the trophic transfer of nutrients in ectotherms in mixed C3 and C4 /crassulacean acid metabolism (CAM) plant landscapes, we found that our lizard species primarily acquired nutrients that originated from C4 /CAM plants. This work adds an important dimension to the general lack of studies using stable isotope analyses to estimate lizard niche partitioning and resource use. PMID:26817923

  16. Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level.

    PubMed

    Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene

    2014-01-01

    Awareness that disease susceptibility is not only dependent on genetic make up, but can be affected by lifestyle decisions, has brought more attention to the role of diet. However, food is often treated as a black box, or the focus is limited to few, well-studied compounds, such as polyphenols, lipids and nutrients. In this work, we applied text mining and Naïve Bayes classification to assemble the knowledge space of food-phytochemical and food-disease associations, where we distinguish between disease prevention/amelioration and disease progression. We subsequently searched for frequently occurring phytochemical-disease pairs and we identified 20,654 phytochemicals from 16,102 plants associated to 1,592 human disease phenotypes. We selected colon cancer as a case study and analyzed our results in three directions; i) one stop legacy knowledge-shop for the effect of food on disease, ii) discovery of novel bioactive compounds with drug-like properties, and iii) discovery of novel health benefits from foods. This works represents a systematized approach to the association of food with health effect, and provides the phytochemical layer of information for nutritional systems biology research. PMID:24453957

  17. Metagenomic analysis of buffalo rumen microbiome: Effect of roughage diet on Dormancy and Sporulation genes.

    PubMed

    Singh, K M; Reddy, B; Patel, A K; Panchasara, H; Parmar, N; Patel, A B; Shah, T M; Bhatt, V D; Joshi, C G

    2014-12-01

    Buffalo rumen microbiome experiences a variety of diet stress and represents reservoir of Dormancy and Sporulation genes. However, the information on genomic responses to such conditions is very limited. The Ion Torrent PGM next generation sequencing technology was used to characterize general microbial diversity and the repertoire of microbial genes present, including genes associated with Dormancy and Sporulation in Mehsani buffalo rumen metagenome. The research findings revealed the abundance of bacteria at the domain level and presence of Dormancy and Sporulation genes which were predominantly associated with the Clostridia and Bacilli taxa belonging to the phyla Firmicutes. Genes associated with Sporulation cluster and Sporulation orphans were increased from 50% to 100% roughage treatment, thereby promoting sporulation all along the treatments. The spore germination is observed to be the highest in the 75% roughage treatment both in the liquid and solid rumen fraction samples with respect to the decrease in the values of the genes associated with spore core dehydration, thereby facilitating spore core hydration which is necessary for spore germination. PMID:25606408

  18. Metagenomic analysis of buffalo rumen microbiome: Effect of roughage diet on Dormancy and Sporulation genes

    PubMed Central

    Singh, K.M.; Reddy, B.; Patel, A.K.; Panchasara, H.; Parmar, N.; Patel, A.B.; Shah, T.M.; Bhatt, V.D.; Joshi, C.G.

    2014-01-01

    Buffalo rumen microbiome experiences a variety of diet stress and represents reservoir of Dormancy and Sporulation genes. However, the information on genomic responses to such conditions is very limited. The Ion Torrent PGM next generation sequencing technology was used to characterize general microbial diversity and the repertoire of microbial genes present, including genes associated with Dormancy and Sporulation in Mehsani buffalo rumen metagenome. The research findings revealed the abundance of bacteria at the domain level and presence of Dormancy and Sporulation genes which were predominantly associated with the Clostridia and Bacilli taxa belonging to the phyla Firmicutes. Genes associated with Sporulation cluster and Sporulation orphans were increased from 50% to 100% roughage treatment, thereby promoting sporulation all along the treatments. The spore germination is observed to be the highest in the 75% roughage treatment both in the liquid and solid rumen fraction samples with respect to the decrease in the values of the genes associated with spore core dehydration, thereby facilitating spore core hydration which is necessary for spore germination. PMID:25606408

  19. Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level

    PubMed Central

    Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene

    2014-01-01

    Awareness that disease susceptibility is not only dependent on genetic make up, but can be affected by lifestyle decisions, has brought more attention to the role of diet. However, food is often treated as a black box, or the focus is limited to few, well-studied compounds, such as polyphenols, lipids and nutrients. In this work, we applied text mining and Naïve Bayes classification to assemble the knowledge space of food-phytochemical and food-disease associations, where we distinguish between disease prevention/amelioration and disease progression. We subsequently searched for frequently occurring phytochemical-disease pairs and we identified 20,654 phytochemicals from 16,102 plants associated to 1,592 human disease phenotypes. We selected colon cancer as a case study and analyzed our results in three directions; i) one stop legacy knowledge-shop for the effect of food on disease, ii) discovery of novel bioactive compounds with drug-like properties, and iii) discovery of novel health benefits from foods. This works represents a systematized approach to the association of food with health effect, and provides the phytochemical layer of information for nutritional systems biology research. PMID:24453957

  20. Impact of low-carbohydrate diet on renal function: a meta-analysis of over 1000 individuals from nine randomised controlled trials.

    PubMed

    Oyabu, Chikako; Hashimoto, Yoshitaka; Fukuda, Takuya; Tanaka, Muhei; Asano, Mai; Yamazaki, Masahiro; Fukui, Michiaki

    2016-08-01

    We aimed to clarify the effect of low-carbohydrate diet (LCD) on renal function in overweight and obese individuals without chronic kidney disease (CKD). Literature searches were performed using EMBASE, MEDLINE and Cochrane Library until December 2015. We selected articles that reported human studies from their inception until December 2015 in English using the following searching terms: 'Low carbohydrate diet' AND ('Clinical trial' OR 'Clinical study' OR 'Clinical investigation' OR 'Observational study' OR 'Cohort study'). We compared the effects of LCD on renal function, defined as change in estimated glomerular filtration rate (eGFR), assessed in randomised-controlled trials. We calculated the mean change in eGFR and the mean change in standard deviations by eGFR or creatinine clearance, and compared the mean change in eGFR and standard deviations in LCD with those in the control diet using fixed-effects models. We selected nine randomised controlled trials including 1687 participants (861 were fed LCD and 826 were fed the control diet). The mean change in eGFR in the LCD group was -4·7 to 24·0 ml/min per 1·73 m2 and that in the control diet group was -4·1 to 10·8 ml/min per 1·73 m2. The mean change in eGFR in the LCD group was greater than that in the control diet (0·13 ml/min per 1·73 m2; 95 % CI 0·00, 0·26). In the present meta-analysis, we identified that the increase in eGFR was greater in LCD compared with the control diet in overweight and obese individuals without CKD. PMID:27346534

  1. Meta-Analysis of Attention-Deficit/Hyperactivity Disorder or Attention-Deficit/Hyperactivity Disorder Symptoms, Restriction Diet, and Synthetic Food Color Additives

    ERIC Educational Resources Information Center

    Nigg, Joel T.; Lewis, Kara; Edinger, Tracy; Falk, Michael

    2012-01-01

    Objective: The role of diet and of food colors in attention-deficit/hyperactivity disorder (ADHD) or its symptoms warrants updated quantitative meta-analysis, in light of recent divergent policy in Europe and the United States. Method: Studies were identified through a literature search using the PubMed, Cochrane Library, and PsycNET databases…

  2. Analysis of production responses to changing crude protein levels in lactating dairy cow diets when evaluated in continuous or change-over experimental designs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate by meta-analysis the effect of experimental design on the production response functions obtained when changing crude protein levels in lactating dairy cow diets. The final database of studies that met the selection criteria contained 55 publications with 2...

  3. Contribution of diet to aggregate arsenic exposures-an analysis across populations.

    PubMed

    Kurzius-Spencer, Margaret; Burgess, Jefferey L; Harris, Robin B; Hartz, Vern; Roberge, Jason; Huang, Shuang; Hsu, Chiu-Hsieh; O'Rourke, M K

    2014-01-01

    The relative contribution of dietary arsenic (As) to aggregate daily exposure has not been well-characterized, especially in relation to the current EPA maximum contaminant level (MCL) of 10 p.p.b. for As in drinking water. Our objectives were to: (1) model exposure to inorganic and total As among non-seafood eaters using subject-specific data, (2) compare the contribution of food, drinking and cooking water to estimated aggregate exposure in households with variable background tap water As levels, and (3) describe the upper distribution of potential dose at different thresholds of tap water As. Dietary As intake was modeled in regional study populations and NHANES 2003-2004 using dietary records in conjunction with published food As residue data. Water As was measured in the regional studies. Among subjects exposed to tap water As >10 p.p.b., aggregate inorganic exposure was 24.5-26.1 μg/day, with approximately 30% of intake from food. Among subjects living in homes with tap water As ≤10, 5 or 3 p.p.b., aggregate inorganic As exposure was 8.6-11.8 μg/day, with 54-85% of intake from food. Median inorganic As potential dose was 0.42-0.50 μg/kg BW/day in subjects exposed to tap water As >10 p.p.b. and less than half that among subjects exposed to tap water As ≤10 p.p.b. The majority of inorganic and total As exposure is attributable to diet in subjects with tap water As

  4. Diet and cancer risk in the Korean population: a meta- analysis.

    PubMed

    Woo, Hae Dong; Park, Sohee; Oh, Kyungwon; Kim, Hyun Ja; Shin, Hae Rim; Moon, Hyun Kyung; Kim, Jeongseon

    2014-01-01

    Many studies have found links between diet and cancer. The summary estimates of the association between dietary factors and cancer risk were investigated using previously reported studies of the Korean population. Gastric cancer risk was inversely associated with the high intake of soy foods [OR (95% CI): 0.32 (0.25-0.40) for soybean, 0.56 (0.45-0.71) for soybean curd, and 0.67 (0.46-0.98) for soymilk], allium vegetables [OR (95% CI): 0.37 (0.26-0.53) for green onion, 0.54 (0.40-0.73) for garlic, and 0.54 (0.35-0.85) for onion], fruits [OR (95% CI): 0.61 (0.42-0.88)], and mushrooms [OR (95% CI): 0.43 (0.21-0.88)]. Salt and Kimchi were associated with an increased gastric cancer risk [OR (95% CI): 1.92 (1.52-2.43) and 2.21 (1.29-3.77), respectively]. Colorectal cancer risk was positively associated with meat intake [OR (95% CI): 1.25 (1.15-1.36)]. Total soy products, soybean curd, and soymilk showed an inverse association with breast cancer risk [OR (95% CI): 0.61 (0.38-0.99), 0.47 (0.34-0.66), and 0.75 (0.57-0.98), respectively]. Green/yellow and light colored vegetables were associated with a reduced risk of breast cancer [OR (95% CI): 0.34 (0.23-0.49) and 0.44 (0.21-0.90), respectively]. Mushroom intake was inversely associated in pre-menopausal women only [OR (95% CI): 0.47 (0.26-0.86)]. In conclusion, soy foods, fruits and vegetables might reduce cancer risk in the Korean population. High salt food might be risk factor for gastric cancer, and intake of high amount of meat might cause colorectal cancer. PMID:25339056

  5. Regime for Bowel Preparation in Patients Scheduled to Colonoscopy: Low-Residue Diet or Clear Liquid Diet? Evidence From Systematic Review With Power Analysis.

    PubMed

    Song, Guo-Min; Tian, Xu; Ma, Li; Yi, Li-Juan; Shuai, Ting; Zeng, Zi; Zeng, Xian-Tao

    2016-01-01

    Clear liquid diet (CLD) is used to perform bowel preparation before colonoscopy traditionally, but several clinical studies indicated that low-residue diet (LRD) generates equal effects to CLD and a conclusive conclusion has not yet been yielded. The systematic review was performed to address this conflict and facilitate informed decision-making eventually. To capture randomized controlled trials (RCTs) comparing LRD with CLD in terms of bowel preparation, a search was performed in PubMed, EMBASE, Cochrane Central Register of Controlled Trials (CENTRAL), Science Direct, recent conference abstracts, Google Scholar, and Clinicaltrials.gov through May 2015. We performed all meta-analyses based on fixed- or random-effects model, which is generated from clinical characteristics and methodology. Moreover, the G*Power software was adopted to achieve statistical power for each outcome. In total, we captured 109 potential citations at initial search stage and 2 topic-related articles were included through other sources. After critical appraisal, 7 RCTs were eligible for our inclusion criteria. Meta-analyses generated similar effects in bowel preparation quality, efficacy of colon cleansing, and compliance with recommended dietary regime when LRD versus CLD regime, but patients who were prescribed to receive LRD have slightly better tolerance (RR, 1.06; 95% CI, 1.02-1.11) and tended to repeat the same preparation regime in future (RR, 1.17; 95% CI, 1.09-1.26) relative to patients in CLD. Importantly, both regimes resulted in similar adverse events (AEs). With the best available evidence, LRD could be recommended to be as standard regime for bowel preparation prior to colonoscopy. PMID:26735547

  6. Retrospective characterization of ontogenetic shifts in killer whale diets via δ13C and δ15N analysis of teeth

    USGS Publications Warehouse

    Newsome, Seth D.; Etnier, Michael A.; Monson, Daniel H.; Fogel, Marilyn L.

    2009-01-01

    Metabolically inert, accretionary structures such as the dentin growth layers in teeth provide a life history record of individual diet with near-annual resolution. We constructed ontogenetic δ13C and δ15N profiles by analyzing tooth dentin growth layers from 13 individual killer whales Orcinus orca collected in the eastern northeast Pacific Ocean between 1961 and 2003. The individuals sampled were 6 to 52 yr old, representing 2 ecotypes—resident and transient—collected across ~25° of latitude. The average isotopic values of transient individuals (n = 10) are consistent with a reliance on mammalian prey, while the average isotopic values of residents (n = 3) are consistent with piscivory. Regardless of ecotype, most individuals show a decrease in δ15N values of ~2.5‰ through the first 3 yr of life, roughly equivalent to a decrease of one trophic level. We interpret this as evidence of gradual weaning, after which, ontogenetic shifts in isotopic values are highly variable. A few individuals (n = 2) maintained relatively stable δ15N and δ13C values throughout the remainder of their lives, whereas δ15N values of most (n = 11) increased by ~1.5‰, suggestive of an ontogenetic increase in trophic level. Significant differences in mean δ13C and δ15N values among transients collected off California suggest that individuality in prey preferences may be prevalent within this ecotype. Our approach provides retrospective individual life history and dietary information that cannot be obtained through traditional field observations of free-ranging and elusive species such as killer whales, including unique historic ecological information that pre-dates modern studies. By providing insights into individual diet composition, stable isotope analysis of teeth and/or bones may be the only means of evaluating a number of hypothesized historical dietary shifts in killer whales of the northeast Pacific Ocean

  7. Retrospective characterization of ontogenetic shifts in killer whale diets via δ13C and δ15N analysis of teeth

    USGS Publications Warehouse

    Newsome, Seth D.; Etnier, Michael A.; Monson, Daniel H.; Fogel, Marilyn L.

    2009-01-01

    Metabolically inert, accretionary structures such as the dentin growth layers in teeth provide a life history record of individual diet with near-annual resolution. We constructed ontogenetic ??13C and ??15N profiles by analyzing tooth dentin growth layers from 13 individual killer whales Orcinus orca collected in the eastern northeast Pacific Ocean between 1961 and 2003. The individuals sampled were 6 to 52 yr old, representing 2 ecotypes-resident and transient - collected across ???25?? of latitude. The average isotopic values of transient individuals (n = 10) are consistent with a reliance on mammalian prey, while the average isotopic values of residents (n = 3) are consistent with piscivory. Regardless of ecotype, most individuals show a decrease in ??15N values of ???2.5% through the first 3 yr of life, roughly equivalent to a decrease of one trophic level. We interpret this as evidence of gradual weaning, after which, ontogenetic shifts in isotopic values are highly variable. A few individuals (n = 2) maintained relatively stable ??15N and ??13C values throughout the remainder of their lives, whereas ??15N values of most (n = 11) increased by ???1.5%, suggestive of an ontogenetic increase in trophic level. Significant differences in mean ??13C and ??15N values among transients collected off California suggest that individuality in prey preferences may be prevalent within this ecotype. Our approach provides retrospective individual life history and dietary information that cannot be obtained through traditional field observations of free-ranging and elusive species such as killer whales, including unique historic ecological information that pre-dates modern studies. By providing insights into individual diet composition, stable isotope analysis of teeth and/or bones may be the only means of evaluating a number of hypothesized historical dietary shifts in killer whales of the northeast Pacific Ocean. ?? Inter-Research 2009.

  8. Long-term effects of low-fat diets either low or high in protein on cardiovascular and metabolic risk factors: a systematic review and meta-analysis

    PubMed Central

    2013-01-01

    Background Meta-analyses of short-term studies indicate favorable effects of higher protein vs. lower protein diets on health outcomes like adiposity or cardiovascular risk factors, but their long-term effects are unknown. Methods Electronic databases (MEDLINE, EMBASE, Cochrane Trial Register) were searched up to August 2012 with no restriction to language or calendar date. A random effect meta-analysis was performed using the Software package by the Cochrane Collaboration Review Manager 5.1. Sensitivity analysis was performed for RCTs with a Jadad Score ≥3, and excluding type 2 diabetic subjects (T2D). Results 15 RCTs met all objectives and were included in the present meta-analysis. No significant differences were observed for weight, waist circumference, fat mass, blood lipids (i.e. total cholesterol, LDL-cholesterol, HDL-cholesterol, triacylglycerols), C-reactive protein, diastolic and systolic blood pressure, fasting glucose and glycosylated hemoglobin. In contrast, improvements of fasting insulin was significantly more pronounced following high protein diets as compared to the low protein counterparts (weighted mean difference: -0.71 μIU/ml, 95% CI -1.36 to -0.05, p = 0.03). Sensitivity analysis of high quality RCTs confirmed the data of the primary analyses, while exclusion of studies with diabetic subjects resulted in an additional benefit of high-protein diets with respect to a more marked increase in HDL-cholesterol. Conclusion According to the present meta-analysis of long-term RCTs, high-protein diets exerted neither specific beneficial nor detrimental effects on outcome markers of obesity, cardiovascular disease or glycemic control. Thus, it seems premature to recommend high-protein diets in the management of overweight and obesity. PMID:23587198

  9. Effects of sampling conditions on DNA-based estimates of American black bear abundance

    USGS Publications Warehouse

    Laufenberg, Jared S.; Van Manen, Frank T.; Clark, Joseph D.

    2013-01-01

    DNA-based capture-mark-recapture techniques are commonly used to estimate American black bear (Ursus americanus) population abundance (N). Although the technique is well established, many questions remain regarding study design. In particular, relationships among N, capture probability of heterogeneity mixtures A and B (pA and pB, respectively, or p, collectively), the proportion of each mixture (π), number of capture occasions (k), and probability of obtaining reliable estimates of N are not fully understood. We investigated these relationships using 1) an empirical dataset of DNA samples for which true N was unknown and 2) simulated datasets with known properties that represented a broader array of sampling conditions. For the empirical data analysis, we used the full closed population with heterogeneity data type in Program MARK to estimate N for a black bear population in Great Smoky Mountains National Park, Tennessee. We systematically reduced the number of those samples used in the analysis to evaluate the effect that changes in capture probabilities may have on parameter estimates. Model-averaged N for females and males were 161 (95% CI = 114–272) and 100 (95% CI = 74–167), respectively (pooled N = 261, 95% CI = 192–419), and the average weekly p was 0.09 for females and 0.12 for males. When we reduced the number of samples of the empirical data, support for heterogeneity models decreased. For the simulation analysis, we generated capture data with individual heterogeneity covering a range of sampling conditions commonly encountered in DNA-based capture-mark-recapture studies and examined the relationships between those conditions and accuracy (i.e., probability of obtaining an estimated N that is within 20% of true N), coverage (i.e., probability that 95% confidence interval includes true N), and precision (i.e., probability of obtaining a coefficient of variation ≤20%) of estimates using logistic regression. The capture probability

  10. From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments

    EPA Science Inventory

    Recent technological advances have driven rapid development of DNA-based methods designed to facilitate detection and monitoring of invasive species in aquatic environments. These tools promise to significantly alleviate difficulties associated with traditional monitoring approac...

  11. DNA-BASED METHODS FOR MONITORING INVASIVE SPECIES: A REVIEW AND PROSPECTUS

    EPA Science Inventory

    The recent explosion of interest in DNA-based tools for species identification has prompted widespread speculation on the future availability of inexpensive, rapid and accurate means of identifying specimens and assessing biodiversity. One applied field that may benefit dramatic...

  12. Diets of nesting laughing gulls (Larus atricilla) at the Virginia Coast Reserve: observations from stable isotope analysis

    USGS Publications Warehouse

    Knoff, A.J.; Macko, S.A.; Erwin, R.M.

    2001-01-01

    Food web studies often ignore details of temporal, spatial, and intrapopulation dietary variation in top-level consumers. In this study, intrapopulation dietary variation of a dominant carnivore, the Laughing Gull (Larus atricilla), was examined using carbon, nitrogen, and sulfur isotope analysis of gull tissues as well as their prey (fish, invertebrates, and insects) from the Virginia Coast Reserve estuarine system. As earlier traditional diet studies found evidence of individual dietary specialization within gull populations, this study used stable isotope analysis to assess specialization in a coastal Laughing Gull population. Specifically, blood, muscle, and feather isotope values indicated significant intrapopulation dietary specialization. Some gulls relied more heavily on estuarine prey (mean blood δ13C = -17.5, δ15N = 12.6, and δ34S = 9.3), whereas others appeared to consume more foods of marine origin (mean blood δ13C = -19.4, δ15N = 14.8, and δ34S = 10.4). It is important to account for such dietary variability when assessing trophic linkages in dynamic estuarine systems.

  13. Diets of nesting laughing gulls (Larus atricilla) at the Virginia Coast Reserve: observations from stable isotope analysis.

    PubMed

    Knoff, A J; Macko, S A; Erwin, R M

    2001-01-01

    Food web studies often ignore details of temporal, spatial, and intrapopulation dietary variation in top-level consumers. In this study, intrapopulation dietary variation of a dominant carnivore, the Laughing Gull (Larus atricilla), was examined using carbon, nitrogen, and sulfur isotope analysis of gull tissues as well as their prey (fish, invertebrates, and insects) from the Virginia Coast Reserve estuarine system. As earlier traditional diet studies found evidence of individual dietary specialization within gull populations, this study used stable isotope analysis to assess specialization in a coastal Laughing Gull population. Specifically, blood, muscle, and feather isotope values indicated significant intrapopulation dietary specialization. Some gulls relied more heavily on estuarine prey (mean blood delta13C = -17.5, delta15N = 12.6, and delta34S = 9.3), whereas others appeared to consume more foods of marine origin (mean blood delta13C = -19.4, delta15N = 14.8, and delta34S = 10.4). It is important to account for such dietary variability when assessing trophic linkages in dynamic estuarine systems. PMID:11558657

  14. Administration of a maple syrup extract to mitigate their hepatic inflammation induced by a high-fat diet: a transcriptome analysis.

    PubMed

    Kamei, Asuka; Watanabe, Yuki; Shinozaki, Fumika; Yasuoka, Akihito; Kondo, Takashi; Ishijima, Tomoko; Toyoda, Tsudoi; Arai, Soichi; Abe, Keiko

    2015-01-01

    Effects of the administration of maple syrup extract (MSX) on hepatic gene expression were investigated in mice fed a high-fat diet. Gene annotation enrichment analysis based on gene ontology revealed some changes in the expression of genes related to lipid metabolism and the immune response in MSX-fed mice. Detailed analysis of these data indicated that MSX ingestion mitigates hepatic inflammation. PMID:25982262

  15. Programmable and Multiparameter DNA-Based Logic Platform For Cancer Recognition and Targeted Therapy

    PubMed Central

    2014-01-01

    The specific inventory of molecules on diseased cell surfaces (e.g., cancer cells) provides clinicians an opportunity for accurate diagnosis and intervention. With the discovery of panels of cancer markers, carrying out analyses of multiple cell-surface markers is conceivable. As a trial to accomplish this, we have recently designed a DNA-based device that is capable of performing autonomous logic-based analysis of two or three cancer cell-surface markers. Combining the specific target-recognition properties of DNA aptamers with toehold-mediated strand displacement reactions, multicellular marker-based cancer analysis can be realized based on modular AND, OR, and NOT Boolean logic gates. Specifically, we report here a general approach for assembling these modular logic gates to execute programmable and higher-order profiling of multiple coexisting cell-surface markers, including several found on cancer cells, with the capacity to report a diagnostic signal and/or deliver targeted photodynamic therapy. The success of this strategy demonstrates the potential of DNA nanotechnology in facilitating targeted disease diagnosis and effective therapy. PMID:25361164

  16. Programmable and multiparameter DNA-based logic platform for cancer recognition and targeted therapy.

    PubMed

    You, Mingxu; Zhu, Guizhi; Chen, Tao; Donovan, Michael J; Tan, Weihong

    2015-01-21

    The specific inventory of molecules on diseased cell surfaces (e.g., cancer cells) provides clinicians an opportunity for accurate diagnosis and intervention. With the discovery of panels of cancer markers, carrying out analyses of multiple cell-surface markers is conceivable. As a trial to accomplish this, we have recently designed a DNA-based device that is capable of performing autonomous logic-based analysis of two or three cancer cell-surface markers. Combining the specific target-recognition properties of DNA aptamers with toehold-mediated strand displacement reactions, multicellular marker-based cancer analysis can be realized based on modular AND, OR, and NOT Boolean logic gates. Specifically, we report here a general approach for assembling these modular logic gates to execute programmable and higher-order profiling of multiple coexisting cell-surface markers, including several found on cancer cells, with the capacity to report a diagnostic signal and/or deliver targeted photodynamic therapy. The success of this strategy demonstrates the potential of DNA nanotechnology in facilitating targeted disease diagnosis and effective therapy. PMID:25361164

  17. Social media interventions for diet and exercise behaviours: a systematic review and meta-analysis of randomised controlled trials

    PubMed Central

    Williams, Gillian; Hamm, Michele P; Shulhan, Jocelyn; Vandermeer, Ben; Hartling, Lisa

    2014-01-01

    Objectives To conduct a systematic review of randomised controlled trials (RCTs) examining the use of social media to promote healthy diet and exercise in the general population. Data sources MEDLINE, CENTRAL, ERIC, PubMed, CINAHL, Academic Search Complete, Alt Health Watch, Health Source, Communication and Mass Media Complete, Web of Knowledge and ProQuest Dissertation and Thesis (2000–2013). Study eligibility criteria RCTs of social media interventions promoting healthy diet and exercise behaviours in the general population were eligible. Interventions using social media, alone or as part of a complex intervention, were included. Study appraisal and synthesis Study quality was assessed using the Cochrane Risk of Bias Tool. We describe the studies according to the target populations, objectives and nature of interventions, outcomes examined, and results and conclusions. We extracted data on the primary and secondary outcomes examined in each study. Where the same outcome was assessed in at least three studies, we combined data in a meta-analysis. Results 22 studies were included. Participants were typically middle-aged Caucasian women of mid-to-high socioeconomic status. There were a variety of interventions, comparison groups and outcomes. All studies showed a decrease in programme usage throughout the intervention period. Overall, no significant differences were found for primary outcomes which varied across studies. Meta-analysis showed no significant differences in changes in physical activity (standardised mean difference (SMD) 0.13 (95% CI −0.04 to 0.30), 12 studies) and weight (SMD −0.00 (95% CI −0.19 to 0.19), 10 studies); however, pooled results from five studies showed a significant decrease in dietary fat consumption with social media (SMD −0.35 (95% CI −0.68 to −0.02)). Conclusions Social media may provide certain advantages for public health interventions; however, studies of social media interventions to date relating to healthy

  18. An Analysis of Diet Quality, How It Controls Fatty Acid Profiles, Isotope Signatures and Stoichiometry in the Malaria Mosquito Anopheles arabiensis

    PubMed Central

    Hood-Nowotny, Rebecca; Schwarzinger, Bettina; Schwarzinger, Clemens; Soliban, Sharon; Madakacherry, Odessa; Aigner, Martina; Watzka, Margarete; Gilles, Jeremie

    2012-01-01

    Background Knowing the underlying mechanisms of mosquito ecology will ensure effective vector management and contribute to the overall goal of malaria control. Mosquito populations show a high degree of population plasticity in response to environmental variability. However, the principle factors controlling population size and fecundity are for the most part unknown. Larval habitat and diet play a crucial role in subsequent mosquito fitness. Developing the most competitive insects for sterile insect technique programmes requires a “production” orientated perspective, to deduce the most effective larval diet formulation; the information gained from this process offers us some insight into the mechanisms and processes taking place in natural native mosquito habitats. Methodology/Principal Findings Fatty acid profiles and de-novo or direct assimilation pathways, of whole-individual mosquitoes reared on a range of larval diets were determined using pyrolysis gas chromatograph/mass spectrometry. We used elemental analysis and isotope ratio mass spectrometry to measure individual-whole-body carbon, nitrogen and phosphorous values and to assess the impact of dietary quality on subsequent population stoichiometry, size, quality and isotopic signature. Diet had the greatest impact on fatty acid (FA) profiles of the mosquitoes, which exhibited a high degree of dietary routing, characteristic of generalist feeders. De-novo synthesis of a number of important FAs was observed. Mosquito C:N stoichiometry was fixed in the teneral stage. Dietary N content had significant influence on mosquito size, and P was shown to be a flexible pool which limited overall population size. Conclusions/Significance Direct routing of FAs was evident but there was ubiquitous de-novo synthesis suggesting mosquito larvae are competent generalist feeders capable of survival on diet with varying characteristics. It was concluded that nitrogen availability in the larval diet controlled teneral

  19. Nutrition and Diet

    MedlinePlus

    ... Thai HbH:Vietnamese Relevant links Living with Thalassemia NUTRITION ▶ Nutrition and DietDiet for the Non-transfused ... booklet ▶ 3 Simple Suggestions for a Healthy Diet Nutrition and Diet Nutritional deficiencies are common in thalassemia, ...

  20. Effect of diet-induced weight loss on muscle strength in adults with overweight or obesity - a systematic review and meta-analysis of clinical trials.

    PubMed

    Zibellini, J; Seimon, R V; Lee, C M Y; Gibson, A A; Hsu, M S H; Sainsbury, A

    2016-08-01

    We conducted a systematic review and meta-analysis to identify how diet-induced weight loss in adults with overweight or obesity impacts on muscle strength. Twenty-seven publications, including 33 interventions, most of which were 8-24 weeks in duration, were included. Meta-analysis of seven interventions measuring knee extensor strength by isokinetic dynamometry in 108 participants found a significant decrease following diet-induced weight loss (-9.0 [95% confidence interval: -13.8, -4.1] N/m, P < 0.001), representing a 7.5% decrease from baseline values. Meta-analysis of handgrip strength from 10 interventions in 231 participants showed a non-significant decrease (-1.7 [-3.6, 0.1] kg, P = 0.070), with significant heterogeneity (I(2)  = 83.9%, P < 0.001). This heterogeneity may have been due to diet type, because there was a significant decrease in handgrip strength in seven interventions in 169 participants involving moderate energy restriction (-2.4 [-4.8, -0.0] kg, P = 0.046), representing a 4.6% decrease from baseline values, but not in three interventions in 62 participants involving very-low-energy diet (-0.4 [-2.0, 1.2] kg, P = 0.610). Because of variability in methodology and muscles tested, no other data could be meta-analyzed, and qualitative assessment of the remaining interventions revealed mixed results. Despite varying methodologies, diets and small sample sizes, these findings suggest a potential adverse effect of diet-induced weight loss on muscle strength. While these findings should not act as a deterrent against weight loss, due to the known health benefits of losing excess weight, they call for strategies to combat strength loss - such as weight training and other exercises - during diet-induced weight loss. © 2016 World Obesity. PMID:27126087

  1. Systematic review and meta-analysis of the association between childhood overweight and obesity and primary school diet and physical activity policies.

    PubMed

    Williams, Andrew James; Henley, William E; Williams, Craig Anthony; Hurst, Alison Jane; Logan, Stuart; Wyatt, Katrina Mary

    2013-01-01

    Obesity is a major public health concern and there are increasing calls for policy intervention. As obesity and the related health conditions develop during childhood, schools are being seen as important locations for obesity prevention, including multifaceted interventions incorporating policy elements. The objective of this systematic review was to evaluate the effects of policies related to diet and physical activity in schools, either alone, or as part of an intervention programme on the weight status of children aged 4 to 11 years. A comprehensive and systematic search of medical, education, exercise science, and social science databases identified 21 studies which met the inclusion criteria. There were no date, location or language restrictions. The identified studies evaluated a range of either, or both, diet and physical activity related policies, or intervention programmes including such policies, using a variety of observational and experimental designs. The policies were clustered into those which sought to affect diet, those which sought to affect physical activity and those which sought to affect both diet and physical activity to undertake random effects meta-analysis. Within the diet cluster, studies of the United States of America National School Lunch and School Breakfast Programs were analysed separately; however there was significant heterogeneity in the pooled results. The pooled effects of the physical activity, and other diet related policies on BMI-SDS were non-significant. The multifaceted interventions tended to include policy elements related to both diet and physical activity (combined cluster), and although these interventions were too varied to pool their results, significant reductions in weight-related outcomes were demonstrated. The evidence from this review suggests that, when implemented alone, school diet and physical activity related policies appear insufficient to prevent or treat overweight or obesity in children, however, they

  2. Can dietary interventions change diet and cardiovascular risk factors? A meta-analysis of randomized controlled trials.

    PubMed Central

    Brunner, E; White, I; Thorogood, M; Bristow, A; Curle, D; Marmot, M

    1997-01-01

    OBJECTIVES: This study evaluated the effectiveness of dietary advice in primary prevention of chronic disease. METHODS: A meta-analysis was conducted of 17 randomized controlled trials of dietary behavior interventions of at least 3 months' duration. Results were analyzed as changes in reported dietary fat intakes and biomedical measures (serum cholesterol, urinary sodium, systolic and diastolic blood pressure) in the intervention group minus changes in the control group at 3 to 6 months and 9 to 18 months of follow-up. RESULTS: After 3 to 6 months, mean net changes in each of the five outcomes favored intervention. For dietary fat as a percentage of food energy, the change was -2.5% (95% confidence interval [CI] = -3.9%, -1.1%). Mean net changes over 9 to 18 months were as follows: serum cholesterol, -0.22 (95% CI = -0.39, -0.05) mmol/L; urinary sodium, -45.0 (95% CI = -57.1, -32.8) mmol/24 hours; systolic blood pressure, -1.9 (95% CI = -3.0, 0.8) mm Hg; and diastolic blood pressure, -1.2 (95% CI = -2.6, 0.2) mm Hg. CONCLUSIONS: Individual dietary interventions in primary prevention can achieve modest improvements in diet and cardiovascular disease risk status that are maintained for 9 to 18 months. PMID:9314790

  3. Preliminary assessment of avian stomach oils: a vector of contaminants to chicks and potential for diet analysis and biomonitoring.

    PubMed

    Foster, Karen L; Wang, Shiway W; Mackay, Don; Mallory, Mark L; Blais, Jules M

    2010-09-01

    Bird species from the order Procellariiformes or petrels, including the northern fulmar (Fulmarus glacialis), produce high lipid and high energy content stomach oils from the prey they consume, which enables them to exploit distant marine food sources. Stomach oils are also used as a food source for chicks and for defensive purposes. Samples of stomach oils from two Arctic colonies, St. George Island Alaska, USA and Cape Vera, Devon Island Nunavut, Canada, were collected and analyzed for organochlorine contaminants. SigmaPCB concentrations ranged from 13 to 236 ng g(-1) wet weight (ww) and SigmaDDT concentrations from 5 to 158 ng g(-1) ww and were similar in both sites, though differences in chemical signatures were apparent. Stomach oils are a rich energy source; however, they may also provide a higher dose of contaminants per unit energy than the direct consumption of prey items, as illustrated using mass and energy balance calculations to estimate chick exposure to SigmaDDT for hypothetical stomach oil and whole prey diets. The results of this study suggest that stomach oils are an important vector of organochlorine contaminants to chicks and should be considered in future risk assessments of northern fulmars and other species of petrels. To our knowledge this is the first study of stomach oils as an overlooked vector of organochlorine contaminants to chicks and as a potentially valuable medium for dietary analysis and noninvasive biomonitoring both of petrel dietary exposure and of marine contaminant concentrations. PMID:20707316

  4. Development of sensitive and rapid analytical methodology for food analysis of 18 mycotoxins included in a total diet study.

    PubMed

    Beltrán, Eduardo; Ibáñez, María; Portolés, Tania; Ripollés, Cristina; Sancho, Juan Vicente; Yusà, Vicent; Marín, Silvia; Hernández, Félix

    2013-06-14

    A rapid and sensitive method for the determination of 18 mycotoxins in 24 different food matrices has been developed and validated. With the exception of beverages and oil samples, a simple extraction with acetonitrile:water 80:20 (0.1% formic acid) was applied. Fruit juice, wine and beer samples were simply diluted with water containing 0.1% formic acid. Oil samples were partitioned with acetonitrile/hexane in order to remove fats. Analyses were made by ultra-high performance liquid chromatography (UHPLC) coupled to tandem mass spectrometry with triple quadrupole. Validation was carried out in all selected matrices using blank samples spiked at two analyte concentrations. Extraction recoveries between 70 and 120% and relative standard deviations lower than 20% were obtained for the wide majority of analyte-matrix combinations. Matrix-matched calibration was used for a correct quantification in order to compensate for matrix effects. Limits of quantification were lower than maximum permitted levels for every regulated mycotoxin-matrix combination. The acquisition of three SRM transitions per compound allowed the unequivocal confirmation of positive samples, supported by the accomplishment of ion intensity ratios and retention time when compared with reference standards. The developed methodology was applied to the analysis of 240 samples within a total diet study performed at Comunidad Valenciana (Spain). The most frequently found mycotoxins were deoxynivalenol, fumonisin B1, ochratoxin A and zearalenone at low μg kg(-1) levels, mainly in bread, breakfast cereals and beer. PMID:23726098

  5. Detection of Trypanosoma brucei spp. in human blood by a nonradioactive branched DNA-based technique.

    PubMed Central

    Harris, E; Detmer, J; Dungan, J; Doua, F; White, T; Kolberg, J A; Urdea, M S; Agabian, N

    1996-01-01

    We have developed a nonradioactive branched DNA (bDNA)-based assay for the diagnosis of the African trypanosomiases in simple buffy coat preparations of human blood. Two repetitive DNA sequences specific to the Trypanosoma brucei complex were chosen as targets of the bDNA assay, a technique which amplifies the signal from a target molecule rather than the target itself. Comparable sensitivities were observed with cloned target sequences, purified T. brucei DNA, procyclic trypanosomes, and bloodstream trypomastigotes. The results of bDNA analysis of human blood samples from Côte d'Ivoire (n = 50) showed excellent agreement with those of buffy coat microscopy. The bDNA technology offers certain advantages over alternative molecular biological techniques, including the simplicity of sample preparation and of the procedure itself, the stability of the reagents, the ability to process large numbers of samples simultaneously, and freedom from crosscontamination artifacts. We have successfully applied the bDNA technique to the detection of T. brucei in clinical samples from regions where T. brucei infection is endemic; to our knowledge, this is the first report of the molecular detection of T. brucei in human blood. PMID:8880488

  6. Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms.

    PubMed

    Krawczyk, Beata; Kur, Józef; Stojowska-Swędrzyńska, Karolina; Śpibida, Marta

    2016-01-01

    A significant number of DNA-based techniques has been introduced into the field of microorganisms' characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before DNA amplification by PCR, known as Ligation-Mediated PCR methods (LM PCR), have been successfully applied for the typing of microorganisms below the species level. These molecular methods include: Amplified Fragment Length Polymorphism (AFLP), Amplification of DNA fragments Surrounding Rare Restriction Sites (ADSRRS), PCR Melting Profiles (PCR MP), Ligation Mediated PCR/Shifter (LM PCR/Shifter), Infrequent-Restriction-Site Amplification (IRS PCR), double digestion Ligation Mediated Suppression PCR (ddLMS PCR). These techniques are now applied more and more often because they involve less time, are comparably inexpensive, and require only standard lab equipment. Here, we present a general review of this group of methods showing their possibilities and limitations. We also identify questions and propose solutions which may be helpful in choosing a particular LM PCR method for the achievement of the required goal. PMID:26885774

  7. Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems

    PubMed Central

    Li, Xianran; Scanlon, Michael J.; Yu, Jianming

    2015-01-01

    DNA base composition is a fundamental genome feature. However, the evolutionary pattern of base composition and its potential causes have not been well understood. Here, we report findings from comparative analysis of base composition at the whole-genome level across 2210 species, the polymorphic-site level across eight population comparison sets, and the mutation-site level in 12 mutation-tracking experiments. We first demonstrate that base composition follows the individual-strand base equality rule at the genome, chromosome and polymorphic-site levels. More intriguingly, clear separation of base-composition values calculated across polymorphic sites was consistently observed between basal and derived groups, suggesting common underlying mechanisms. Individuals in the derived groups show an A&T-increase/G&C-decrease pattern compared with the basal groups. Spontaneous and induced mutation experiments indicated these patterns of base composition change can emerge across mutation sites. With base-composition across polymorphic sites as a genome phenotype, genome scans with human 1000 Genomes and HapMap3 data identified a set of significant genomic regions enriched with Gene Ontology terms for DNA repair. For three DNA repair genes (BRIP1, PMS2P3 and TTDN), ENCODE data provided evidence for interaction between genomic regions containing these genes and regions containing the significant SNPs. Our findings provide insights into the mechanisms of genome evolution. PMID:25765652

  8. Extensive impact of saturated fatty acids on metabolic and cardiovascular profile in rats with diet-induced obesity: a canonical analysis

    PubMed Central

    2013-01-01

    Background Although hypercaloric interventions are associated with nutritional, endocrine, metabolic, and cardiovascular disorders in obesity experiments, a rational distinction between the effects of excess adiposity and the individual roles of dietary macronutrients in relation to these disturbances has not previously been studied. This investigation analyzed the correlation between ingested macronutrients (including sucrose and saturated and unsaturated fatty acids) plus body adiposity and metabolic, hormonal, and cardiovascular effects in rats with diet-induced obesity. Methods Normotensive Wistar-Kyoto rats were submitted to Control (CD; 3.2 Kcal/g) and Hypercaloric (HD; 4.6 Kcal/g) diets for 20 weeks followed by nutritional evaluation involving body weight and adiposity measurement. Metabolic and hormonal parameters included glycemia, insulin, insulin resistance, and leptin. Cardiovascular analysis included systolic blood pressure profile, echocardiography, morphometric study of myocardial morphology, and myosin heavy chain (MHC) protein expression. Canonical correlation analysis was used to evaluate the relationships between dietary macronutrients plus adiposity and metabolic, hormonal, and cardiovascular parameters. Results Although final group body weights did not differ, HD presented higher adiposity than CD. Diet induced hyperglycemia while insulin and leptin levels remained unchanged. In a cardiovascular context, systolic blood pressure increased with time only in HD. Additionally, in vivo echocardiography revealed cardiac hypertrophy and improved systolic performance in HD compared to CD; and while cardiomyocyte size was unchanged by diet, nuclear volume and collagen interstitial fraction both increased in HD. Also HD exhibited higher relative β-MHC content and β/α-MHC ratio than their Control counterparts. Importantly, body adiposity was weakly associated with cardiovascular effects, as saturated fatty acid intake was directly associated with most

  9. Stable Isotope (δ13C, δ15N, δ34S) Analysis and Satellite Telemetry Depict the Complexity of Gray Wolf (Canis lupus) Diets in Southwest Alaska

    NASA Astrophysics Data System (ADS)

    Stanek, A.; Watts, D. E.; Cohn, B. R.; Spencer, P.; Mangipane, B.; Welker, J. M.

    2010-12-01

    Throughout Alaska, gray wolves (Canis lupus) are a top predator of large ungulates. While they primarily rely on ungulates such as moose (Alces alces) and caribou (Rangifer tarandus) as food, they are opportunistic and use alternative resources. The variation and supplemental protein sources in wolf diet has not been studied extensively on live animals currently using the landscape. With large seasonal influxes of Pacific salmon (Oncorhynchus sp.) into Alaska, terrestrial carnivore use of marine species is of particular interest. Using stable isotope (δ13C, δ15N, δ34S) analysis of wolf guard hair and blood, this study aims to determine the proportion of marine derived nutrients (MDN) in the diet of wolf packs within and surrounding Lake Clark National Park and Preserve and Alaska Peninsula and Becharof National Wildlife Refuges in Southwest Alaska. Satellite telemetry from the animals sampled facilitates quantification of landscape use patterns in correspondence with isotopic traits. Wolf pack territories within and surrounding the Lake Clark region appear to vary in spatial extent and in availability of MDN, such as salmon. Initial analysis shows that two packs with smaller home ranges, centrally located around areas with greater salmon availability, have enriched δ15N values compared to packs that have larger home ranges not centralized around salmon spawning waters. This pattern of isotopic enrichment is found in red blood cells, blood serum and hair, representing diets over different time scales. The enrichment in both blood and hair indicates a sustained use of MDN over the previous six to nine months. In the Lake Clark region, simple mixing model estimates suggest that up to 30% of wolf pack diets may be from marine sources. In contrast, packs with larger home ranges and less access to salmon have stable isotope values representative of a terrestrial diet.

  10. Reconstructing Ancient Egyptian Diet through Bone Elemental Analysis Using LIBS (Qubbet el Hawa Cemetery).

    PubMed

    Al-Khafif, Ghada Darwish; El-Banna, Rokia

    2015-01-01

    One of the most important advantages of LIBS that make it suitable for the analysis of archeological materials is that it is a quasi-nondestructive technique. Archeological mandibles excavated from Qubbet el Hawa Cemetery, Aswan, were subjected to elemental analysis in order to reconstruct the dietary patterns of the middle class of the Aswan population throughout three successive eras: the First Intermediate Period (FIP), the Middle Kingdom (MK), and the Second Intermediate Period (SIP). The bone Sr/Ca and Ba/Ca ratios were significantly correlated, so the Sr/Ca ratios are considered to represent the ante-mortem values. It was suggested that the significantly low FIP Sr/Ca compared to that of both the MK and the SIP was attributed to the consumption of unusual sorts of food and imported cereals during years of famine, while the MK Sr/Ca was considered to represent the amelioration of climatic, social, economic, and political conditions in this era of state socialism. The SIP Sr/Ca, which is nearly the same as that of the MK, was considered to be the reflection of the continuity of the individualism respect and state socialism and a reflection of agriculture conditions amelioration under the reign of the 17th Dynasty in Upper Egypt. PMID:26345727

  11. Reconstructing Ancient Egyptian Diet through Bone Elemental Analysis Using LIBS (Qubbet el Hawa Cemetery)

    PubMed Central

    Al-Khafif, Ghada Darwish; El-Banna, Rokia

    2015-01-01

    One of the most important advantages of LIBS that make it suitable for the analysis of archeological materials is that it is a quasi-nondestructive technique. Archeological mandibles excavated from Qubbet el Hawa Cemetery, Aswan, were subjected to elemental analysis in order to reconstruct the dietary patterns of the middle class of the Aswan population throughout three successive eras: the First Intermediate Period (FIP), the Middle Kingdom (MK), and the Second Intermediate Period (SIP). The bone Sr/Ca and Ba/Ca ratios were significantly correlated, so the Sr/Ca ratios are considered to represent the ante-mortem values. It was suggested that the significantly low FIP Sr/Ca compared to that of both the MK and the SIP was attributed to the consumption of unusual sorts of food and imported cereals during years of famine, while the MK Sr/Ca was considered to represent the amelioration of climatic, social, economic, and political conditions in this era of state socialism. The SIP Sr/Ca, which is nearly the same as that of the MK, was considered to be the reflection of the continuity of the individualism respect and state socialism and a reflection of agriculture conditions amelioration under the reign of the 17th Dynasty in Upper Egypt. PMID:26345727

  12. Effects of plant stanol or sterol-enriched diets on lipid profiles in patients treated with statins: systematic review and meta-analysis.

    PubMed

    Han, Shufen; Jiao, Jun; Xu, Jiaying; Zimmermann, Diane; Actis-Goretta, Lucas; Guan, Lei; Zhao, Youyou; Qin, Liqiang

    2016-01-01

    Efficacy and safety data from trials with suitable endpoints have shown that non-statin medication in combination with a statin is a potential strategy to further reduce cardiovascular events. We aimed to evaluate the overall effect of stanol- or sterol-enriched diets on serum lipid profiles in patients treated with statins by conducting a meta-analysis of randomized controlled trials (RCTs). We used the PubMed, Cochrane library and ClinicalTrials.gov databases to search for literature published up to December 2015. Trials were included in the analysis if they were RCTs evaluating the effect of plant stanols or sterols in patients under statin therapy that reported corresponding data on serum lipid profiles. We included 15 RCTs involving a total of 500 participants. Stanol- or sterol-enriched diets in combination with statins, compared with statins alone, produced significant reductions in total cholesterol of 0.30 mmol/L (95% CI -0.36 to -0.25) and low-density lipoprotein (LDL) cholesterol of 0.30 mmol/L (95% CI -0.35 to -0.25), but not in high-density lipoprotein cholesterol or triglycerides. These results persisted in the subgroup analysis. Our meta-analysis provides further evidence that stanol- or sterol-enriched diets additionally lower total cholesterol and LDL-cholesterol levels in patients treated with statins beyond that achieved by statins alone. PMID:27539156

  13. Effects of plant stanol or sterol-enriched diets on lipid profiles in patients treated with statins: systematic review and meta-analysis

    PubMed Central

    Han, Shufen; Jiao, Jun; Xu, Jiaying; Zimmermann, Diane; Actis-Goretta, Lucas; Guan, Lei; Zhao, Youyou; Qin, Liqiang

    2016-01-01

    Efficacy and safety data from trials with suitable endpoints have shown that non-statin medication in combination with a statin is a potential strategy to further reduce cardiovascular events. We aimed to evaluate the overall effect of stanol- or sterol-enriched diets on serum lipid profiles in patients treated with statins by conducting a meta-analysis of randomized controlled trials (RCTs). We used the PubMed, Cochrane library and ClinicalTrials.gov databases to search for literature published up to December 2015. Trials were included in the analysis if they were RCTs evaluating the effect of plant stanols or sterols in patients under statin therapy that reported corresponding data on serum lipid profiles. We included 15 RCTs involving a total of 500 participants. Stanol- or sterol-enriched diets in combination with statins, compared with statins alone, produced significant reductions in total cholesterol of 0.30 mmol/L (95% CI −0.36 to −0.25) and low-density lipoprotein (LDL) cholesterol of 0.30 mmol/L (95% CI −0.35 to −0.25), but not in high-density lipoprotein cholesterol or triglycerides. These results persisted in the subgroup analysis. Our meta-analysis provides further evidence that stanol- or sterol-enriched diets additionally lower total cholesterol and LDL-cholesterol levels in patients treated with statins beyond that achieved by statins alone. PMID:27539156

  14. Quantitative analysis of diet structure by real-time PCR, reveals different feeding patterns by two dominant grasshopper species

    PubMed Central

    Huang, Xunbing; Wu, Huihui; McNeill, Mark Richard; Qin, Xinghu; Ma, Jingchuan; Tu, Xiongbing; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Zhang, Zehua

    2016-01-01

    Studies on grasshopper diets have historically employed a range of methodologies, each with certain advantages and disadvantages. For example, some methodologies are qualitative instead of quantitative. Others require long experimental periods or examine population-level effects, only. In this study, we used real-time PCR to examine diets of individual grasshoppers. The method has the advantage of being both fast and quantitative. Using two grasshopper species, Oedaleus asiaticus and Dasyhippus barbipes, we designed ITS primer sequences for their three main host plants, Stipa krylovii, Leymus chinensis and Cleistogenes squarrosa and used real-time PCR method to test diet structure both qualitatively and quantitatively. The lowest detection efficiency of the three grass species was ~80% with a strong correlation between actual and PCR-measured food intake. We found that Oedaleus asiaticus maintained an unchanged diet structure across grasslands with different grass communities. By comparison, Dasyhippus barbipes changed its diet structure. These results revealed why O. asiaticus distribution is mainly confined to Stipa-dominated grassland, and D. barbipes is more widely distributed across Inner Mongolia. Overall, real-time PCR was shown to be a useful tool for investigating grasshopper diets, which in turn offers some insight into grasshopper distributions and improved pest management. PMID:27562455

  15. Quantitative analysis of diet structure by real-time PCR, reveals different feeding patterns by two dominant grasshopper species.

    PubMed

    Huang, Xunbing; Wu, Huihui; McNeill, Mark Richard; Qin, Xinghu; Ma, Jingchuan; Tu, Xiongbing; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Zhang, Zehua

    2016-01-01

    Studies on grasshopper diets have historically employed a range of methodologies, each with certain advantages and disadvantages. For example, some methodologies are qualitative instead of quantitative. Others require long experimental periods or examine population-level effects, only. In this study, we used real-time PCR to examine diets of individual grasshoppers. The method has the advantage of being both fast and quantitative. Using two grasshopper species, Oedaleus asiaticus and Dasyhippus barbipes, we designed ITS primer sequences for their three main host plants, Stipa krylovii, Leymus chinensis and Cleistogenes squarrosa and used real-time PCR method to test diet structure both qualitatively and quantitatively. The lowest detection efficiency of the three grass species was ~80% with a strong correlation between actual and PCR-measured food intake. We found that Oedaleus asiaticus maintained an unchanged diet structure across grasslands with different grass communities. By comparison, Dasyhippus barbipes changed its diet structure. These results revealed why O. asiaticus distribution is mainly confined to Stipa-dominated grassland, and D. barbipes is more widely distributed across Inner Mongolia. Overall, real-time PCR was shown to be a useful tool for investigating grasshopper diets, which in turn offers some insight into grasshopper distributions and improved pest management. PMID:27562455

  16. Termites in the hominin diet: a meta-analysis of termite genera, species and castes as a dietary supplement for South African robust australopithecines.

    PubMed

    Lesnik, Julie J

    2014-06-01

    Termite foraging by chimpanzees and present-day modern humans is a well-documented phenomenon, making it a plausible hypothesis that early hominins were also utilizing this resource. Hominin termite foraging has been credited by some to be the explanation for the unexpected carbon isotope signatures present in South African hominin teeth, which suggest the diet was different from that of extant non-human great apes, consisting of a significant amount of resources that are not from woody-plants. Grass-eating termites are one potential resource that could contribute to the carbon signature. However, not all termites eat grasses, and in fact, the termites that are most widely consumed by chimpanzees and by many present-day human populations at best have a mixed diet that includes small amounts of grasses. Here I review the ecology of termites and how it affects their desirability as a food resource for hominins, and conduct a meta-analysis of nutritional values for various genera, species and castes from the literature. Termites are very diverse, even within species, and this variability affects both their carbon signatures and nutritional value, hindering generalizations regarding the contribution of termites to the hominin diet. It is concluded here that a combination of soldiers and alates of the genus Macrotermes be used to model the insectivory component of the Plio-Pleistocene hominin diet due to their significant amounts of energy-yielding nutrients and potential role as a critical resource for supporting larger-brained hominins. PMID:24613098

  17. Induction of Olfaction and Cancer-Related Genes in Mice Fed a High-Fat Diet as Assessed through the Mode-of-Action by Network Identification Analysis

    PubMed Central

    Choi, Youngshim; Hur, Cheol-Goo; Park, Taesun

    2013-01-01

    The pathophysiological mechanisms underlying the development of obesity and metabolic diseases are not well understood. To gain more insight into the genetic mediators associated with the onset and progression of diet-induced obesity and metabolic diseases, we studied the molecular changes in response to a high-fat diet (HFD) by using a mode-of-action by network identification (MNI) analysis. Oligo DNA microarray analysis was performed on visceral and subcutaneous adipose tissues and muscles of male C57BL/6N mice fed a normal diet or HFD for 2, 4, 8, and 12 weeks. Each of these data was queried against the MNI algorithm, and the lists of top 5 highly ranked genes and gene ontology (GO)-annotated pathways that were significantly overrepresented among the 100 highest ranked genes at each time point in the 3 different tissues of mice fed the HFD were considered in the present study. The 40 highest ranked genes identified by MNI analysis at each time point in the different tissues of mice with diet-induced obesity were subjected to clustering based on their temporal patterns. On the basis of the above-mentioned results, we investigated the sequential induction of distinct olfactory receptors and the stimulation of cancer-related genes during the development of obesity in both adipose tissues and muscles. The top 5 genes recognized using the MNI analysis at each time point and gene cluster identified based on their temporal patterns in the peripheral tissues of mice provided novel and often surprising insights into the potential genetic mediators for obesity progression. PMID:23555558

  18. A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

    PubMed Central

    Ratnasingham, Sujeevan; Hebert, Paul D. N.

    2013-01-01

    Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs), these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI) gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL) and four established (ABGD, CROP, GMYC, jMOTU) algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN) system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth. PMID:23861743

  19. Practical aspects of DNA-based forensic studies in dentistry

    PubMed Central

    Muruganandhan, J; Sivakumar, G

    2011-01-01

    Forensic dentistry as a science has evolved from simple methods of age estimation and bite-mark analysis, to a new era of genetic and serological investigations. DNA analysis in forensic science requires a sample or source from either an individual (living or dead) or a crime/incident site. The orofacial region is a good source of such material, due to the fact that certain oral tissues are relatively resistant to environmental degradation and destruction by thermal, electrical, and mechanical insult. Dentists may be called upon to provide samples and expert analysis in many such situations. Sources include soft and hard tissues of teeth and jaws, saliva, biopsy material, and mucosal swabs. Tissue samples should be handled with care, and correct protocol in collection and preparation has to be followed. This ensures a high yield of the required DNA. Hard tissues like teeth require specialized procedures to extract the genetic material. Research has shown that there is a wide variation in the quality and quantity of DNA extracted from different individuals from the same site even under similar conditions. This necessitates calibration of the various methods to achieve best results. DNA analysis can provide highly accurate identification if used correctly. Here a description of the various sources in the oral region has been provided from which samples could be forwarded to the forensic laboratory. Most commonly employed techniques of collection and handling for laboratory procedures have been outlined. PMID:22022138

  20. Mediterranean diet and risk of endometrial cancer: a pooled analysis of three italian case-control studies

    PubMed Central

    Filomeno, M; Bosetti, C; Bidoli, E; Levi, F; Serraino, D; Montella, M; La Vecchia, C; Tavani, A

    2015-01-01

    Background: Some components of the Mediterranean diet have favourable effects on endometrial cancer, and the Mediterranean diet as a whole has been shown to have a beneficial role on various neoplasms. Methods: We analysed this issue pooling data from three case-control studies carried out between 1983 and 2006 in various Italian areas and in the Swiss Canton of Vaud. Cases were 1411 women with incident, histologically confirmed endometrial cancer, and controls were 3668 patients in hospital for acute diseases. We measured the adherence to the Mediterranean diet using a Mediterranean Diet Score (MDS), based on the nine dietary components characteristics of this diet, that is, high intake of vegetables, fruits/nuts, cereals, legumes, fish; low intake of dairy products and meat; high monounsaturated to saturated fatty acid ratio; and moderate alcohol intake. We estimated the odds ratios (OR) and the corresponding 95% confidence intervals (CI) for increasing levels of the MDS (varying from 0, no adherence, to 9, maximum adherence) using multiple logistic regression models, adjusted for major confounding factors. Results: The adjusted OR for a 6–9 components of the MDS (high adherence) compared with 0–3 (low adherence) was 0.43 (95% CI 0.34–0.56). The OR for an increment of one component of MDS diet was 0.84 (95% CI 0.80–0.88). The association was consistent in strata of various covariates, although somewhat stronger in older women, in never oral contraceptive users and in hormone-replacement therapy users. Conclusions: Our study provides evidence for a beneficial role of the Mediterranean diet on endometrial cancer risk, suggesting a favourable effect of a combination of foods rich in antioxidants, fibres, phytochemicals, and unsaturated fatty acids. PMID:26010500

  1. Multi-Scale Effects of Nestling Diet on Breeding Performance in a Terrestrial Top Predator Inferred from Stable Isotope Analysis

    PubMed Central

    Resano-Mayor, Jaime; Hernández-Matías, Antonio; Real, Joan; Moleón, Marcos; Parés, Francesc; Inger, Richard; Bearhop, Stuart

    2014-01-01

    Inter-individual diet variation within populations is likely to have important ecological and evolutionary implications. The diet-fitness relationships at the individual level and the emerging population processes are, however, poorly understood for most avian predators inhabiting complex terrestrial ecosystems. In this study, we use an isotopic approach to assess the trophic ecology of nestlings in a long-lived raptor, the Bonelli’s eagle Aquila fasciata, and investigate whether nestling dietary breath and main prey consumption can affect the species’ reproductive performance at two spatial scales: territories within populations and populations over a large geographic area. At the territory level, those breeding pairs whose nestlings consumed similar diets to the overall population (i.e. moderate consumption of preferred prey, but complemented by alternative prey categories) or those disproportionally consuming preferred prey were more likely to fledge two chicks. An increase in the diet diversity, however, related negatively with productivity. The age and replacements of breeding pair members had also an influence on productivity, with more fledglings associated to adult pairs with few replacements, as expected in long-lived species. At the population level, mean productivity was higher in those population-years with lower dietary breadth and higher diet similarity among territories, which was related to an overall higher consumption of preferred prey. Thus, we revealed a correspondence in diet-fitness relationships at two spatial scales: territories and populations. We suggest that stable isotope analyses may be a powerful tool to monitor the diet of terrestrial avian predators on large spatio-temporal scales, which could serve to detect potential changes in the availability of those prey on which predators depend for breeding. We encourage ecologists and evolutionary and conservation biologists concerned with the multi-scale fitness consequences of inter

  2. DNA based electrolyte/separator for lithium battery application

    NASA Astrophysics Data System (ADS)

    Kumar, Jitendra; Ouchen, Fahima; Smarra, Devin A.; Subramanyam, Guru; Grote, James G.

    2015-09-01

    In this study, we demonstrated the use of DNA-CTMA (DC) in combination with PolyVinylidene Fluoride (PVDF) as a host matrix or separator for Lithium based electrolyte to form solid polymer/gel like electrolyte for potential application in Li-ion batteries. The addition of DC provided a better thermal stability of the composite electrolyte as shown by the thermos-gravimetric analysis (TGA). The AC conductivity measurements suggest that the addition of DC to the gel electrolyte had no effect on the overall ionic conductivity of the composite. The obtained films are flexible with high mechanical stretch-ability as compared to the gel type electrolytes only.

  3. Metabolite production during in vitro colonic fermentation of dietary fiber: analysis and comparison of two European diets.

    PubMed

    Tabernero, Maria; Venema, Koen; Maathuis, Annet J H; Saura-Calixto, Fulgencio D

    2011-08-24

    Metabolite production and antioxidant released during colonic fermentation of naturally occurring dietary fiber (DF) from two European diets (Mediterranean and Scandinavian) were determined. With this aim, DF and associated components were isolated from both whole diets, as well as from cereals and fruits and vegetables comprising the diets. DF was used as substrate for colonic fermentation in a dynamic in vitro model of the colon, samples were collected, and fermentation metabolites were analyzed. Statistical differences between samples were observed in the concentrations of short-chain fatty acids and ammonia and in the ratio acetate/propionate/butyrate. Whole grain cereal DF generated a larger amount of propionate than refined flour cereal DF. Fruit and vegetable DF generated higher amounts of butyrate than cereal DF. Most antioxidant compounds were released from DF during in vitro colonic fermentation. It is concluded that different sources of DF may play a specific role in health maintenance mediated by metabolites produced during colonic fermentation. PMID:21761861

  4. DNA-Based Asymmetric Catalysis: Role of Ionic Solvents and Glymes.

    PubMed

    Zhao, Hua; Shen, Kai

    2014-01-01

    Recently, DNA has been evaluated as a chiral scaffold for metal complexes to construct so called 'DNA-based hybrid catalysts', a robust and inexpensive alternative to enzymes. The unique chiral structure of DNA allows the hybrid catalysts to catalyze various asymmetric synthesis reactions. However, most current studies used aqueous buffers as solvents for these asymmetric reactions, where substrates/products are typically suspended in the solutions. The mass transfer limitation usually requires a long reaction time. To overcome this hurdle and to advance DNA-based asymmetric catalysis, we evaluated a series of ionic liquids (ILs), inorganic salts, deep eutectic solvents (DES), glymes, glycols, acetonitrile and methanol as co-solvents/additives for the DNA-based asymmetric Michael addition. In general, these additives induce indistinguishable changes to the DNA B-form duplex conformation as suggested by circular dichroism (CD) spectroscopy, but impose a significant influence on the catalytic efficiency of the DNA-based hybrid catalyst. Conventional organic solvents (e.g. acetonitrile and methanol) led to poor product yields and/or low enantioselectivities. Most ILs and inorganic salts cause the deactivation of the hybrid catalyst except 0.2 M [BMIM][CF3COO] (95.4% ee and 93% yield) and 0.2 M [BMIM]Cl (93.7% ee and 89% yield). Several other additives have also been found to improve the catalytic efficiency of the DNA-based hybrid catalyst (control reaction without additive gives >99% ee and 87% yield): 0.4 M glycerol (>99% ee and 96% yield at 5 °C or 96.2% ee and 83% yield at room temperature), 0.2 M choline chloride/glycerol (1:2) (92.4% ee and 90% yield at 5 °C or 94.0% ee and 88% yield at room temperature), and 0.5 M dipropylene glycol dimethyl ether (>99% ee and 87% yield at room temperature). The use of some co-solvents/additives allows the Michael addition to be performed at a higher temperature (e.g. room temperature vs 5 °C) and a shorter reaction time (24

  5. Intelligent DNA-based molecular diagnostics using linked genetic markers

    SciTech Connect

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  6. Temporal and spatial trends in prey composition of wahoo Acanthocybium solandri: a diet analysis from the central North Pacific Ocean using visual and DNA bar-coding techniques.

    PubMed

    Oyafuso, Z S; Toonen, R J; Franklin, E C

    2016-04-01

    A diet analysis was conducted on 444 wahoo Acanthocybium solandri caught in the central North Pacific Ocean longline fishery and a nearshore troll fishery surrounding the Hawaiian Islands from June to December 2014. In addition to traditional observational methods of stomach contents, a DNA bar-coding approach was integrated into the analysis by sequencing the cytochrome c oxidase subunit 1 (COI) region of the mtDNA genome to taxonomically identify individual prey items that could not be classified visually to species. For nearshore-caught A. solandri, juvenile pre-settlement reef fish species from various families dominated the prey composition during the summer months, followed primarily by Carangidae in autumn months. Gempylidae, Echeneidae and Scombridae were dominant prey taxa from the offshore fishery. Molidae was a common prey family found in stomachs collected north-east of the Hawaiian Archipelago while tetraodontiform reef fishes, known to have extended pelagic stages, were prominent prey items south-west of the Hawaiian Islands. The diet composition of A. solandri was indicative of an adaptive feeder and thus revealed dominant geographic and seasonal abundances of certain taxa from various ecosystems in the marine environment. The addition of molecular bar-coding to the traditional visual method of prey identifications allowed for a more comprehensive range of the prey field of A. solandri to be identified and should be used as a standard component in future diet studies. PMID:27059148

  7. DNA-based identification of Calendula officinalis (Asteraceae)1

    PubMed Central

    Schmiderer, Corinna; Lukas, Brigitte; Ruzicka, Joana; Novak, Johannes

    2015-01-01

    Premise of the study: For the economically important species Calendula officinalis, a fast identification assay based on high-resolution melting curve analysis was designed. This assay was developed to distinguish C. officinalis from other species of the genus and other Asteraceae genera, and to detect C. officinalis as an adulterant of saffron samples. Methods and Results: For this study, five markers (ITS, rbcL, 5′ trnK-matK, psbA-trnH, trnL-trnF) of 10 Calendula species were sequenced and analyzed for species-specific mutations. With the application of two developed primer pairs located in the trnK 5′ intron and trnL-trnF, C. officinalis could be distinguished from other species of the genus and all outgroup samples tested. Adulterations of Calendula DNA in saffron could be detected down to 0.01%. Conclusions: With the developed assay, C. officinalis can be reliably identified and admixtures of this species as adulterant of saffron can be revealed at low levels. PMID:26649268

  8. Variation in DNA Base Excision Repair Genes in Fuchs Endothelial Corneal Dystrophy

    PubMed Central

    Wójcik, Katarzyna A.; Synowiec, Ewelina; Polakowski, Piotr; Błasiak, Janusz; Szaflik, Jerzy; Szaflik, Jacek P.

    2015-01-01

    Background Fuchs endothelial corneal dystrophy (FECD) is a corneal disease characterized by abnormalities in the Descemet membrane and the corneal endothelium. The etiology of this disease is poorly understood. An increased level of oxidative DNA damage reported in FECD corneas suggests a role of DNA base excision repair (BER) genes in its pathogenesis. In this work, we searched for the association between variation of the PARP-1, NEIL1, POLG, and XRCC1 genes and FECD occurrence. Material/Methods This study was conducted on 250 FECD patients and 353 controls using polymerase chain reaction-restriction fragment length polymorphism, high-resolution melting analysis, and the TaqMan® SNP Genotyping Assay. Results We observed that the A/A genotype and the A allele of the c.1196A>G polymorphism of the XRCC1 gene were positively correlated with an increased FECD occurrence, whereas the G allele had the opposite effect. A weak association between the C/G genotype of the g.46438521G>C polymorphism of the NEIL1 gene and an increased incidence of FECD was also detected. Haplotypes of both polymorphisms of the XRCC1 were associated with FECD occurrence. No association of the c.2285T>C, c.–1370T>A and c.580C>T polymorphisms of the PARP-1, POLG and XRCC1 genes, respectively, with FECD occurrence was observed. Conclusions Our results suggest that the c.1196A>G polymorphism in the XRCC1 gene may be an independent genetic risk factor for FECD. PMID:26388025

  9. Developmental plasticity in Tenebrio molitor (Coleoptera: Tenebrionidae): Analysis of Instar Variation in Number and Development Time under Different Diets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The variation in instar number and the pattern of sequential instar development time of Tenebrio molitor L. (Coleoptera: Tenebrionidae) was studied under 4 different diet regimes. Addition of dietary supplements consisting of dry potato or a mix of dry potato and dry egg whites significantly reduced...

  10. Combined effects of aerobic exercise and diet on lipids and lipoproteins in overweight and obese adults: a meta-analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study used the aggregate data meta-analytic approach to determine the combined effects of aerobic exercise and diet on lipids and lipoproteins in overweight and obese adults. Twelve studies representing 859 men and women (443 intervention, 416 control) were included. Using random-effects models...