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Sample records for dna-based diet analysis

  1. Fast and efficient DNA-based method for winter diet analysis from stools of three cervids: moose, red deer, and roe deer.

    PubMed

    Czernik, Marta; Taberlet, Pierre; Swisłocka, Magdalena; Czajkowska, Magdalena; Duda, Norbert; Ratkiewicz, Mirosław

    2013-01-01

    Effects of cervid browsing on timber production, especially during winter, lead to economic losses in forest management. The aim of this study was to present an efficient DNA-based method which allows qualitative assessment of the winter diet from stools of moose (Alces alces), roe deer (Capreolus capreolus), and red deer (Cervus elaphus). The preliminary results of the diet composition of the three cervids from Poland were also presented with a special emphasis on moose. The electropherograms of the chloroplast intron trnL (UAA) P6 loop amplification products using g (fluorescence-labeled) and h primers revealed differences in the length of PCR products among various plant species eaten by these herbivores. In addition, the usage of species-specific primers allowed unambiguous identification of different gymnosperms and angiosperms. The preliminary moose diet analysis, based on winter fecal samples from the entire range of moose occurrence in Poland, revealed the presence of 15 to 24 tree, shrub, and herbaceous species. This fast, cost-efficient, and simple method proved also to be reliable for the diet analysis of red deer and roe deer. It may be a valuable tool in forest and conservation management, as well as a way of enhancing ecological studies focusing on the impact of herbivores on the ecosystems and their possible food niche overlap.

  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. 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.

  4. Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces.

    PubMed

    Pegard, Anthony; Miquel, Christian; Valentini, Alice; Coissac, Eric; Bouvier, Frédéric; François, Dominique; Taberlet, Pierre; Engel, Erwan; Pompanon, François

    2009-07-08

    Because of the demand for controlling livestock diets, two methods that characterize the DNA of plants present in feces were developed. After DNA extraction from fecal samples, a short fragment of the chloroplastic trnL intron was amplified by PCR using a universal primer pair for plants. The first method generates a signature that is the electrophoretic migration pattern of the PCR product. The second method consists of sequencing several hundred DNA fragments from the PCR product through pyrosequencing. These methods were validated with a blind analysis of feces from concentrate- and pasture-fed lambs. The signature method allowed differentiation of the two diets and confirmed the presence of concentrate in one of them. The pyrosequencing method allowed the identification of up to 25 taxa in a diet. These methods are complementary to the chemical methods already used. They could be applied to the control of diets and the study of food preferences.

  5. Forensic analysis of hallucinogenic fungi: a DNA-based approach.

    PubMed

    Nugent, Kimberly G; Saville, Barry J

    2004-03-10

    Hallucinogenic fungi synthesize two controlled substances, psilocin and psilocybin. Possession of the fungal species that contain these compounds is a criminal offence in North America. Some related species that are morphologically similar, do not contain the controlled substances. Therefore, unambiguous identification of fungi to the species level is critical in determining if a mushroom is illegal. We investigate a phylogenetic approach for the identification of species that contain the psychoactive compounds. We analyzed 35 North American specimens representing seven different genera of hallucinogenic and non-hallucinogenic mushrooms. We amplified and sequenced the internal transcribed spacer region of the rDNA (ITS-1) and a 5' portion of the nuclear large ribosomal subunit of rRNA (nLSU rRNA or 28S). ITS-1 locus sequence data was highly variable and produced a phylogenetic resolution that was not consistent with morphological identifications. In contrast, the nLSU rRNA data clustered isolates from the same species and separated hallucinogen containing and non-hallucinogen containing isolates into distinct clades. With this information, we propose an approach that combines the specificity of PCR detection and the resolving power of phylogenetic analysis to efficiently and unambiguously identify hallucinogenic fungal specimens for legal purposes.

  6. The impact of chimerism in DNA-based forensic sex determination analysis.

    PubMed

    George, Renjith; Donald, Preethy Mary; Nagraj, Sumanth Kumbargere; Idiculla, Jose Joy; Hj Ismail, Rashid

    2013-01-01

    Sex determination is the most important step in personal identification in forensic investigations. DNA-based sex determination analysis is comparatively more reliable than the other conventional methods of sex determination analysis. Advanced technology like real-time polymerase chain reaction (PCR) offers accurate and reproducible results and is at the level of legal acceptance. But still there are situations like chimerism where an individual possess both male and female specific factors together in their body. Sex determination analysis in such cases can give erroneous results. This paper discusses the phenomenon of chimerism and its impact on sex determination analysis in forensic investigations.

  7. 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...

  8. 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

  9. An Efficient Approach in Analysis of DNA Base Calling Using Neural Fuzzy Model

    PubMed Central

    2017-01-01

    This paper presented the issues of true representation and a reliable measure for analyzing the DNA base calling is provided. The method implemented dealt with the data set quality in analyzing DNA sequencing, it is investigating solution of the problem of using Neurofuzzy techniques for predicting the confidence value for each base in DNA base calling regarding collecting the data for each base in DNA, and the simulation model of designing the ANFIS contains three subsystems and main system; obtain the three features from the subsystems and in the main system and use the three features to predict the confidence value for each base. This is achieving effective results with high performance in employment. PMID:28261268

  10. 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.

  11. 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

  12. 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.

  13. 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

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

    PubMed

    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.

  15. 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.

  16. Pioneer identification of fake tiger claws using morphometric and DNA-based analysis in wildlife forensics in India.

    PubMed

    Vipin; Sharma, Vinita; Sharma, Chandra Prakash; Kumar, Ved Prakash; Goyal, Surendra Prakash

    2016-09-01

    The illegal trade in wildlife is a serious threat to the existence of wild animals throughout the world. The short supply and high demand for wildlife articles have caused an influx of many different forms of fake wildlife articles into this trade. The task of identifying the materials used in making such articles poses challenges in wildlife forensics as different approaches are required for species identification. Claws constitute 3.8% of the illegal animal parts (n=2899) received at the Wildlife Institute of India (WII) for species identification. We describe the identification of seized suspected tiger claws (n=18) using a combined approach of morphometric and DNA-based analysis. The differential keratin density, determined using X-ray radiographs, indicated that none of the 18 claws were of any large cat but were fake. We determined three claw measurements, viz. ac (from the external coronary dermo-epidermal interface to the epidermis of the skin fold connecting the palmar flanges of the coronary horn), bc (from the claw tip to the epidermis of the skin fold connecting the palmar flanges of the coronary horn) and the ratio bc/ac, for all the seized (n=18), tiger (n=23) and leopard (n=49) claws. Univariate and multivariate statistical analyses were performed using SPSS. A scatter plot generated using canonical discriminant function analysis revealed that of the 18 seized claws, 14 claws formed a cluster separate from the clusters of the tiger and leopard claws, whereas the remaining four claws were within the leopard cluster. Because a discrepancy was observed between the X-ray images and the measurements of these four claws, one of the claw that clustered with the leopard claws was chosen randomly and DNA analysis carried out using the cyt b (137bp) and 16S rRNA (410bp) genes. A BLAST search and comparison with the reference database at WII indicated that the keratin material of the claw was derived from Bos taurus (cattle). This is a pioneering discovery, and

  17. DNA-based probes for flow cytometry analysis of endocytosis and recycling.

    PubMed

    Dumont, Claire; Czuba, Ewa; Chen, Moore; Villadangos, Jose A; Johnston, Angus P R; Mintern, Justine D

    2016-12-26

    The internalization of proteins plays a key role in cell development, cell signaling and immunity. We have previously developed a specific hybridization internalization probe (SHIP) to quantitate the internalization of proteins and particles into cells. Herein, we extend the utility of SHIP to examine both the endocytosis and recycling of surface receptors using flow cytometry. SHIP was used to monitor endocytosis of membrane-bound transferrin receptor (TFR) and its soluble ligand transferrin (TF). SHIP enabled measurements of the proportion of surface molecules internalized, the internalization kinetics and the proportion and rate of internalized molecules that recycle to the cell surface with time. Using this method, we have demonstrated the internalization and recycling of holo-TF and an antibody against the TFR behave differently. This assay therefore highlights the implications of receptor internalization and recycling, where the internalization of the receptor-antibody complex behaves differently to the receptor-ligand complex. In addition, we observe distinct internalization patterns for these molecules expressed by different subpopulations of primary cells. SHIP provides a convenient and high throughput technique for analysis of trafficking parameters for both cell surface receptors and their ligands.

  18. Studying Seabird Diet through Genetic Analysis of Faeces: A Case Study on Macaroni Penguins (Eudyptes chrysolophus)

    PubMed Central

    Deagle, Bruce E.; Gales, Nick J.; Evans, Karen; Jarman, Simon N.; Robinson, Sarah; Trebilco, Rowan; Hindell, Mark A.

    2007-01-01

    Background Determination of seabird diet usually relies on the analysis of stomach-content remains obtained through stomach flushing; this technique is both invasive and logistically difficult. We evaluate the usefulness of DNA-based faecal analysis in a dietary study on chick-rearing macaroni penguins (Eudyptes chrysolophus) at Heard Island. Conventional stomach-content data was also collected, allowing comparison of the approaches. Methodology/Principal Findings Prey-specific PCR tests were used to detect dietary DNA in faecal samples and amplified prey DNA was cloned and sequenced. Of the 88 faecal samples collected, 39 contained detectable DNA from one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in the early (guard) stage of chick-rearing, and detection of DNA from the myctophid fish Krefftichthys anderssoni and amphipods became more common in samples collected in the later (crèche) stage. These trends followed those observed in the penguins' stomach contents. In euphausiid-specific clone libraries the proportion of sequences from the two dominant euphausiid prey species (Euphausia vallentini and Thysanoessa macrura) changed over the sampling period; again, this reflected the trend in the stomach content data. Analysis of prey sequences in universal clone libraries revealed a higher diversity of fish prey than identified in the stomachs, but non-fish prey were not well represented. Conclusions/Significance The present study is one of the first to examine the full breadth of a predator's diet using DNA-based faecal analysis. We discuss methodological difficulties encountered and suggest possible refinements. Overall, the ability of the DNA-based approach to detect temporal variation in the diet of macaroni penguins indicates this non-invasive method will be generally useful for monitoring population-level dietary trends in seabirds. PMID:17786203

  19. Analysis of bacterial core communities in the central Baltic by comparative RNA-DNA-based fingerprinting provides links to structure-function relationships.

    PubMed

    Brettar, Ingrid; Christen, Richard; Höfle, Manfred G

    2012-01-01

    Understanding structure-function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.

  20. Tooth wear: diet analysis and advice.

    PubMed

    Young, William George

    2005-04-01

    Diet analysis and advice for patients with tooth wear is potentially the most logical intervention to arrest attrition, erosion and abrasion. It is saliva that protects the teeth against corrosion by the acids which soften enamel and make it susceptible to wear. Thus the lifestyles and diet of patients at risk need to be analysed for sources of acid and reasons for lost salivary protection. Medical conditions which put patients at risk of tooth wear are principally: asthma, bulimia nervosa, caffeine addiction, diabetes mellitus, exercise dehydration, functional depression, gastroesophageal reflux in alcoholism, hypertension and syndromes with salivary hypofunction. The sources of acid are various, but loss of salivary protection is the common theme. In healthy young Australians, soft drinks are the main source of acid, and exercise dehydration the main reason for loss of salivary protection. In the medically compromised, diet acids and gastroesophageal reflux are the sources, but medications are the main reasons for lost salivary protection. Diet advice for patients with tooth wear must: promote a healthy lifestyle and diet strategy that conserves the teeth by natural means of salivary stimulation; and address the specific needs of the patients' oral and medical conditions. Individualised, patient-empowering erosion WATCH strategies; on Water, Acid, Taste, Calcium and Health, are urgently required to combat the emerging epidemic of tooth wear currently being experienced in westernised societies.

  1. 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

  2. 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.

  3. Weight-loss dieting behavior: an economic analysis.

    PubMed

    Rosin, Odelia

    2012-07-01

    In light of the widespread phenomena of diet failure and excessive dieting, this paper presents a theoretical economic analysis of the decision-making process of weight-loss dieting. The paper incorporates behavioral elements involved in the process of dieting: effort exerted in dieting, influence of social norms concerning body weight, time-inconsistent present biased preferences, and a distinction between naiveté and sophistication. The model explains cyclic dieting and provides interesting insights on the extent of weight-loss dieting. The extent of dieting is an increasing function of initial body weight and a decreasing function of the effort exerted in dieting and the strength of social norms concerning ideal weight. Income and diet strictness have an ambiguous effect. In addition, greater dieting efforts are not necessarily balanced against a slowdown in body metabolism or a higher initial body weight.

  4. DNA based molecular motors

    NASA Astrophysics Data System (ADS)

    Michaelis, Jens; Muschielok, Adam; Andrecka, Joanna; Kügel, Wolfgang; Moffitt, Jeffrey R.

    2009-12-01

    Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid-a process that is driven by one of the most powerful molecular motors.

  5. 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...

  6. 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.

  7. Surface-enhanced Raman detection of RNA and DNA bases following flow-injection analysis or HPLC separation

    NASA Astrophysics Data System (ADS)

    Cotton, Therese M.; Sheng, Rong-Sheng; Ni, Fan

    1990-11-01

    The goal of this study is to develop Surface-enhanced Raman scattering (SERS) detection methods for flow injection analysis (FIA) and high performance liquid chromatography (HPLC). Nucleic acid bases have been chosen for analysis because of their importance in life processes. The advantages to the use of SERS-based detection include its sensitivity, specificity and versatility. With the development of improved methodology, the detection limits should be comparable to UV spectroscopy. However, the specificity is considerably superior to that obtained with electronic spectroscopy in that the Raman spectrum provides a molecular fingerprint of the individual analytes. Raman spectroscopy is very versatile: aqueous samples, gases and solids can be analyzed with equal facility. The results presented here demonstrate that SERS can be used as a detection method for both FIA and HPLC detection. In the following experiments Ag sols have been used as the active substrate. The effect of various parameters such as temperature, pH, flow rate, and the nature of the interface between the HPLC system and the Raman spectrometer have been examined. One of the most significant findings is that the temperature of the Ag sol/HPLC effluent mixture has a dramatic effect on the SERS intensities. This effect is a result of increased colloid aggregation at higher temperatures. Aggregation is known to produce greater enhancement in SERS and proceeds much more rapidly at elevated temperatures. An increase in the temperature of the Ag sol enables SERS detection under flowing conditions and in real time. This is a substantial improvement over many of the previous attempts to interface SERS detection to FIA or HPLC. In most of the previous studies, it was necessary to stop the flow as the analyte eluted from the chromatogram and measure the SERS spectra under static conditions.

  8. Detection of Herpesviridae in whole blood by multiplex PCR DNA-based microarray analysis after hematopoietic stem cell transplantation.

    PubMed

    Debaugnies, France; Busson, Laurent; Ferster, Alina; Lewalle, Philippe; Azzi, Nadira; Aoun, Mickael; Verhaegen, Godelieve; Mahadeb, Bhavna; de Marchin, Jérôme; Vandenberg, Olivier; Hallin, Marie

    2014-07-01

    Viral infections are important causes of morbidity and mortality in patients after hematopoietic stem cell transplantation. The monitoring by PCR of Herpesviridae loads in blood samples has become a critical part of posttransplant follow-up, representing mounting costs for the laboratory. In this study, we assessed the clinical performance of the multiplex PCR DNA microarray Clart Entherpex kit for detection of cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesvirus 6 (HHV-6) as a screening test for virological follow-up. Two hundred fifty-five blood samples from 16 transplanted patients, prospectively tested by routine PCR assays, were analyzed by microarray. Routine PCR detected single or multiple viruses in 42% and 10% of the samples, respectively. Microarray detected single or multiple viruses in 34% and 18% of the samples, respectively. Microarray results correlated well with CMV and EBV detections by routine PCR (kappa tests = 0.79 and 0.78, respectively), whereas a weak correlation was observed with HHV-6 (0.43). HHV-7 was also detected in 48 samples by microarray. In conclusion, the microarray is a reliable screening assay for a posttransplant virological follow-up to detect CMV and EBV infections in blood. However, positive samples must be subsequently confirmed and viral loads must be quantified by PCR assays. Limitations were identified regarding HHV-6 detection. Although it is promising, is easy to use as a first-line test, and allows a reduction in the cost of analysis without undue delay in the reporting of the final quantitative result to the clinician, some characteristics of this microarray should be improved, particularly regarding quality control and the targeted virus panel, such that it could then be used as a routine test.

  9. Complete sequence analysis of 18S rDNA based on genomic DNA extraction from individual Demodex mites (Acari: Demodicidae).

    PubMed

    Zhao, Ya-E; Xu, Ji-Ru; Hu, Li; Wu, Li-Ping; Wang, Zheng-Hang

    2012-05-01

    The study for the first time attempted to accomplish 18S ribosomal DNA (rDNA) complete sequence amplification and analysis for three Demodex species (Demodex folliculorum, Demodex brevis and Demodex canis) based on gDNA extraction from individual mites. The mites were treated by DNA Release Additive and Hot Start II DNA Polymerase so as to promote mite disruption and increase PCR specificity. Determination of D. folliculorum gDNA showed that the gDNA yield reached the highest at 1 mite, tending to descend with the increase of mite number. The individual mite gDNA was successfully used for 18S rDNA fragment (about 900 bp) amplification examination. The alignments of 18S rDNA complete sequences of individual mite samples and those of pooled mite samples ( ≥ 1000mites/sample) showed over 97% identities for each species, indicating that the gDNA extracted from a single individual mite was as satisfactory as that from pooled mites for PCR amplification. Further pairwise sequence analyses showed that average divergence, genetic distance, transition/transversion or phylogenetic tree could not effectively identify the three Demodex species, largely due to the differentiation in the D. canis isolates. It can be concluded that the individual Demodex mite gDNA can satisfy the molecular study of Demodex. 18S rDNA complete sequence is suitable for interfamily identification in Cheyletoidea, but whether it is suitable for intrafamily identification cannot be confirmed until the ascertainment of the types of Demodex mites parasitizing in dogs.

  10. Intraguild Predation Among Three Common Coccinellids (Coleoptera: Coccinellidae) in China: Detection Using DNA-Based Gut-Content Analysis.

    PubMed

    Yang, Fan; Wang, Qian; Wang, Dongmei; Xu, Bin; Xu, Jianxiang; Lu, Yanhui; Harwood, James D

    2016-12-26

    The ubiquity of intraguild predation (IGP) has been widely recognized for predatory coccinellids (Coleoptera: Coccinellidae). In Chinese agroecosystems, three species (Coccinella septempunctata L., Harmonia axyridis (Pallas), and Propylea japonica (Thunberg)) are particularly common, but there is little information of interactions occurring between them. In no-choice laboratory feeding trials, differential directional predation was observed between species: C. septempunctata preyed on eggs of P. japonica more than H. axyridis and H. axyridis consumed eggs of C. septempunctata and P. japonica equally, whereas P. japonica had a very low predation rate on eggs of the other two species. In choice trials, C. septempunctata and P. japonica larvae preyed less on H. axyridis eggs than those of P. japonica and C. septempunctata, respectively, contrasting with H. axyridis larvae, which showed similar preference for both species. Species-specific primers were developed for each coccinellid and used to determine the relative frequency of prey consumption in the field. Prior to field-based analysis, primer specificity was confirmed and consumption of prey elicited a positive reaction success, and detection time varied between different predator-prey combinations. Predators were then collected from cotton agroecosystems and, interestingly, no DNA of C. septempunctata was found in P. japonica, but all other predator-prey combinations yielded positive documentation of IGP in the field, with the greatest rate of 9% of C. septempunctata testing positive for H. axyridis DNA. This study confirmed the frequency of IGP among three common coccinellids in Chinese agroecosystems and the likelihood for interference to the biological control services provided by these important natural enemies.

  11. 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].

  12. 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.

  13. DNA-based hybrid catalysis.

    PubMed

    Rioz-Martínez, Ana; Roelfes, Gerard

    2015-04-01

    In the past decade, DNA-based hybrid catalysis has merged as a promising novel approach to homogeneous (asymmetric) catalysis. A DNA hybrid catalysts comprises a transition metal complex that is covalently or supramolecularly bound to DNA. The chiral microenvironment and the second coordination sphere interactions provided by the DNA are key to achieve high enantioselectivities and, often, additional rate accelerations in catalysis. Nowadays, current efforts are focused on improved designs, understanding the origin of the enantioselectivity and DNA-induced rate accelerations, expanding the catalytic scope of the concept and further increasing the practicality of the method for applications in synthesis. Herein, the recent developments will be reviewed and the perspectives for the emerging field of DNA-based hybrid catalysis will be discussed.

  14. Neutron activation analysis of total diet food composites for iodine

    SciTech Connect

    Allegrini, M.; Boyer, K.W.; Tanner, J.T.

    1981-09-01

    The iodine content of Total Diet food composites was measured using neutron activation analysis. The interfering element chlorine was separated using a modified combustion and gas phase procedure. The average recovery was 94.8% (standard deviation 2.9) for the 10 matrices that were tested. In addition, iodine was measured in National Bureau of Standards Standard Reference Materials, which have no certified values for this element. Preliminary findings of iodine content of adult Total Diet market baskets collected during Fiscal Year 1980 in different regions of the United States ranged from 292 to 901 ..mu..g/day for a 2900 kcal intake.

  15. 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...

  16. Molecular analysis of the diets of snakes: changes in prey exploitation during development of the rare smooth snake Coronella austriaca.

    PubMed

    Brown, David S; Ebenezer, Katie L; Symondson, William O C

    2014-08-01

    Reptiles are declining in many parts of the world, mainly due to habitat loss and environmental change. A major factor in this is availability of suitable food. For many animals, dietary requirements shift during developmental stages and a habitat will only be suitable for conserving a species if it supports all stages. Conventional methods for establishing diet often rely on visual recognition of morphologically identifiable features of prey in faeces, regurgitation or stomach contents, which suffer from biases and poor resolution of taxa. DNA-based techniques facilitate noninvasive analysis of diet from faeces without these constraints. We tested the hypothesis that diet changes during growth stages of smooth snakes (Coronella austriaca), which have a highly restricted distribution in the UK but are widespread in continental Europe. Small numbers of the sympatric grass snake (Natrix natrix) were analysed for comparison. Faecal samples were collected from snakes and prey DNA analysed using PCR, targeting amphibians, reptiles, mammals and invertebrates. Over 85% of smooth snakes were found to have eaten reptiles and 28% had eaten mammals. Predation on mammals increased with age and was entirely absent among juveniles and subadults. Predation on reptiles did not change ontogenetically. Smooth snakes may, therefore, be restricted to areas of sufficiently high reptile densities to support young snakes.

  17. Detecting Chemically Modified DNA Bases Using Surface Enhanced Raman Spectroscopy.

    PubMed

    Barhoumi, Aoune; Halas, Naomi J

    2011-12-15

    Post-translational modifications of DNA- changes in the chemical structure of individual bases that occur without changes in the DNA sequence- are known to alter gene expression. They are believed to result in frequently deleterious phenotypic changes, such as cancer. Methylation of adenine, methylation and hydroxymethylation of cytosine, and guanine oxidation are the primary DNA base modifications identified to date. Here we show it is possible to use surface enhanced Raman spectroscopy (SERS) to detect these primary DNA base modifications. SERS detection of modified DNA bases is label-free and requires minimal additional sample preparation, reducing the possibility of additional chemical modifications induced prior to measurement. This approach shows the feasibility of DNA base modification assessment as a potentially routine analysis that may be further developed for clinical diagnostics.

  18. DNA-based soft phases.

    PubMed

    Bellini, Tommaso; Cerbino, Roberto; Zanchetta, Giuliano

    2012-01-01

    This chapter reviews the state-of-the-art in the study of molecular or colloidal systems whose mutual interactions are mediated by DNA molecules. In the last decade, the robust current knowledge of DNA interactions has enabled an impressive growth of self-assembled DNA-based structures that depend crucially on the properties of DNA-DNA interactions. In many cases, structures are built on design by exploiting the programmable selectivity of DNA interactions and the modularity of their strength. The study of DNA-based materials is definitely an emerging field in condensed matter physics, nanotechnology, and material science. This chapter will consider both systems that are entirely constructed by DNA and hybrid systems in which latex or metal colloidal particles are coated by DNA strands. We will confine our discussion to systems in which DNA-mediated interactions promote the formation of "phases," that is structures extending on length scales much larger than the building blocks. Their self-assembly typically involves a large number of interacting particles and often features hierarchical stages of structuring. Because of the possibility of fine-tuning the geometry and strength of the DNA-mediated interactions, these systems are characterized by a wide variety of patterns of self-assembly, ranging from amorphous, to liquid crystalline, to crystalline in one, two, or three dimensions.

  19. Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes.

    PubMed

    Hambäck, Peter A; Weingartner, Elisabeth; Dalén, Love; Wirta, Helena; Roslin, Tomas

    2016-12-01

    Inflow of matter and organisms may strongly affect the local density and diversity of organisms. This effect is particularly evident on shores where organisms with aquatic larval stages enter the terrestrial food web. The identities of such trophic links are not easily estimated as spiders, a dominant group of shoreline predator, have external digestion. We compared trophic links and the prey diversity of spiders on different shore types along the Baltic Sea: on open shores and on shores with a reed belt bordering the water. A priori, we hypothesized that the physical structure of the shoreline reduces the flow between ecosystem and the subsidies across the sea-land interface. To circumvent the lack of morphologically detectable remains of spider prey, we used a combination of stable isotope and molecular gut content analyses. The two tools used for diet analysis revealed complementary information on spider diets. The stable isotope analysis indicated that spiders on open shores had a marine signal of carbon isotopes, while spiders on reedy shores had a terrestrial signal. The molecular analysis revealed a diverse array of dipteran and lepidopteran prey, where spiders on open and reedy shores shared a similar diet with a comparable proportion of chironomids, the larvae of which live in the marine system. Comparing the methods suggests that differences in isotope composition of the two spider groups occurred because of differences in the chironomid diets: as larvae, chironomids of reedy shores likely fed on terrestrial detritus and acquired a terrestrial isotope signature, while chironomids of open shores utilized an algal diet and acquired a marine isotope signature. Our results illustrate how different methods of diet reconstruction may shed light on complementary aspects of nutrient transfer. Overall, they reveal that reed belts can reduce connectivity between habitats, but also function as a source of food for predators.

  20. 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

  1. Physiological effects of diet mixing on consumer fitness: a meta-analysis.

    PubMed

    Lefcheck, Jonathan S; Whalen, Matthew A; Davenport, Theresa M; Stone, Joshua P; Duffy, J Emmett

    2013-03-01

    The degree of dietary generalism among consumers has important consequences for population, community, and ecosystem processes, yet the effects on consumer fitness of mixing food types have not been examined comprehensively. We conducted a meta-analysis of 161 peer-reviewed studies reporting 493 experimental manipulations of prey diversity to test whether diet mixing enhances consumer fitness based on the intrinsic nutritional quality of foods and consumer physiology. Averaged across studies, mixed diets conferred significantly higher fitness than the average of single-species diets, but not the best single prey species. More than half of individual experiments, however, showed maximal growth and reproduction on mixed diets, consistent with the predicted benefits of a balanced diet. Mixed diets including chemically defended prey were no better than the average prey type, opposing the prediction that a diverse diet dilutes toxins. Finally, mixed-model analysis showed that the effect of diet mixing was stronger for herbivores than for higher trophic levels. The generally weak evidence for the nutritional benefits of diet mixing in these primarily laboratory experiments suggests that diet generalism is not strongly favored by the inherent physiological benefits of mixing food types, but is more likely driven by ecological and environmental influences on consumer foraging.

  2. 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 ...

  3. 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...

  4. Development of a quantitation approach for total human and male DNA based on real time PCR followed by high resolution melting analysis.

    PubMed

    Ginart, Santiago; Caputo, Mariela; Alechine, Evguenia; Corach, Daniel; Sala, Andrea

    2016-10-01

    We developed and validated a total human DNA quantitation technique that simultaneously allows male DNA detection. This assay, called Amel-Y, is a duplex Real Time PCR followed by HRM (high resolution melting) analysis using the intercalating dye SYTO9. Amel-Y duplex produces two amplicons, one for the amelogenin gene (106/112 bp, female/male) and another (84 bp) corresponding to human Y chromosome-specific fragment to detect male DNA. After HRM analysis, two melting peaks differing in 5.3°C-5.5°C are detected if both male and female DNA are present and only one if only female DNA is present. For specificity assessment, the inclusion of high concentrations of bacterial and fungal DNA in the quantitation reactions allowed discarding species cross-reactivity. A set of crime scene evidence from forensic casework has been quantified with commercial kits and compared with Amel-Y duplex. Our method detected male DNA from a concentration of 18 pg/μL and supports autosomal/Y DNA detection ratio up to 200:1. A limitation of the technique is its inability to quantify male and female donnors in a mixed sample. The Amel-Y duplex demonstrated to be an efficient system for quantifying total human DNA being a specific, rapid, sensitive, and cost-effective method suitable for mixed DNA samples and applicable to any field where human DNA quantification is required, such as molecular diagnosis, population genetics, and forensic identification.

  5. 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.

  6. Identification of the DNA Bases of a DNase I Footprint by the Use of Dye Primer Sequencing on an Automated Capillary DNA Analysis Instrument

    PubMed Central

    Zianni, Michael; Tessanne, Kimberly; Merighi, Massimo; Laguna, Rick; Tabita, F.R.

    2006-01-01

    We have adapted the techniques of DNA footprint analysis to an Applied Biosystems 3730 DNA Analyzer. The use of fluorescently labeled primers eliminates the need for radioactively labeled nucleotides, as well as slab gel electrophoresis, and takes advantage of commonly available automated fluorescent capillary electrophoresis instruments. With fluorescently labeled primers and dideoxynucleotide DNA sequencing, we have shown that the terminal base of each digested fragment may be accurately identified with a capillary-based instrument. Polymerase chain reaction (PCR) was performed with a 6FAM-labeled primer to amplify a typical target promoter region. This PCR product was then incubated with a transcriptional activator protein, or bovine serum albumin as a control, and then partially digested with DNase I. A clone of the promoter was sequenced with the Thermo Sequenase Dye Primer Manual Cycle Sequencing kit (USB) and the FAM-labeled primer. Through the use of Genemapper software, the Thermo sequenase and DNasei digestion products were accurately aligned, providing a ready means to assign correct nucleotides to each peak from the DNA footprint. This method was used to characterize the binding of two different transcriptional activator proteins to their respective promoter regions. PMID:16741237

  7. Epigenetic clock analysis of diet, exercise, education, and lifestyle factors

    PubMed Central

    Lu, Ake T.; Chen, Brian H.; Ferrucci, Luigi; Ritz, Beate; Bandinelli, Stefania; Neuhouser, Marian L.; Beasley, Jeannette M.; Snetselaar, Linda; Wallace, Robert B.; Tsao, Philip S.; Absher, Devin; Assimes, Themistocles L.; Stewart, James D.; Li, Yun; Hou, Lifang; Baccarelli, Andrea A.; Whitsel, Eric A.; Horvath, Steve

    2017-01-01

    Behavioral and lifestyle factors have been shown to relate to a number of health-related outcomes, yet there is a need for studies that examine their relationship to molecular aging rates. Toward this end, we use recent epigenetic biomarkers of age that have previously been shown to predict all-cause mortality, chronic conditions and age-related functional decline. We analyze cross-sectional data from 4,173 postmenopausal female participants from the Women's Health Initiative, as well as 402 male and female participants from the Italian cohort study, Invecchiare nel Chianti. Extrinsic epigenetic age acceleration (EEAA) exhibits significant associations with fish intake (p=0.02), moderate alcohol consumption (p=0.01), education (p=3×10-5), BMI (p=0.01), and blood carotenoid levels (p=1×10-5)—an indicator of fruit and vegetable consumption, whereas intrinsic epigenetic age acceleration (IEAA) is associated with poultry intake (p=0.03) and BMI (p=0.05). Both EEAA and IEAA were also found to relate to indicators of metabolic syndrome, which appear to mediate their associations with BMI. Metformin—the first-line medication for the treatment of type 2 diabetes—does not delay epigenetic aging in this observational study. Finally, longitudinal data suggests that an increase in BMI is associated with increase in both EEAA and IEAA. Overall, the epigenetic age analysis of blood confirms the conventional wisdom regarding the benefits of eating a high plant diet with lean meats, moderate alcohol consumption, physical activity, and education, as well as the health risks of obesity and metabolic syndrome. PMID:28198702

  8. Epigenetic clock analysis of diet, exercise, education, and lifestyle factors.

    PubMed

    Quach, Austin; Levine, Morgan E; Tanaka, Toshiko; Lu, Ake T; Chen, Brian H; Ferrucci, Luigi; Ritz, Beate; Bandinelli, Stefania; Neuhouser, Marian L; Beasley, Jeannette M; Snetselaar, Linda; Wallace, Robert B; Tsao, Philip S; Absher, Devin; Assimes, Themistocles L; Stewart, James D; Li, Yun; Hou, Lifang; Baccarelli, Andrea A; Whitsel, Eric A; Horvath, Steve

    2017-02-14

    Behavioral and lifestyle factors have been shown to relate to a number of health-related outcomes, yet there is a need for studies that examine their relationship to molecular aging rates. Toward this end, we use recent epigenetic biomarkers of age that have previously been shown to predict all-cause mortality, chronic conditions, and age-related functional decline. We analyze cross-sectional data from 4,173 postmenopausal female participants from the Women's Health Initiative, as well as 402 male and female participants from the Italian cohort study, Invecchiare nel Chianti.Extrinsic epigenetic age acceleration (EEAA) exhibits significant associations with fish intake (p=0.02), moderate alcohol consumption (p=0.01), education (p=3x10(-5)), BMI (p=0.01), and blood carotenoid levels (p=1x10(-5))-an indicator of fruit and vegetable consumption, whereas intrinsic epigenetic age acceleration (IEAA) is associated with poultry intake (p=0.03) and BMI (p=0.05). Both EEAA and IEAA were also found to relate to indicators of metabolic syndrome, which appear to mediate their associations with BMI. Metformin-the first-line medication for the treatment of type 2 diabetes-does not delay epigenetic aging in this observational study. Finally, longitudinal data suggests that an increase in BMI is associated with increase in both EEAA and IEAA.Overall, the epigenetic age analysis of blood confirms the conventional wisdom regarding the benefits of eating a high plant diet with lean meats, moderate alcohol consumption, physical activity, and education, as well as the health risks of obesity and metabolic syndrome.

  9. 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

  10. 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.

  11. 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.

  12. Challenges and progress in making DNA-based AIS early ...

    EPA Pesticide Factsheets

    The ability of DNA barcoding to find additional species in hard-to-sample locations or hard-to-identify samples is well established. Nevertheless, adoption of DNA barcoding into regular monitoring programs has been slow, in part due to issues of standardization and interpretation that need resolving. In this presentation, we describe our progress towards incorporating DNA-based identification into broad-spectrum aquatic invasive species early-detection monitoring in the Laurentian Great Lakes. Our work uses community biodiversity information as the basis for evaluating survey performance for various taxonomic groups. Issues we are tackling in bringing DNA-based data to bear on AIS monitoring design include: 1) Standardizing methodology and work flow from field collection and sample handling through bioinformatics post-processing; 2) Determining detection sensitivity and accounting for inter-species differences in DNA amplification and primer affinity; 3) Differentiating sequencing and barcoding errors from legitimate new finds when range and natural history information is limited; and 4) Accounting for the different nature of morphology- vs. DNA-based biodiversity information in subsequent analysis (e.g., via species accumulation curves, multi-metric indices). not applicable

  13. DNA Based Electrochromic and Photovoltaic Cells

    DTIC Science & Technology

    2012-01-01

    SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON a. REPORT...9550-09-1-0647 final 01-09-2009 ; 30-11-2011 DNA Based Electrochromic and Photovoltaic Cells FA 9550-09-1-0647 Pawlicka, Agnieszka, J. Instituto de...as well as DNA-CTMA and DNA-DODA were also obtained and characterized. High ionic conductivity results combined with transparency and adhesion to the

  14. Analysis Extract. AFSC 4D0X1 Diet Therapy (Active Duty)

    DTIC Science & Technology

    2002-07-01

    87* 22* V0140 Diet(s) exp- Kosher Diet Active Active Active Active AD...98 % 94 % Total in group: 23* 29* 52* 41* 119* V0140 Diet(s) exp- Kosher Diet...13* 8* V0140 Diet(s) exp- Kosher Diet AETC ACC AMC AFMC PACAF USAFE

  15. Multiphoton excitation of fluorescent DNA base analogs.

    PubMed

    Katilius, Evaldas; Woodbury, Neal W

    2006-01-01

    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 x 10(-50) cm(4)s (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.

  16. 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.

  17. Microarray analysis of diet-induced alterations in gene expression in the ACI rat prostate.

    PubMed

    Reyes, Niradiz; Iatropoulos, Michael; Mittelman, Abraham; Geliebter, Jan

    2002-08-01

    The natural history of prostate cancer is a multistage process that involves the transition from normal tissue to subclinical cancer, with progression to carcinoma in situ and eventually metastatic disease. Evidence suggests that a high-fat diet plays a critical role in the biology and progression of the disease. ACI rats were maintained for two generations on high beef fat or control diets for 18 months. Affymetrix microarrays were used to analyze the mRNA expression levels in the dorsolateral prostates of rats on the different diets. Approximately 4752 genes and expressed sequence tag (EST) were expressed in the prostates of rats on either diet. Twenty-seven genes were upregulated and 28 genes downregulated in the high beef fat diet. Data analysis indicated that a high beef fat diet affects the expression of genes involved in inflammation, glucose and fatty acid metabolism, androgen metabolism, potential tumor suppression and protein kinase activity, as well as intracellular and extracellular matrix molecules, growth factors and androgen responsive genes. Results from these and future studies will lead to a better understanding of the effect of diet on gene expression in the prostate and facilitate the rational design and assessment of potential dietary programs for prostate cancer prevention.

  18. A bibliometric analysis of diets and breast cancer research.

    PubMed

    Kotepui, Manas; Wannaiampikul, Sivaporn; Chupeerach, Chaowanee; Duangmano, Suwit

    2014-01-01

    Breast cancer is the most common cancer among women worldwide. The primary aim of this work was to provide an in-depth evaluation of research publications in the field of diets and breast cancer. The impact of economic outcome on national academic productivity was also investigated. Data were retrieved using Pubmed for English-language publications. The search included all research for which articles included words relating to "diets and breast cancer". Population and national income data were obtained from publicly available databases. Impact factors for journals were obtained from Journal Citation Reports® (Thomson Scientific). There were 2,396 publications from 60 countries in 384 journals with an impact factor. Among them, 1,652 (68.94%) publications were Original articles. The United States had the highest quantity (51% of total) and highest of mean impact factor (8.852) for publication. Sweden had the highest productivity of publication when adjusted for number of population (6 publications per million population). Publications from the Asian nation increased from 5.3% in 2006 to 14.6% in 2012. The Original article type was also associated with geography (p<0.001; OR=2.183; 95%CI=1.526-3.123), Asian countries produced more proportion of Original articles (82%) than those of rest of the world (67.6%). Diets and breast cancer-associated research output continues to increase annually worldwide including publications from Asian countries. Although the United States produced the most publications, European nations per capita were higher in publication output.

  19. 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.; 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%).

  20. 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...

  1. 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.

  2. Engineering DNA-based functional materials.

    PubMed

    Roh, Young Hoon; Ruiz, Roanna C H; Peng, Songming; Lee, Jong Bum; Luo, Dan

    2011-12-01

    While DNA is a genetic material, it is also an inherently polymeric material made from repeating units called nucleotides. Although DNA's biological functions have been studied for decades, the polymeric features of DNA have not been extensively exploited until recently. In this tutorial review, we focus on two aspects of using DNA as a polymeric material: (1) the engineering methods, and (2) the potential real-world applications. More specifically, various strategies for constructing DNA-based building blocks and materials are introduced based on DNA topologies, which include linear, branched/dendritic, and networked. Different applications in nanotechnology, medicine, and biotechnology are further reviewed.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. A simple DNA-based translation system.

    PubMed

    Garibotti, Alejandra V; Liao, Shiping; Seeman, Nadrian C

    2007-02-01

    We have used DNA double crossover (DX) molecules to produce a translation system that generates unique molecular products. The particular species of DX molecule used contains an even number of half-turns between crossover points, so there is a continuous strand on both sides of the molecule. One of these strands acts as the input strand containing the message, and a second strand acts as the product of translation. The crossover strands carry the "code" that connects the two sides of the molecule. This system is more robust, more extendable, and simpler than previous DNA-based translation systems that have been reported. It is designed to be useful in a variety of applications that utilize the concept of translating from one code to another.

  10. DNA base identification by electron microscopy.

    PubMed

    Bell, David C; Thomas, W Kelley; Murtagh, Katelyn M; Dionne, Cheryl A; Graham, Adam C; Anderson, Jobriah E; Glover, William R

    2012-10-01

    Advances in DNA sequencing, based on fluorescent microscopy, have transformed many areas of biological research. However, only relatively short molecules can be sequenced by these technologies. Dramatic improvements in genomic research will require accurate sequencing of long (>10,000 base-pairs), intact DNA molecules. Our approach directly visualizes the sequence of DNA molecules using electron microscopy. This report represents the first identification of DNA base pairs within intact DNA molecules by electron microscopy. By enzymatically incorporating modified bases, which contain atoms of increased atomic number, direct visualization and identification of individually labeled bases within a synthetic 3,272 base-pair DNA molecule and a 7,249 base-pair viral genome have been accomplished. This proof of principle is made possible by the use of a dUTP nucleotide, substituted with a single mercury atom attached to the nitrogenous base. One of these contrast-enhanced, heavy-atom-labeled bases is paired with each adenosine base in the template molecule and then built into a double-stranded DNA molecule by a template-directed DNA polymerase enzyme. This modification is small enough to allow very long molecules with labels at each A-U position. Image contrast is further enhanced by using annular dark-field scanning transmission electron microscopy (ADF-STEM). Further refinements to identify additional base types and more precisely determine the location of identified bases would allow full sequencing of long, intact DNA molecules, significantly improving the pace of complex genomic discoveries.

  11. Application of DNA-based methods in forensic entomology.

    PubMed

    Wells, Jeffrey D; Stevens, Jamie R

    2008-01-01

    A forensic entomological investigation can benefit from a variety of widely practiced molecular genotyping methods. The most commonly used is DNA-based specimen identification. Other applications include the identification of insect gut contents and the characterization of the population genetic structure of a forensically important insect species. The proper application of these procedures demands that the analyst be technically expert. However, one must also be aware of the extensive list of standards and expectations that many legal systems have developed for forensic DNA analysis. We summarize the DNA techniques that are currently used in, or have been proposed for, forensic entomology and review established genetic analyses from other scientific fields that address questions similar to those in forensic entomology. We describe how accepted standards for forensic DNA practice and method validation are likely to apply to insect evidence used in a death or other forensic entomological investigation.

  12. 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.

  13. 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

  14. 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…

  15. 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

  16. Variation in winter diet of southern Beaufort Sea polar bears inferred from stable isotope analysis

    USGS Publications Warehouse

    Bentzen, T.W.; Follmann, E.H.; Amstrup, Steven C.; York, G.S.; Wooller, M.J.; O'Hara, T. M.

    2007-01-01

    Ringed seals (Phoca hispida Schreber, 1775 = Pusa hispida (Schreber, 1775)) and bearded seals (Erignathus barbatus (Erxleben, 1777)) represent the majority of the polar bear (Ursus maritimus Phipps, 1774) annual diet. However, remains of lower trophic level bowhead whales (Balaena mysticetus L., 1758) are available in the southern Beaufort Sea and their dietary contribution to polar bears has been unknown. We used stable isotope (13C/12C, δ13C, 15N/14N, and δ15N) analysis to determine the diet composition of polar bears sampled along Alaska’s Beaufort Sea coast in March and April 2003 and 2004. The mean δ15N values of polar bear blood cells were 19.5‰ (SD = 0.7‰) in 2003 and 19.9‰ (SD = 0.7‰) in 2004. Mixing models indicated bowhead whales composed 11%–26% (95% CI) of the diets of sampled polar bears in 2003, and 0%–14% (95% CI) in 2004. This suggests significant variability in the proportion of lower trophic level prey in polar bear diets among individuals and between years. Polar bears depend on sea ice for hunting seals, and the temporal and spatial availabilities of sea ice are projected to decline. Consumption of low trophic level foods documented here suggests bears may increasingly scavenge such foods in the future.

  17. Nutritional analysis of blenderized enteral diets in the Philippines.

    PubMed

    Sullivan, Mary M; Sorreda-Esguerra, Pearl; Platon, Maria Bernadette; Castro, Cynthia G; Chou, Nancy R; Shott, Susan; Comer, Gail M; Alarcon, Pedro

    2004-01-01

    The objective of this study was to analyze the nutritional quality and viscosity of blenderized enteral tube feedings (BTFs) from four hospitals in the Philippines. Samples of two different BTFs (one standard and one modified) were collected from each hospital on three separate occasions and analyzed for macronutrients, micronutrients, and viscosity. There was considerable variation among the BTFs for the concentrations of most nutrients measured. For standard BTF samples, the caloric density ranged from 66-123 kcal/100g and the percentages of total weight for protein, carbohydrate, and fat ranged from 1.5-4.0%, 8.6-21.4%, and 0.27-3.40%, respectively. Levels of specific vitamins were undetectable in 10 standard and 15 modified BTF samples. In samples where vitamin levels were detectable, results were: vitamin A, 625-8850 IU/kg; riboflavin, 0.40-5.00 mg/kg; and pyridoxine, 0.14-3.00 mg/kg. Mineral concentrations also varied greatly (eg calcium, 64-524 mg/kg; sodium, 148-886 mg/kg; iron, 3.0-13.7 mg/kg; and zinc, 1.8- 11.5 mg/kg). Correlation coefficients were statistically significant only for carbohydrate (r = 0.48, P = 0.017). Measured values tended to be lower than expected values for all nutrients, although the difference was statistically significant only for calories (P = 0.023). The viscosity of BTF samples ranged from 2.3-45,060 centipoise, excluding three samples that were too viscous for analysis. This study demonstrates that hospital prepared blenderized enteral tube feedings render unpredictable levels of micronutrients and macronutrients and appear likely to deliver less than the desired amounts of nutrients. Additionally, the viscosity of these feedings may be unsuitable for infusion through feeding tubes.

  18. Alternative DNA base pairing through metal coordination.

    PubMed

    Clever, Guido H; Shionoya, Mitsuhiko

    2012-01-01

    Base-pairing in the naturally occurring DNA and RNA oligonucleotide duplexes is based on π-stacking, hydrogen bonding, and shape complementarity between the nucleobases adenine, thymine, guanine, and cytosine as well as on the hydrophobic-hydrophilic balance in aqueous media. This complex system of multiple supramolecular interactions is the product of a long-term evolutionary process and thus highly optimized to serve its biological functions such as information storage and processing. After the successful implementation of automated DNA synthesis, chemists have begun to introduce artificial modifications inside the core of the DNA double helix in order to study various aspects of base pairing, generate new base pairs orthogonal to the natural ones, and equip the biopolymer with entirely new functions. The idea to replace the hydrogen bonding interactions with metal coordination between ligand-like nucleosides and suitable transition metal ions culminated in the development of a plethora of artificial base-pairing systems termed "metal base-pairs" which were shown to strongly enhance the DNA duplex stability. Furthermore, they show great potential for the use of DNA as a molecular wire in nanoscale electronic architectures. Although single electrons have proven to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides was identified as a serious obstacle. By exchanging some or all of the Watson-Crick base pairs in DNA with metal complexes, this problem may be solved. In the future, these research efforts are supposed to lead to DNA-like materials with superior conductivity for nano-electronic applications. Other fields of potential application such as DNA-based supramolecular architecture and catalysis may be strongly influenced by these developments as well. This text is meant to illustrate the basic concepts of metal-base pairing and give an outline over recent developments in this field.

  19. Analysis of the rumen bacterial diversity of goats during shift from forage to concentrate diet.

    PubMed

    Grilli, Diego Javier; Fliegerová, Kateřina; Kopečný, Jan; Lama, Sebastián Paez; Egea, Vanina; Sohaefer, Noelia; Pereyra, Celia; Ruiz, María Soledad; Sosa, Miguel Angel; Arenas, Graciela Nora; Mrázek, Jakub

    2016-12-01

    High-grain feeding used in the animal production is known to affect the host rumen bacterial community, but our understanding of consequent changes in goats is limited. This study was therefore aimed to evaluate bacterial population dynamics during 20 days adaptation of 4 ruminally cannulated goats to the high-grain diet (grain: hay - ratio of 40:60). The dietary transition of goats from the forage to the high-grain-diet resulted in the significant decrease of rumen fluid pH, which was however still higher than value established for acute or subacute ruminal acidosis was not diagnosed in studied animals. DGGE analysis demonstrated distinct ruminal microbial populations in hay-fed and grain-fed animals, but the substantial animal-to-animal variation were detected. Quantitative PCR showed for grain-fed animals significantly higher number of bacteria belonging to Clostridium leptum group at 10 days after the incorporation of corn into the diet and significantly lower concentration of bacteria belonging to Actinobacteria phylum at the day 20 after dietary change. Taxonomic distribution analysed by NGS at day 20 revealed the similar prevalence of the phyla Firmicutes and Bacteroidetes in all goats, significantly higher presence of the unclassified genus of groups of Bacteroidales and Ruminococcaceae in grain-fed animals and significantly higher presence the genus Prevotella and Butyrivibrio in the forage-fed animals. The three different culture-independent methods used in this study show that high proportion of concentrate in goat diet does not induce any serious disturbance of their rumen ecosystem and indicate the good adaptive response of caprine ruminal bacteria to incorporation of corn into the diet.

  20. Kinematic gait analysis and lactation performance in dairy cows fed a diet supplemented with zinc, manganese, copper and cobalt.

    PubMed

    Yamamoto, Satoshi; Ito, Kazuhiko; Suzuki, Kii; Matsushima, Yuki; Watanabe, Izumi; Watanabe, Yutaka; Abiko, Keima; Kamada, Toshihiko; Sato, Kan

    2014-03-01

    This study investigated how supplementation of the diet of dairy cows with trace minerals (zinc, manganese, copper and cobalt) affected kinematic gait parameters and lactation performance. Eight Holstein cows were divided into two groups, with each group receiving a different dietary treatment (control diet, or control diet supplemented with trace minerals) in a two-period crossover design. Kinematic gait parameters were calculated by using image analysis software. Compared to cows fed the control diet, cows that received the trace mineral-supplemented diet exhibited significantly increased walking and stepping rates, and had a shorter stance duration. Feed intake and milk production increased in cows fed the trace mineral-supplemented diet compared with control groups. The plasma manganese concentration was not different in control and experimental cows. In contrast, cobalt was only detected in the plasma of cows fed the supplemented diet. These results provide the first evidence that trace mineral supplementation of the diet of dairy cows affects locomotion, and that the associated gait changes can be detected by using kinematic gait analysis. Moreover, trace mineral supplementation improved milk production and only minimally altered blood and physiological parameters in dairy cows.

  1. 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

  2. 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

  3. PCB congener patterns in rats consuming diets containing Great Lakes salmon: Analysis of fish, diets, and adipose tissue

    SciTech Connect

    Jordan, S.A.; Feeley, M.M.

    1999-02-01

    As part of a multidisciplinary toxicological investigation into Great Lakes contaminants, chinook salmon were collected from lake Huron (LH) and Lake Ontario (LO) and incorporated into standard rat diets as 20 or 100% of the protein complement. Final PCB concentrations in the experiment ranged from 3.15 ng/g in the control diet to 1,080 ngg in the high-dose LO diet, with maximal estimated daily consumption by the rats of 82 {micro}g PCBs/kg body wt in the LO20 dietary group. Seventeen PCB congeners, PCB 85, 99, 101, 105, 110, 118, 128, 129, 132, 138, 149, 153, 170, 177, 180, 187, and 199, occurred at > 3.0% of the total PCBs in the fish with no major site differences. Cumulatively, these 17 congeners accounted for up to 75% of the total PCBs in the fish compared to 44 and 54% in two commercial Aroclors, 1254 and 1260, respectively. PCB 77 was the major dioxin-like congener in the fish, followed by PCB 126 and then PCB 169. All major dietary congeners bioaccumulated in the adipose tissue of the rats with the exception of PCB congeners 101, 110, 132, and 149.

  4. 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.

  5. 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.

  6. The first New Zealanders: patterns of diet and mobility revealed through isotope analysis.

    PubMed

    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.

  7. 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

  8. Molecular Diet Analysis of Two African Free-Tailed Bats (Molossidae) Using High Throughput Sequencing

    PubMed Central

    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

  9. 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

  10. NMR metabolomic analysis of fecal water from subjects on a vegetarian diet.

    PubMed

    Pettersson, Jenny; Karlsson, Pernilla Christina; Choi, Young Hae; Verpoorte, Robert; Rafter, Joseph James; Bohlin, Lars

    2008-06-01

    A vegetarian diet rich in phytochemicals may prevent colon carcinogenesis by affecting biochemical processes in the colonic mucosa. Compounds passing the digestive system reaching the colon could potentially be detected in fecal water. We previously reported that intact fecal water samples from human volunteers significantly decreased prostaglandin production and COX-2 protein expression in colonic cells. The aim with the present study was to further study the composition of the fecal waters, using NMR spectroscopy and multivariate data analysis, and to trace the COX-2 inhibiting activity. Intact fecal water samples and fractions thereof were analyzed for their ability to inhibit prostaglandin E2 production in the human colon cell line HT-29. The majority of the tested aqueous phases derived from intact fecal water showed ability to inhibit prostaglandin production in cells (13.8+/-1.34% inhibition, p=0.01). NMR analysis indicated the presence of significant quantities of amino acids and fatty acids. Major metabolites included; acetic acid, butanoic acid, propanoic acid, glutamic acid and alanine. Smaller amounts of glycine and fumaric acid, which are known to have anti-inflammatory and anti-tumorigenic properties, were also detected. This study describes for the first time NMR metabolomic analysis of fecal water from subjects on a vegetarian diet.

  11. 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

  12. 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

  13. 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

  14. Bland diet

    MedlinePlus

    Heartburn - bland diet; Nausea - bland diet; Diarrhea - bland diet; Peptic ulcer - bland diet ... changes to help treat ulcers, heartburn, nausea, vomiting, diarrhea, and gas. You may also need a bland ...

  15. Effect of vegetarian diets on zinc status: a systematic review and meta-analysis of studies in humans.

    PubMed

    Foster, Meika; Chu, Anna; Petocz, Peter; Samman, Samir

    2013-08-15

    Plant-based diets contain less saturated fat and cholesterol and more folate, fibre and phytochemicals than omnivorous diets, but some micronutrients, especially zinc, are poorly bioavailable. The findings of studies exploring the zinc intake and zinc status in populations that habitually consume vegetarian diets are inconsistent. This study aims to investigate the effects of plant-based diets on dietary zinc intake and status in humans using systematic review and meta-analysis techniques. Thirty-four studies were included in the systematic review. Of these, 26 studies (reporting 48 comparisons) compared males and/or females consuming vegetarian diets with non-vegetarian groups and were included in meta-analyses. Dietary zinc intakes and serum zinc concentrations were significantly lower (-0.88 ± 0.15 mg day(-1), P < 0.001 and -0.93 ± 0.27 µmol L(-1), P = 0.001 respectively; mean ± standard error) in populations that followed habitual vegetarian diets compared with non-vegetarians. Secondary analyses showed greater impact of vegetarian diets on the zinc intake and status of females, vegetarians from developing countries and vegans. Populations that habitually consume vegetarian diets have low zinc intakes and status. Not all vegetarian categories impact zinc status to the same extent, but a lack of consistency in defining vegetarian diets for research purposes makes dietary assessment difficult. Dietary practices that increase zinc bioavailability, the consumption of foods fortified with zinc or low-dose supplementation are strategies that should be considered for improving the zinc status of vegetarians with low zinc intakes or serum zinc concentrations at the lower end of the reference range.

  16. 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

  17. 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

  18. Transcriptomic analysis of the effects of a fish oil enriched diet on murine brains.

    PubMed

    Hammamieh, Rasha; Chakraborty, Nabarun; 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

  19. 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

  20. DNA base excision repair nanosystem engineering: model development.

    PubMed

    Sokhansanj, B A

    2005-01-01

    DNA base damage results from a combination of endogenous sources, (normal metabolism, increased metabolism due to obesity, stress from diseases such as arthritis and diabetes, and ischemia) and the environment (ingested toxins, ionizing radiation, etc.). If unrepaired DNA base damage can lead to diminished cell function, and potentially diseases and eventually mutations that lead to cancer. Sophisticated DNA repair mechanisms have evolved in all living cells to preserve the integrity of inherited genetic information and transcriptional control. Understanding a system like DNA repair is greatly enhanced by using engineering methods, in particular modeling interactions and using predictive simulation to analyze the impact of perturbations. We describe the use of such a "nanosystem engineering" approach to analyze the DNA base excision repair pathway in human cells, and use simulation to predict the impact of varying enzyme concentration on DNA repair capacity.

  1. Antibody-controlled actuation of DNA-based molecular circuits

    NASA Astrophysics Data System (ADS)

    Engelen, Wouter; Meijer, Lenny H. H.; Somers, Bram; de Greef, Tom F. A.; Merkx, Maarten

    2017-02-01

    DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody-epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.

  2. Forensic aspects of DNA-based human identity testing.

    PubMed

    Roper, Stephen M; Tatum, Owatha L

    2008-01-01

    The forensic applications of DNA-based human identity laboratory testing are often underappreciated. Molecular biology has seen an exponential improvement in the accuracy and statistical power provided by identity testing in the past decade. This technology, dependent upon an individual's unique DNA sequence, has cemented the use of DNA technology in the forensic laboratory. This paper will discuss the state of modern DNA-based identity testing, describe the technology used to perform this testing, and describe its use as it relates to forensic applications. We will also compare individual technologies, including polymerase chain reaction (PCR) and Southern Blotting, that are used to detect the molecular differences that make all individuals unique. An increasing reliance on DNA-based identity testing dictates that healthcare providers develop an understanding of the background, techniques, and guiding principles of this important forensic tool.

  3. 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.

  4. 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.

  5. DNA-based methods of geochemical prospecting

    DOEpatents

    Ashby, Matthew [Mill Valley, CA

    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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

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

    PubMed

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

    1997-10-01

    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.

  12. 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

  13. DNA-based cryptographic methods for data hiding in DNA media.

    PubMed

    Marwan, Samiha; Shawish, Ahmed; Nagaty, Khaled

    2016-12-01

    Information security can be achieved using cryptography, steganography or a combination of them, where data is firstly encrypted using any of the available cryptography techniques and then hid into any hiding medium. Recently, the famous genomic DNA has been introduced as a hiding medium, known as DNA steganography, due to its notable ability to hide huge data sets with a high level of randomness and hence security. Despite the numerous cryptography techniques, to our knowledge only the vigenere cipher and the DNA-based playfair cipher have been combined with the DNA steganography, which keeps space for investigation of other techniques and coming up with new improvements. This paper presents a comprehensive analysis between the DNA-based playfair, vigenere, RSA and the AES ciphers, each combined with a DNA hiding technique. The conducted analysis reports the performance diversity of each combined technique in terms of security, speed, hiding capacity in addition to both key size and data size. Moreover, this paper proposes a modification of the current combined DNA-based playfair cipher technique, which makes it not only simple and fast but also provides a significantly higher hiding capacity and security. The conducted extensive experimental studies confirm such outstanding performance in comparison with all the discussed combined techniques.

  14. 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.

  15. [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.

  16. Vegetarian Diet

    MedlinePlus

    ... animal products The lacto vegetarian diet, which includes plant foods plus dairy products The lacto-ovo vegetarian diet, which includes both dairy products and eggs People who follow vegetarian diets can get ...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. IsoWeb: a bayesian isotope mixing model for diet analysis of the whole food web.

    PubMed

    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.

  2. Long-term effectiveness of diet-plus-exercise interventions vs. diet-only interventions for weight loss: a meta-analysis.

    PubMed

    Wu, T; Gao, X; Chen, M; van Dam, R M

    2009-05-01

    Diet and exercise are two of the commonest strategies to reduce weight. Whether a diet-plus-exercise intervention is more effective for weight loss than a diet-only intervention in the long-term has not been conclusively established. The objective of this study was to systemically review the effect of diet-plus-exercise interventions vs. diet-only interventions on both long-term and short-term weight loss. Studies were retrieved by searching MEDLINE and Cochrane Library (1966 - June 2008). Studies were included if they were randomized controlled trials comparing the effect of diet-plus-exercise interventions vs. diet-only interventions on weight loss for a minimum of 6 months among obese or overweight adults. Eighteen studies met our inclusion criteria. Data were independently extracted by two investigators using a standardized protocol. We found that the overall standardized mean differences between diet-plus-exercise interventions and diet-only interventions at the end of follow-up were -0.25 (95% confidence interval [CI]-0.36 to -0.14), with a P-value for heterogeneity of 0.4. Because there were two outcome measurements, weight (kg) and body mass index (kg m(-2)), we also stratified the results by weight and body mass index outcome. The pooled weight loss was 1.14 kg (95% CI 0.21 to 2.07) or 0.50 kg m(-2) (95% CI 0.21 to 0.79) greater for the diet-plus-exercise group than the diet-only group. We did not detect significant heterogeneity in either stratum. Even in studies lasting 2 years or longer, diet-plus-exercise interventions provided significantly greater weight loss than diet-only interventions. In summary, a combined diet-plus-exercise programme provided greater long-term weight loss than a diet-only programme. However, both diet-only and diet-plus-exercise programmes are associated with partial weight regain, and future studies should explore better strategies to limit weight regain and achieve greater long-term weight loss.

  3. 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…

  4. 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.

  5. Envisioning the molecular choreography of DNA base excision repair.

    PubMed

    Parikh, S S; Mol, C D; Hosfield, D J; Tainer, J A

    1999-02-01

    Recent breakthroughs integrate individual DNA repair enzyme structures, biochemistry and biology to outline the structural cell biology of the DNA base excision repair pathways that are essential to genome integrity. Thus, we are starting to envision how the actions, movements, steps, partners and timing of DNA repair enzymes, which together define their molecular choreography, are elegantly controlled by both the nature of the DNA damage and the structural chemistry of the participating enzymes and the DNA double helix.

  6. DNA-based computing of strategic assignment problems.

    PubMed

    Shu, Jian-Jun; Wang, Qi-Wen; Yong, Kian-Yan

    2011-05-06

    DNA-based computing is a novel technique to tackle computationally difficult problems, in which computing time grows exponentially corresponding to problematic size. A strategic assignment problem is a typical nondeterministic polynomial problem, which is often associated with strategy applications. In this Letter, a new approach dealing with strategic assignment problems is proposed based on manipulating DNA strands, which is believed to be better than the conventional silicon-based computing in solving the same problem.

  7. 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.

  8. Comparative analysis of the composition of intestinal bacterial communities in Dastarcus helophoroides fed different diets.

    PubMed

    Wang, Wei-Wei; He, Cai; Cui, Jun; Wang, Hai-Dong; Li, Meng-Lou

    2014-01-01

    The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides.

  9. Comparative Analysis of the Composition of Intestinal Bacterial Communities in Dastarcus helophoroides Fed Different Diets

    PubMed Central

    Wang, Wei-Wei; He, Cai; Cui, Jun; Wang, Hai-Dong; Li, Meng-Lou

    2014-01-01

    The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides. PMID:25199878

  10. Antibody-controlled actuation of DNA-based molecular circuits

    PubMed Central

    Engelen, Wouter; Meijer, Lenny H. H.; Somers, Bram; de Greef, Tom F. A.; Merkx, Maarten

    2017-01-01

    DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody–epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification. PMID:28211541

  11. Development of DNA-based Identification methods to track the ...

    EPA Pesticide Factsheets

    The ability to track the identity and abundance of larval fish, which are ubiquitous during spawning season, may lead to a greater understanding of fish species distributions in Great Lakes nearshore areas including early-detection of invasive fish species before they become established. However, larval fish are notoriously hard to identify using traditional morphological techniques. While DNA-based identification methods could increase the ability of aquatic resource managers to determine larval fish composition, use of these methods in aquatic surveys is still uncommon and presents many challenges. In response to this need, we have been working with the U. S. Fish and Wildlife Service to develop field and laboratory methods to facilitate the identification of larval fish using DNA-meta-barcoding. In 2012, we initiated a pilot-project to develop a workflow for conducting DNA-based identification, and compared the species composition at sites within the St. Louis River Estuary of Lake Superior using traditional identification versus DNA meta-barcoding. In 2013, we extended this research to conduct DNA-identification of fish larvae collected from multiple nearshore areas of the Great Lakes by the USFWS. The species composition of larval fish generally mirrored that of fish species known from the same areas, but was influenced by the timing and intensity of sampling. Results indicate that DNA-based identification needs only very low levels of biomass to detect pre

  12. Integrating DNA-based data into bioassessments improves ...

    EPA Pesticide Factsheets

    The integration of DNA-based identification methods into bioassessments could result in more accurate representations of species distributions and species-habitat relationships. DNA-based approaches may be particularly informative for tracking the distributions of rare and/or invasive species that can comprise a small proportion of samples or are difficult to identify morphologically. In 2012 and 2013, we used a combination of morphological and DNA-based methods (meta-barcoding) to identify fish eggs and larvae collected in the St. Louis River estuary area, Minnesota. We found a large proportion of cases where a lack of agreement occurred between species identified at a site using morphological versus DNA identification, prompting a discussion of how to best reconcile these differences. Choices made during sampling collection, DNA amplification/extraction, and bioinformatics processing influence the DNA-morphology match. The distribution of some species (including several invasives) and their relationships to habitat changed after DNA-data was incorporated. Results highlight how incorporating of DNA-data may get us closer to the “truth”, which has large ramifications in the search for rare species and when understanding the environmental drivers of species distributions is important for management. not applicable

  13. DNA-based random number generation in security circuitry.

    PubMed

    Gearheart, Christy M; Arazi, Benjamin; Rouchka, Eric C

    2010-06-01

    DNA-based circuit design is an area of research in which traditional silicon-based technologies are replaced by naturally occurring phenomena taken from biochemistry and molecular biology. This research focuses on further developing DNA-based methodologies to mimic digital data manipulation. While exhibiting fundamental principles, this work was done in conjunction with the vision that DNA-based circuitry, when the technology matures, will form the basis for a tamper-proof security module, revolutionizing the meaning and concept of tamper-proofing and possibly preventing it altogether based on accurate scientific observations. A paramount part of such a solution would be self-generation of random numbers. A novel prototype schema employs solid phase synthesis of oligonucleotides for random construction of DNA sequences; temporary storage and retrieval is achieved through plasmid vectors. A discussion of how to evaluate sequence randomness is included, as well as how these techniques are applied to a simulation of the random number generation circuitry. Simulation results show generated sequences successfully pass three selected NIST random number generation tests specified for security applications.

  14. Associations of the Baltic Sea diet with cardiometabolic risk factors--a meta-analysis of three Finnish studies.

    PubMed

    Kanerva, Noora; Kaartinen, Niina E; Rissanen, Harri; Knekt, Paul; Eriksson, Johan G; Sääksjärvi, Katri; Sundvall, Jouko; Männistö, Satu

    2014-08-28

    Dyslipidaemia, hypertension and low-grade inflammation increase the risk of CVD. In the present meta-analysis, we examined whether adherence to a healthy Nordic diet, also called the Baltic Sea diet, may associate with a lower risk of these cardiometabolic risk factors. In 2001-2007, three cross-sectional Finnish studies were conducted: the Dietary, Lifestyle and Genetic Determinants of Obesity and Metabolic Syndrome study (n 4776); Health 2000 Survey (n 5180); Helsinki Birth Cohort Study (n 1972). The following parameters were assessed in these three studies: blood pressure, total, HDL- and LDL-cholesterol, TAG and high-sensitivity C-reactive protein (hs-CRP); a validated FFQ was used to assess the participants' dietary intakes. The Baltic Sea Diet Score (BSDS) was developed based on the healthy Nordic diet. All studies assessed confounding variables, such as physical activity and BMI, based on standardised questionnaires and measurements. The random-effects meta-analysis provided summary estimates for OR and 95 % CI by the BSDS quintiles. In the meta-analysis, the risk of elevated hs-CRP concentration was lower among men (OR 0·58, 95 % CI 0·43, 0·78) and women (OR 0·73, 95 % CI 0·58, 0·91) in the highest BSDS quintile than among those in the lowest BSDS quintile. In contrast, the risk of lowered HDL-cholesterol concentration was higher among women (OR 1·67, 95 % CI 1·12, 2·48) in the highest BSDS quintile than among those in the lowest BSDS quintile. However, no other associations were found. In conclusion, the associations between the adherence to the healthy Nordic diet and cardiometabolic risk factors are equivocal. Longitudinal studies are needed to further examine this hypothesis.

  15. 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.

  16. Chronic kidney disease progression: a retrospective analysis of 3-year adherence to a low protein diet.

    PubMed

    Rizzetto, Felipe; Leal, Viviane de Oliveira; Bastos, Leonardo Soares; Fouque, Denis; Mafra, Denise

    2017-11-01

    The potential benefits and dangers of dietary protein restriction in chronic kidney disease (CKD) are still controversial. Thus, the aim of this study is to evaluate the effect of low protein diet (LPD) on the renal function in nondialysis CKD patients. A retrospective study was conducted from 321 nondialysis CKD patient's medical files (65.1 ± 12.7 yrs, 58.2% men). These patients received individualized dietary protein prescription (0.6-0.8 g protein/kg/day). Protein intake was evaluated by food diary and 24 h-food recall. Adherence to the LPD was considered when patients intake from 90 to 110% of the prescribed amount of protein. The patients were divided into 4 groups: (G1) adherent diabetes mellitus (DM) patients (n = 83); (G2) non-adherent DM patients (n = 106); (G3) adherent non-DM patients (n = 75); (G4) non-adherent non-DM patients (n = 57). Renal function was assessed by estimated glomerular filtration rate (eGFR). Both groups of patients (DM and non-DM) that adhered to the LPD showed significant improvement in eGFR (G1: 38.7 ± 13.2 mL/min to 51.1 ± 17.0 mL/min (p < 0.001); G3: 35.1 ± 16.8 mL/min to 46.8 ± 21.4 mL/min (p < 0.001)). In adherent patients, no differences in albumin and BMI were observed at the end of follow up. In non-adherent patients, eGFR significantly decreased in DM group (G2: 44.2 ± 18.5 mL/min to 38.2 ± 15.8 mL/min (p = 0.003)). According to multivariate analysis, annual changes in eGFR were not independent associated with age, gender, BMI, lipid profile, bicarbonate or smoking status. In summary, adherence to low protein diet could be able to improve serum creatinine and eGFR, well-known markers of renal function. However, prospective studies are needed to control confounders which affect renal function and CKD progression.

  17. 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.

  18. 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

  19. Longitudinal analysis of short-term high-fat diet on endothelial senescence in baboons

    PubMed Central

    Shi, Qiang; Hornsby, Peter J; Meng, Qinghe; VandeBerg, Jane F; VandeBerg, John L

    2013-01-01

    A high-fat diet is a major risk factor for atherosclerosis. We conducted a longitudinal investigation to determine whether vascular endothelial senescence is involved in the mechanism by which a high-fat diet promotes atherogenesis. We challenged 10 baboons (Papio sp.) with a high-cholesterol high-fat (HCHF) diet for 7 weeks. In addition to multiple changes in plasma lipid profiles, inflammatory status, and endothelial functions in each individual, we found that levels of total serum cholesterol (TSC) and monocyte chemotactic protein-1 (MCP-1) were negatively and significantly correlated with endothelial nitric oxide synthase (eNOS) levels in endothelial cells while the levels of tumor necrosis factor α (TNF-α) and interleukin 6 (IL-6) were significantly correlated with nitric oxide levels in plasma within this time window. Most important, we observed that senescence-associated β-galactosidase (SA-β-gal) activities in endothelial cells harvested at 7 weeks after initiation of HCHF diet were significantly elevated by comparison with cells isolated from the same animals prior to dietary challenge. The SA-β-gal activities correlated significantly with the elevations of TSC, LDL-cholesterol, HDL-cholesterol, and IL-8 after 7 weeks of HCHF diet and with the changes of TSC and TNF-α levels after 3 weeks of HCHF diet. Our data indicate that the HCHF diet caused hyperlipidemia and prominent inflammation, which subsequently will cause endothelial dysfunction and promote senescence. The present study is the first to demonstrate the sequential and interactive changes as a consequence of an HCHF dietary challenge and establish a potential mechanism underlying the etiology of diet-induced atherogenesis in a nonhuman primate. PMID:23991345

  20. 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

  1. 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

  2. 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.

  3. Low Carbohydrate versus Isoenergetic Balanced Diets for Reducing Weight and Cardiovascular Risk: A Systematic Review and Meta-Analysis

    PubMed Central

    Naude, Celeste E.; Schoonees, Anel; Senekal, Marjanne; Young, Taryn; Garner, Paul; Volmink, Jimmy

    2014-01-01

    Background Some popular weight loss diets restricting carbohydrates (CHO) claim to be more effective, and have additional health benefits in preventing cardiovascular disease compared to balanced weight loss diets. Methods and Findings We compared the effects of low CHO and isoenergetic balanced weight loss diets in overweight and obese adults assessed in randomised controlled trials (minimum follow-up of 12 weeks), and summarised the effects on weight, as well as cardiovascular and diabetes risk. Dietary criteria were derived from existing macronutrient recommendations. We searched Medline, EMBASE and CENTRAL (19 March 2014). Analysis was stratified by outcomes at 3–6 months and 1–2 years, and participants with diabetes were analysed separately. We evaluated dietary adherence and used GRADE to assess the quality of evidence. We calculated mean differences (MD) and performed random-effects meta-analysis. Nineteen trials were included (n = 3209); 3 had adequate allocation concealment. In non-diabetic participants, our analysis showed little or no difference in mean weight loss in the two groups at 3–6 months (MD 0.74 kg, 95%CI −1.49 to 0.01 kg; I2 = 53%; n = 1745, 14 trials; moderate quality evidence) and 1–2 years (MD 0.48 kg, 95%CI −1.44 kg to 0.49 kg; I2 = 12%; n = 1025; 7 trials, moderate quality evidence). Furthermore, little or no difference was detected at 3–6 months and 1–2 years for blood pressure, LDL, HDL and total cholesterol, triglycerides and fasting blood glucose (>914 participants). In diabetic participants, findings showed a similar pattern. Conclusions Trials show weight loss in the short-term irrespective of whether the diet is low CHO or balanced. There is probably little or no difference in weight loss and changes in cardiovascular risk factors up to two years of follow-up when overweight and obese adults, with or without type 2 diabetes, are randomised to low CHO diets and isoenergetic balanced weight loss

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. Controlling charge current through a DNA based molecular transistor

    NASA Astrophysics Data System (ADS)

    Behnia, S.; Fathizadeh, S.; Ziaei, J.

    2017-01-01

    Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I-V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive.

  10. Quantum interference in DNA bases probed by graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Jeong, Heejeong; Seul Kim, Han; Lee, Sung-Hoon; Lee, Dongho; Hoon Kim, Yong; Huh, Nam

    2013-07-01

    Based on first-principles nonequilibrium Green's function calculations, we demonstrate quantum interference (QI) effects on the tunneling conductance of deoxyribonucleic acid bases placed between zigzag graphene nanoribbon electrodes. With the analogy of QI in hydrocarbon ring structures, we hypothesize that QI can be well preserved in the π-π coupling between the carbon-based electrode and a single DNA base. We demonstrate indications of QI, such as destructively interfered anti-resonance or Fano-resonance, that affect the variation of tunneling conductance depending on the orientation of a base. We find that guanine, with a 10-fold higher transverse conductance, can be singled out from the other bases.

  11. Modeling the bandstructures of B-DNA base stacks

    NASA Astrophysics Data System (ADS)

    Rengifo, E.; Murillo, G.; Arce, J. C.

    2013-05-01

    A pseudohelical approximation for the calculation of the bandstructures of DNA base homostacks in B conformation is introduced. It consists of choosing a unit cell of only two nucleobases with relative parallel displacement and twist that locally mimic the helical conformation. It is tested employing the extended Hückel method with a unique Wolfsberg-Helmholtz parameter. The resulting bandgaps and ionization potential trend agree well with the ones reported in the literature employing the full screw-axis symmetry and higher levels of theory. The electron and hole effective masses extracted from the bandstructures follow the same trends as the experimentally reported mobilities.

  12. 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

  13. 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.

  14. Plasmid DNA-based gene transfer with ultrasound and microbubbles.

    PubMed

    Taniyama, Yoshiaki; Azuma, Junya; Rakugi, Hiromi; Morishita, Ryuichi

    2011-12-01

    Gene therapy offers a novel approach for the prevention and treatment of a variety of diseases, but it is not yet a common option in the real world because of various problems. Viral vectors show high efficiency of gene transfer, but they have some problems with toxicity and immunity. On the other hand, plasmid DNA-based gene transfer is very safe, but its efficiency is relatively low. Especially, plasmid DNA gene therapy is used for cardiovascular disease because plasmid DNA transfer is possible for cardiac or skeletal muscle. Clinical angiogenic gene therapy using plasmid DNA gene transfer has been attempted in patients with peripheral artery disease, but a Phase III clinical trial did not show sufficient efficiency. Recently, a Phase III clinical trial of hepatocyte growth factor gene therapy in peripheral artery disease (PAD) showed improvement of ischemic ulcers, but it could not salvage limbs from amputation. In addition, a Phase I/II clinical study of fibroblast growth factor gene therapy in PAD extended amputation-free survival, but it seemed to fail in Phase III. In this situation, we and others have developed plasmid DNA-based gene transfer using ultrasound with microbubbles to enhance its efficiency while maintaining safety. Ultrasound-mediated gene transfer has been reported to augment the gene transfer efficiency and select the target organ using cationic microbubble phospholipids which bind negatively charged DNA. Ultrasound with microbubblesis likely to create new therapeutic options inavariety of diseases.

  15. The effect of vegetarian diets on iron status in adults: A systematic review and meta-analysis.

    PubMed

    Haider, Lisa M; Schwingshackl, Lukas; Hoffmann, Georg; Ekmekcioglu, Cem

    2016-11-23

    Background Vegetarian diets exclude meat, seafood, and products containing these foods. Although the vegetarian lifestyle could lead to a better health status in adults, it may also bear risks for certain nutritional deficiencies. Cross-sectional studies and narrative reviews have shown that the iron status of vegetarians is compromised by the absence of highly bioavailable haem-iron in meatless diets and the inhibiting effect of certain components present in plant foods on non-haem iron bioavailability. Methods The databases Pubmed, Scopus, Embase, and Cochrane Central Register of Controlled Trials were searched for studies comparing serum ferritin, as the major laboratory parameter for iron status of adult vegetarians with non-vegetarian control groups. A qualitative review was conducted as well as an inverse-variance random-effects meta-analysis to pool available data. In addition the effect of vegetarian diets according to gender was investigated with a subgroup analysis. The results were validated using a sensitivity analysis. Results A total of 27 cross-sectional studies and 3 interventional studies were selected for the systematic review. The meta-analysis which combined data of 24 cross-sectional studies showed that adult vegetarians have significantly lower serum ferritin levels than their non-vegetarian controls (-29.71 µg/l, 95% CI [-39.69, -19.73], p<0.01). Inclusion of semi-vegetarian diets did not change the results considerably (-23.27 µg/l, 95% CI [-29.77, -16.76], p<0.01). The effects were more pronounced in men (-61.88 µg/l, 95% CI [-85.59, -38.17], p<0.01) than in both premenopausal women (-17.70 μg/l, 95% CI [-29.80, -5.60], p<0.01) and all women (-13.50 μg/l, 95% CI [-22.96, -4.04], p<0.01), respectively. Conclusions In conclusion our results showed that vegetarians are more likely to have lower iron stores compared with non-vegetarians. However, since high iron stores are also a risk factor for certain non-communicable diseases, such

  16. Stable isotope ratio analysis as a tool to discriminate between rainbow trout (O. mykiss) fed diets based on plant or fish-meal proteins.

    PubMed

    Moreno-Rojas, J M; Tulli, F; Messina, M; Tibaldi, E; Guillou, C

    2008-12-01

    The use of stable isotope ratio analysis (SIRA) as a rapid analytical tool to characterize and discriminate farmed fish on the basis of the feedstuffs included in the diet formulation is discussed. Two isoproteic (44.8%) and isolipidic (19.6%) extruded diets were formulated: a fish-meal-based diet (FM diet), containing fish meal as the sole protein source; a plant-protein-based diet (PP diet), where pea protein concentrate and wheat gluten meal replaced 80% of fish meal protein. The diets were fed to eight groups of rainbow trout (initial body weight: 106.6g) for 103 days in two daily meals under controlled rearing conditions. Growth performance (final body weight: 318.5 g; specific growth rate: 1.06%) and feed-to-gain ratio (0.79) were not affected by the dietary treatment. The differences in isotopic values of the two diets were clearly reflected in the different carbon and nitrogen isotopic values in rainbow trout fillets. The delta(13)C and delta(15)N values of muscle of farmed rainbow trout showed differences between farmed fish fed a fish-protein-based diet (-20.47 +/- 0.34 and 12.38 +/- 0.57 for delta(13)C and delta(15)N, respectively) and those fed a plant-protein-based diet (-23.96 +/- 0.38 and 7.15 +/- 0.51 for delta(13)C and delta(15)N, respectively). The results suggest that SIRA provides a robust and verifiable analytical tool to discriminate between fish fed on a plant or a fish protein diet.

  17. 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...

  18. 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...

  19. 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...

  20. Northern Goshawk diet in Minnesota: An Analysis using video recording systems

    USGS Publications Warehouse

    Smithers, B.L.; Boal, C.W.; Andersen, D.E.

    2005-01-01

    We used video-recording systems to collect diet information at 13 Northern Goshawk (Accipiter gentilis) nests in Minnesota during the 2000, 2001, and 2002 breeding seasons. We collected 4871 hr of video footage, from which 652 prey deliveries were recorded. The majority of prey deliveries identified were mammals (62%), whereas birds (38%) composed a smaller proportion of diet. Mammals accounted for 61% of biomass delivered, and avian prey items accounted for 39% of prey biomass. Sciurids and leporids accounted for 70% of the identified prey. Red squirrel (Tamiasciurus hudsonicus), eastern chipmunk (Tamias striatus), and snowshoe hare (Lepus americanus) were the dominant mammals identified in the diet, while American Crow (Corvus brachyrhynchos) and Ruffed Grouse (Bonasa umbellus) were the dominant avian prey delivered to nests. On average, breeding goshawks delivered 2.12 prey items/d, and each delivery averaged 275 g for a total of 551 g delivered/d. However, daily (P < 0.001) and hourly (P = 0.01) delivery rates varied among nests. Delivery rates (P = 0.01) and biomass delivered (P = 0.038) increased with brood size. Diversity and equitability of prey used was similar among nests and was low throughout the study area, most likely due to the dominance of red squirrel in the diet. ?? 2005 The Raptor Research Foundation, Inc.

  1. 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...

  2. A preliminary study of a Peruvian diet using dietary analysis and hair mineral content as indicators.

    PubMed

    Tueller, Daniel J; Eggett, Dennis L; Parker, Tory L

    2013-11-01

    Observations among former American residents living long-term in Peru suggested that hair health improved while in Peru. To determine if a Peruvian diet correlates with hair composition, dietary intake of nutrients and mineral content of hair were measured among Peruvian and matched US residents. Selected foods from Peru were also analyzed for mineral and antioxidant content and compared with equivalent foods available in the USA. Statistically significant differences between Peruvian and US residents' hair were found for sodium (decreased in Peru, p = 0.007) and vanadium (decreased in Peru, p = 0.03). Differences in hair composition between residencies may be explained by lower dietary sodium and vanadium intake among Peruvian residents or by lower concentrations of these minerals in Peruvian drinking water. Many significant mineral differences were also identified between Peruvian foods and their US equivalents. Although no statistically significant correlations between dietary intake and hair mineral content were found, results indicate that a Peruvian diet contributes differently to hair composition than a US diet. More research is needed to elucidate the link between a Peruvian diet and specific aspects of hair health.

  3. 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.

  4. A comparative analysis of the evolutionary relationship between diet and enzyme targeting in bats, marsupials and other mammals

    PubMed Central

    Birdsey, Graeme M; Lewin, Jackie; Holbrook, Joanna D; Simpson, Victor R; Cunningham, Andrew A; Danpure, Christopher J

    2005-01-01

    The subcellular distribution of the enzyme alanine : glyoxylate aminotransferase (AGT) in the livers of different mammals appears to be related to their natural diets. Thus, AGT tends to be mitochondrial in carnivores, peroxisomal in herbivores, and both mitochondrial and peroxisomal in omnivores. To what extent this relationship is an incidental consequence of phylogenetic structure or an evolutionarily meaningful adaptive response to changes in dietary selection pressure is unknown. In order to distinguish between these two possibilities, we have determined the subcellular distribution of AGT in the livers of 22 new mammalian species, including members of three orders not studied before. In addition, we have analysed the statistical relationship between AGT distribution and diet in all 77 mammalian species, from 12 different orders, for which the distribution is currently known. Our analysis shows that there is a highly significant correlation between AGT distribution and diet, independent of phylogeny. This finding is compatible with the suggestion that the variable intracellular targeting of AGT is an adaptive response to episodic changes in dietary selection pressure. To our knowledge, this is the first example of such a response being manifested at the molecular and cellular levels across the breadth of Mammalia. PMID:15888416

  5. 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

    2016-01-01

    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.

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

    PubMed

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

    2015-09-18

    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.

  7. Therapeutic option of plasmid-DNA based gene transfer.

    PubMed

    Taniyama, Yoshiaki; Azuma, Junya; Kunugiza, Yasuo; Iekushi, Kazuma; Rakugi, Hiromi; Morishita, Ryuichi

    2012-01-01

    Gene therapy offers a novel approach for the prevention and treatment of a variety of diseases, but it is not yet a common method in clinical cases because of various problems. Viral vectors show high efficiency of gene transfer, but they have some problems with toxicity and immunity. On the other hand, plasmid deoxyribonucleic acid (DNA)-based gene transfer is very safe, but its efficiency is relatively low. Especially, plasmid DNA gene therapy is used for cardiovascular disease because plasmid DNA transfer is possible for cardiac or skeletal muscle. Clinical angiogenic gene therapy using plasmid DNA gene transfer has been attempted in patients with peripheral artery disease, but a phase III clinical trial did not show sufficient efficiency. In this situation, more efficient plasmid DNA gene transfer is needed all over the world. This review focuses on plasmid DNA gene transfer and its enhancement, including ultrasound with microbubbles, electroporation, hydrodynamic method, gene gun, jet injection, cationic lipids and cationic polymers.

  8. Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.

    PubMed

    Markegard, Cade B; Mazaheripour, Amir; Jocson, Jonah-Micah; Burke, Anthony M; Dickson, Mary N; Gorodetsky, Alon A; Nguyen, Hung D

    2015-09-03

    Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks.

  9. The Five Immune Forces Impacting DNA-Based Cancer Immunotherapeutic Strategy

    PubMed Central

    Amara, Suneetha; Tiriveedhi, Venkataswarup

    2017-01-01

    DNA-based vaccine strategy is increasingly realized as a viable cancer treatment approach. Strategies to enhance immunogenicity utilizing tumor associated antigens have been investigated in several pre-clinical and clinical studies. The promising outcomes of these studies have suggested that DNA-based vaccines induce potent T-cell effector responses and at the same time cause only minimal side-effects to cancer patients. However, the immune evasive tumor microenvironment is still an important hindrance to a long-term vaccine success. Several options are currently under various stages of study to overcome immune inhibitory effect in tumor microenvironment. Some of these approaches include, but are not limited to, identification of neoantigens, mutanome studies, designing fusion plasmids, vaccine adjuvant modifications, and co-treatment with immune-checkpoint inhibitors. In this review, we follow a Porter’s analysis analogy, otherwise commonly used in business models, to analyze various immune-forces that determine the potential success and sustainable positive outcomes following DNA vaccination using non-viral tumor associated antigens in treatment against cancer. PMID:28304339

  10. Chemically-modified graphenes for oxidation of DNA bases: analytical parameters.

    PubMed

    Goh, Madeline Shuhua; Bonanni, Alessandra; Ambrosi, Adriano; Sofer, Zdeněk; Pumera, Martin

    2011-11-21

    We studied the electroanalytical performances of chemically-modified graphenes (CMGs) containing different defect densities and amounts of oxygen-containing groups, namely graphite oxide (GPO), graphene oxide (GO), thermally reduced graphene oxide (TR-GO) and electrochemically reduced graphene oxide (ER-GO) by comparing the sensitivity, selectivity, linearity and repeatability towards the oxidation of DNA bases. We have observed that for differential pulse voltammetric (DPV) detection of adenine and cytosine, all CMGs showed enhanced sensitivity to oxidation, while for guanine and thymine, ER-GO and TR-GO exhibited much improved sensitivity over bare glassy carbon (GC) as well as over GPO and GO. There is also significant selectivity enhancement when using GPO for adenine and TR-GO for thymine. Our results have uncovered that the differences in surface functionalities, structure and defects of various CMGs largely influence their electrochemical behaviour in detecting the oxidation of DNA bases. The findings in this report will provide a useful guide for the future development of label-free electrochemical devices for DNA analysis.

  11. Ab initio Study of Naptho-Homologated DNA Bases

    SciTech Connect

    Sumpter, Bobby G; Vazquez-Mayagoitia, Alvaro; Huertas, Oscar; Fuentes-Cabrera, Miguel A; Orozco, Modesto; Luque, Javier

    2008-01-01

    Naptho-homologated DNA bases have been recently used to build a new type of size expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naptho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like form of naptho-thymine (yyT) and naptho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naptho-guanine (yyG) and naptho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphto-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naptho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.

  12. A meta-analysis of feed digestion in dairy cows. 1. The effects of forage and concentrate factors on total diet digestibility.

    PubMed

    Nousiainen, J; Rinne, M; Huhtanen, P

    2009-10-01

    A meta-analysis based on published experiments with lactating dairy cows was conducted to study the effects of dietary forage and concentrate factors on apparent total diet digestibility. A data set was collected that included a total of 497 dietary treatment means from 92 studies. The diets were based on grass silage or on legume or whole-crop cereal silages partly or completely substituted for grass silage. The silages were supplemented with concentrates given at a flat rate within a dietary comparison. For the statistical evaluation, the data were divided into 5 subsets to quantify silage (digestibility, 42 diets in 17 studies; fermentation characteristics, 108 diets in 39 studies) and concentrate (amount of supplementation, 142 diets in 59 studies; concentration of crude protein, 215 diets in 82 studies; carbohydrate composition, 66 diets in 23 studies) factors on total diet digestibility. The diet digestibility of dairy cows was determined by total fecal collection or by using acid-insoluble ash as an internal marker. Diet organic matter digestibility (OMD) at a maintenance level of feeding (OMD(m)) was estimated using sheep in vivo or corresponding in vitro digestibility values for the forage and reported ingredient and chemical composition values, with tabulated digestibility coefficients for the concentrate components of the diet. A mixed model regression analysis was used to detect the responses of different dietary factors on apparent total diet digestibility. Improved silage OMD(m) resulting from earlier harvest was translated into improved production-level OMD in cows (OMD(p)). The effects of silage fermentation characteristics on OMD(p) were quantitatively small, although sometimes significant. Concentrate supplementation improved total diet OMD(m), but this was not realized in lactating dairy cows because of linearly decreased neutral detergent fiber (NDF) digestibility as concentrate intake increased. Increasing the concentrate crude protein amount

  13. 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

  14. 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.

  15. Evolution of stenophagy in spiders (Araneae): evidence based on the comparative analysis of spider diets.

    PubMed

    Pekár, Stano; Coddington, Jonathan A; Blackledge, Todd A

    2012-03-01

    Stenophagy (narrow diet breadth) represents an extreme of trophic specialization in carnivores, but little is known about the forces driving its evolution. We used spiders, the most diversified group of terrestrial predators, to investigate whether stenophagy (1) promoted diversification; (2) was phylogenetically conserved and evolutionarily derived state; and (3) was determined either by geographical distribution and foraging guild. We used published data on the prey of almost 600 species. Six categories of stenophagy were found: myrmecophagy, araneophagy, lepidopterophagy, termitophagy, dipterophagy, and crustaceophagy. We found that the species diversity of euryphagous genera and families was similar to stenophagous genera and families. At the family level, stenophagy evolved repeatedly and independently. Within families, the basal condition was oligophagy or euryphagy. Most types of stenophagy were clearly derived: myrmecophagy in Zodariidae; lepidopterophagy in Araneidae; dipterophagy in Theridiidae. In contrast, araneophagy was confined to basal and intermediate lineages, suggesting its ancestral condition. The diet breadth of species from the tropics and subtropics was less diverse than species from the temperate zone. Diet breadth was lower in cursorial spiders compared to web-building species. Thus, the evolution of stenophagy in spiders appears to be complex and governed by phylogeny as well as by ecological determinants.

  16. Adherence to Mediterranean diet and risk of developing cognitive disorders: An updated systematic review and meta-analysis of prospective cohort studies

    PubMed Central

    Wu, Lei; Sun, Dali

    2017-01-01

    Recent articles have presented inconsistent findings on the impact of Mediterranean diet in the occurrence of cognitive disorders; therefore, we performed an updated systematic review and meta-analysis to evaluate the potential association and dose-response pattern with accumulating evidence. We searched the PubMed and the Embase for the records relevant to this topic. A generic inverse-variance method was used to pool the outcome data for continuous variable, and categories of high vs. low, median vs. low of Mediterranean diet score with a random-effects model. Generalized least-squares trend estimation model was used to estimate the potential dose-response patterns of Mediterranean diet score on incident cognitive disorders. We identified 9 cohort studies involving 34,168 participants. Compared with the lowest category, the pooled analysis showed that the highest Mediterranean diet score was inversely associated with the developing of cognitive disorders, and the pooled RR (95% CI) was 0.79 (0.70, 0.90). Mediterranean diet score of the median category was not significantly associated with cognitive disorders. Dose-response analysis indicated a trend of an approximately linear relationship of the Mediterranean diet score with the incident risk of cognitive disorders. Further studies of randomized controlled trials are warranted to confirm the observed association in different populations. PMID:28112268

  17. Analysis of hepatic gene expression profile in a spontaneous mouse model of type 2 diabetes under a high sucrose diet.

    PubMed

    Nojima, Koji; Sugimoto, Ken; Ueda, Hironori; Babaya, Naru; Ikegami, Hiroshi; Rakugi, Hiromi

    2013-01-01

    Both genetic factors and diabetogenic environmental factors, such as a high-sucrose diet (HSD), are involved in the development of type 2 diabetes. In this study, the Nagoya-Shibata-Yasuda (NSY) mouse, an animal model of type 2 diabetes and C3H mice used as controls, were fed a HSD, a high-fat diet (HFD) or a regular diet (RD) from weaning. In C3H mice, HFD significantly increased body weight gain, but maintained glucose tolerance. In contrast, in NSY mice, HSD resulted in increased body weight gain and liver steatosis and increased glucose intolerance to a greater extent than HFD. Furthermore, we performed DNA microarray analysis to detect differences in hepatic gene expression levels in both strains under HSD. We then performed RT-PCR analysis on selected genes to evaluate basal expression level under RD and changes under HSD conditions. HSD-fed NSY, but not C3H mice, exhibited increased hepatic expression levels of Pparg2, an isoform of Pparg as well as G0s2, a target of Pparg, which are known to be adipocyte-specific genes. Compared to RD-fed C3H mice, hepatic expression levels of Kat2b (transcriptional regulation), Hsd3b5 (steroid hormone metabolism) and Cyp7b1 (bile acid metabolism) were initially lower in RD-fed NSY mice, and were further decreased in HSD-fed NSY mice. Expression of Metallothionein (Mt1) and Metallothionein 2 (Mt2) was significantly lower in NSY mice compared to C3H mice, irrespective of dietary condition. These data suggest that elucidation of this heterogeneity in response to HSD might contribute to further understanding of the gene-environment interactions leading to diabetes in humans.

  18. An exploratory analysis of the suitability of diets fed to a flightless insectivore, the North Island brown kiwi (Apteryx mantelli), in New Zealand.

    PubMed

    Potter, Murray A; Hendriks, Wouter H; Lentle, Roger G; Thomas, Donald V; Minson, Charlotte J; Pindur, Nicola B

    2010-01-01

    The ingredients and the macro- and micro-nutrient contents of diets that are fed to captive kiwi at seven New Zealand holding facilities were subject to analysis. The nutrient compositions were compared across facilities and with an estimate of the nutrient composition of the diets of wild kiwi based on the intake of various dietary ingredients reported in the literature. A total of 20 ingredients were used, the number and proportion of these ingredients varied greatly between facilities. Six of the diets were based primarily on meat and three comprised a mixture of meat and cat biscuits. Just one included a proprietary insectivore mix. Nutrient content varied greatly between the seven diets, organic matter ranging from 91.8 to 95.6%, crude protein from 41.9 to 62.9%, and crude fat from 9.0 to 28.7% of dry matter content. Large variations were found in the total content and profile of amino acids and of fatty acids of the diets. The nutrient content of all seven diets differed from that of the natural diet of wild kiwi. Hence, the presence of nutrient deficiencies in the current formulations cannot be excluded.

  19. 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

  20. 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.

  1. Mesozooplankton Grazing on Picocyanobacteria in the Baltic Sea as Inferred from Molecular Diet Analysis

    PubMed Central

    Motwani, Nisha H.; Gorokhova, Elena

    2013-01-01

    Our current knowledge on the microbial component of zooplankton diet is limited, and it is generally assumed that bacteria-sized prey is not directly consumed by most mesozooplankton grazers in the marine food webs. We questioned this assumption and conducted field and laboratory studies to examine picocyanobacteria contribution to the diets of Baltic Sea zooplankton, including copepods. First, qPCR targeting ITS-1 rDNA sequence of the picocyanobacteria Synechococcus spp. was used to examine picocyanobacterial DNA occurrence in the guts of Baltic zooplankton (copepods, cladocerans and rotifers). All field-collected zooplankton were found to consume picocyanobacteria in substantial quantities. In terms of Synechococcus quantity, the individual gut content was highest in cladocerans, whereas biomass-specific gut content was highest in rotifers and copepod nauplii. Moreover, the gut content in copepods was positively related to the picocyanobacteria abundance and negatively to the total phytoplankton abundance in the water column at the time of sampling. This indicates that increased availability of picocyanobacteria resulted in the increased intake of this prey and that copepods may rely more on picoplankton when food in the preferred size range declines. Second, a feeding experiments with a laboratory reared copepod Acartia tonsa fed a mixture of the picocyanobacterium Synechococcus bacillaris and microalga Rhodomonas salina confirmed that copepods ingested Synechococcus, even when the alternative food was plentiful. Finally, palatability of the picocyanobacteria for A. tonsa was demonstrated using uptake of 13C by the copepods as a proxy for carbon uptake in feeding experiment with 13C-labeled S. bacillaris. These findings suggest that, if abundant, picoplankton may become an important component of mesozooplankton diet, which needs to be accounted for in food web models and productivity assessments. PMID:24260175

  2. Transcriptome analysis of the effects of chitosan on the hyperlipidemia and oxidative stress in high-fat diet fed mice.

    PubMed

    Wang, Bin; Zhang, Sicong; Wang, Xiaoya; Yang, Shuo; Jiang, Qixing; Xu, Yanshun; Xia, Wenshui

    2017-04-03

    Transcriptome analysis was performed to investigate the alterations in gene expression after chitosan (CS) treatment on the liver of mice fed with high-fat diet (HFD). The results showed that the body weight, the liver weight and the epididymal fat mass of HFD mice, which were 62.98%, 46.51% and 239.37%, respectively, higher than those of control mice, could be significantly decreased by chitosan supplementation. Also, high-fat diet increased both plasma lipid and liver lipid as compared with the control mice. Chitosan supplementation decreased the plasma lipid and liver lipid, increased the lipoprotein lipase (LPL) and hepatic lipase (HL) activity, increased T-AOC and decreased MDA in the liver and the epididymis adipose as compared with the HFD mice. Transcriptome analysis indicated that increased Mups, Lcn2, Gstm3 and CYP2E1 expressions clearly indicated HFD induced lipid metabolism disorder and oxidative damage. Especially, chitosan treatment decreased the Mup17 and Lcn2 expressions by 64.32% and 82.43% respectively as compared with those of HFD mice. These results indicated that chitosan possess the ability to improve the impairment of lipid metabolism as strongly associated with increased Mups expressions and gene expressions related to oxidative stress.

  3. 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

  4. Adherence to the Mediterranean diet is inversely associated with metabolic syndrome occurrence: a meta-analysis of observational studies.

    PubMed

    Godos, Justyna; Zappalà, Gaetano; Bernardini, Sergio; Giambini, Ilio; Bes-Rastrollo, Maira; Martinez-Gonzalez, Miguel

    2017-03-01

    Diet plays a role in the onset and progression of metabolic disorders, including metabolic syndrome (MetS). We aimed to systematically review and conduct a quantitative meta-analysis of results from observational cross-sectional and prospective cohort studies on adherence to the Mediterranean dietary pattern and risk of MetS. Literature databases including PubMed, SCOPUS and EMBASE were searched from the beginning to May 2016. Eight cross-sectional and four prospective studies were included in this meta-analysis, accounting for a total of 33,847 individuals and 6342 cases of MetS. High adherence to the Mediterranean diet was associated with a risk of MetS (RR: 0.81, 95%CI: 0.71, 0.92). Regarding individual components of the MetS, the inverse associations were significant for waist circumference, blood pressure and low HDL-C levels. In conclusion, adoption of a Mediterranean dietary pattern was associated with lower risk of the MetS and it can be proposed for the primary prevention of the MetS.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. Stability and proton transfer in DNA base pairs of AMD473-DNA adduct

    NASA Astrophysics Data System (ADS)

    Sarmah, Pubalee; Deka, Ramesh C.

    2011-05-01

    We investigate the energetics of four different adducts of cisplatin analogue cis-[PtCl 2(NH 3)(2-picoline)] (AMD473) with a duplex DNA using DFT/ONIOM methods to probe their stabilities. Further, we study the possibilities of proton transfer between DNA base pairs of the most stable drug-DNA adduct. The adduct b(2-picoline trans to 3'-G and 2-methyl group directs to the DNA major groove) is found to be the most stable configuration among all the possible adducts. From the proton transfer analysis we found that the single proton transfer between N1 position of guanine (G) and N3 position of cytosine (C) of each GC pair gives a structure energetically as stable as the original one.

  14. 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

  15. Manta birostris, predator of the deep? Insight into the diet of the giant manta ray through stable isotope analysis

    PubMed Central

    Couturier, Lydie I. E.; Marshall, Andrea D.; Richardson, Anthony J.; Weeks, Scarla J.; Bennett, Michael B.

    2016-01-01

    The characterization of diet for the giant manta ray Manta birostris has been problematic given their large-scale movement patterns and the difficulty in obtaining stomach contents from this species. The large majority of existing information is based on observational data limited to feeding events at the sea surface during daylight. Recently discovered aggregation sites for the giant manta ray off mainland Ecuador are some of the most accessible to date and provide a unique opportunity for researchers to gather much needed information on this elusive species. To assess how important surface zooplankton is to giant manta ray diet, we conducted stable isotope analysis (15N and 13C) on M. birostris muscle and surface zooplankton. Trophic position estimates placed M. birostris overall at a secondary consumer level of approximately 3.4 but there was large variation in δ15N and δ13C values among individuals. Manta birostris muscle tissue δ13C values were also not consistent with this species feeding predominantly on surface zooplankton and suggest that the majority of dietary intake is of mesopelagic origin. Given the conservative life history and fisheries pressure on large planktivores, knowledge of their trophic role and foraging strategies is essential to better understand their ecology and develop effective conservation measures. PMID:28018660

  16. Amniotic fluid metabolomics and biochemistry analysis provides novel insights into the diet-regulated foetal growth in a pig model

    PubMed Central

    Wan, Jin; Jiang, Fei; Zhang, Jiao; Xu, Qingsong; Chen, Daiwen; Yu, Bing; Mao, Xiangbing; Yu, Jie; Luo, Yuheng; He, Jun

    2017-01-01

    Foetal loss and intrauterine growth restriction are major problems in mammals, but there are few effective ways in preventing it. Intriguingly, chitosan oligosaccharide (COS), a biomaterial derived from chitosan, can promote foetal survival and growth. Therefore, we have investigated how COS affects foetal survival and growth in a pig model. Fifty-two sows were divided into two treatment groups (n = 26) and fed either solely a control diet or a control diet that includes 100 mg/kg COS. Amniotic fluid and foetus samples from six sows that were of average body weight in each group were collected on gestation day 35. We applied a 1H NMR-based metabolomics approach combined with biochemistry analysis to track the changes that occurred in the amniotic fluid of pregnant sows after COS intervention. Maternal COS inclusion had enhanced (P < 0.05) the foetal survival rate and size at 35 days. COS supplementation had both increased (P < 0.05) SOD, CAT and T-AOC activities and elevated (P < 0.05) IL-10, IgG and IgM concentrations in the amniotic fluid. Moreover, COS had affected (P < 0.05) the amniotic fluid’s lysine, citrate, glucose and hypoxanthine levels. Overall, COS inclusion induced amniotic fluid antioxidant status and metabolic profiles modifications characterising improvements in foetal survival and growth in a pig model. PMID:28300194

  17. Manta birostris, predator of the deep? Insight into the diet of the giant manta ray through stable isotope analysis.

    PubMed

    Burgess, Katherine B; Couturier, Lydie I E; Marshall, Andrea D; Richardson, Anthony J; Weeks, Scarla J; Bennett, Michael B

    2016-11-01

    The characterization of diet for the giant manta ray Manta birostris has been problematic given their large-scale movement patterns and the difficulty in obtaining stomach contents from this species. The large majority of existing information is based on observational data limited to feeding events at the sea surface during daylight. Recently discovered aggregation sites for the giant manta ray off mainland Ecuador are some of the most accessible to date and provide a unique opportunity for researchers to gather much needed information on this elusive species. To assess how important surface zooplankton is to giant manta ray diet, we conducted stable isotope analysis ((15)N and (13)C) on M. birostris muscle and surface zooplankton. Trophic position estimates placed M. birostris overall at a secondary consumer level of approximately 3.4 but there was large variation in δ(15)N and δ(13)C values among individuals. Manta birostris muscle tissue δ(13)C values were also not consistent with this species feeding predominantly on surface zooplankton and suggest that the majority of dietary intake is of mesopelagic origin. Given the conservative life history and fisheries pressure on large planktivores, knowledge of their trophic role and foraging strategies is essential to better understand their ecology and develop effective conservation measures.

  18. 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

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

    PubMed

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

    2016-03-15

    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.

  20. DNA-based nanobiostructured devices: The role of quasiperiodicity and correlation effects

    NASA Astrophysics Data System (ADS)

    Albuquerque, E. L.; Fulco, U. L.; Freire, V. N.; Caetano, E. W. S.; Lyra, M. L.; de Moura, F. A. B. F.

    2014-02-01

    , promote an electronic self-trapping, thus opening up the possibility of controlling the spreading of the electronic density by an external field. The main features of DNA-based nanobiostructured devices presented in this review will include their electronic density of states, energy profiles, thermodynamic properties, localization, correlation effects, scale laws, fractal and multifractal analysis, and anhydrous crystals of their bases, among others. New features, like other nanobiostructured devices, as well as the future directions in this field are also presented and discussed.

  1. Bioarchaeological analysis of diet during the Coles Creek period in the southern Lower Mississippi Valley.

    PubMed

    Listi, Ginesse A

    2011-01-01

    The timing of the dietary shift from foraging to maize agriculture, and the speed at which such practices were adopted, are important considerations in the cultural evolution of the New World. In the southern Lower Mississippi Valley, maize agriculture traditionally was believed to have been practiced during the Coles Creek period (A.D. 700-1200); however, direct evidence for maize is lacking in the archaeological record prior to A.D. 1000. The present study examines Coles Creek diet from a bioarchaeological perspective. Oral-health indicators, including abscesses, antemortem tooth loss, calculus, carious lesions, periodontal disease, and tooth wear, were evaluated in a regional, temporal context. Data were collected from 288 dentitions from eight sites in the southern Lower Mississippi Valley that range in date from 800 B.C. to A.D. 1200. The sample then was separated into Pre-Coles Creek and Coles Creek categories and statistical analyses were used to assess temporal variation in pathology load. Results indicate that pathology load in the Coles Creek sample is slightly heavier than the Pre-Coles Creek sample; however, the differences are not substantial. Furthermore, data suggest that regional differences in resource exploitation existed between the Lower Mississippi Valley and populations elsewhere in the eastern United States. Specifically, the presence of starchy native plants other than maize in the diet likely contributed to a high pathology load for early hunter-gatherers. Ultimately, data from this study complement the archaeological, botanical, and zooarchaeological records and indicate that Coles Creek subsistence was not based on maize agriculture.

  2. Analysis of rumen microbial populations in lactating dairy cattle fed diets varying in carbohydrate profiles and Saccharomyces cerevisiae fermentation product.

    PubMed

    Mullins, C R; Mamedova, L K; Carpenter, A J; Ying, Y; Allen, M S; Yoon, I; Bradford, B J

    2013-09-01

    The rumen microbial ecosystem is a critical factor that links diets to bovine physiology and productivity; however, information about dietary effects on microbial populations has generally been limited to small numbers of samples and qualitative assessment. To assess whether consistent shifts in microbial populations occur in response to common dietary manipulations in dairy cattle, samples of rumen contents were collected from 2 studies for analysis by quantitative real-time PCR (qPCR). In one study, lactating Holstein cows (n=8) were fed diets in which a nonforage fiber source replaced an increasing proportion of forages and concentrates in a 4×4 Latin square design, and samples of ruminal digesta were collected at 9-h intervals over 3 d at the end of each period. In the second study, lactating Holstein cows (n=15) were fed diets with or without the inclusion of a Saccharomyces cerevisiae fermentation product (SCFP) in a crossover design. In this study, rumen liquid and solid samples were collected during total rumen evacuations before and after feeding in a 42-h period. In total, 146 samples of ruminal digesta were used for microbial DNA isolation and analysis by qPCR. Validated primer sets were used to quantify total bacterial and anaerobic fungal populations as well as 12 well-studied bacterial taxa. The relative abundance of the target populations was similar to those previously reported. No significant treatment effects were observed for any target population. A significant interaction of treatment and dry matter intake was observed, however, for the abundance of Eubacterium ruminantium. Increasing dry matter intake was associated with a quadratic decrease in E. ruminantium populations in control animals but with a quadratic increase in E.ruminantium populations in cows fed SCFP. Analysis of sample time effects revealed that Fibrobacter succinogenes and fungal populations were more abundant postfeeding, whereas Ruminococcus albus tended to be more abundant

  3. 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.

  4. Effect of phenolic radicals on the geometry and electronic structure of DNA base pairs: computational study

    NASA Astrophysics Data System (ADS)

    Zarei, Mohammad; Seif, Abdolvahab; Azizi, Khaled; Zarei, Mohanna; Bahrami, Jamil

    2016-04-01

    In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

  5. How to make DNA count: DNA-based diagnostic tools in veterinary parasitology.

    PubMed

    Hunt, P W; Lello, J

    2012-05-04

    Traditional methods for the diagnosis of parasitic helminth infections of livestock have a number of limitations, such as the inability to distinguish mixed-species infections, a heavy reliance on technical experience and also sub-sampling errors. Some of these limitations may be overcome through the development of rapid and accurate DNA-based tests. For example, DNA-based tests can specifically detect individual species in a mixed infection at either the larval or egg stages, in the absence of morphological differences among species. Even so, some diagnostic problems remain the same, irrespective of whether a DNA-based or traditional method is used. For example, sub-sampling errors from an aggregated distribution are likely to persist. It is proposed, however, that DNA-based diagnostic technologies offer an opportunity to expand diagnostic capabilities, and are discussed in the current review. The future introduction of DNA-based diagnostic technologies into routine diagnostic settings will also be discussed.

  6. Diverticulitis Diet

    MedlinePlus

    ... allowed on a clear liquid diet include: Broth Fruit juices without pulp, such as apple juice Ice chips ... skin) Eggs, fish and poultry Refined white bread Fruit and vegetable juice with no pulp Low-fiber cereals Milk, yogurt ...

  7. Diet & Nutrition

    MedlinePlus

    ... Omega-3 Publication Diet and MS Research Review Paper With increasing interest in the possible role of ... for people with MS. A recent research review paper by Pavan Bhargava, MD, provides information and current ...

  8. 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 ...

  9. Gout Diet

    MedlinePlus

    ... Nutrition and healthy eating By Mayo Clinic Staff Gout, a painful form of arthritis, occurs when high ... is eliminated from the body in urine. A gout diet may help decrease uric acid levels in ...

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

    PubMed

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

    2013-01-06

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

  11. Heart disease and diet

    MedlinePlus

    Diet - heart disease; CAD - diet; Coronary artery disease - diet; Coronary heart disease - diet ... diet and lifestyle can reduce your risk of: Heart disease, heart attacks, and stroke Conditions that lead ...

  12. A DNA-based semantic fusion model for remote sensing data.

    PubMed

    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.

  13. 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

  14. Automated DNA-based plant identification for large-scale biodiversity assessment.

    PubMed

    Papadopoulou, Anna; Chesters, Douglas; Coronado, Indiana; De la Cadena, Gissela; Cardoso, Anabela; Reyes, Jazmina C; Maes, Jean-Michel; Rueda, Ricardo M; Gómez-Zurita, Jesús

    2015-01-01

    Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable, markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic inference. We describe the strategies used to establish these steps and the optimization of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.

  15. 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

  16. [Estimation of the intake of radioactive cesium based on analysis of total diet samples in Nagoya].

    PubMed

    Miyazaki, Hitoshi; Kato, Haruyasu; Kato, Yukari; Tsuchiyama, Tomoyuki; Terada, Hisaya

    2013-01-01

    Food samples were purchased in Nagoya based on daily intake in the Tokai region, and prepared as total diet samples according to the market basket method. The contents of radioactive cesium (Cs) were determined by using a γ-ray spectrometer with a germanium semiconductor detector, and a committed effective dose was estimated. Radioactive Cs was not detected in samples collected in 2006 before the Fukushima nuclear plant accident. Radioactive Cs was detected in samples prepared in August, 2011, five months after the accident. The sources were sugar and confectioneries (3rd food group), other vegetables, seaweeds and mushrooms (8th food group) and fishes, shellfishes and processed seafoods (10th food group). Only Cs-137 was detected in samples prepared in August, 2012, one year and five months after the accident. The sources were the 8th and the 10th food groups. The estimated committed effective dose for radioactive Cs was 0.0015 mSv in 2011 and 0.00016 mSv in 2012.

  17. A molecular analysis of ground sloth diet through the last glaciation.

    PubMed

    Hofreiter, M; Poinar, H N; Spaulding, W G; Bauer, K; Martin, P S; Possnert, G; Pääbo, S

    2000-12-01

    DNA was extracted from five coprolites, excavated in Gypsum Cave, Nevada and radiocarbon dated to approximately 11 000, 20 000 and 28 500 years BP. All coprolites contained mitochondrial DNA sequences identical to a DNA sequence determined from a bone of the extinct ground sloth Nothrotheriops shastensis. A 157-bp fragment of the chloroplast gene for the large subunit of the ribulosebisphosphate carboxylase (rbcL) was amplified from the boluses and several hundred clones were sequenced. In addition, the same DNA fragment was sequenced from 99 plant species that occur in the vicinity of Gypsum Cave today. When these were compared to the DNA sequences in GenBank, 69 were correctly (two incorrectly) assigned to taxonomic orders. The plant sequences from the five coprolites as well as from one previously studied coprolite were compared to rbcL sequences in GenBank and the contemporary plant species. Thirteen families or orders of plants that formed part of the diet of the Shasta ground sloth could be identified, showing that the ground sloth was feeding on trees as well as herbs and grasses. The plants in the boluses further indicate that the climate 11 000 years BP was dryer than 20 000 and 28 500 years BP. However, the sloths seem to have visited water sources more frequently at 11 000 BP than at earlier times.

  18. 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.

  19. 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.

  20. 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

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

    PubMed Central

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

    2016-01-01

    Abstract 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

  2. 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.

  3. [Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?].

    PubMed

    Brovarets', O O

    2013-01-01

    At the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that the Löwdin's G*.C* DNA base pair formed by the mutagenic tautomers can acquire, as the A-T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G.C-->G*.C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.

  4. 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...

  5. 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…

  6. Effects of high-protein diets on body weight, glycaemic control, blood lipids and blood pressure in type 2 diabetes: meta-analysis of randomised controlled trials.

    PubMed

    Dong, Jia-Yi; Zhang, Zeng-Li; Wang, Pei-Yu; Qin, Li-Qiang

    2013-09-14

    High-protein diets are popular for weight management, but the health effects of such diets in diabetic persons are inconclusive. The aim of the present meta-analysis was to examine the effects of high-protein diets on body weight and metabolic risk factors in patients with type 2 diabetes. We searched the PubMed and Cochrane Library databases for relevant randomised trials up to August 2012. Either a fixed- or a random-effects model was used to combine the net changes in each outcome from baseline to the end of the intervention. Overall, nine trials including a total of 418 diabetic patients met our inclusion criteria. The study duration ranged from 4 to 24 weeks. The actual intake of dietary protein ranged from 25 to 32% of total energy in the intervention groups and from 15 to 20% in the control groups. Compared with the control diets, high-protein diets resulted in more weight loss (pooled mean difference: 22.08, 95% CI 23.25, 20.90 kg). High-protein diets significantly decreased glycated Hb A1C (HbA1C) levels by 0.52 (95% CI 20.90, 20.14) %, but did not affect the fasting blood glucose levels. There were no differences in lipid profiles. The pooled net changes in systolic and diastolic blood pressure were 23.13 (95% CI 26.58, 0.32)mmHg and 21.86 (95% CI 24.26, 0.56) mmHg, respectively. However, two studies reported a large influence on weight loss and HbA1C levels, respectively. In summary, high-protein diets (within 6 months) may have some beneficial effects on weight loss, HbA1C levels and blood pressure in patients with type 2 diabetes. However, further investigations are still required to draw a conclusion.

  7. A further subgroup analysis of the effects of the DASH diet and three dietary sodium levels on blood pressure: results of the DASH-Sodium Trial.

    PubMed

    Bray, George A; Vollmer, William M; Sacks, Frank M; Obarzanek, Eva; Svetkey, Laura P; Appel, Lawrence J

    2004-07-15

    This study presents an extensive analysis of the effects on blood pressure (BP) of changes in sodium intake over a wide array of subgroups, including joint subgroups defined by age and hypertension status, race or ethnicity and hypertension status, and gender and race or ethnicity. Participants were given 3 levels of sodium (50, 100, and 150 mmol/2,100 kcal) for 30 days while consuming the Dietary Approaches to Stop Hypertension (DASH) diet (rich in fruits, vegetables, and low-fat dairy) or a more typical American diet. Within each diet and subgroup, there was a general pattern such that the lower the sodium level, the greater the mean reduction in BP. Sodium reduction from 100 to 50 mmol/2,100 kcal generally had twice the effect on BP as reduction from 150 to 100 mmol/2,100 kcal. Age had a strong and graded influence on the effect of sodium within the typical and DASH diets, respectively: -4.8 and -1.0 mm Hg systolic for 23 to 41 years, -5.9 and -1.8 mm Hg for 42 to 47 years, -7.5 and -4.3 mm Hg for 48 to 54 years, and -8.1 and -6.0 mm Hg for 55 to 76 years. The influence of age on the effect of sodium reduction was particularly strong in nonhypertensive patients: -3.7 mm Hg systolic for <45 years and -7.0 mm Hg for >45 years with the typical diet and -0.7 and -2.8 mm Hg with the DASH diet. Reduced sodium intake and the DASH diet should be advocated for the prevention and treatment of high BP, particularly because the benefits to BP strengthen as subjects enter middle age, when the rate of cardiovascular disease increases sharply.

  8. 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

  9. 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.

  10. 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

  11. 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

  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. 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...

  14. 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...

  15. Toward DNA-based Security Circuitry: First Step - Random Number Generation.

    PubMed

    Bogard, Christy M; Arazi, Benjamin; Rouchka, Eric C

    2008-08-10

    DNA-based circuit design is an area of research in which traditional silicon-based technologies are replaced by naturally occurring phenomena taken from biochemistry and molecular biology. Our team investigates the implications of DNA-based circuit design in serving security applications. As an initial step we develop a random number generation circuitry. A novel prototype schema employs solid-phase synthesis of oligonucleotides for random construction of DNA sequences. Temporary storage and retrieval is achieved through plasmid vectors.

  16. 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

  17. Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes.

    PubMed

    Li, Yougen; Cu, Yen Thi Hong; Luo, Dan

    2005-07-01

    Rapid, multiplexed, sensitive and specific molecular detection is of great demand in gene profiling, drug screening, clinical diagnostics and environmental analysis. One of the major challenges in multiplexed analysis is to identify each specific reaction with a distinct label or 'code'. Two encoding strategies are currently used: positional encoding, in which every potential reaction is preassigned a particular position on a solid-phase support such as a DNA microarray, and reaction encoding, where every possible reaction is uniquely tagged with a code that is most often optical or particle based. The micrometer size, polydispersity, complex fabrication process and nonbiocompatibility of current codes limit their usability. Here we demonstrate the synthesis of dendrimer-like DNA-based, fluorescence-intensity-coded nanobarcodes, which contain a built-in code and a probe for molecular recognition. Their application to multiplexed detection of the DNA of several pathogens is first shown using fluorescence microscopy and dot blotting, and further demonstrated using flow cytometry that resulted in detection that was sensitive (attomole) and rapid.

  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. Sodium in diet

    MedlinePlus

    Diet - sodium (salt); Hyponatremia - sodium in diet; Hypernatremia - sodium in diet; Heart failure - sodium in diet ... The body uses sodium to control blood pressure and blood volume. Your body also needs sodium for your muscles and nerves to work ...

  20. Potassium in diet

    MedlinePlus

    ... the diet; Hypokalemia - potassium in the diet; Chronic kidney disease - potassium in diet; Kidney failure - potassium in diet ... are also excellent sources of potassium. People with kidney problems, especially those on dialysis, should not eat ...

  1. Metabolomic analysis of the effects of chronic arsenic exposure in a mouse model of diet-induced fatty liver disease

    PubMed Central

    Shi, Xue; Wei, Xiaoli; Koo, Imhoi; Schmidt, Robin H.; Yin, Xinmin; Kim, Seong Ho; Vaughn, Andrew; McClain, Craig J.; Arteel, Gavin E.

    2014-01-01

    Arsenic is a widely-distributed environmental component that is associated with a variety of cancer and non-cancer adverse health effects. Additional lifestyle factors, such as diet, contribute to the manifestation of disease. Recently, arsenic was found to increase inflammation and liver injury in a dietary model of fatty liver disease. The purpose of the present study was to investigate potential mechanisms of this diet-environment interaction via a high throughput metabolomics approach. GC×GC-TOF MS was used to identify metabolites that were significantly increased or decreased in the livers of mice fed a Western diet (a diet high in fat and cholesterol) and co-exposed to arsenic-contaminated drinking water. The results showed that there are distinct hepatic metabolomic profiles associated with eating a high fat diet, drinking arsenic-contaminated water, and the combination of the two. Among the metabolites that were decreased when arsenic exposure was combined with a high fat diet were short-chain and medium-chain fatty acid metabolites and the anti-inflammatory amino acid, glycine. These results are consistent with the observed increase in inflammation and cell death in the livers of these mice, and they point to potentially novel mechanisms by which these metabolic pathways could be altered by arsenic in the context of diet-induced fatty liver disease. PMID:24328084

  2. Measurement of oxidative DNA damage by gas chromatography-mass spectrometry: ethanethiol prevents artifactual generation of oxidized DNA bases.

    PubMed

    Jenner, A; England, T G; Aruoma, O I; Halliwell, B

    1998-04-15

    Analysis of oxidative damage to DNA bases by GC-MS enables identification of a range of base oxidation products, but requires a derivatization procedure. However, derivatization at high temperature in the presence of air can cause 'artifactual' oxidation of some undamaged bases, leading to an overestimation of their oxidation products, including 8-hydroxyguanine. Therefore derivatization conditions that could minimize this problem were investigated. Decreasing derivatization temperature to 23 degrees C lowered levels of 8-hydroxyguanine, 8-hydroxyadenine, 5-hydroxycytosine and 5-(hydroxymethyl)uracil measured by GC-MS in hydrolysed calf thymus DNA. Addition of the reducing agent ethanethiol (5%, v/v) to DNA samples during trimethylsilylation at 90 degrees C also decreased levels of these four oxidized DNA bases as well as 5-hydroxyuracil. Removal of guanine from hydrolysed DNA samples by treatment with guanase, prior to derivatization, resulted in 8-hydroxyguanine levels (54-59 pmol/mg of DNA) that were significantly lower than samples not pretreated with guanase, independent of the derivatization conditions used. Only hydrolysed DNA samples that were derivatized at 23 degrees C in the presence of ethanethiol produced 8-hydroxyguanine levels (56+/-8 pmol/mg of DNA) that were as low as those of guanase-pretreated samples. Levels of other oxidized bases were similar to samples derivatized at 23 degrees C without ethanethiol, except for 5-hydroxycytosine and 5-hydroxyuracil, which were further decreased by ethanethiol. Levels of 8-hydroxyguanine, 8-hydroxyadenine and 5-hydroxycytosine measured in hydrolysed calf thymus DNA by the improved procedures described here were comparable with those reported previously by HPLC with electrochemical detection and by GC-MS with prepurification to remove undamaged base. We conclude that artifactual oxidation of DNA bases during derivatization can be prevented by decreasing the temperature to 23 degrees C, removing air from the

  3. 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

    2013-08-22

    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

  4. 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

  5. Effects of the Dietary Approach to Stop Hypertension (DASH) diet on cardiovascular risk factors: a systematic review and meta-analysis.

    PubMed

    Siervo, Mario; Lara, Jose; Chowdhury, Shakir; Ashor, Ammar; Oggioni, Clio; Mathers, John C

    2015-01-14

    The Dietary Approach to Stop Hypertension (DASH) is recommended to lower blood pressure (BP), but its effects on cardiometabolic biomarkers are unclear. A systematic review and meta-analysis of randomised controlled trials (RCT) was conducted to determine the effects of the DASH diet on cardiovascular risk factors. Medline, Embase and Scopus databases were searched from inception to December 2013. Inclusion criteria were as follows: (1) DASH diet; (2) RCT; (3) risk factors including systolic and diastolic BP and glucose, HDL, LDL, TAG and total cholesterol concentrations; (4) control group. Random-effects models were used to determine the pooled effect sizes. Meta-regression analyses were carried out to examine the association between effect sizes, baseline values of the risk factors, BMI, age, quality of trials, salt intake and study duration. A total of twenty articles reporting data for 1917 participants were included in the meta-analysis. The duration of interventions ranged from 2 to 24 weeks. The DASH diet was found to result in significant decreases in systolic BP ( - 5·2 mmHg, 95% CI - 7·0, - 3·4; P< 0·001) and diastolic BP ( - 2·6 mmHg, 95% CI - 3·5, - 1·7; P< 0·001) and in the concentrations of total cholesterol ( - 0·20 mmol/l, 95% CI - 0·31, - 0·10; P< 0·001) and LDL ( - 0·10 mmol/l, 95% CI - 0·20, - 0·01; P= 0·03). Changes in both systolic and diastolic BP were greater in participants with higher baseline BP or BMI. These changes predicted a reduction of approximately 13% in the 10-year Framingham risk score for CVD. The DASH diet improved cardiovascular risk factors and appeared to have greater beneficial effects in subjects with an increased cardiometabolic risk. The DASH diet is an effective nutritional strategy to prevent CVD.

  6. 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.

  7. Long-Term use of Modified Diets in Huntington's Disease: A Descriptive Clinical Practice Analysis on Improving Dietary Enjoyment.

    PubMed

    Moorhouse, Bronwyn; Fisher, Caroline A

    2016-01-01

    Dysphagia is a very common occurrence in Huntington's disease (HD). As such, many people with HD require texture modified diets. This commentary discusses the implications for individuals living long-term on modified diets, including the loss of sensory stimulation and dietary enjoyment. Clinical practice analyses of two interventions aimed at promoting dietary satisfaction and involvement in food preparation for those with HD are described and parameters for future research are discussed.

  8. Identification of species with DNA-based technology: current progress and challenges.

    PubMed

    Pereira, Filipe; Carneiro, João; Amorim, António

    2008-01-01

    One of the grand challenges of modern biology is to develop accurate and reliable technologies for a rapid screening of DNA sequence variation. This topic of research is of prime importance for the detection and identification of species in numerous fields of investigation, such as taxonomy, epidemiology, forensics, archaeology or ecology. Molecular identification is also central for the diagnosis, treatment and control of infections caused by different pathogens. In recent years, a variety of DNA-based approaches have been developed for the identification of individuals in a myriad of taxonomic groups. Here, we provide an overview of most commonly used assays, with emphasis on those based on DNA hybridizations, restriction enzymes, random PCR amplifications, species-specific PCR primers and DNA sequencing. A critical evaluation of all methods is presented focusing on their discriminatory power, reproducibility and user-friendliness. Having in mind that the current trend is to develop small-scale devices with a high-throughput capacity, we briefly review recent technological achievements for DNA analysis that offer great potentials for the identification of species.

  9. DNA-based identification of spices: DNA isolation, whole genome amplification, and polymerase chain reaction.

    PubMed

    Focke, Felix; Haase, Ilka; Fischer, Markus

    2011-01-26

    Usually spices are identified morphologically using simple methods like magnifying glasses or microscopic instruments. On the other hand, molecular biological methods like the polymerase chain reaction (PCR) enable an accurate and specific detection also in complex matrices. Generally, the origins of spices are plants with diverse genetic backgrounds and relationships. The processing methods used for the production of spices are complex and individual. Consequently, the development of a reliable DNA-based method for spice analysis is a challenging intention. However, once established, this method will be easily adapted to less difficult food matrices. In the current study, several alternative methods for the isolation of DNA from spices have been developed and evaluated in detail with regard to (i) its purity (photometric), (ii) yield (fluorimetric methods), and (iii) its amplifiability (PCR). Whole genome amplification methods were used to preamplify isolates to improve the ratio between amplifiable DNA and inhibiting substances. Specific primer sets were designed, and the PCR conditions were optimized to detect 18 spices selectively. Assays of self-made spice mixtures were performed to proof the applicability of the developed methods.

  10. DNA base pair stacks with high electric conductance: a systematic structural search.

    PubMed

    Berlin, Yuri A; Voityuk, Alexander A; Ratner, Mark A

    2012-09-25

    We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes. The results of this work may provide guidance for the construction of DNA devices and DNA-based elements of nanoscale molecular circuits. Several factors that cause changes of step parameters favorable to the formation of the predicted stack conformation with high electric conductance of DNA molecules are also discussed; favorable geometries may enhance the conductivity by factors as large as 15.

  11. Life history and cost analysis for continuous rearing of Podisus maculiventris (Say) (Heteroptera: Pentatomidae) on a zoophytophagous artificial diet.

    PubMed

    Coudron, T A; Wittmeyer, J; Kim, Y

    2002-12-01

    The impact of a zoophytophagous, insect-free artificial diet upon the developmental rate, life table parameters, and fertility table parameters was examined over 11 consecutive generations for domesticated and wild colonies of Podisus maculiventris (Say) (Heteroptera: Pentatomidae). This study showed that the developmental time, preoviposition period, fecundity, and nymphal survival improved in the domestic colony when fed an insect-free artificial diet for 11 consecutive generations, but remained relatively constant for the wild colony, as did reproductive rate and intrinsic rate of increase. Although, after 11 generations of adaptation to an artificial diet feeding regime, all reproductive and fertility table parameters were still significantly lower than when fed on T. ni larvae as the natural prey, the realized cost of rearing either colony on the artificial diet approached 1.2 times the cost of rearing these insects on a natural prey. This is a significant achievement in the effort to develop cost-effective artificial diets for the mass-rearing of beneficial pentatomids, and has positive implications for the use of one artificial diet to efficiently rear several beneficial insects.

  12. 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

  13. 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.

  14. Suction sampling as a significant source of error in molecular analysis of predator diets.

    PubMed

    King, R A; Davey, J S; Bell, J R; Read, D S; Bohan, D A; Symondson, W O C

    2012-06-01

    The molecular detection of predation is a fast growing field, allowing highly specific and sensitive detection of prey DNA within the gut contents or faeces of a predator. Like all molecular methods, this technique is prone to potential sources of error that can result in both false positive and false negative results. Here, we test the hypothesis that the use of suction samplers to collect predators from the field for later molecular analysis of predation will lead to high numbers of false positive results. We show that, contrary to previous published work, the use of suction samplers resulted in previously starved predators testing positive for aphid and collembolan DNA, either as a results of ectopic contamination or active predation in the collecting cup/bag. The contradictory evidence for false positive results, across different sampling protocols, sampling devices and different predator-prey systems, highlights the need for experimentation prior to mass field collections of predators to find techniques that minimise the risk of false positives.

  15. Dietary changes needed to reach nutritional adequacy without increasing diet cost according to income: An analysis among French adults

    PubMed Central

    Maillot, Matthieu; Vieux, Florent; Delaere, Fabien; Lluch, Anne; Darmon, Nicole

    2017-01-01

    Objective To explore the dietary changes needed to achieve nutritional adequacy across income levels at constant energy and diet cost. Materials and methods Individual diet modelling was used to design iso-caloric, nutritionally adequate optimised diets for each observed diet in a sample of adult normo-reporters aged ≥20 years (n = 1,719) from the Individual and National Dietary Survey (INCA2), 2006–2007. Diet cost was estimated from mean national food prices (2006–2007). A first set of free-cost models explored the impact of optimisation on the variation of diet cost. A second set of iso-cost models explored the dietary changes induced by the optimisation with cost set equal to the observed one. Analyses of dietary changes were conducted by income quintiles, adjusting for energy intake, sociodemographic and socioeconomic variables, and smoking status. Results The cost of observed diets increased with increasing income quintiles. In free-cost models, the optimisation increased diet cost on average (+0.22 ± 1.03 euros/d) and within each income quintile, with no significant difference between quintiles, but with systematic increases for observed costs lower than 3.85 euros/d. In iso-cost models, it was possible to design nutritionally adequate diets whatever the initial observed cost. On average, the optimisation at iso-cost increased fruits and vegetables (+171 g/day), starchy foods (+121 g/d), water and beverages (+91 g/d), and dairy products (+20 g/d), and decreased the other food groups (e.g. mixed dishes and salted snacks), leading to increased total diet weight (+300 g/d). Those changes were mostly similar across income quintiles, but lower-income individuals needed to introduce significantly more fruit and vegetables than higher-income ones. Conclusions In France, the dietary changes needed to reach nutritional adequacy without increasing cost are similar regardless of income, but may be more difficult to implement when the budget for food is lower than

  16. 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

  17. Measurement of inelastic cross sections for low-energy electron scattering from DNA bases

    PubMed Central

    Michaud, Marc; Bazin, Marc.; Sanche, Léon

    2013-01-01

    Purpose Determine experimentally the absolute cross sections (CS) to deposit various amount of energies into DNA bases by low-energy electron (LEE) impact. Materials and methods Electron energy loss (EEL) spectra of DNA bases are recorded for different LEE impact energies on the molecules deposited at very low coverage on an inert argon (Ar) substrate. Following their normalisation to the effective incident electron current and molecular surface number density, the EEL spectra are then fitted with multiple Gaussian functions in order to delimit the various excitation energy regions. The CS to excite a molecule into its various excitation modes are finally obtained from computing the area under the corresponding Gaussians. Results The EEL spectra and absolute CS for the electronic excitations of pyrimidine and the DNA bases thymine, adenine, and cytosine by electron impacts below 18 eV are reported for the molecules deposited at about monolayer coverage on a solid Ar substrate. Conclusions The CS for electronic excitations of DNA bases by LEE impact are found to lie within the 10−16 – 10−18 cm2 range. The large value of the total ionisation CS indicates that ionisation of DNA bases by LEE is an important dissipative process via which ionising radiation degrades and is absorbed in DNA. PMID:21615242

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

    PubMed

    Darling, John A; Mahon, Andrew R

    2011-10-01

    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 improve on traditional monitoring approaches by enhancing detection sensitivity, reducing analytical turnaround times and monitoring costs, and increasing specificity of target identifications. However, despite the promise of DNA-based monitoring methods, the adoption of these tools in decision-making frameworks remains challenging. Here, rather than explore technical aspects of method development, we examine impediments to effective translation of those methods into management contexts. In addition to surveying current use of DNA-based tools for aquatic invasive species monitoring, we explore potential sources of uncertainty associated with molecular technologies and possibilities for limiting that uncertainty and effectively communicating its implications for decision-making. We pay particular attention to the recent adoption of DNA-based methods for detection of invasive Asian carp species in the United States Great Lakes region, as this example illustrates many of the challenges associated with applying molecular tools to achieve desired management outcomes. Our goal is to provide a useful assessment of the obstacles associated with integrating DNA-based methods into aquatic invasive species management, and to offer recommendations for future efforts aimed at overcoming those obstacles.

  19. 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

  20. Multi-scale effects of nestling diet on breeding performance in a terrestrial top predator inferred from stable isotope analysis.

    PubMed

    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

  1. Comparison of reducing epicardial fat by exercise, diet or bariatric surgery weight loss strategies: a systematic review and meta-analysis.

    PubMed

    Rabkin, S W; Campbell, H

    2015-05-01

    The objectives were to determine whether epicardial fat (EAT) is subject to modification, and whether various strategies accomplish this end point and the relationship between weight loss and EAT. A systematic review of the literature following meta-analysis guidelines was conducted using the search strategy 'epicardial fat' OR 'epicardial adipose tissue' AND 'diet' OR 'exercise' OR 'bariatric surgery (BS)' OR 'change in body weight' limited to humans. Eleven articles were identified with 12 intervention approaches of which eight studies showed a statistically significant reduction in EAT. A random-effects meta-analysis suggests an overall significant reduction of 1.12 standardized units (95% CI = [-1.71, -0.54], P value < 0.01). While there is a large amount of heterogeneity across study groups, a substantial amount of this variability can be accounted for by considering intervention type and change in body mass index (BMI). These variables were incorporated into a random-effects meta-regression model. Using this analysis, significant EAT reduction occurred with diet and BS but not with exercise. BMI reductions correlated significantly with EAT reductions for diet-based interventions, i.e. for some but not all interventions. In conclusion, EAT, a factor that is significantly associated with coronary artery disease, can be modified. The type of intervention, in addition to the amount of weight loss achieved, is predictive of the amount of EAT reduction.

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

    PubMed

    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.

  3. 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

  4. Descriptive sensory analysis of meat from broilers fed diets containing vitamin E or beta-carotene as antioxidants and different supplemental fats.

    PubMed

    Ruiz, J A; Guerrero, L; Arnau, J; Guardia, M D; Esteve-Garcia, E

    2001-07-01

    The objective of this study was to investigate the effects of dietary fat (lard, sunflower oil, and olive oil) and supplementation of alpha-tocopheryl acetate or beta-carotene on descriptive sensory changes in broiler leg meat as evaluated by a trained panel. Twenty-five descriptors were analyzed from chicken leg meat: 11 in raw meat and 14 in cooked meat. Rancid values were very low, possibly because samples were consumed between 1 and 4 d after slaughter, which maybe insufficient time for oxidative processes to decrease meat sensory quality. However, samples supplemented with vitamin E showed lower rancidity levels, although the differences were only significant when compared to a beta-carotene diet, whereas the control treatment showed intermediate scores. Beta-carotene modified texture scores compared to the control diet, although the differences were only significant in initial juiciness and teeth adhesion compared to the vitamin E treatment and in tenderness compared to the control. In addition, juiciness and tenderness were positively correlated according to the principal component analysis of sensory attributes. The effect of dietary fat on analyzed attributes was lower than the effect of dietary antioxidant. The most important effect of fat type was on hardness of internal fat. Chickens whose diets were supplemented with lard had higher scored values than chickens whose diets were supplemented with vegetable oils. However, type of fat added to diet did not significantly influence rancidity values. These results indicate that an increase in the degree of unsaturation of fat in meat does not cause an increase in the oxidation levels detected by the panel under the conditions of short-term storage.

  5. DPT tautomerisation of the wobble guanine·thymine DNA base mispair is not mutagenic: QM and QTAIM arguments.

    PubMed

    Brovarets', Ol'ha O; Zhurakivsky, Roman O; Hovorun, Dmytro M

    2015-01-01

    We have shown for the first time, connecting QM methods with QTAIM analysis and using the methodology of the sweeps of the energetical, electron-topological and geometrical parameters, that the tautomerisation of the wobble guanine·thymine (wG·T) DNA base mispair into the wG(*)·T(*) base mispair induced by the double proton transfer (DPT), which undergoes a concerted asynchronous pathway, is not mutagenic. The wG·T → wG(*)·T(*) DPT tautomerisation does not result in the transition of the G base into its mutagenic tautomeric form G(*) able to mispair with the T base within the Watson-Crick base pairing scheme. This observation is explained by the so-called quantum protection of the wG·T DNA base mispair from its mutagenic tautomerisation - the dynamical non-stability of the tautomerised wG(*)·T(*) base mispair and significantly negative value of the Gibbs free energy of activation for the reverse reaction of the wG·T → wG(*)·T(*) DPT tautomerisation.

  6. Detection of genetically modified organisms in foods by protein- and DNA-based techniques: bridging the methods.

    PubMed

    van Duijn, Gert J; van Biert, Ria; Bleeker-Marcelis, Henriette; Van Boeijen, Ineke; Adan, Abdi Jama; Jhakrie, Soeniei; Hessing, Martin

    2002-01-01

    According to European Commission (EC) Regulation 1139/98, foods and food ingredients that are to be delivered to the final consumer in which either protein or DNA resulting from genetic modification is present, shall be subject to additional specific labeling requirements. Since 1994, genetically altered tomatoes, squash, potatoes, canola, cotton, and soy have been on the market. Recently, insect-resistant and herbicide-tolerant maize varieties have been introduced. Soy and maize are 2 of the most important vegetable crops in the world. During the past 4 years, both protein- and DNA-based methods have been developed and applied for detection of transgenic soy and maize, and their derivatives. For protein-based detection, specific monoclonal and polyclonal antibodies have been developed; for immunochemical detection, Western blot analysis and enzyme-linked immunosorbent assays are the most prominent examples. For detection of genetically modified organisms (GMOs) at the level of DNA, polymerase chain reaction-based methods are mainly used. For these reactions, highly specific primer sets are needed. This study compares the principally different methods. Specificity of methods and the possible risks of false-positive or false-negative results are considered in relation to sampling, matrix effects, and food processing procedures. In addition, quantitative aspects of protein- and DNA-based GM detection methods are presented and discussed. This is especially relevant as EC regulation 49/2000, which defines a threshold for an unintentional comingling of 1%, came into force on April 10, 2000.

  7. [Risk-benefit analysis of a hCG-500 kcal reducing diet (cura romana) in females].

    PubMed

    Rabe, T; Richter, S; Kiesel, L; Runnebaum, B

    1987-05-01

    The British physician A.T.W. Simeons described in 1954 a new method for dieting. He combined a reduction diet (500 kcal per day) with daily injections of the pregnancy hormone human chorionic gonadotropin (hCG) (125 IU i.m.). According to Simeons the patient should not lose more weight during a 4-to-6 weeks' diet than without hCG, but the injections should facilitate to maintain the diet and to lose body weight at specific parts of the body (e.g. hip, belly, thigh). After the first publication various studies conducted with male and female patients analysed the efficacy of the "Cura romana". 10 of these studies showed positive and another 10 studies negative results with regard to hCG-related weight reduction. Two of these studies with positive results were double-blind studies (hCG vs. placebo). Most of them were reports on therapeutical experiences and were not controlled studies. According to these reports the body proportions normalized and the feeling of hunger was tolerable. Four out of 10 studies with negative results were controlled studies (hCG vs. control without hCG), whereas 6 were double-blind studies. These studies showed a significant weight reduction during dieting, but no differences between treatment groups in respect of body weight, body proportions and feeling of hunger. One of them is the only German study conducted by Rabe et al. in 1981 in which 82 randomised premenopausal volunteers had been dieting either with hCG or without hCG injections. In recent publications describing mostly well-documented double-blind studies authors largely reject hCG administration in dieting. Supporters of the hCG diet must prove the efficacy of this method in controlled studies according to the German Drug Law. Until then the opinion of the German steroid toxicology panel is still valid, that hCG is ineffective in dieting and should not be used (Bolt 1982 a, 1982 b).

  8. Ontogenetic shifts in the diet of plains hog-nosed snakes (Heterodon nasicus) revealed by stable isotope analysis.

    PubMed

    Durso, Andrew M; Mullin, Stephen J

    2017-02-01

    Wild snake diets are difficult to study using traditional methods, but stable isotopes offer several advantages, including integrating dietary information over time, providing data from individuals that have not fed recently, and avoiding bias towards slowly-digesting prey items. We used stable isotope signatures of carbon and nitrogen from scale tissue, red blood cells, and blood plasma to assess the diet of wild plains hog-nosed snakes (Heterodon nasicus) in Illinois. We developed Bayesian mixing models which, taken together, predicted that H. nasicus shifted from a juvenile diet predominantly (31-63%) composed of six-lined racerunners (Aspidoscelis sexlineatus) and their eggs to an adult diet predominantly (44-56%) composed of eggs of the aquatic turtles Chrysemys picta and Chelydra serpentina, with a contribution from toads (Anaxyrus sp.; 6-27%) during their adolescent years. These results agreed with sparse data from gut contents. Combining traditional and isotopic techniques for studying the diets of wild snakes can increase the utility of both types of data.

  9. The effects of adding fat to diets of lactating dairy cows on total-tract neutral detergent fiber digestibility: A meta-analysis.

    PubMed

    Weld, K A; Armentano, L E

    2017-03-01

    The objective of this meta-analysis was to determine the effects of supplemental fat on fiber digestibility in lactating dairy cattle. Published papers that evaluated the effects of adding fat to the diets of lactating dairy cattle on total-tract neutral detergent fiber digestibility (ttNDFd) and dry matter intake (DMI) were compiled. The final data set included 108 fat-supplemented treatment means, not including low-fat controls, from 38 publications. The fat-supplemented treatment means exhibited a wide range of ttNDFd (49.4% ± 9.3, mean ± standard deviation) and DMI (21.3 kg/d ± 3.5). Observations were summarized as the difference between the treatment means for fat-supplemented diets minus their respective low-fat control means. Additionally, those differences were divided by the difference in diet fatty acid (FA) concentration between the treatment and control diets. Treatment means were categorized by the type of fat supplement. Supplementing 3% FA in the diet as medium-chain fats (containing predominately 12- and 14-carbon saturated FA) or unsaturated vegetable oil decreased ttNDFd by 8.0 and 1.2 percentage units, respectively. Adding 3% calcium salts of long-chain FA or saturated fats increased ttNDFd by 3.2 and 1.3 percentage units, respectively. No other fat supplement type affected ttNDFd. Except for saturated fats and animal-vegetable fats, supplementing dietary fat decreased DMI. When the values for changes in ttNDFd are regressed on changes in DMI there was a positive relationship, though the coefficient of determination is only 0.20. When changes in ttNDFd were regressed on changes in DMI, within individual fat supplement types, there was no relationship within calcium salt supplements. There was a positive relationship between changes in ttNDFd and changes in DMI for saturated fats. Neither relationship suggested that the increased ttNDFd with calcium salts or saturated FA was due to decreased DMI for these fat sources. A subset of the means

  10. 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.

  11. Diet history: Method and applications.

    PubMed

    Morán Fagúndez, Luis Juan; Rivera Torres, Alejandra; González Sánchez, María Eugenia; de Torres Aured, Mari Lourdes; Pérez Rodrigo, Carmen; Irles Rocamora, José Antonio

    2015-02-26

    The diet history is a traditional method of analysis of food intake. In its traditional structure consists of three components that provide an overall information of the usual food consumption pattern of the individual and also detailed information on certain foods. The information is collected in an interview and requires highly experienced qualified interviewers. The quality of information depends largely on the skills of the interviewer. It is mostly used in clinical practice. It has also been used in studies of diet and health relationship to investigate the usual diet in the past. The high cost and long duration of the interview limit their usefulness in large epidemiological studies.

  12. Anharmonic Vibrational Signatures of DNA Bases and Watson-Crick Base Pairs

    NASA Astrophysics Data System (ADS)

    Wang, Gui-xiu; Ma, Xiao-yan; Wang, Jian-ping

    2009-12-01

    Changes of molecular structure and associated charge distributions, and changes of anharmonic vibrational parameters from DNA base monomers to the Watson-Crick base pairs, have been investigated at the density functional theory level. Through examination of the NH2, N-H, and C = O stretching vibrational modes that are involved in the multiple H-bonds in the base pairs, sensitivity of their diagonal and off-diagonal anharmonicities, as well as anharmonic vibrational couplings, to the structure change are predicted. Our results reveal the intrinsic connection between the anharmonic vibrational potentials, H-bonding, and electrostatic interactions in DNA bases.

  13. FRET based characterization of DNA-based assemblies

    NASA Astrophysics Data System (ADS)

    Buckhout-White, Susan; Gray, Rochester; Ancona, Mario; Goldman, Ellen R.; Medintz, Igor L.

    2014-05-01

    The "spectroscopic ruler" based on fluorescence resonance energy transfer (FRET) is explored as a method for detailed structural characterization of DNA nanostructures in solution. The approach is most directly useful for assessing the positional relationships among chromophores organized by the DNA, but it can also be used to characterize the geometry and kinematics of the DNA scaffold itself. By accumulating data for the distances separating various donor-acceptor pairs, and correlating them with the expected distances, one can quantify the shape and deformability of the structure. A 8x16nm "mini-origami" rectangle is used as the model test structure and the dye-pairs are chosen to investigate anisotropy in the origami's mechanical properties. Not unexpectedly, our analysis finds a strong anisotropy in the stiffness, with the measured spacing across the origami weave deviating much more from expectation than the spacing aligned along the weave pattern.

  14. 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.

  15. A strand graph semantics for DNA-based computation.

    PubMed

    Petersen, Rasmus L; Lakin, Matthew R; Phillips, Andrew

    2016-06-13

    DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental techniques improve, it is important for modelling languages to keep pace with the complexity of structures that can be realised experimentally. In this paper we present a process calculus for modelling DNA strand displacement computations involving rich secondary structures, including DNA branches and loops. We prove that our calculus is also sufficiently expressive to model previous work on non-branching structures, and propose a mapping from our calculus to a canonical strand graph representation, in which vertices represent DNA strands, ordered sites represent domains, and edges between sites represent bonds between domains. We define interactions between strands by means of strand graph rewriting, and prove the correspondence between the process calculus and strand graph behaviours. Finally, we propose a mapping from strand graphs to an efficient implementation, which we use to perform modelling and simulation of DNA strand displacement systems with rich secondary structure.

  16. 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

  17. Effects of aerobic exercise, diet, or both on lipids and lipoproteins in adults: a meta-analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    BACKGROUND: Studies addressing the effects of aerobic exercise (E), diet (D), or both (ED) on lipids and lipoproteins have led to conflicting results. OBJECTIVE: Determine the effects of E, D, and ED on lipids and lipoproteins. METHODS: Using the aggregate data meta-analytic approach, studies were ...

  18. 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...

  19. Gene expression analysis between rainbow trout strains with different susceptibility to enteritis when reared on plant-based diets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. However, total replacement of fishmeal with plant proteins in diets causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selectiv...

  20. Diet or exercise interventions vs combined behavioral weight management programs: a systematic review and meta-analysis of direct comparisons.

    PubMed

    Johns, David J; Hartmann-Boyce, Jamie; Jebb, Susan A; Aveyard, Paul

    2014-10-01

    Weight loss can reduce the health risks associated with being overweight or obese. However, the most effective method of weight loss remains unclear. Some programs emphasize physical activity, others diet, but existing evidence is mixed as to whether these are more effective individually or in combination. We aimed to examine the clinical effectiveness of combined behavioral weight management programs (BWMPs) targeting weight loss in comparison to single component programs, using within study comparisons. We included randomized controlled trials of combined BWMPs compared with diet-only or physical activity-only programs with at least 12 months of follow-up, conducted in overweight and obese adults (body mass index ≥25). Systematic searches of nine databases were run and two reviewers extracted data independently. Random effects meta-analyses were conducted for mean difference in weight change at 3 to 6 months and 12 to 18 months using a baseline observation carried forward approach for combined BWMPs vs diet-only BWMPs and combined BWMPs vs physical activity-only BWMPs. In total, eight studies were included, representing 1,022 participants, the majority of whom were women. Six studies met the inclusion criteria for combined BWMP vs diet-only. Pooled results showed no significant difference in weight loss from baseline or at 3 to 6 months between the BWMPs and diet-only arms (-0.62 kg; 95% CI -1.67 to 0.44). However, at 12 months, a significantly greater weight-loss was detected in the combined BWMPs (-1.72 kg; 95% CI -2.80 to -0.64). Five studies met the inclusion criteria for combined BWMP vs physical activity-only. Pooled results showed significantly greater weight loss in the combined BWMPs at 3 to 6 months (-5.33 kg; 95% CI -7.61 to -3.04) and 12 to 18 months (-6.29 kg; 95% CI -7.33 to -5.25). Weight loss is similar in the short-term for diet-only and combined BWMPs but in the longer-term weight loss is increased when diet and physical activity are combined

  1. Nutrition and Diet

    MedlinePlus

    ... Thai HbH:Vietnamese Relevant links Living with Thalassemia NUTRITION ▶ Nutrition and DietDiet for the Non-transfused ... Nutrition with Connie Schroepfer, MS, RD: Dec 2016 Nutrition and Diet Nutritional deficiencies are common in thalassemia, ...

  2. Diet - liver disease

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/002441.htm Diet - liver disease To use the sharing features on this page, please enable JavaScript. Some people with liver disease must eat a special diet. This diet ...

  3. Diet myths and facts

    MedlinePlus

    Obesity - diet myths and facts; Overweight - diet myths and fact; Weight-loss diet myths and facts ... evidence: using the proposed effect of breakfast on obesity to show 2 practices that distort scientific evidence. ...

  4. Does Diet-Induced Weight Loss Lead to Bone Loss in Overweight or Obese Adults? A Systematic Review and Meta-Analysis of Clinical Trials.

    PubMed

    Zibellini, Jessica; Seimon, Radhika V; Lee, Crystal M Y; Gibson, Alice A; Hsu, Michelle S H; Shapses, Sue A; Nguyen, Tuan V; Sainsbury, Amanda

    2015-12-01

    Diet-induced weight loss has been suggested to be harmful to bone health. We conducted a systematic review and meta-analysis (using a random-effects model) to quantify the effect of diet-induced weight loss on bone. We included 41 publications involving overweight or obese but otherwise healthy adults who followed a dietary weight-loss intervention. The primary outcomes examined were changes from baseline in total hip, lumbar spine, and total body bone mineral density (BMD), as assessed by dual-energy X-ray absorptiometry (DXA). Secondary outcomes were markers of bone turnover. Diet-induced weight loss was associated with significant decreases of 0.010 to 0.015 g/cm(2) in total hip BMD for interventions of 6, 12, or 24 (but not 3) months' duration (95% confidence intervals [CIs], -0.014 to -0.005, -0.021 to -0.008, and -0.024 to -0.000 g/cm(2), at 6, 12, and 24 months, respectively). There was, however, no statistically significant effect of diet-induced weight loss on lumbar spine or whole-body BMD for interventions of 3 to 24 months' duration, except for a significant decrease in total body BMD (-0.011 g/cm(2); 95% CI, -0.018 to -0.003 g/cm(2)) after 6 months. Although no statistically significant changes occurred in serum concentrations of N-terminal propeptide of type I procollagen (P1NP), interventions of 2 or 3 months in duration (but not of 6, 12, or 24 months' duration) induced significant increases in serum concentrations of osteocalcin (0.26 nmol/L; 95% CI, 0.13 to 0.39 nmol/L), C-terminal telopeptide of type I collagen (CTX) (4.72 nmol/L; 95% CI, 2.12 to 7.30 nmol/L) or N-terminal telopeptide of type I collagen (NTX) (3.70 nmol/L; 95% CI, 0.90 to 6.50 nmol/L bone collagen equivalents [BCEs]), indicating an early effect of diet-induced weight loss to promote bone breakdown. These data show that in overweight and obese individuals, a single diet-induced weight-loss intervention induces a small decrease in total hip BMD, but not lumbar spine

  5. Forensic aspects of mass disasters: strategic considerations for DNA-based human identification.

    PubMed

    Budowle, Bruce; Bieber, Frederick R; Eisenberg, Arthur J

    2005-07-01

    Many mass disasters result in loss of lives. Law enforcement and/or public safety and health officials often have the responsibility for identifying the human remains found at the scene, so they can be returned to their families. The recovered human remains range from being relatively intact to highly degraded. DNA-based identity testing is a powerful tool for victim identification in that the data are not restricted to any particular one to one body landmark comparison and DNA profile comparisons can be used to associate separated remains or body parts. Even though DNA typing is straightforward, a disaster is a chaotic environment that can complicate effective identification of the remains. With some planning, or at least identification of the salient features to consider, stress can be reduced for those involved in the identification process. General guidelines are provided for developing an action plan for identification of human remains from a mass disaster by DNA analysis. These include: (1) sample collection, preservation, shipping and storage; (2) tracking and chain of custody issues; (3) laboratory facilities; (4) quality assurance and quality control practices; (5) parsing out work; (6) extraction and typing; (7) interpretation of results; (8) automation; (9) software for tracking and managing data; (10) the use of an advisory panel; (11) education and communication; and (12) privacy issues. In addition, key technologies that may facilitate the identification process are discussed, such as resin based DNA extraction, real-time PCR for quantitation of DNA, use of mini-STRs, SNP detection procedures, and software. Many of the features necessary for DNA typing of human remains from a mass disaster are the same as those for missing persons' cases. Therefore, developing a missing persons DNA identification program would also provide the basis for a mass disaster human remains DNA identification program.

  6. Cost-Effectiveness Analysis of a Low-Fat Diet in the Prevention of Breast and Ovarian Cancer

    PubMed Central

    BÓS, ANTÔNIO M.; HOWARD, BARBARA V.; BERESFORD, SHIRLEY A. A.; URBAN, NICOLE; TINKER, LESLEY F.; WATERS, HUGH; BÓS, ÂNGELO J.; CHLEBOWSKI, ROWAN; ENNIS, JACQUELINE M.

    2015-01-01

    Background Results of the Women’s Health Initiative Randomized Controlled Dietary Modification Trial (WHI-DM) suggest that a low-fat diet may be associated with beneficial health outcomes for specific groups of women. Objective The objective is to assess how cost-effective the WHI-DM would be if implemented as a public health intervention and under the sponsorship of private health insurers and Medicare. Breast and ovarian cancers are the health outcomes of interest. Participants Two groups of WHI-DM participants form the target population for this analysis: participants consuming >36.8% of energy from fat at baseline, and participants at high risk for breast cancer with 32% or more of energy from fat at baseline. Methods This study uses Markov cohort modeling, following societal and health care payer perspectives, with Monte Carlo simulations and one-way sensitivity analyses. WHI-DM records, nationally representative prices, and published estimates of medical care costs were the sources of cost information. Simulations were performed for hypothetical cohorts of women aged 50, 55, 60, 65, or 70 years at the beginning of the intervention. Effectiveness was estimated by quality-adjusted life years (QALYs) and the main outcome measure was the incremental cost-effectiveness ratio (ICER). Results Following the societal perspective, the ICERs for the 50-year old cohort are $13,773/QALY (95% confidence interval $7,482 to $20,916) for women consuming >36.8% of energy from fat at baseline and $10,544/QALY ($2,096 to $23,673) for women at high risk for breast cancer. The comparable ICER from a private health care payer perspective is $66,059/QALY ($30,155 to $121,087) and from a Medicare perspective, it is $15,051/QALY ($6,565 to $25,105). Conclusions The WHI-DM is a cost-effective strategy for the prevention of breast and ovarian cancers in the target population, from both societal and Medicare perspectives. Private health care payers have a relative short time-frame to

  7. Potential for DNA-based ID of Great Lakes fauna: Species inventories vs. barcode libraries

    EPA Science Inventory

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However the abil...

  8. Comparison of High vs. Normal/Low Protein Diets on Renal Function in Subjects without Chronic Kidney Disease: A Systematic Review and Meta-Analysis

    PubMed Central

    Schwingshackl, Lukas; Hoffmann, Georg

    2014-01-01

    Background It was the aim of the present systematic review and meta-analysis to investigate the effects of high protein (HP) versus normal/low protein (LP/NP) diets on parameters of renal function in subjects without chronic kidney disease. Methods Queries of literature were performed using the electronic databases MEDLINE, EMBASE, and the Cochrane Trial Register until 27th February 2014. Study specific weighted mean differences (MD) were pooled using a random effect model by the Cochrane software package Review Manager 5.1. Findings 30 studies including 2160 subjects met the objectives and were included in the meta-analyses. HP regimens resulted in a significantly more pronounced increase in glomerular filtration rate [MD: 7.18 ml/min/1.73 m2, 95% CI 4.45 to 9.91, p<0.001], serum urea [MD: 1.75 mmol/l, 95% CI 1.13 to 237, p<0.001], and urinary calcium excretion [MD: 25.43 mg/24h, 95% CI 13.62 to 37.24, p<0.001] when compared to the respective LP/NP protocol. Conclusion HP diets were associated with increased GFR, serum urea, urinary calcium excretion, and serum concentrations of uric acid. In the light of the high risk of kidney disease among obese, weight reduction programs recommending HP diets especially from animal sources should be handled with caution. PMID:24852037

  9. Maternal eating disorder and infant diet. A latent class analysis based on the Norwegian Mother and Child Cohort Study (MoBa).

    PubMed

    Torgersen, Leila; Ystrom, Eivind; Siega-Riz, Anna Maria; Berg, Cecilie Knoph; Zerwas, Stephanie C; Reichborn-Kjennerud, Ted; Bulik, Cynthia M

    2015-01-01

    Knowledge of infant diet and feeding practices among children of mothers with eating disorders is essential to promote healthy eating in these children. This study compared the dietary patterns of 6-month-old children of mothers with anorexia nervosa, bulimia nervosa, binge eating disorder, and eating disorder not otherwise specified-purging subtype, to the diet of children of mothers with no eating disorders (reference group). The study was based on 53,879 mothers in the Norwegian Mother and Child Cohort Study (MoBa). Latent class analysis (LCA) was used to identify discrete latent classes of infant diet based on the mothers' responses to questions about 16 food items. LCA identified five classes, characterized by primarily homemade vegetarian food (4% of infants), homemade traditional food (8%), commercial cereals (35%), commercial jarred baby food (39%), and a mix of all food groups (11%). The association between latent dietary classes and maternal eating disorders were estimated by multinomial logistic regression. Infants of mothers with bulimia nervosa had a lower probability of being in the homemade traditional food class compared to the commercial jarred baby food class, than the referent (O.R. 0.59; 95% CI 0.36-0.99). Infants of mothers with binge eating disorder had a lower probability of being in the homemade vegetarian class compared to the commercial jarred baby food class (O.R. 0.77; 95% CI 0.60-0.99), but only before adjusting for relevant confounders. Anorexia nervosa and eating disorder not otherwise specified-purging subtype were not statistically significantly associated with any of the dietary classes. These results suggest that maternal eating disorders may to some extent influence the child's diet at 6 months; however, the extent to which these differences influence child health and development remains an area for further inquiry.

  10. Weight losses with low-energy formula diets in obese patients with and without type 2 diabetes: systematic review and meta-analysis

    PubMed Central

    Leslie, W S; Taylor, R; Harris, L; Lean, M E J

    2017-01-01

    Aim: To provide a systematic review, of published data, to compare weight losses following very low calorie (<800 kcal per day VLCD) or low-energy liquid-formula (>800 kcal per day LELD) diets, in people with and without type 2 diabetes mellitus (T2DM). Methods: Systematic electronic searches of Medline (1946–2015) and Embase (1947–2015) to identify published studies using formula total diet replacement diets (VLCD/LELD). Random effects meta-analysis using weighted mean difference (WMD) in body weight between groups (with and without diabetes) as the summary estimate. Results: Final weight loss, in the five included studies, weighted for study sizes, (n=569, mean BMI=35.5–42.6 kg/m2), was not significantly different between participants with and without T2DM: −1.2 kg; 95% CI: −4.1 to 1.6 kg). Rates of weight loss were also similar in the two groups −0.6 kg per week (T2DM) and 0.5 kg per week (no diabetes), and for VLCD (<800 kcal per day) and LELD (>800 kcal per day). Conclusions: Weight losses with liquid-formula diets are very similar for VLCD and LELD and for obese subjects with or without T2DM. They can potentially achieve new weight loss/ maintenance targets of >15–20% for people with severe and medically complicated obesity. PMID:27698345

  11. Vacuum-Ultraviolet photoionization studies of the microhydrationof DNA bases (Guanine, Cytosine, Adenine and Thymine)

    SciTech Connect

    Belau, L.; Wilson, K.R.; Leone, S.R.; Musahid, Ahmed

    2007-01-22

    In this work, we report on a photoionization study of the microhydration of the four DNA bases. Gas-phase clusters of water with DNA bases [guanine (G), cytosine (C), adenine (A), and thymine (T)] are generated via thermal vaporization of the bases and expansion of the resultant vapor in a continuous supersonic jet expansion of water seeded in Ar. The resulting clusters are investigated by single-photon ionization with tunable vacuum-ultraviolet synchrotron radiation and mass analyzed using reflectron mass spectrometry. Photoionization efficiency (PIE) curves are recorded for the DNA bases and the following water (W) clusters: G, GW{sub n} (n = 1-3); C, CW{sub n} (n = 1-3); A, AW{sub n} (n = 1,2); and T, TW{sub n} (n = 1-3). Appearance energies (AE) are derived from the onset of these PIE curves (all energies in eV): G (8.1 {+-} 0.1), GW (8.0 {+-} 0.1), GW{sub 2} (8.0 {+-} 0.1), and GW{sub 3} (8.0); C (8.65 {+-} 0.05), CW (8.45 {+-} 0.05), CW{sub 2} (8.4 {+-} 0.1), and CW{sub 3} (8.3 {+-} 0.1); A (8.30 {+-} 0.05), AW (8.20 {+-} 0.05), and AW{sub 2} (8.1 {+-} 0.1); T (8.90 {+-} 0.05); and TW (8.75 {+-} 0.05), TW{sub 2} (8.6 {+-} 0.1), and TW{sub 3} (8.6 {+-} 0.1). The AEs of the DNA bases decrease slightly with the addition of water molecules (up to three) but do not converge to values found for photoinduced electron removal from DNA bases in solution.

  12. Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health

    PubMed Central

    Kelder, T; Stroeve, J H M; Bijlsma, S; Radonjic, M; Roeselers, G

    2014-01-01

    Background: Recent evidence suggests that the gut microbiota plays an important role in human metabolism and energy homeostasis and is therefore a relevant factor in the assessment of metabolic health and flexibility. Understanding of these host–microbiome interactions aids the design of nutritional strategies that act via modulation of the microbiota. Nevertheless, relating gut microbiota composition to host health states remains challenging because of the sheer complexity of these ecosystems and the large degrees of interindividual variation in human microbiota composition. Methods: We assessed fecal microbiota composition and host response patterns of metabolic and inflammatory markers in 10 apparently healthy men subjected to a high-fat high-caloric diet (HFHC, 1300 kcal/day extra) for 4 weeks. DNA was isolated from stool and barcoded 16S rRNA gene amplicons were sequenced. Metabolic health parameters, including anthropomorphic and blood parameters, where determined at t=0 and t=4 weeks. Results: A correlation network approach revealed diet-induced changes in Bacteroides levels related to changes in carbohydrate oxidation rates, whereas the change in Firmicutes correlates with changes in fat oxidation. These results were confirmed by multivariate models. We identified correlations between microbial diversity indices and several inflammation-related host parameters that suggest a relation between diet-induced changes in gut microbiota diversity and inflammatory processes. Conclusions: This approach allowed us to identify significant correlations between abundances of microbial taxa and diet-induced shifts in several metabolic health parameters. Constructed correlation networks provide an overview of these relations, revealing groups of correlations that are of particular interest for explaining host health aspects through changes in the gut microbiota. PMID:24979151

  13. Diet and mobility in a late Neolithic population of coastal Oman inferred from radiocarbon dating and stable isotope analysis.

    PubMed

    Zazzo, Antoine; Munoz, Olivia; Saliège, Jean-François

    2014-03-01

    In Oman, the presence of highly productive marine environments, coupled with relatively limited land resources, have led to intense exploitation of coastal resources, but the question of the seasonality of occupation of coastal sites remains open. Our aim is to evaluate the contribution of marine resources to the diet of the Neolithic population of Ra's al-Hamra 5 (RH-5) to shed new light on its mobility, using stable isotopes and radiocarbon ((14)C) dating as dietary tracers. Charcoal, shell, human bone and enamel apatite from eight contemporary graves were sampled. Graves are thought to provide the best chance to obtain marine and terrestrial remains that were contemporary with the human remains in order to calculate the marine reservoir effect (MRE) for this period. Inter-individual variation in human bone apatite δ(13)C value is small, suggesting a homogenous diet. Bone apatite (14)C ages are very close to the shell ages while enamel is significantly younger and plots near the charcoal ages. Older enamel ages were obtained when a stronger acetic treatment was used, demonstrating that the young ages are due to diagenetic alteration rather than a diachronic change in diet and that only bone apatite retained in vivo dietary signals. Bone ages indicate a heavy reliance on marine resources and it is therefore unlikely that the individuals analyzed here were leaving the coast seasonally, although mobility along the coast cannot be excluded.

  14. Integrating DNA-based data into bioassessments improves our understanding of species distributions and species habitat relationships

    EPA Science Inventory

    The integration of DNA-based identification methods into bioassessments could result in more accurate representations of species distributions and species-habitat relationships. DNA-based approaches may be particularly informative for tracking the distributions of rare and/or inv...

  15. Hidden Conformation Events in DNA Base Extrusions: A Generalized Ensemble Path Optimization and Equilibrium Simulation Study

    PubMed Central

    Cao, Liaoran; Lv, Chao; Yang, Wei

    2013-01-01

    DNA base extrusion is a crucial component of many biomolecular processes. Elucidating how bases are selectively extruded from the interiors of double-strand DNAs is pivotal to accurately understanding and efficiently sampling this general type of conformational transitions. In this work, the on-the-path random walk (OTPRW) method, which is the first generalized ensemble sampling scheme designed for finite-temperature-string path optimizations, was improved and applied to obtain the minimum free energy path (MFEP) and the free energy profile of a classical B-DNA major-groove base extrusion pathway. Along the MFEP, an intermediate state and the corresponding transition state were located and characterized. The MFEP result suggests that a base-plane-elongation event rather than the commonly focused base-flipping event is dominant in the transition state formation portion of the pathway; and the energetic penalty at the transition state is mainly introduced by the stretching of the Watson-Crick base pair. Moreover to facilitate the essential base-plane-elongation dynamics, the surrounding environment of the flipped base needs to be intimately involved. Further taking the advantage of the extended-dynamics nature of the OTPRW Hamiltonian, an equilibrium generalized ensemble simulation was performed along the optimized path; and based on the collected samples, several base-flipping (opening) angle collective variables were evaluated. In consistence with the MFEP result, the collective variable analysis result reveals that none of these commonly employed flipping (opening) angles alone can adequately represent the base extrusion pathway, especially in the pre-transition-state portion. As further revealed by the collective variable analysis, the base-pairing partner of the extrusion target undergoes a series of in-plane rotations to facilitate the base-plane-elongation dynamics. A base-plane rotation angle is identified to be a possible reaction coordinate to represent

  16. Negative stereotypes of the Scottish diet: A qualitative analysis of deep-fried Mars bar references in bestselling newspapers in Scotland, 2011-14.

    PubMed

    Knight, Christine

    2016-08-01

    The Scottish diet is associated in the UK media and popular discourse with unhealthy deep-fried foods. In addition to the stereotype's negative effects on perceptions of Scottish food, culture and people, there is evidence that the stereotype of the Scottish diet has negative effects on food behaviour and public health in Scotland, having been shown to encourage consumption of deep-fried foods and discourage positive dietary change. The most notorious deep-fried food associated with Scotland is the deep-fried Mars bar (DFMB), arguably invented in Stonehaven (near Aberdeen), and first reported in the Scottish and UK press in 1995. This article reports findings from an analysis of newspaper references to the DFMB in the two highest selling newspapers in Scotland, the Scottish Sun and the Daily Record, between 2011 and 2014. A keyword search ("deep fried Mars bar") using the online media database Lexis Library generated 97 unique records, and the resulting dataset was analysed thematically and discursively. Analysis showed that both newspapers clearly associated the DFMB with Scotland. Further, both newspapers portrayed the DFMB and the broader "deep-fried" Scottish diet stereotype ambivalently (mixed positive and negative associations). However, the Daily Record actively criticised the DFMB stereotype much more often than did the Scottish Sun. These findings suggest that the Scottish population encounters different messages in the press about food and nutrition from people elsewhere in the UK, and that these messages vary depending on choice of media in Scotland. Given the known negative effects of the stereotype, differences in Scottish media discourse should be considered a potential factor in persistent health inequalities affecting Scotland. Educational efforts, and opening discussion with journalists and amongst the Scottish public, may be helpful.

  17. Evaluating marine diets through radiocarbon dating and stable isotope analysis of victims of the AD79 eruption of Vesuvius.

    PubMed

    Craig, Oliver E; Bondioli, Luca; Fattore, Luciano; Higham, Tom; Hedges, Robert

    2013-11-01

    The stable carbon (δ(13) C) and nitrogen (δ(15) N) isotope values of bone collagen are frequently used in paleodietary studies to assess the marine contribution to an individual's diet. Surprisingly, the relationship between stable isotope these values characteristics and the percentage of marine foods in diet has never been effectively demonstrated. To clarify this relationship, the stable isotope values and radiocarbon dates of nine humans and one sheep from Herculaneum, all who perished simultaneously during the AD 79 eruption of Vesuvius, were determined. Significant differences were found in the radiocarbon dates which are attributable to the incorporation of "old" carbon from the marine reservoir. The magnitude of the observed differences was linearly correlated with both δ(13) C and δ(15) N values allowing the response of each isotope to increasing marine carbon in collagen to be independently verified. Regression analyses showed that for every 1‰ enrichment in δ(13) C and δ(15) N, 56 years and 34 years were added to the radiocarbon age, respectively. Predictions of the maximum marine reservoir age differed considerably depending on which stable isotope was considered. This discrepancy is attributed to some degree of macronutrient scrambling whereby nitrogen from marine protein is preferentially incorporated in collagen over marine carbon. It is suggested that the macronutrient scrambling explains the observed relationship between δ(13) C and δ(15) N from Roman coastal sites and should be considered when interpreting any diet which is not dominated by protein. Nevertheless, without knowing the degree of macronutrient scrambling in different dietary scenarios, the accuracy of dietary reconstructions is severely compromised.

  18. Fish diets in a freshwater-deprived semiarid estuary (The Coorong, Australia) as inferred by stable isotope analysis

    NASA Astrophysics Data System (ADS)

    Lamontagne, S.; Deegan, B. M.; Aldridge, K. T.; Brookes, J. D.; Geddes, M. C.

    2016-09-01

    In 2007, high rates of water extraction combined with a regional drought stopped freshwater discharge to the Coorong, a ∼120 km estuarine and coastal lagoon system at the outlet of the River Murray (Australia). The sources of organic matter sustaining the Coorong food web in the absence of river-borne organic matter and nutrient inputs were evaluated by measuring δ13C, δ15N and δ34S in large-bodied fish and their prey. In general, the δ34S of the food web (mean = 11.3‰; range = 4.32-18.9‰) suggested a comparable contribution from autochthonous pelagic (∼21‰) and benthic (<5‰) primary production. A relatively high δ13C in all organisms (-20 to -9.2‰) was also consistent with a dominant contribution from autochtonous sources to the food web. A Bayesian mixing model framework (SIMMR) was used to estimate the diet of large-bodied fish for statistically-determined prey groups based on their similarity in isotopic composition. Argyrosomus japonicus preyed primarily on Fish Group 1 (small pelagic fish like galaxiids and Hyperlophus vittatus), Rhombosolea tapirina on Invertebrate Group 2 (polychaetes like Capitella spp.) but Acanthopagrus butcheri fed on a wide variety of fish and invertebrate groups. A partial switch in diet to other prey groups suggested larger Ar. japonicus fed on larger prey, such as crabs and adult Aldrichetta forsteri. Despite being numerically abundant at the time, Fish Group 2 (benthic species) was a relatively low proportion of large-bodied fish diets. This probably reflected the tendency of some salt-tolerant members of this group (such as Atherinosoma microstoma) to prefer hypersaline habitats, which the large-bodied fish avoided. As the heavily preyed-on Fish Group 1 included species with a marine component to their life-cycle, marine productivity may also help to maintain this estuarine ecosystem in the absence of river-borne organic matter inputs.

  19. Reactions of DNA bases with the anti-cancer nitrogen mustard mechlorethamine: A quantum chemical study

    NASA Astrophysics Data System (ADS)

    Shukla, P. K.; Mishra, P. C.; Suhai, S.

    2007-12-01

    Reactions of the aziridinium ion of mechlorethamine (AZ+1) at the N7, N3 and O6 sites of guanine, N7, N3 and N1 sites of adenine, O2 and N3 sites of cytosine, and O2 and O4 sites of thymine were studied using density functional theory (B3LYP) and the MP2 method in gas phase and aqueous media. The calculations explain the mechanism of alkylation of the DNA bases and show that the reactions of the AZ+1 ion would be most likely to occur at the N7 site of guanine and the N3 site of adenine while it would be much less likely to occur at the carbonyl oxygen sites of the DNA bases.

  20. Microwave-Induced Inactivation of DNA-Based Hybrid Catalyst in Asymmetric Catalysis

    PubMed Central

    Zhao, Hua; Shen, Kai

    2015-01-01

    DNA-based hybrid catalysts have gained strong interests in asymmetric reactions. However, to maintain the high enantioselectivity, these reactions are usually conducted at relatively low temperatures (e.g. < 5 °C) for 2–3 days. Aiming to improve the reaction’s turnover rate, we evaluated microwave irradiation with simultaneous cooling as potential energy source since this method has been widely used to accelerate various chemical and enzymatic reactions. However, our data indicated that microwave irradiation induced an inactivation of DNA-based hybrid catalyst even at low temperatures (such as 5 °C). Circular dichroism (CD) spectra and gel electrophoresis of DNA suggest that microwave exposure degrades DNA molecules and disrupts DNA double-stranded structures, causing changes of DNA–metal ligand binding properties and thus poor DNA catalytic performance. PMID:26712696

  1. DNA Bases Thymine and Adenine in Bio-Organic Light Emitting Diodes

    DTIC Science & Technology

    2014-11-24

    DNA Bases Thymine and Adenine in Bio-Organic Light Emitting Diodes Eliot F. Gomez1, Vishak Venkatraman1, James G. Grote2 & Andrew J. Steckl1...45433-7707 USA. We report on the use of nucleic acid bases (NBs) in organic light emitting diodes (OLEDs). NBs are small molecules that are the basic...polymer has been a frequent natural material integrated in electronic devices. DNA has been used in organic light - emitting diodes (OLEDs)4,5,7–14

  2. Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers.

    PubMed

    Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

    2010-12-09

    The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

  3. DNA-based dye lasers: progress in this half a decade

    NASA Astrophysics Data System (ADS)

    Kawabe, Yutaka

    2016-09-01

    After the invention of DNA-surfactant films and the proposal of dye doping into them by Ogata, many applications were demonstrated. Among them tunable thin film laser is one of the most attractive functional devices. Development and progress in DNA based lasers after the first observation of amplified spontaneous emission (ASE) by us has been reviewed in a former paper published in 2011.1 In this proceeding, progresses in the subsequent half a decade are described.

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

    PubMed Central

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

    2015-01-01

    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 through February 2011. Twenty-four publications met inclusion criteria for synthetic food colors; 10 additional studies informed analysis of dietary restriction. A random-effects meta-analytic model generated summary effect sizes. Results Restriction diets reduced ADHD symptoms at an effect of g = 0.29 (95% CI, 0.07–0.53). For food colors, parent reports yielded an effect size of g = 0.18 (95% CI, 0.08–0.24; p = .0007), which decreased to 0.12 (95% CI, 0.01–0.23; p < .05) after adjustment for possible publication bias. The effect was reliable in studies restricted to food color additives (g = 0.21, 95% CI = 0.06–0.36) but did not survive correction for possible publication bias and was not reliable in studies confined to Food and Drug Administration–approved food colors. Teacher/observer reports yielded a nonsignificant effect of 0.07 (95% CI = −0.03 to 0.18; p = .14). However, high-quality studies confined to color additives yielded a reliable effect (g = 0.22, 95% CI = 0.10–0.41, p = .030) that survived correction. In psychometric tests of attention, the summary effect size was 0.27 (95% CI = 0.07–0.47; p = .007) and survived correction. An estimated 8% of children with ADHD may have symptoms related to synthetic food colors. Conclusions A restriction diet benefits some children with ADHD. Effects of food colors were notable were but susceptible to publication bias or were derived from small, nongeneralizable samples. Renewed investigation of diet and ADHD is warranted. PMID:22176942

  5. DNA-based biosensors for Hg(2+) determination by polythymine-methylene blue modified electrodes.

    PubMed

    Tortolini, Cristina; Bollella, Paolo; Antonelli, Marta Letizia; Antiochia, Riccarda; Mazzei, Franco; Favero, Gabriele

    2015-05-15

    In this work we have developed a new electrochemical DNA-based biosensor for the selective determination of the Hg(2+) ion by the use of different electrodes modified with polythymine, bearing methylene blue, as redox probe, in 3' position. The determination of Hg(2+) can be employed with an excellent degree of selectivity by the use of DNA biosensors through the formation of the complex Thymine-Hg-Thymine (T-Hg-T): in fact, Hg(2+) tends to bind two thymines, generating a T-Hg-T complex with a formation constant higher than that one of the coupling Adenine-Thymine, which can be employed for a selective, fast and cost-effective Hg(2+) detection. The presence of the Hg(2+) in solution leads to the formation of T-Hg-T complex thus causing the "hairpin-like" folding of oligonucleotide, leading to an improved electronic exchange of methylene blue with the electrode surface due to the reduced distance and thus to an increase of the faradic current which is detected by means of square wave voltammetry (SWV). To test the feasibility of this kind of biosensor to be applied to the analysis of Hg(2+) we have developed several biosensors configuration by modifying the electrochemical sensor transducer: (a) Au electrode; (b) Au screen-printed electrode (SPE). The proposed system, allows the determination of Hg(2+) in the range 0.2-100 nM (0.05-20 ppb), with a sensitivity 0.327 µA/nM, LOD 0.1 nM (0.02 ppb), LOQ 0.2 nM (0.05 ppb) and RSD ≤4.3% when Au electrode is used as electrochemical transducer; on the other hand, in the case of Au SPE the linear range is 0.2-50 nM (0.05-10 ppb), with a sensitivity 0.285 µA/nM, while LOD and LOQ are the same as previously and RSD is ≤3.8%. This enabled the detection of mercury in real samples (waters and fishes) with good accuracy (recoveries 92-101% on waters and 92-107% on fishes, respectively) and reproducibility (RSD ≤9.6% for measurements on waters and ≤8.8% on fishes, respectively).

  6. High-speed DNA-based rolling motors powered by RNase H.

    PubMed

    Yehl, Kevin; Mugler, Andrew; Vivek, Skanda; Liu, Yang; Zhang, Yun; Fan, Mengzhen; Weeks, Eric R; Salaita, Khalid

    2016-02-01

    DNA-based machines that walk by converting chemical energy into controlled motion could be of use in applications such as next-generation sensors, drug-delivery platforms and biological computing. Despite their exquisite programmability, DNA-based walkers are challenging to work with because of their low fidelity and slow rates (∼1 nm min(-1)). Here we report DNA-based machines that roll rather than walk, and consequently have a maximum speed and processivity that is three orders of magnitude greater than the maximum for conventional DNA motors. The motors are made from DNA-coated spherical particles that hybridize to a surface modified with complementary RNA; the motion is achieved through the addition of RNase H, which selectively hydrolyses the hybridized RNA. The spherical motors can move in a self-avoiding manner, and anisotropic particles, such as dimerized or rod-shaped particles, can travel linearly without a track or external force. We also show that the motors can be used to detect single nucleotide polymorphism by measuring particle displacement using a smartphone camera.

  7. High-speed DNA-based rolling motors powered by RNase H

    NASA Astrophysics Data System (ADS)

    Yehl, Kevin; Mugler, Andrew; Vivek, Skanda; Liu, Yang; Zhang, Yun; Fan, Mengzhen; Weeks, Eric R.; Salaita, Khalid

    2016-02-01

    DNA-based machines that walk by converting chemical energy into controlled motion could be of use in applications such as next-generation sensors, drug-delivery platforms and biological computing. Despite their exquisite programmability, DNA-based walkers are challenging to work with because of their low fidelity and slow rates (˜1 nm min-1). Here we report DNA-based machines that roll rather than walk, and consequently have a maximum speed and processivity that is three orders of magnitude greater than the maximum for conventional DNA motors. The motors are made from DNA-coated spherical particles that hybridize to a surface modified with complementary RNA; the motion is achieved through the addition of RNase H, which selectively hydrolyses the hybridized RNA. The spherical motors can move in a self-avoiding manner, and anisotropic particles, such as dimerized or rod-shaped particles, can travel linearly without a track or external force. We also show that the motors can be used to detect single nucleotide polymorphism by measuring particle displacement using a smartphone camera.

  8. High-speed DNA-based rolling motors powered by RNase H

    PubMed Central

    Yehl, Kevin; Mugler, Andrew; Vivek, Skanda; Liu, Yang; Zhang, Yun; Fan, Mengzhen; Weeks, Eric R.

    2016-01-01

    DNA-based machines that walk by converting chemical energy into controlled motion could be of use in applications such as next generation sensors, drug delivery platforms, and biological computing. Despite their exquisite programmability, DNA-based walkers are, however, challenging to work with due to their low fidelity and slow rates (~1 nm/min). Here, we report DNA-based machines that roll rather than walk, and consequently have a maximum speed and processivity that is three-orders of magnitude greater than conventional DNA motors. The motors are made from DNA-coated spherical particles that hybridise to a surface modified with complementary RNA; motion is achieved through the addition of RNase H, which selectively hydrolyses hybridised RNA. Spherical motors move in a self-avoiding manner, whereas anisotropic particles, such as dimerised particles or rod-shaped particles travel linearly without a track or external force. Finally, we demonstrate detection of single nucleotide polymorphism by measuring particle displacement using a smartphone camera. PMID:26619152

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

    PubMed Central

    Abu-Salah, Khalid M.; Zourob, Mohammed M.; Mouffouk, Fouzi; Alrokayan, Salman A.; Alaamery, Manal A.; Ansari, Anees A.

    2015-01-01

    Detection of disease at an early stage is one of the biggest challenges in medicine. Different disciplines of science are working together in this regard. The goal of nanodiagnostics is to provide more accurate tools for earlier diagnosis, to reduce cost and to simplify healthcare delivery of effective and personalized medicine, especially with regard to chronic diseases (e.g., diabetes and cardiovascular diseases) that have high healthcare costs. Up-to-date results suggest that DNA-based nanobiosensors could be used effectively to provide simple, fast, cost-effective, sensitive and specific detection of some genetic, cancer, and infectious diseases. In addition, they could potentially be used as a platform to detect immunodeficiency, and neurological and other diseases. This review examines different types of DNA-based nanobiosensors, the basic principles upon which they are based and their advantages and potential in diagnosis of acute and chronic diseases. We discuss recent trends and applications of new strategies for DNA-based nanobiosensors, and emphasize the challenges in translating basic research to the clinical laboratory. PMID:26102488

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

    PubMed

    Abu-Salah, Khalid M; Zourob, Mohammed M; Mouffouk, Fouzi; Alrokayan, Salman A; Alaamery, Manal A; Ansari, Anees A

    2015-06-19

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

  11. Re-evaluation of the traditional diet-heart hypothesis: analysis of recovered data from Minnesota Coronary Experiment (1968-73)

    PubMed Central

    Zamora, Daisy; Majchrzak-Hong, Sharon; Faurot, Keturah R; Broste, Steven K; Frantz, Robert P; Davis, John M; Ringel, Amit; Suchindran, Chirayath M; Hibbeln, Joseph R

    2016-01-01

    Objective To examine the traditional diet-heart hypothesis through recovery and analysis of previously unpublished data from the Minnesota Coronary Experiment (MCE) and to put findings in the context of existing diet-heart randomized controlled trials through a systematic review and meta-analysis. Design The MCE (1968-73) is a double blind randomized controlled trial designed to test whether replacement of saturated fat with vegetable oil rich in linoleic acid reduces coronary heart disease and death by lowering serum cholesterol. Recovered MCE unpublished documents and raw data were analyzed according to hypotheses prespecified by original investigators. Further, a systematic review and meta-analyses of randomized controlled trials that lowered serum cholesterol by providing vegetable oil rich in linoleic acid in place of saturated fat without confounding by concomitant interventions was conducted. Setting One nursing home and six state mental hospitals in Minnesota, United States. Participants Unpublished documents with completed analyses for the randomized cohort of 9423 women and men aged 20-97; longitudinal data on serum cholesterol for the 2355 participants exposed to the study diets for a year or more; 149 completed autopsy files. Interventions Serum cholesterol lowering diet that replaced saturated fat with linoleic acid (from corn oil and corn oil polyunsaturated margarine). Control diet was high in saturated fat from animal fats, common margarines, and shortenings. Main outcome measures Death from all causes; association between changes in serum cholesterol and death; and coronary atherosclerosis and myocardial infarcts detected at autopsy. Results The intervention group had significant reduction in serum cholesterol compared with controls (mean change from baseline −13.8% v −1.0%; P<0.001). Kaplan Meier graphs showed no mortality benefit for the intervention group in the full randomized cohort or for any prespecified subgroup. There was a 22

  12. Suggested Citations for the DHQ II & Diet*Calc

    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.

  13. [Critical analysis of the diet quality of the Brazilian population according to the Healthy Eating Index: a systematic review].

    PubMed

    Moreira, Patrícia Regina Silva; Rocha, Naruna Pereira; Milagres, Luana Cupertino; de Novaes, Juliana Farias

    2015-12-01

    In light of the importance of studying instruments that assess the food quality of the population, this study sought to conduct a systematic review of the quality of the diet of the Brazilian population using the Healthy Eating Index (HEI) and duly analyzing its methodology and results. The major electronic databases were used for the selection of studies. After the searches with the key words, 32 articles were included in this review. The growing interest of the scientific community in addressing this issue was observed, with recent studies using this instrument in Brazil. Methodological issues of articles were evaluated and discussed taking into consideration the revised versions and adaptations of the HEI. Some common results were highlighted among the studies such as low consumption of fruit, vegetables and/or dairy products, and the wider consumption of meat and eggs, cholesterol, total fat and saturated fat. Among the articles that address the HEI and socioeconomic aspects it was seen that quality of diet improves both in accordance with the increasing level of education of parents and with the family income in the population studied. The HEI can be used to monitor changes in dietary patterns and also as a nutrition education and health promotion tool.

  14. DNA-based determination of microbial biomass suitable for frozen and alkaline soil samples

    NASA Astrophysics Data System (ADS)

    Semenov, Mikhail; Blagodatskaya, Evgeniya; Kogut, Boris; Kuzyakov, Yakov

    2015-04-01

    Microbial biomass is a sensitive indicator of changes due to soil management, long before other basic soil measures such as Corg or Ntot. Improvement of methods for determination of microbial biomass still remains relevant, and these methods should be correctly applicable for the soil samples being in various state. This study was designed to demonstrate the applicability of DNA-based determination of microbial biomass under conditions when the common basic approaches, namely chloroform fumigation-extraction (CFE) and substrate-induced respiration (SIR), are restricted by certain soil properties, experimental designs or research needs, e.g. in frozen, alkaline or carbonaceous soils. We compared microbial biomass determined by CFE, SIR and by DNA approaches in the range of neutral and slightly alkaline Chernozem and alkaline Calcisol of semi-arid climate. The samples of natural and agricultural ecosystems were taken throughout the soil profile from long-term static field experiments in the European part of Russia. Extraction and subsequent quantification of dsDNA revealed a strong agreement with SIR and CFE when analyzing the microbial biomass content in soils with pH below 8. The conversion factors (FDNA) from dsDNA to SIR-Cmic (5.10) and CFE-Cmic (4.41) were obtained by testing a range of the soil samples down to 1.5 m depth and indicated a good reproducibility of DNA-based estimations. In alkaline soils (pH > 8), CO2 retention due to alkaline pH and exchange with carbonates resulted in a strong underestimation of soil microbial biomass by SIR or even in the absence of any CO2 emission, especially at low absolute values of microbial biomass in subsoil. Correction of CO2 efflux by theoretical retention pH-dependent factors caused overestimation of SIR-biomass. In alkaline conditions, DNA extraction proved to be a reliable alternative for microbial biomass determination. Moreover, the DNA-based approach can serve as an excellent alternative enabling correct

  15. Efficacy of interventions that include diet, aerobic and resistance training components for type 2 diabetes prevention: a systematic review with meta-analysis.

    PubMed

    Aguiar, Elroy J; Morgan, Philip J; Collins, Clare E; Plotnikoff, Ronald C; Callister, Robin

    2014-01-15

    Current recommendations for the prevention of type 2 diabetes advise modification of diet and exercise behaviors including both aerobic and resistance training. However, the efficacy of multi-component interventions involving a combination of these three components has not been established. The aims of this review were to systematically review and meta-analyze the evidence on multi-component (diet + aerobic exercise + resistance training) lifestyle interventions for type 2 diabetes prevention. Eight electronic databases (Medline, Embase, SportDiscus, Web of Science, CINAHL, Informit health collection, Cochrane library and Scopus) were searched up to June 2013. Eligible studies 1) recruited prediabetic adults or individuals at risk of type 2 diabetes; 2) conducted diet and exercise [including both physical activity/aerobic and resistance training] programs; and 3) reported weight and plasma glucose outcomes. In total, 23 articles from eight studies were eligible including five randomized controlled trials, one quasi-experimental, one two-group comparison and one single-group pre-post study. Four studies had a low risk of bias (score ≥ 6/10). Median intervention length was 12 months (range 4-48 months) with a follow-up of 18 months (range 6.5-48 months). The diet and exercise interventions varied slightly in terms of their specific prescriptions. Meta-analysis favored interventions over controls for weight loss (-3.79 kg [-6.13, -1.46; 95% CI], Z = 3.19, P = 0.001) and fasting plasma glucose (-0.13 mmol.L⁻¹ [-0.24, -0.02; 95% CI], Z = 2.42, P = 0.02). Diabetes incidence was only reported in two studies, with reductions of 58% and 56% versus control groups. In summary, multi-component lifestyle type 2 diabetes prevention interventions that include diet and both aerobic and resistance exercise training are modestly effective in inducing weight loss and improving impaired fasting glucose, glucose tolerance, dietary and exercise outcomes

  16. A Metabolomic Analysis of Omega-3 Fatty Acid-Mediated Attenuation of Western Diet-Induced Nonalcoholic Steatohepatitis in LDLR-/- Mice

    PubMed Central

    Depner, Christopher M.; Traber, Maret G.; Bobe, Gerd; Kensicki, Elizabeth; Bohren, Kurt M.; Milne, Ginger; Jump, Donald B.

    2013-01-01

    Background Nonalcoholic steatohepatitis (NASH) is a progressive form of nonalcoholic fatty liver disease and a risk factor for cirrhosis, hepatocellular carcinoma and liver failure. Previously, we reported that dietary docosahexaenoic acid (DHA, 22:6,n-3) was more effective than eicosapentaenoic acid (EPA, 20:5,n-3) at reversing western diet (WD) induced NASH in LDLR-/- mice. Methods Using livers from our previous study, we carried out a global non-targeted metabolomic approach to quantify diet-induced changes in hepatic metabolism. Results Livers from WD + olive oil (WD + O)-fed mice displayed histological and gene expression features consistent with NASH. The metabolomic analysis of 320 metabolites established that the WD and n-3 polyunsaturated fatty acid (PUFA) supplementation had broad effects on all major metabolic pathways. Livers from WD + O-fed mice were enriched in saturated (SFA) and monounsaturated fatty acids (MUFA), palmitoyl-sphingomyelin, cholesterol, n-6 PUFA, n-6 PUFA-containing phosphoglycerolipids, n-6 PUFA-derived oxidized lipids (12-HETE) and depleted of C20-22 n-3 PUFA-containing phosphoglycerolipids, C20-22 n-3 PUFA-derived oxidized lipids (18-HEPE, 17,18-DiHETE) and S-lactoylglutathione, a methylglyoxal detoxification product. WD + DHA was more effective than WD + EPA at attenuating WD + O-induced changes in NASH gene expression markers, n-6 PUFA and oxidized lipids, citrate and S-lactosyl glutathione. Diet-induced changes in hepatic MUFA and sphingolipid content were associated with changes in expression of enzymes involved in MUFA and sphingolipid synthesis. Changes in hepatic oxidized fatty acids and S-lactoylglutathione, however, correlated with hepatic n-3 and n-6 C20-22 PUFA content. Hepatic C20-22 n-3 PUFA content was inversely associated with hepatic α-tocopherol and ascorbate content and positively associated with urinary F2- and F3-isoprostanes, revealing diet effects on whole body oxidative stress. Conclusion DHA regulation of

  17. Efficacy of interventions that include diet, aerobic and resistance training components for type 2 diabetes prevention: a systematic review with meta-analysis

    PubMed Central

    2014-01-01

    Current recommendations for the prevention of type 2 diabetes advise modification of diet and exercise behaviors including both aerobic and resistance training. However, the efficacy of multi-component interventions involving a combination of these three components has not been established. The aims of this review were to systematically review and meta-analyze the evidence on multi-component (diet + aerobic exercise + resistance training) lifestyle interventions for type 2 diabetes prevention. Eight electronic databases (Medline, Embase, SportDiscus, Web of Science, CINAHL, Informit health collection, Cochrane library and Scopus) were searched up to June 2013. Eligible studies 1) recruited prediabetic adults or individuals at risk of type 2 diabetes; 2) conducted diet and exercise [including both physical activity/aerobic and resistance training] programs; and 3) reported weight and plasma glucose outcomes. In total, 23 articles from eight studies were eligible including five randomized controlled trials, one quasi-experimental, one two-group comparison and one single-group pre-post study. Four studies had a low risk of bias (score ≥ 6/10). Median intervention length was 12 months (range 4–48 months) with a follow-up of 18 months (range 6.5 - 48 months). The diet and exercise interventions varied slightly in terms of their specific prescriptions. Meta-analysis favored interventions over controls for weight loss (-3.79 kg [-6.13, -1.46; 95% CI], Z = 3.19, P = 0.001) and fasting plasma glucose (-0.13 mmol.L-1 [-0.24, -0.02; 95% CI], Z = 2.42, P = 0.02). Diabetes incidence was only reported in two studies, with reductions of 58% and 56% versus control groups. In summary, multi-component lifestyle type 2 diabetes prevention interventions that include diet and both aerobic and resistance exercise training are modestly effective in inducing weight loss and improving impaired fasting glucose, glucose tolerance, dietary and exercise

  18. A Survey on the Effect of Livestock Production System and Finishing Diet on Sensory Characteristics of Foal Meat Using Generalized Procrustes Analysis.

    PubMed

    Lorenzo, José M; Purriños, Laura; Carballo, Javier

    2016-01-01

    The influence of livestock production system [Freedom Extensive System (FES) versus Semi-Extensive System (SES)] and finishing feed (1.5 kg versus 3.0 kg of commercial feed in the finishing period) diet on sensory properties of foal meat using Generalized Procrustes Analysis (GPA) was studied. For this work, a total of 24 foals (8 from FES and 16 from SES) were used. Samples were evaluated by eight panelists for eight sensory attributes: colour, marbling, odour intensity, sweetness, springiness, hardness, chewiness, and juiciness. Data were analyzed using a GPA to minimize differences among testers. Highly appreciated sensory properties (odour intensity, red colour, marbling, and juiciness) were mostly associated with foals from the Semi-Extensive System. On the other hand, the three groups studied (FES, 1.5SES, and 3SES) were clearly recognized by panelists on the consensus configuration and they were clearly separated on the map. This study concluded that sensory characteristics of foal meat from a Semi-Extensive Production System with a finishing diet of 3 kg concentrate were more preferable than the other ones.

  19. A Survey on the Effect of Livestock Production System and Finishing Diet on Sensory Characteristics of Foal Meat Using Generalized Procrustes Analysis

    PubMed Central

    Lorenzo, José M.; Purriños, Laura; Carballo, Javier

    2016-01-01

    The influence of livestock production system [Freedom Extensive System (FES) versus Semi-Extensive System (SES)] and finishing feed (1.5 kg versus 3.0 kg of commercial feed in the finishing period) diet on sensory properties of foal meat using Generalized Procrustes Analysis (GPA) was studied. For this work, a total of 24 foals (8 from FES and 16 from SES) were used. Samples were evaluated by eight panelists for eight sensory attributes: colour, marbling, odour intensity, sweetness, springiness, hardness, chewiness, and juiciness. Data were analyzed using a GPA to minimize differences among testers. Highly appreciated sensory properties (odour intensity, red colour, marbling, and juiciness) were mostly associated with foals from the Semi-Extensive System. On the other hand, the three groups studied (FES, 1.5SES, and 3SES) were clearly recognized by panelists on the consensus configuration and they were clearly separated on the map. This study concluded that sensory characteristics of foal meat from a Semi-Extensive Production System with a finishing diet of 3 kg concentrate were more preferable than the other ones. PMID:27006978

  20. Exploring the contribution and significance of animal protein in the diet of bonobos by stable isotope ratio analysis of hair

    PubMed Central

    Oelze, Vicky M.; Fuller, Benjamin T.; Richards, Michael P.; Fruth, Barbara; Surbeck, Martin; Hublin, Jean-Jacques; Hohmann, Gottfried

    2011-01-01

    In primates, age, sex, and social status can strongly influence access to food resources. In Pan, these criteria are assumed to influence access to vertebrate meat. However, the significance of meat in terms of its role in the nutrition of Pan is still debated. Here we present a study using stable carbon and nitrogen isotope ratios in hair samples from habituated, wild bonobos (Pan paniscus) to explore these issues. Over a period of 5 mo hair samples were collected from fresh bonobo nests at LuiKotale, Democratic Republic of Congo. Hair samples were assigned to known individuals and were of sufficient length to allow the evaluation of isotopic variation over several months. Samples of plant foods and sympatric fauna were also analyzed. The δ13C and δ15N results of the bonobo hair were remarkably homogeneous over time and for the group as a whole. There are no differences in diet between the sexes. Within the group of males, however, there was a positive correlation between dominance status and δ15N. The isotopic data indicate that the contribution of fauna to bonobo diet is marginal and that plant food is the dietary protein source. In only some cases did elevated δ15N hair values correlate with observed faunivory and not correspond to the δ15N measured in the dominant plant foods. Given the large variation in hunting and meat eating of Pan across the African continent, the detection of seasonal changes in faunivory by elevated δ15N values in sectioned ape hair is a promising approach. PMID:21628564

  1. Caffeine in the diet

    MedlinePlus

    Diet - caffeine ... Caffeine is absorbed and passes quickly into the brain. It does not collect in the bloodstream or ... been consumed. There is no nutritional need for caffeine. It can be avoided in the diet. Caffeine ...

  2. Diets for constipation.

    PubMed

    Bae, Sun Hwan

    2014-12-01

    Chronic constipation is a very common disease in children. Successful treatment of constipation can be achieved not only with medication but also with lifestyle changes, including a proper diet. Diets including fruits, fluids, and probiotics are good for constipation. Some dietary components are helpful for constipation, and some are harmful. In this study, we present diets related to constipation from the literature, and propose some perspectives regarding diets related to constipation.

  3. Diets for Constipation

    PubMed Central

    2014-01-01

    Chronic constipation is a very common disease in children. Successful treatment of constipation can be achieved not only with medication but also with lifestyle changes, including a proper diet. Diets including fruits, fluids, and probiotics are good for constipation. Some dietary components are helpful for constipation, and some are harmful. In this study, we present diets related to constipation from the literature, and propose some perspectives regarding diets related to constipation. PMID:25587519

  4. Diet, Nutrition, and Cancer Epigenetics.

    PubMed

    Sapienza, Carmen; Issa, Jean-Pierre

    2016-07-17

    The search for a connection between diet and human cancer has a long history in cancer research, as has interest in the mechanisms by which dietary factors might increase or decrease cancer risk. The realization that altering diet can alter the epigenetic state of genes and that these epigenetic alterations might increase or decrease cancer risk is a more modern notion, driven largely by studies in animal models. The connections between diet and epigenetic alterations, on the one hand, and between epigenetic alterations and cancer, on the other, are supported by both observational studies in humans as well as animal models. However, the conclusion that diet is linked directly to epigenetic alterations and that these epigenetic alterations directly increase or decrease the risk of human cancer is much less certain. We suggest that true and measurable effects of diet or dietary supplements on epigenotype and cancer risk are most likely to be observed in longitudinal studies and at the extremes of the intersection of dietary risk factors and human population variability. Careful analysis of such outlier populations is most likely to shed light on the molecular mechanisms by which suspected environmental risk factors drive the process of carcinogenesis.

  5. Low-carbohydrate diets.

    PubMed

    Last, Allen R; Wilson, Stephen A

    2006-06-01

    Americans spend dollar 33 billion annually on weight loss products and services, and a large portion of this money is spent on low-carbohydrate diets. Because of their higher protein and fat content and lower fiber and carbohydrate content, concerns have been raised about the potential health consequences of low-carbohydrate diets. Published long-term data are lacking. Short-term studies comparing traditional low-fat diets with low-carbohydrate diets found lower triglyceride levels, higher high-density lipoprotein cholesterol levels, similar low-density lipoprotein cholesterol levels, and lower A1C levels in persons on low-carbohydrate diets. These diets induce greater weight loss at three and six months than traditional low-fat diets; however, by one year there is no significant difference in maintained weight loss. Weight loss is directly related to calorie content and the ability to maintain caloric restriction; the proportions of nutrients in the diet are irrelevant. Low-carbohydrate diets had lower dropout rates than low-fat diets in several studies, possibly because of the high protein content and low glycemic index, which can be appetite suppressing. Data indicate that low-carbohydrate diets are a safe, reasonable alternative to low-fat diets for weight loss. Additional studies are needed to investigate the long-term safety and effectiveness of these and other approaches to weight loss.

  6. A scenario-based dieting self-efficacy scale: the DIET-SE.

    PubMed

    Stich, Christine; Knäuper, Bärbel; Tint, Ami

    2009-03-01

    The article discusses a scenario-based dieting self-efficacy scale, the DIET-SE, developed from dieter's inventory of eating temptations (DIET). The DIET-SE consists of items that describe scenarios of eating temptations for a range of dieting situations, including high-caloric food temptations. Four studies assessed the psychometric properties of the 11-item DIET-SE. Exploratory factor analysis (N = 392) and confirmatory factors analysis (N = 124) revealed three internally consistent and reliable factors representing challenges to adhere to a diet (high-caloric food temptations [HCF], social and internal factors [SIF], negative emotional events [NEE]). Convergent validity is established with other measures of dieting self-efficacy, as well as measures of eating disinhibition, susceptibility to hunger, and weight loss competency. Criterion-related validity is provided through the assessment of goal adherence, and predictive validity is established for dieters' actual food intake (N = 68). The DIET-SE represents a short, reliable, and valid scenario-based measure of dieting self-efficacy.

  7. Diet for rapid weight loss

    MedlinePlus

    ... diet; VLCD; Low-calorie diet; LCD; Very low energy diet; Weight loss - rapid weight loss; Overweight - rapid ... AM, Aveyard P. Clinical effectiveness of very-low-energy diets in the management of weight loss: a ...

  8. Is Dieting OK for Kids?

    MedlinePlus

    ... Room? What Happens in the Operating Room? Is Dieting OK for Kids? KidsHealth > For Kids > Is Dieting ... not — diet this way. Why? Let's find out. Dieting to Lose Weight All foods and many drinks ...

  9. High blood pressure and diet

    MedlinePlus

    ... increase the potassium in your diet or use salt substitutes (which often contain potassium). People who have kidney ... consume. Alternative Names Hypertension - diet Images DASH diet Low sodium diet References American Heart Association Nutrition Committee; Lichtenstein ...

  10. Dairy goat kids fed liquid diets in substitution of goat milk and slaughtered at different ages: an economic viability analysis using Monte Carlo techniques.

    PubMed

    Knupp, L S; Veloso, C M; Marcondes, M I; Silveira, T S; Silva, A L; Souza, N O; Knupp, S N R; Cannas, A

    2016-03-01

    The aim of this study was to analyze the economic viability of producing dairy goat kids fed liquid diets in alternative of goat milk and slaughtered at two different ages. Forty-eight male newborn Saanen and Alpine kids were selected and allocated to four groups using a completely randomized factorial design: goat milk (GM), cow milk (CM), commercial milk replacer (CMR) and fermented cow colostrum (FC). Each group was then divided into two groups: slaughter at 60 and 90 days of age. The animals received Tifton hay and concentrate ad libitum. The values of total costs of liquid and solid feed plus labor, income and average gross margin were calculated. The data were then analyzed using the Monte Carlo techniques with the @Risk 5.5 software, with 1000 iterations of the variables being studied through the model. The kids fed GM and CMR generated negative profitability values when slaughtered at 60 days (US$ -16.4 and US$ -2.17, respectively) and also at 90 days (US$ -30.8 and US$ -0.18, respectively). The risk analysis showed that there is a 98% probability that profitability would be negative when GM is used. In this regard, CM and FC presented low risk when the kids were slaughtered at 60 days (8.5% and 21.2%, respectively) and an even lower risk when animals were slaughtered at 90 days (5.2% and 3.8%, respectively). The kids fed CM and slaughtered at 90 days presented the highest average gross income (US$ 67.88) and also average gross margin (US$ 18.43/animal). For the 60-day rearing regime to be economically viable, the CMR cost should not exceed 11.47% of the animal-selling price. This implies that the replacer cannot cost more than US$ 0.39 and 0.43/kg for the 60- and 90-day feeding regimes, respectively. The sensitivity analysis showed that the variables with the greatest impact on the final model's results were animal selling price, liquid diet cost, final weight at slaughter and labor. In conclusion, the production of male dairy goat kids can be economically

  11. Qualitative analysis of human milk produced by women consuming a maize-predominant diet typical of rural Mexico.

    PubMed

    Villalpando, S; Butte, N F; Flores-Huerta, S; Thotathuchery, M

    1998-01-01

    The milk composition of women on a typical rural Mexican diet was compared with that secreted by American women, consuming a diet typical of affluent countries. Milk concentrations of free fatty acids, cholesterol, total amino acids, and selected key minerals were analyzed at 4 or 6 months postpartum. The total milk fat concentration was lower in the Otomi (22.7 +/- 6.7 mg/g milk) than in the American women (31.3 +/- 5.4 mg/g milk, p = 0.001). Although the absolute concentration did not differ, cholesterol, expressed in terms of total lipid, was higher in the Otomi milk (3.9 +/- 1.1 vs. 3.1 +/- 0.7 mg/g fat, p = 0.005). Saturated medium-chain (C10:0-C14:0) and unsaturated intermediate-chain fatty acids (C16:1 and C18:2) were higher in the Otomi than in the American milk (p < 0.03). The concentrations of C16:0, C18:0, and C18:1 were significantly lower in Otomi than in American milk. The milk concentrations of protein and nonprotein nitrogen were comparable between the two groups. The concentrations of serine, proline, cystine, methionine, and tryptophan were higher in the Otomi than in the American milk (p < 0.05-0.001). The concentrations of valine and isoleucine were significantly lower in the Otomi milk (p = 0.05). Expressed per gram of milk protein, the cystine, methionine, lysine, and tryptophan concentrations were higher, and the glutamine/glutamate, valine, isoleucine, and arginine levels were lower in the Otomi milk. The concentrations of phosphorus and copper were lower in the Otomi than in the American milk at 4 months postpartum (p = 0.05). These differences in milk fatty acid and amino acid patterns and mineral content are unlikely to affect infant growth, but may have other biological consequences yet to be ascertained.

  12. [Sustainable diet: history lessons].

    PubMed

    Fatati, Giuseppe

    2015-11-01

    Global dietary patterns changed dramatically in the past 50 years, presenting both a boom and a threat to the health and well-being of populations everywhere. We need sustainable diets, with low-input, local and seasonal agro-ecological food productions as well as short distance production-consumption nets for fair trade. The development of a global food system able to guarantee everyone a balanced food intake requires health professionals an awareness and a commitment to increasingly complex education. Dietary changes such as the adherence of to the Mediterranean Dietary Pattern can reduce the environmental footprint and thus the use of natural resources. Increased focus on improving the utilization of freshwater fishes and the correct use of the waters of rivers and lakes should also be encouraged. Cultural heritage, food quality and culinary skills are other key aspects determining sustainable dietary patterns and food security. The Mediterranean street food (Mediterraneità), for intrinsic characteristics, can represent valid model to address the main issues concerning the sustainable food system. The issues of sustainability offer a great opportunity to nutritional science and scientists to play a more central role in the political analysis of future food systems. We are confident that preserve the past helps us understand the present and build for the future, the Mediterranean lifestyle is much more than the Mediterranean diet and, finally, the rivers and the lakes may be our future.

  13. Implementation of Arithmetic and Nonarithmetic Functions on a Label-free and DNA-based Platform

    PubMed Central

    Wang, Kun; He, Mengqi; Wang, Jin; He, Ronghuan; Wang, Jianhua

    2016-01-01

    A series of complex logic gates were constructed based on graphene oxide and DNA-templated silver nanoclusters to perform both arithmetic and nonarithmetic functions. For the purpose of satisfying the requirements of progressive computational complexity and cost-effectiveness, a label-free and universal platform was developed by integration of various functions, including half adder, half subtractor, multiplexer and demultiplexer. The label-free system avoided laborious modification of biomolecules. The designed DNA-based logic gates can be implemented with readout of near-infrared fluorescence, and exhibit great potential applications in the field of bioimaging as well as disease diagnosis. PMID:27713517

  14. Implementation of Arithmetic and Nonarithmetic Functions on a Label-free and DNA-based Platform

    NASA Astrophysics Data System (ADS)

    Wang, Kun; He, Mengqi; Wang, Jin; He, Ronghuan; Wang, Jianhua

    2016-10-01

    A series of complex logic gates were constructed based on graphene oxide and DNA-templated silver nanoclusters to perform both arithmetic and nonarithmetic functions. For the purpose of satisfying the requirements of progressive computational complexity and cost-effectiveness, a label-free and universal platform was developed by integration of various functions, including half adder, half subtractor, multiplexer and demultiplexer. The label-free system avoided laborious modification of biomolecules. The designed DNA-based logic gates can be implemented with readout of near-infrared fluorescence, and exhibit great potential applications in the field of bioimaging as well as disease diagnosis.

  15. On the role of DNA in DNA-based catalytic enantioselective conjugate addition reactions.

    PubMed

    Dijk, Ewold W; Boersma, Arnold J; Feringa, Ben L; Roelfes, Gerard

    2010-09-07

    A kinetic study of DNA-based catalytic enantioselective Friedel-Crafts alkylation and Michael addition reactions showed that DNA affects the rate of these reactions significantly. Whereas in the presence of DNA, a large acceleration was found for the Friedel-Crafts alkylation and a modest acceleration in the Michael addition of dimethyl malonate, a deceleration was observed when using nitromethane as nucleophile. Also, the enantioselectivities proved to be dependent on the DNA sequence. In comparison with the previously reported Diels-Alder reaction, the results presented here suggest that DNA plays a similar role in both cycloaddition and conjugate addition reactions.

  16. Diet analysis by next-generation sequencing indicates the frequent consumption of introduced plants by the critically endangered red-headed wood pigeon (Columba janthina nitens) in oceanic island habitats.

    PubMed

    Ando, Haruko; Setsuko, Suzuki; Horikoshi, Kazuo; Suzuki, Hajime; Umehara, Shoko; Inoue-Murayama, Miho; Isagi, Yuji

    2013-10-01

    Oceanic island ecosystems are vulnerable to the introduction of alien species, and they provide a habitat for many endangered species. Knowing the diet of an endangered animal is important for appropriate nature restoration efforts on oceanic islands because introduced species may be a major component of the diets of some endangered species. DNA barcoding techniques together with next-generation sequencing may provide more detailed information on animal diets than other traditional methods. We performed a diet analysis using 48 fecal samples from the critically endangered red-headed wood pigeon that is endemic to the Ogasawara Islands based on chloroplast trnL P6 loop sequences. The frequency of each detected plant taxa was compared with a microhistological analysis of the same sample set. The DNA barcoding approach detected a much larger number of plants than the microhistological analysis. Plants that were difficult to identify by microhistological analysis after being digested in the pigeon stomachs were frequently identified only by DNA barcoding. The results of the barcoding analysis indicated the frequent consumption of introduced species, in addition to several native species, by the red-headed wood pigeon. The rapid eradication of specific introduced species may reduce the food resources available to this endangered bird; thus, balancing eradication efforts with the restoration of native food plants should be considered. Although some technical problems still exist, the trnL approach to next-generation sequencing may contribute to a better understanding of oceanic island ecosystems and their conservation.

  17. Diet analysis by next-generation sequencing indicates the frequent consumption of introduced plants by the critically endangered red-headed wood pigeon (Columba janthina nitens) in oceanic island habitats

    PubMed Central

    Ando, Haruko; Setsuko, Suzuki; Horikoshi, Kazuo; Suzuki, Hajime; Umehara, Shoko; Inoue-Murayama, Miho; Isagi, Yuji

    2013-01-01

    Oceanic island ecosystems are vulnerable to the introduction of alien species, and they provide a habitat for many endangered species. Knowing the diet of an endangered animal is important for appropriate nature restoration efforts on oceanic islands because introduced species may be a major component of the diets of some endangered species. DNA barcoding techniques together with next-generation sequencing may provide more detailed information on animal diets than other traditional methods. We performed a diet analysis using 48 fecal samples from the critically endangered red-headed wood pigeon that is endemic to the Ogasawara Islands based on chloroplast trnL P6 loop sequences. The frequency of each detected plant taxa was compared with a microhistological analysis of the same sample set. The DNA barcoding approach detected a much larger number of plants than the microhistological analysis. Plants that were difficult to identify by microhistological analysis after being digested in the pigeon stomachs were frequently identified only by DNA barcoding. The results of the barcoding analysis indicated the frequent consumption of introduced species, in addition to several native species, by the red-headed wood pigeon. The rapid eradication of specific introduced species may reduce the food resources available to this endangered bird; thus, balancing eradication efforts with the restoration of native food plants should be considered. Although some technical problems still exist, the trnL approach to next-generation sequencing may contribute to a better understanding of oceanic island ecosystems and their conservation. PMID:24324859

  18. Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production

    PubMed Central

    Xiang, Ruidong; McNally, Jody; Rowe, Suzanne; Jonker, Arjan; Pinares-Patino, Cesar S.; Oddy, V. Hutton; Vercoe, Phil E.; McEwan, John C.; Dalrymple, Brian P.

    2016-01-01

    Ruminants obtain nutrients from microbial fermentation of plant material, primarily in their rumen, a multilayered forestomach. How the different layers of the rumen wall respond to diet and influence microbial fermentation, and how these process are regulated, is not well understood. Gene expression correlation networks were constructed from full thickness rumen wall transcriptomes of 24 sheep fed two different amounts and qualities of a forage and measured for methane production. The network contained two major negatively correlated gene sub-networks predominantly representing the epithelial and muscle layers of the rumen wall. Within the epithelium sub-network gene clusters representing lipid/oxo-acid metabolism, general metabolism and proliferating and differentiating cells were identified. The expression of cell cycle and metabolic genes was positively correlated with dry matter intake, ruminal short chain fatty acid concentrations and methane production. A weak correlation between lipid/oxo-acid metabolism genes and methane yield was observed. Feed consumption level explained the majority of gene expression variation, particularly for the cell cycle genes. Many known stratified epithelium transcription factors had significantly enriched targets in the epithelial gene clusters. The expression patterns of the transcription factors and their targets in proliferating and differentiating skin is mirrored in the rumen, suggesting conservation of regulatory systems. PMID:27966600

  19. Analysis of veterinary drug residues in fish and shrimp composites collected during the Canadian Total Diet Study, 1993-2004.

    PubMed

    Tittlemier, S A; Van de Riet, J; Burns, G; Potter, R; Murphy, C; Rourke, W; Pearce, H; Cao, X L; Dabekai, R W; Dufresne, G

    2007-01-01

    Thirty shrimp, marine fish, freshwater fish, and canned fish composite samples collected and prepared as part of the Canadian Total Diet Study were analysed for 39 different veterinary drug residues. The analyses were undertaken to obtain baseline data that could be used to estimate the dietary exposure of Canadians to these residues. The most frequently observed residue was AOZ (four out of 30 samples), the metabolite of furazolidone, at a range of 0.50 to 2.0 ng g(-1) wet weight. Other residues detected included enrofloxacin (three samples; 0.3-0.73 ng g(-1)), leucomalachite green (three samples; 0.73-1.2 ng g(-1)), oxolinic acid (two samples; 0.3-4.3 ng g(-1)), AMOZ (the metabolite of furaltadone; one sample; 0.40 ng g(-1)), chloramphenicol (one sample; 0.40 ng g(-1)), and SEM (the metabolite of nitrofurazone; one sample; 0.8 ng g(-1)). The results of this survey indicate that Canadians are exposed to low ng g-1 concentrations of some banned and unapproved veterinary drug residues via the consumption of certain fish and shrimp.

  20. Metabolomic Analysis of Diet-Induced Type 2 Diabetes Using UPLC/MS Integrated with Pattern Recognition Approach

    PubMed Central

    Sun, Hui; Zhang, Shuxiang; Zhang, Aihua; Yan, Guangli; Wu, Xiuhong; Han, Ying; Wang, Xijun

    2014-01-01

    Metabolomics represents an emerging discipline concerned with comprehensive assessment of small molecule endogenous metabolites in biological systems and provides a powerful approach insight into the mechanisms of diseases. Type 2 diabetes (T2D), called the burden of the 21st century, is growing with an epidemic rate. However, its precise molecular mechanism has not been comprehensively explored. In this study, we applied urinary metabolomics based on the UPLC/MS integrated with pattern recognition approaches to discover differentiating metabolites, to characterize and explore metabolic pathway disruption in an experimental model for high-fat-diet induced T2D. Six differentiating urinary metabolites were found in the negative mode, and two (2-(4-hydroxy-3-methoxy-phenyl) acetaldehyde sulfate, 2-phenylethanol glucuronide) of which were identified involving the key metabolic pathways linked to pentose and glucuronate interconversions, starch, sucrose metabolism and tyrosine metabolism. Our study provides new insight into pathophysiologic mechanisms and may enhance the understanding of T2D pathogenesis. PMID:24671089

  1. Effect of maternal diet on offspring coping styles in rodents: a systematic review and meta-analysis.

    PubMed

    Besson, Anne A; Lagisz, Malgorzata; Senior, Alistair M; Hector, Katie L; Nakagawa, Shinichi

    2016-11-01

    Maternal nutrition can have long-term effects on offspring morphology, physiology and behaviours. However, it is unclear whether mothers 'program' offspring behavioural coping strategy (proactive/reactive) according to the predicted nutritional quality of their future environment. We conducted a systematic review on this topic and meta-analytically synthesized relevant experimental data on mice and rats (46 studies). We included data from experiments where dams were subjected to caloric restriction, protein restriction or overfeeding around gestation and subsequently measured offspring activity, exploration, or anxiety. Overall, little evidence existed for effects of maternal nutrition on the three investigated behavioural traits. The high heterogeneity observed in the data set suggests that maternal programming may sometimes occur. However, because offspring had access to a balanced diet before testing, behaviours may have been reprogrammed. Our results may indicate that reprogrammed behaviours could ameliorate negative effects associated with sub-optimal nutrition in early life. Further, our systematic review revealed clear knowledge gaps and fruitful future research avenues.

  2. Metabolomic Analysis of Biochemical Changes in the Plasma of High-Fat Diet and Streptozotocin-Induced Diabetic Rats after Treatment with Isoflavones Extract of Radix Puerariae

    PubMed Central

    2016-01-01

    The main purpose of this study was to investigate the protective effects of total isoflavones from Radix Puerariae (PTIF) in diabetic rats. Diabetes was induced by a high-fat diet and intraperitoneal injection of low-dose streptozotocin (STZ; 40 mg/kg). At 26 weeks onwards, PTIF 421 mg/kg was administrated to the rats once daily consecutively for 10 weeks. Metabolic profiling changes were analyzed by Ultraperformance Liquid Chromatography-Quadrupole-Exactive Orbitrap-Mass Spectrometry (UPLC-Q-Exactive Orbitrap-MS). The principal component discriminant analysis (PCA-DA), partial least-squares discriminant analysis (PLS-DA), and orthogonal partial least-squares discriminant analysis (OPLS-DA) were used for multivariate analysis. Moreover, free amino acids in serum were determined by high-performance liquid chromatography with fluorescence detector (HPLC-FLD). Additionally, oxidative stress and inflammatory cytokines were evaluated. Eleven potential metabolite biomarkers, which are mainly related to the coagulation, lipid metabolism, and amino acid metabolism, have been identified. PCA-DA scores plots indicated that biochemical changes in diabetic rats were gradually restored to normal after administration of PTIF. Furthermore, the levels of BCAAs, glutamate, arginine, and tyrosine were significantly increased in diabetic rats. Treatment with PTIF could regulate the disturbed amino acid metabolism. Consequently, PTIF has great therapeutic potential in the treatment of DM by improving metabolism disorders and inhibiting oxidative damage. PMID:27042190

  3. Assessing macroinvertebrate biodiversity in freshwater ecosystems: Advances and challenges in dna-based approaches

    USGS Publications Warehouse

    Pfrender, M.E.; Ferrington, L.C.; Hawkins, C.P.; Hartzell, P.L.; Bagley, M.; Jackson, S.; Courtney, G.W.; Larsen, D.P.; Creutzburg, B.R.; Levesque, C.A.; Epler, J.H.; Morse, J.C.; Fend, S.; Petersen, M.J.; Ruiter, D.; Schindel, D.; Whiting, M.

    2010-01-01

    Assessing the biodiversity of macroinvertebrate fauna in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify water quality and measure the efficacy of remediation and restoration efforts. The accuracy and precision of biodiversity assessments based on standard morphological identifications are often limited by taxonomic resolution and sample size. Morphologically based identifications are laborious and costly, significantly constraining the sample sizes that can be processed. We suggest that the development of an assay platform based on DNA signatures will increase the precision and ease of quantifying biodiversity in freshwater ecosystems. Advances in this area will be particularly relevant for benthic and planktonic invertebrates, which are often monitored by regulatory agencies. Adopting a genetic assessment platform will alleviate some of the current limitations to biodiversity assessment strategies. We discuss the benefits and challenges associated with DNA-based assessments and the methods that are currently available. As recent advances in microarray and next-generation sequencing technologies will facilitate a transition to DNA-based assessment approaches, future research efforts should focus on methods for data collection, assay platform development, establishing linkages between DNA signatures and well-resolved taxonomies, and bioinformatics. ?? 2010 by The University of Chicago Press.

  4. Genome size and DNA base composition of geophytes: the mirror of phenology and ecology?

    PubMed Central

    Veselý, Pavel; Bureš, Petr; Šmarda, Petr; Pavlíček, Tomáš

    2012-01-01

    Background and Aims Genome size is known to affect various plant traits such as stomatal size, seed mass, and flower or shoot phenology. However, these associations are not well understood for species with very large genomes, which are laregly represented by geophytic plants. No detailed associations are known between DNA base composition and genome size or species ecology. Methods Genome sizes and GC contents were measured in 219 geophytes together with tentative morpho-anatomical and ecological traits. Key Results Increased genome size was associated with earliness of flowering and tendency to grow in humid conditions, and there was a positive correlation between an increase in stomatal size in species with extremely large genomes. Seed mass of geophytes was closely related to their ecology, but not to genomic parameters. Genomic DNA GC content showed a unimodal relationship with genome size but no relationship with species ecology. Conclusions Evolution of genome size in geophytes is closely related to their ecology and phenology and is also associated with remarkable changes in DNA base composition. Although geophytism together with producing larger cells appears to be an advantageous strategy for fast development of an organism in seasonal habitats, the drought sensitivity of large stomata may restrict the occurrence of geophytes with very large genomes to regions not subject to water stress. PMID:22021815

  5. Structuring polymers for delivery of DNA-based therapeutics: updated insights.

    PubMed

    Gupta, Madhu; Tiwari, Shailja; Vyas, Suresh

    2012-01-01

    Gene therapy offers greater opportunities for treating numerous incurable diseases from genetic disorders, infections, and cancer. However, development of appropriate delivery systems could be one of the most important factors to overcome numerous biological barriers for delivery of various therapeutic molecules. A number of nonviral polymer-mediated vectors have been developed for DNA delivery and offer the potential to surmount the associated problems of their viral counterpart. To address the concerns associated with safety issues, a wide range of polymeric vectors are available and have been utilized successfully to deliver their therapeutics in vivo. Today's research is mainly focused on the various natural or synthetic polymer-based delivery carriers that protect the DNA molecule from degradation, which offer specific targeting to the desired cells after systemic administration, have transfection efficiencies equivalent to virus-mediated gene delivery, and have long-term gene expression through sustained-release mechanisms. This review explores an updated overview of different nonviral polymeric delivery system for delivery of DNA-based therapeutics. These polymeric carriers have been evaluated in vitro and in vivo and are being utilized in various stages of clinical evaluation. Continued research and understanding of the principles of polymer-based gene delivery systems will enable us to develop new and efficient delivery systems for the delivery of DNA-based therapeutics to achieve the goal of efficacious and specific gene therapy for a vast array of clinical disorders as the therapeutic solutions of tomorrow.

  6. The photoinduced transformation of fluorescent DNA base analogue tC triggers DNA melting.

    PubMed

    Preus, Søren; Jønck, Søren; Pittelkow, Michael; Dierckx, Anke; Karpkird, Thitinun; Albinsson, Bo; Wilhelmsson, L Marcus

    2013-08-01

    While fluorescent analogues of the canonical nucleobases have proven to be highly valuable in a large number of applications, up until today, fluorescent DNA base analogues remain virtually inapplicable for single-molecule fluorescence experiments which require extremely bright and photostable dyes. Insight into the photodegradation processes of these fluorophores is thus a key step in the continuous development towards dyes with improved performances. Here, we show that the commercially available fluorescent nucleobase analogue tC under intense long-term illumination and in the presence of O2 is degraded to form a single photoreaction product which we suggest to be the sulfoxide form of tC. The photoproduct is characterized by a blue-shifted absorption and a less intense fluorescence compared to that of tC. Interestingly, when tC is positioned inside double-stranded DNA this photodriven conversion of tC to its photoproduct greatly reduces the duplex stability of the overall double helix in which the probe is positioned. Since tC can be excited selectively at 400 nm, well outside the absorption band of the natural DNA bases, this observation points towards the application of tC as a general light-triggered switch of DNA duplex stability.

  7. Immunization of the Female Genital Tract with a DNA-Based Vaccine

    PubMed Central

    Livingston, Julie B.; Lu, Shan; Robinson, Harriet; Anderson, Deborah J.

    1998-01-01

    Vaccines are being sought for contraception and the prevention of sexually transmitted diseases. However, progress is slow in this area largely because of lack of information on induction of protective immune responses in genital tract mucosa. In this study, we investigated whether in vivo transfection with a model DNA-based antigen delivered by gene gun technology would induce an antibody response detectable in vaginal secretions. Female rats were immunized with plasmids encoding human growth hormone (HGH) under the control of a cytomegalovirus promoter (pCMV/HGH) via vaginal mucosa (V), Peyer’s patch (PP), and/or abdominal skin (S) routes. Localization of HGH in the target tissues demonstrated that all three sites can be transfected in vivo with pCMV/HGH. Vaginal tissues expressed roughly the same level of plasmid as skin. Antibodies to HGH were detectable in serum and vaginal secretions in rats immunized with pCMV/HGH. In the rats primed and boosted vaginally, vaginal immunoglobulin A (IgA) and IgG antibody titers to HGH were sustained for at least 14 weeks, whereas rats immunized via other routes and protocols (S/V, S/S, PP/PP, or PP/V) did not consistently sustain significant vaginal antibody titers beyond week 6. DNA-based immunizations administered by the gene gun may be an effective method of inducing local immunity in the female genital tract. PMID:9423874

  8. Analysis of Total Food Intake and Composition of Individual's Diet Based on the U.S. Department of Agriculture's 1994-96, 1998 Continuing Survey of Food Intakes by Individuals (CSFII) (Final Report)

    EPA Science Inventory

    EPA released the final report, Analysis of Total Food Intake and Composition of Individual’s Diet Based on USDA’s 1994-1996, 98 Continuing Survey of Food Intakes by Individuals (CSFII). The consumption of food by the general population is a significant route of potential ...

  9. Effect of diet on mortality and cancer recurrence among cancer survivors: a systematic review and meta-analysis of cohort studies

    PubMed Central

    Schwedhelm, Carolina; Boeing, Heiner; Hoffmann, Georg; Aleksandrova, Krasimira

    2016-01-01

    Context: Evidence of an association between dietary patterns and individual foods and the risk of overall mortality among cancer survivors has not been reviewed systematically. Objective: The aim of this meta-analysis of cohort studies was to investigate the association between food intake and dietary patterns and overall mortality among cancer survivors. Data Sources: The PubMed and Embase databases were searched. Study Selection: A total of 117 studies enrolling 209 597 cancer survivors were included. Data Extraction: The following data were extracted: study location, types of outcome, population characteristics, dietary assessment method, risk estimates, and adjustment factors. Results: Higher intakes of vegetables and fish were inversely associated with overall mortality, and higher alcohol consumption was positively associated with overall mortality (RR, 1.08; 95%CI, 1.02–1.16). Adherence to the highest category of diet quality was inversely associated with overall mortality (RR, 0.78; 95%CI, 0.72–0.85; postdiagnosis RR, 0.79; 95%CI, 0.71–0.89), as was adherence to the highest category of a prudent/healthy dietary pattern (RR, 0.81; 95%CI, 0.67–0.98; postdiagnosis RR, 0.77; 95%CI, 0.60–0.99). The Western dietary pattern was associated with increased risk of overall mortality (RR, 1.46; 95%CI, 1.27–1.68; postdiagnosis RR, 1.51; 95%CI, 1.24–1.85). Conclusion: Adherence to a high-quality diet and a prudent/healthy dietary pattern is inversely associated with overall mortality among cancer survivors, whereas a Western dietary pattern is positively associated with overall mortality in this population. PMID:27864535

  10. Exposure to 1800 MHz radiofrequency electromagnetic radiation induces oxidative DNA base damage in a mouse spermatocyte-derived cell line.

    PubMed

    Liu, Chuan; Duan, Weixia; Xu, Shangcheng; Chen, Chunhai; He, Mindi; Zhang, Lei; Yu, Zhengping; Zhou, Zhou

    2013-03-27

    Whether exposure to radiofrequency electromagnetic radiation (RF-EMR) emitted from mobile phones can induce DNA damage in male germ cells remains unclear. In this study, we conducted a 24h intermittent exposure (5 min on and 10 min off) of a mouse spermatocyte-derived GC-2 cell line to 1800 MHz Global System for Mobile Communication (GSM) signals in GSM-Talk mode at specific absorption rates (SAR) of 1 W/kg, 2 W/kg or 4 W/kg. Subsequently, through the use of formamidopyrimidine DNA glycosylase (FPG) in a modified comet assay, we determined that the extent of DNA migration was significantly increased at a SAR of 4 W/kg. Flow cytometry analysis demonstrated that levels of the DNA adduct 8-oxoguanine (8-oxoG) were also increased at a SAR of 4 W/kg. These increases were concomitant with similar increases in the generation of reactive oxygen species (ROS); these phenomena were mitigated by co-treatment with the antioxidant α-tocopherol. However, no detectable DNA strand breakage was observed by the alkaline comet assay. Taking together, these findings may imply the novel possibility that RF-EMR with insufficient energy for the direct induction of DNA strand breaks may produce genotoxicity through oxidative DNA base damage in male germ cells.

  11. [Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

    PubMed

    Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I

    2013-01-01

    To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

  12. ITS1-rDNA-based methodology to identify world-wide hake species of the Genus Merluccius.

    PubMed

    Pérez, Montse; Vieites, Juan M; Presa, Pablo

    2005-06-29

    Species-specific DNA-based tags are valuable tools for the management of both fisheries and commercial fish products. In this study, we have developed a two-step molecular tool to detect the presence of hake DNA (Merluccius spp.) and to identify the exact hake species present in an blind sample. The first test involves PCR amplification of an ITS1-rDNA fragment of 193 bp using nested primers that are interspecifically conserved in Merluccius spp. and Atlantic cod, Gadus morhua. The second test consists of the PCR amplification of a 602-659 bp DNA fragment spanning part of the ribosomal cluster 18S-ITS1-5.8S and digesting it with four restriction enzymes whose targets map at interspecifically nonconserved sites of the ITS1. Alternatively, the identification of hake species can be achieved by FINS or BLAST, using the nucleotide sequence of either the whole ITS1 sequence or its nested fragment of 193 bp. Because of their high reproducibility and ease of execution, these procedures allow for routine analysis and constitute high reliable tools for the rapid identification of 12 species of hake.

  13. Diet and Physical Activity Interventions to Prevent or Treat Obesity in South Asian Children and Adults: A Systematic Review and Meta-Analysis

    PubMed Central

    Brown, Tamara; Smith, Sarah; Bhopal, Raj; Kasim, Adetayo; Summerbell, Carolyn

    2015-01-01

    Background and Aims: The metabolic risks associated with obesity are greater for South Asian populations compared with White or other ethnic groups, and levels of obesity in childhood are known to track into adulthood. Tackling obesity in South Asians is therefore a high priority. The rationale for this systematic review is the suggestion that there may be differential effectiveness in diet and physical activity interventions in South Asian populations compared with other ethnicities. The research territory of the present review is an emergent, rather than mature, field of enquiry, but is urgently needed. Thus the aim of this systematic review and meta-analysis was to assess the effectiveness of diet and physical activity interventions to prevent or treat obesity in South Asians living in or outside of South Asia and to describe the characteristics of effective interventions. Methods: Systematic review of any type of lifestyle intervention, of any length of follow-up that reported any anthropometric measure for children or adults of South Asian ethnicity. There was no restriction on the type of comparator; randomised controlled trials, controlled clinical trials, and before-after studies were included. A comprehensive search strategy was implemented in five electronic databases: ASSIA, Cochrane Controlled Trials Register, Embase, Medline and Social Sciences Citation Index. The search was limited to English language abstracts published between January 2006 and January 2014. References were screened; data extraction and quality assessment were carried out by two reviewers. Results are presented in narrative synthesis and meta-analysis. Results: Twenty-nine studies were included, seven children, 21 adult and one mixed age. No studies in children under six were identified. Sixteen studies were conducted in South Asia, ten in Europe and three in USA. Effective or promising trials include physical activity interventions in South Asian men in Norway and South Asian school

  14. Monetary Diet Cost, Diet Quality, and Parental Socioeconomic Status in Spanish Youth

    PubMed Central

    Ribas-Barba, Lourdes; Pérez-Rodrigo, Carmen; Bawaked, Rowaedh Ahmed; Fíto, Montserrat; Serra-Majem, Lluis

    2016-01-01

    Background Using a food-based analysis, healthy dietary patterns in adults are more expensive than less healthy ones; studies are needed in youth. Therefore, the objective of the present study was to determine relationships between monetary daily diet cost, diet quality, and parental socioeconomic status. Design and Methods Data were obtained from a representative national sample of 3534 children and young people in Spain, aged 2 to 24 years. Dietary assessment was performed with a 24-hour recall. Mediterranean diet adherence was measured by the KIDMED questionnaire. Average food cost was calculated from official Spanish government data. Monetary daily diet cost was expressed as euros per day (€/d) and euros per day standardized to a 1000kcal diet (€/1000kcal/d). Results Mean monetary daily diet cost was 3.16±1.57€/d (1.56±0.72€/1000kcal/d). Socioeconomic status was positively associated with monetary daily diet cost and diet quality measured by the KIDMED index (€/d and €/1000kcal/d, p<0.019). High Mediterranean diet adherence (KIDMED score 8–12) was 0.71 €/d (0.28€/1000kcal/d) more expensive than low compliance (KIDMED score 0–3). Analysis for nonlinear association between the KIDMED index and monetary daily diet cost per1000kcal showed no further cost increases beyond a KIDMED score of 8 (linear p<0.001; nonlinear p = 0.010). Conclusion Higher monetary daily diet cost is associated with healthy eating in Spanish youth. Higher socioeconomic status is a determinant for higher monetary daily diet cost and quality. PMID:27622518

  15. Alternate‐day versus daily energy restriction diets: which is more effective for weight loss? A systematic review and meta‐analysis

    PubMed Central

    Garcia‐Alvarez, A.; Alzahrnai, A. H.; Karanxha, J.; Stretchberry, D. R.; Contrera, K. J.; Utria, A. F.; Cheskin, L. J.

    2016-01-01

    Summary Background Alternate‐day‐fasting (ADF) has been proposed as an effective dieting method. Studies have found that it also can increase life span in rodents, and reduce inflammation in humans. The aim of this paper was to systematically review the efficacy of ADF compared to very‐low‐calorie dieting (VLCD) in terms of weight loss, and reduction of fat mass and fat‐free mass. Methods Systematic review: PubMed literature searches were performed. Fixed review procedures were applied. Studies were evaluated for quality. Twenty‐eight studies were included. Meta‐analysis: 10/28 studies (four ADF and six matched VLCD) were further analyzed. Results After adjustment for BMI and duration, there was no significant difference in mean body weight loss (VLCD 0.88 kg more weight loss than ADF, 95% CI: −4.32, 2.56) or fat‐free mass (VLCD 1.69 kg more fat‐free mass loss than ADF, 95% CI: −3.62, 0.23); there was a significant difference observed in fat mass (ADF 3.31 kg more fat mass loss than VLCD, 95% CI: 0.05, 6.56). Meta‐analysis showed that, among ADF studies, the pooled change in body weight, fat mass and fat‐free mass was 4.30 kg (95% CI: 3.41, 5.20), 4.06 kg (95% CI: 2.99, 5.13) and 0.72 kg (95% CI: −0.07, 1.51), respectively, while among VLCD studies, the pooled change was 6.28 kg (95% CI: 6.08, 6.49), 4.22 kg (95% CI: 3.95, 4.50) and 2.24 kg (95% CI: 1.95, 2.52), respectively. Conclusions Our results from both the systematic review and the meta‐analysis suggest that ADF is an efficacious dietary method, and may be superior to VLCD for some patients because of ease of compliance, greater fat‐mass loss and relative preservation of fat‐free mass. Head‐to‐head randomized clinical trials are needed to further assess relative efficacy of these two approaches. PMID:27708846

  16. Evaluation of bias on the assessment of diet breadth of herbivorous insects using molecular methods.

    PubMed

    De la Cadena, Gissela; Papadopoulou, Anna; Maes, Jean-Michel; Gómez-Zurita, Jesús

    2017-04-01

    The interactions between herbivores and their host plants play a key role in ecological processes. Understanding the width and nature of these interactions is fundamental to ecology and conservation. Recent research on DNA-based inference of trophic associations suggests that the host range of phytophagous insects in the tropics may be wider than previously thought based on traditional observation. However, the reliability of molecular inference of ecological associations, still strongly dependent on PCR and thus exposed to the risk of contamination with environmental DNA, is under debate. Here, we explored alternative procedures to reduce the chance of amplification of external, nondiet DNA, including surface decontamination and analysis of mid/hind guts, comparing the results with those obtained using the standard protocol. We studied 261 specimens in eight species of Neotropical Chrysomelidae that yielded 316 psbA-trnH intergenic spacer sequences (cpDNA marker of putative diets) from unique and multiple-band PCR results. The taxonomic identity of these sequences was inferred using the automated pipeline BAGpipe, yielding results consistent with 31 plant families. Regardless of the protocol used, a wide taxonomic spectrum of food was inferred for all chrysomelid species. Canonical Correspondence Analysis using these data revealed significant differences attributed mainly to species (expectedly, since they represent different ecologies), but also to treatment (untreated vs. cleaned/gut samples) and PCR results (single vs. multiple bands). Molecular identification of diets is not straightforward and, regardless of the species' niche breadth, combining approaches that reduce external contamination and studying multiple individuals per species may help increasing confidence in results.

  17. Efficacy of aerobic exercise and a prudent diet for improving selected lipids and lipoproteins in adults: a meta-analysis of randomized controlled trials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Studies addressing the effects of aerobic exercise and a prudent diet on lipid and lipoprotein concentrations in adults have reached conflicting conclusions. The purpose of this study was to determine the effects of aerobic exercise combined with a prudent diet on lipid and lipoprotein concentration...

  18. Efficacy of aerobic exercise and a prudent diet for improving selected lipids and lipoproteins in adults: A meta-analysis of andomized controlled trials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Studies addressing the effects of aerobic exercise and a prudent diet on lipid and lipoprotein concentrations in adults have reached conflicting conclusions. The purpose of this study was to determine the effects of aerobic exercise combined with a prudent diet on lipid and lipoprotein concentration...

  19. Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

    PubMed

    Takezawa, Yusuke; Shionoya, Mitsuhiko

    2012-12-18

    With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional

  20. Thermodynamics of weight loss diets.

    PubMed

    Fine, Eugene J; Feinman, Richard D

    2004-12-08

    BACKGROUND: It is commonly held that "a calorie is a calorie", i.e. that diets of equal caloric content will result in identical weight change independent of macronutrient composition, and appeal is frequently made to the laws of thermodynamics. We have previously shown that thermodynamics does not support such a view and that diets of different macronutrient content may be expected to induce different changes in body mass. Low carbohydrate diets in particular have claimed a "metabolic advantage" meaning more weight loss than in isocaloric diets of higher carbohydrate content. In this review, for pedagogic clarity, we reframe the theoretical discussion to directly link thermodynamic inefficiency to weight change. The problem in outline: Is metabolic advantage theoretically possible? If so, what biochemical mechanisms might plausibly explain it? Finally, what experimental evidence exists to determine whether it does or does not occur? RESULTS: Reduced thermodynamic efficiency will result in increased weight loss. The laws of thermodynamics are silent on the existence of variable thermodynamic efficiency in metabolic processes. Therefore such variability is permitted and can be related to differences in weight lost. The existence of variable efficiency and metabolic advantage is therefore an empiric question rather than a theoretical one, confirmed by many experimental isocaloric studies, pending a properly performed meta-analysis. Mechanisms are as yet unknown, but plausible mechanisms at the metabolic level are proposed. CONCLUSIONS: Variable thermodynamic efficiency due to dietary manipulation is permitted by physical laws, is supported by much experimental data, and may be reasonably explained by plausible mechanisms.

  1. Anionic magnetite nanoparticle conjugated with pyrrolidinyl peptide nucleic acid for DNA base discrimination

    NASA Astrophysics Data System (ADS)

    Khadsai, Sudarat; Rutnakornpituk, Boonjira; Vilaivan, Tirayut; Nakkuntod, Maliwan; Rutnakornpituk, Metha

    2016-09-01

    Magnetite nanoparticles (MNPs) were surface modified with anionic poly( N-acryloyl glycine) (PNAG) and streptavidin for specific interaction with biotin-conjugated pyrrolidinyl peptide nucleic acid (PNA). Hydrodynamic size ( D h) of PNAG-grafted MNPs varied from 334 to 496 nm depending on the loading ratio of the MNP to NAG in the reaction. UV-visible and fluorescence spectrophotometries were used to confirm the successful immobilization of streptavidin and PNA on the MNPs. About 291 pmol of the PNA/mg MNP was immobilized on the particle surface. The PNA-functionalized MNPs were effectively used as solid supports to differentiate between fully complementary and non-complementary/single-base mismatch DNA using the PNA probe. These novel anionic MNPs can be efficiently applicable for use as a magnetically guidable support for DNA base discrimination.

  2. Recent advances in DNA-based electrochemical biosensors for heavy metal ion detection: A review.

    PubMed

    Saidur, M R; Aziz, A R Abdul; Basirun, W J

    2017-04-15

    The presence of heavy metal in food chains due to the rapid industrialization poses a serious threat on the environment. Therefore, detection and monitoring of heavy metals contamination are gaining more attention nowadays. However, the current analytical methods (based on spectroscopy) for the detection of heavy metal contamination are often very expensive, tedious and can only be handled by trained personnel. DNA biosensors, which are based on electrochemical transduction, is a sensitive but inexpensive method of detection. The principles, sensitivity, selectivity and challenges of electrochemical biosensors are discussed in this review. This review also highlights the major advances of DNA-based electrochemical biosensors for the detection of heavy metal ions such as Hg(2+), Ag(+), Cu(2+) and Pb(2+).

  3. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

    PubMed Central

    2016-01-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  4. Angular distributions in the double ionization of DNA bases by electron impact

    NASA Astrophysics Data System (ADS)

    Khelladi, M. F.; Mansouri, A.; Dal Cappello, C.; Charpentier, I.; Hervieux, P. A.; Ruiz-Lopez, M. F.; Roy, A. C.

    2016-11-01

    Ab initio calculations of the five-fold differential cross sections for electron-impact double ionization of thymine, cytosine, adenine and guanine are performed in the first Born approximation for an incident energy close to 5500 eV. The wavefunctions of the DNA bases are constructed using the multi-center wave functions from the Gaussian 03 program. These multi-center wave functions are converted into single-center expansions of Slater-type functions. For the final state, the two ejected electrons are described by two Coulomb wave functions. The electron-electron repulsion between the two ejected electrons is also taken into account. Mechanisms of the double ionization are discussed for each case and the best choices of the kinematical parameters are determined for next experiments.

  5. Fast parallel DNA-based algorithms for molecular computation: quadratic congruence and factoring integers.

    PubMed

    Chang, Weng-Long

    2012-03-01

    Assume that n is a positive integer. If there is an integer such that M (2) ≡ C (mod n), i.e., the congruence has a solution, then C is said to be a quadratic congruence (mod n). If the congruence does not have a solution, then C is said to be a quadratic noncongruence (mod n). The task of solving the problem is central to many important applications, the most obvious being cryptography. In this article, we describe a DNA-based algorithm for solving quadratic congruence and factoring integers. In additional to this novel contribution, we also show the utility of our encoding scheme, and of the algorithm's submodules. We demonstrate how a variety of arithmetic, shifted and comparative operations, namely bitwise and full addition, subtraction, left shifter and comparison perhaps are performed using strands of DNA.

  6. Fast parallel molecular algorithms for DNA-based computation: factoring integers.

    PubMed

    Chang, Weng-Long; Guo, Minyi; Ho, Michael Shan-Hui

    2005-06-01

    The RSA public-key cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA public-key cryptosystem is based on the difficulty of factoring the product of two large prime numbers. This paper demonstrates to factor the product of two large prime numbers, and is a breakthrough in basic biological operations using a molecular computer. In order to achieve this, we propose three DNA-based algorithms for parallel subtractor, parallel comparator, and parallel modular arithmetic that formally verify our designed molecular solutions for factoring the product of two large prime numbers. Furthermore, this work indicates that the cryptosystems using public-key are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations.

  7. Ab initio Calculations of Electronic Fingerprints of DNA bases on Graphene

    NASA Astrophysics Data System (ADS)

    Ahmed, Towfiq; Rehr, John J.; Kilina, Svetlana; Das, Tanmoy; Haraldsen, Jason T.; Balatsky, Alexander V.

    2012-02-01

    We have carried out first principles DFT calculations of the electronic local density of states (LDOS) of DNA nucleotide bases (A,C,G,T) adsorbed on graphene using LDA with ultra-soft pseudo-potentials. We have also calculated the longitudinal transmission currents T(E) through graphene nano-pores as an individual DNA base passes through it, using a non-equilibrium Green's function (NEGF) formalism. We observe several dominant base-dependent features in the LDOS and T(E) in an energy range within a few eV of the Fermi level. These features can serve as electronic fingerprints for the identification of individual bases from dI/dV measurements in scanning tunneling spectroscopy (STS) and nano-pore experiments. Thus these electronic signatures can provide an alternative approach to DNA sequencing.

  8. A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs

    NASA Astrophysics Data System (ADS)

    Shukla, P. K.; Ganapathy, Vinay; Mishra, P. C.

    2011-09-01

    Methylation of the DNA bases in the Watson-Crick GC and AT base pairs by the methyldiazonium ion was investigated employing density functional and second order Møller-Plesset (MP2) perturbation theories. Methylation at the N3, N7 and O6 sites of guanine, N1, N3 and N7 sites of adenine, O2 and N3 sites of cytosine and the O2 and O4 sites of thymine were considered. The computed reactivities for methylation follow the order N7(guanine) > N3(adenine) > O6(guanine) which is in agreement with experiment. The base pairing in DNA is found to play a significant role with regard to reactivities of the different sites.

  9. Aviram-Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps

    NASA Astrophysics Data System (ADS)

    Agapito, Luis A.; Gayles, Jacob; Wolowiec, Christian; Kioussis, Nicholas

    2012-04-01

    We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab initio non-equilibrium Green’s function (NEGF) theory to determine the electrical response of graphene—base-pair—graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the cytosine-guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the thymine-adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps.

  10. The role of DNA base excision repair in brain homeostasis and disease.

    PubMed

    Akbari, Mansour; Morevati, Marya; Croteau, Deborah; Bohr, Vilhelm A

    2015-08-01

    Chemical modification and spontaneous loss of nucleotide bases from DNA are estimated to occur at the rate of thousands per human cell per day. DNA base excision repair (BER) is a critical mechanism for repairing such lesions in nuclear and mitochondrial DNA. Defective expression or function of proteins required for BER or proteins that regulate BER have been consistently associated with neurological dysfunction and disease in humans. Recent studies suggest that DNA lesions in the nuclear and mitochondrial compartments and the cellular response to those lesions have a profound effect on cellular energy homeostasis, mitochondrial function and cellular bioenergetics, with especially strong influence on neurological function. Further studies in this area could lead to novel approaches to prevent and treat human neurodegenerative disease.

  11. DNA-Based Characterization and Identification of Arbuscular Mycorrhizal Fungi Species.

    PubMed

    Senés-Guerrero, Carolina; Schüßler, Arthur

    2016-01-01

    Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most land plants. They have great ecological and economic importance as they can improve plant nutrition, plant water supply, soil structure, and plant resistance to pathogens. We describe two approaches for the DNA-based characterization and identification of AMF, which both can be used for single fungal spores, soil, or roots samples and resolve closely related AMF species: (a) Sanger sequencing of a 1.5 kb extended rDNA-barcode from clone libraries, e.g., to characterize AMF isolates, and (b) high throughput 454 GS-FLX+ pyrosequencing of a 0.8 kb rDNA fragment, e.g., for in-field monitoring.

  12. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs.

    PubMed

    Fang, Wei; Chen, Ji; Rossi, Mariana; Feng, Yexin; Li, Xin-Zheng; Michaelides, Angelos

    2016-06-02

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general.

  13. Transcriptome analysis on the inflammatory cell infiltration of nonalcoholic steatohepatitis in bama minipigs induced by a long-term high-fat, high-sucrose diet.

    PubMed

    Xia, Jihan; Yuan, Jing; Xin, Leilei; Zhang, Yuanyuan; Kong, Siyuan; Chen, Yaoxing; Yang, Shulin; Li, Kui

    2014-01-01

    Long-term adherence to a high-fat, high-calorie diet influences human health and causes obesity, metabolic syndrome and nonalcoholic steatohepatitis (NASH). Inflammation plays a key role in the development of NASH; however, the mechanism of inflammation induced by over-nutrition remains largely unknown. In this study, we fed Bama minipigs a high-fat, high-sucrose diet (HFHSD) for 23 months. The pigs exhibited characteristics of metabolic syndrome and developed steatohepatitis with greatly increased numbers of inflammatory cells, such as lymphocytes (2.27-fold, P<0.05), Kupffer cells (2.59-fold, P<0.05), eosinophils (1.42-fold, P<0.05) and neutrophils (2.77-fold, P<0.05). High-throughput RNA sequencing (RNA-seq) was performed to explore the systemic transcriptome of the pig liver during inflammation. Approximately 18.2 gigabases of raw sequence data were generated, and over 303 million high-quality reads were assembled into 21,126 unigenes. RNA-seq data analysis showed that 822 genes were differentially expressed in liver (P<0.05) between the HFHSD and control groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the process of inflammation involved the inflammatory signal transduction-related toll-like receptor, MAPK, and PPAR signaling pathways; the cytokine-related chemokine signaling, cytokine-cytokine receptor interaction, and IL2, IL4, IL6, and IL12 signaling pathways; the leukocyte receptor signaling-related T cell, B cell, and natural killer cell signaling pathways; inflammatory cell migration and invasion- related pathways; and other pathways. Moreover, we identified several differentially expressed inflammation-related genes between the two groups, including FOS, JUN, TLR7, MYC, PIK3CD, VAV3, IL2RB and IL4R, that could be potential targets for further investigation. Our study suggested that long-term HFHSD induced obesity and liver inflammation, providing basic insight into the molecular mechanism of this condition and laying the

  14. Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C3'- and C5'-deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3'- and C5'-deoxyribose-phospate cross sections, differing by less than 10%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

  15. Insight into the interaction between DNA bases and defective graphenes: covalent or non-covalent.

    PubMed

    Xu, Zhenfeng; Meher, Biswa Ranjan; Eustache, Darnashley; Wang, Yixuan

    2014-02-01

    Although some metal clusters and molecules were found to more significantly bind to defective graphenes than to pristine graphenes, exhibiting chemisorptions on defective graphenes, the present investigation shows that the adsorption of DNA bases on mono- and di-vacant defective graphenes does not show much difference from that on pristine graphene, and is still dominantly driven by noncovalent interactions. In the present study the adsorptions of the nucleobases, adenine (A), cytosine (C), guanine, (G), and thymine (T) on pristine and defective graphenes, are fully optimized using a hybrid-meta GGA density functional theory (DFT), M06-2X/6-31G*, and the adsorption energies are then refined with both M06-2X and B97-D/6-311++G**. Graphene is modeled as nano-clusters of C₇₂H₂₄, C₇₁H₂₄, and C₇₀H₂₄ for pristine, mono- and di-vacant defective graphenes, respectively, supplemented by a few larger ones. The result shows that guanine has the maximum adsorption energy in all of the three adsorption systems; and the sequence of the adsorption strength is G>A>T>C on the pristine and di-vacant graphene and G>T>A>C on the mono-vacant graphene. In addition, the binding energies of the DNA bases with the pristine graphene are less than the corresponding ones with di-vacant defective graphene; however, they are greater than those of mono-vacant graphene with guanine and adenine, while it is dramatic that the binding energies of mono-vacant graphene with thymine and cytosine appear larger than those of pristine graphene.

  16. Insight into the Interaction between DNA Bases and Defective Graphenes: Covalent or Non-covalent

    PubMed Central

    Xu, Zhenfeng; Meher, Biswa Ranjan; Eustache, Darnashley; Wang, Yixuan

    2013-01-01

    Although some metal clusters and molecules were found to more significantly bind to defective graphenes than to pristine graphenes, exhibiting chemisorptions on defective graphenes, the present investigation shows that the adsorption of DNA bases on mono- and di-vacant defective graphenes does not show much difference from that on pristine graphene, and is still dominantly driven by noncovalent interactions. In the present study the adsorptions of the nucleobases, adenine (A), cytosine (C), guanine, (G), and thymine (T) on pristine and defective graphenes, are fully optimized using a hybrid-meta GGA density functional theory (DFT), M06-2X/6-31G*, and the adsorption energies are then refined with both M06-2X and B97-D/6-311++G**. Graphene is modeled as nano-clusters of C72H24, C71H24, and C70H24 for pristine, mono- and divacant defective graphenes, respectively, supplemented by a few larger ones. The result shows that guanine has the maximum adsorption energy in all of the three adsorption systems; and the sequence of the adsorption strength is G>A>T>C on the pristine and di-vacant graphene and G>T>A>C on the mono-vacant graphene. In addition, the binding energies of the DNA bases with the pristine graphene are less than the corresponding ones with di-vacant defective graphene; however, they are greater than those of mono-vacant graphene with guanine and adenine, while it is dramatic that the binding energies of mono-vacant graphene with thymine and cytosine appear larger than those of pristine graphene. PMID:24215998

  17. Diet counseling in a multicultural society.

    PubMed

    Kittler, P G; Sucher, K P

    1990-01-01

    Successful diet counseling is dependent on culturally sensitive communication strategies. Health care practitioners can improve cross-cultured counseling through a four-step process. First, they must become familiar with their own cultural heritages. Second, they must become acquainted with the cultural background of each client. Third, through an in-depth cross-cultural interview, they must establish the client's cultural background, food habit adaptations made in the United States, and personal preferences. Fourth, they must modify diets based on unbiased analysis of the dietary data. The best chance for compliance occurs when diets are modified with consideration for client's cultural and personal preferences.

  18. Diet Therapy Specialist.

    ERIC Educational Resources Information Center

    Air Force Training Command, Sheppard AFB, TX.

    This four-volume student text is intended for use in training Air Force diet therapy specialists. The first volume, a study guide and workbook for self-directed instruction, covers nutrition, food processing and preparation, therapeutic diets, security precautions in medical food service, procedures for ordering equipment and supplies, food…

  19. Understanding the DASH diet

    MedlinePlus

    ... help lower blood pressure. To follow the DASH diet for weight loss, you eat plenty of: Non-starchy vegetables and ... Waugh R, Sherwood A. Effects of the DASH diet alone and in ... loss on blood pressure and cardiovascular biomarkers in men ...

  20. The amplification effect of functionalized gold nanoparticles on the binding of anticancer drug dacarbazine to DNA and DNA bases

    NASA Astrophysics Data System (ADS)

    Shen, Qin; Wang, Xuemei; Fu, Degang

    2008-11-01

    The promising application of functionalized gold nanoparticles to amplify the performance of biosensors and relevant biomolecular recognition processes has been explored in this paper. Our observations illustrate the apparent enhancement effect of the gold nanoparticles on the electrochemical response of the anticancer drug dacarbazine (DTIC) binding to DNA and DNA bases, indicating that these functionalized gold nanoparticles could readily facilitate the specific interactions between DTIC and DNA/DNA bases. This raises the potential valuable applications of these biocompatible nanoparticles in the promising biosensors and biomedical engineering.

  1. Diet and Inflammatory Bowel Disease.

    PubMed

    Knight-Sepulveda, Karina; Kais, Susan; Santaolalla, Rebeca; Abreu, Maria T

    2015-08-01

    Patients with inflammatory bowel disease (IBD) are increasingly becoming interested in nonpharmacologic approaches to managing their disease. One of the most frequently asked questions of IBD patients is what they should eat. The role of diet has become very important in the prevention and treatment of IBD. Although there is a general lack of rigorous scientific evidence that demonstrates which diet is best for certain patients, several diets-such as the low-fermentable oligosaccharide, disaccharide, monosaccharide, and polyol diet; the specific carbohydrate diet; the anti-inflammatory diet; and the Paleolithic diet-have become popular. This article discusses the diets commonly recommended to IBD patients and reviews the supporting data.

  2. The effects of low carbohydrate diets on liver function tests in nonalcoholic fatty liver disease: A systematic review and meta-analysis of clinical trials

    PubMed Central

    Haghighatdoost, Fahimeh; Salehi-Abargouei, Amin; Surkan, Pamela J.; Azadbakht, Leila

    2016-01-01

    Background: Although several observational and experimental studies have examined the effects of low carbohydrate diets (LCDs) on nonalcoholic fatty liver disease (NAFLD), there are considerable inconsistencies among studies. We summarized the effect of LCDs on liver function tests, including intrahepatic lipid content (IHLC), alanine transaminase (ALT), aspartate aminotransferases (AST), and gamma-glutamyl transferase (GGT) in patients with NAFLD. Materials and Methods: PubMed, ISI Web of Science, Scopus, and Google Scholar databases were searched for relevant publications until July 2014, resulting in ten relevant papers that were included in meta-analysis. Related articles were found by searching Medical Subject Heading terms of “NAFLD” in combination with “low carbohydrate”. For this meta-analysis, we used mean differences and standard errors of liver function biomarkers. Summary effect and corresponding confidence interval (CI) were estimated using random effect models. Heterogeneity between studies was assessed using Cochran's Q- and I-squared tests. Results: Our search led to ten eligible papers that evaluated serum ALT levels (n = 238), nine reported serum AST levels (n = 216), five reported serum GGT concentrations (n = 91), and four assessed IHLC (n = 50). LCD decreased IHLC by −11.53% (95% CI: −18.10, −4.96; I2 = 83.2%). However, the effect of LCD on liver enzymes was not significant. Mean differences for the effects of LCDs on ALT, AST, and GGT were −4.35 IU/L (95% CI: −12.91, 4.20; I2 = 87.9%), −1.44 IU/L (95% CI: −4.98, 2.10; I2 = 61.4%), and −7.85 IU/L (95% CI: −29.65, 13.96; I2 = 99.4%), respectively. Conclusion: LCD consumption in subjects with NAFLD led to a significant reduction in IHLC, but did not significantly affect the concentration of liver enzymes. PMID:27904598

  3. Parental encouragement of dieting promotes daughters' early dieting.

    PubMed

    Balantekin, Katherine N; Savage, Jennifer S; Marini, Michele E; Birch, Leann L

    2014-09-01

    Dieting to lose weight is common among female adolescents. This research investigated the association between maternal and paternal encouragement to diet and their daughters' self-reported "early dieting" (prior to age 11 y) and adolescent dieting (between 11 y and 15 y), and how parental encouragement to diet is related to changes in daughters' BMI percentiles. Participants in this study were 174 non-Hispanic white girls and their parents, assessed when daughters were 9-, 11-, 13-, and 15 y. The Parent Encouragement of Child Weight Loss Scale was used to measure encouragement to diet. Logistic regression was used to examine the relationship between parental encouragement to diet and daughters' reports of dieting by 11 y and by 15 y, adjusting for daughters' weight status at baseline. Compared with girls whose mothers didn't encourage dieting, girls who were encouraged to diet were twice as likely to diet by 11 y; girls who were encouraged by their fathers were also twice as likely to diet by 11 y. Girls who were encouraged to diet by both parents were 8 times more likely to report early dieting than girls who were not. Neither maternal nor paternal encouragement predicted the emergence of dieting during adolescence. Girls who dieted and had parental encouragement to do so had increases in BMI percentile from 9 y to 15 y. Findings reveal that parental encouragement to diet may be counterproductive and that parents need alternative approaches to promote healthy patterns of intake and growth among young girls.

  4. Diet Therapy Career Ladder, AFSC 926XO.

    DTIC Science & Technology

    1985-12-01

    diet . On the other hand, first-termers in AFSC tend to have experience with more types of thera- peutic diets , such as gluten restricted, high...DENTAL SOFT DIET 96 95 95 DIABETIC DIET 96 95 96 k FAT CONTROLLED, CHOLESTEROL RESTRICTED DIET 91 92 92 FAT FREE TEST DIET 60 71 70 FAT RESTRICTED DIET ...ELIMINATION DIET 36 45 46 CARBOHYDRATE TEST DIET , 150GM AND 300GM 40 62 69 - GLUTEN RESTRICTED DIET 30 40 55 . HIGH POTASSIUM DIET

  5. "Nano-oddities": unusual nucleic acid assemblies for DNA-based nanostructures and nanodevices.

    PubMed

    Yatsunyk, Liliya A; Mendoza, Oscar; Mergny, Jean-Louis

    2014-06-17

    CONSPECTUS: DNA is an attractive polymer building material for nanodevices and nanostructures due to its ability for self-recognition and self-assembly. Assembly relies on the formation of base-specific interactions that allow strands to adopt structures in a controllable fashion. Most DNA-based higher order structures such as DNA cages, 2D and 3D DNA crystals, or origamis are based on DNA double helices stabilized by Watson-Crick complementarity. A number of nonclassical pairing patterns are possible between or among DNA strands; these interactions result in formation of unusual structures that include, but are not limited to, G-quadruplexes, i-motifs, triplexes, and parallel-stranded duplexes. These structures create greater diversity of DNA-based building blocks for nanomaterials and have certain advantages over conventional duplex DNA, such as enhanced thermal stability and sensitivity to chemical stimuli. In this Account, we briefly introduce these alternative DNA structures and describe in detail their utilization in a variety of nanomaterials and nanomachines. The field of DNA "nano-oddities" emerged in the late 1990s when for the first time a DNA nanomachine was designed based on equilibrium between B-DNA and noncanonical, left-handed Z-DNA. Soon after, "proof-of-principle" DNA nanomachines based on several DNA "oddities" were reported. These machines were set in motion by the addition of complementary strands (a principle used by many B-DNA-based nanodevices), by the addition of selected cations, small molecules, or proteins, or by a change in pH or temperature. Today, we have fair understanding of the mechanism of action of these devices, excellent control over their performance, and knowledge of basic principles of their design. pH sensors and pH-controlled devices occupy a central niche in the field. They are usually based on i-motifs or triplex DNA, are amazingly simple, robust, and reversible, and create no waste apart from salt and water. G

  6. Evaluation of Diet-Related Infographics on Pinterest for Use of Behavior Change Theories: A Content Analysis

    PubMed Central

    Strickling, Kate; Payne, Hannah E; Jensen, Kayla C; West, Joshua H

    2016-01-01

    Background There is increasing interest in Pinterest as a method of disseminating health information. However, it is unclear whether the health information promoted on Pinterest is evidence-based or incorporates behavior change theory. Objectives The objective of the study was to determine the presence of health behavior theory (HBT) constructs in pins found on Pinterest and assess the relationship between various pin characteristics and the likelihood of inclusion of HBT. Methods A content analysis was conducted on pins collected from Pinterest identified with the search terms “nutrition infographic” and “healthy eating infographic.” The coding rubric included HBT constructs, pin characteristics, and visual communication tools. Each HBT construct was coded as present or not present (yes=1, no=0). A total theory score was calculated by summing the values for each of the 9 constructs (range 0-9). Adjusted regression analysis was used to identify factors associated with the inclusion of health behavior change theory in pins (P<.05). Results The mean total theory score was 2.03 (SD 1.2). Perceived benefits were present most often (170/236, 72%), followed by behavioral capability (123/238, 51.7%) and perceived severity (79/236, 33.5%). The construct that appeared the least was self-regulation/self-control (2/237, 0.8%). Pin characteristics associated with the inclusion of HBT included a large amount of text (P=.01), photographs of real people (P=.001), cartoon pictures of food (P=.01), and the presence of references (P=.001). The number of repins (P=.04), likes (P=.01), and comments (P=.01) were positively associated with the inclusion of HBT. Conclusions These findings suggest that current Pinterest infographics targeting healthy eating contain few HBT elements. Health professionals and organizations should create and disseminate infographics that contain more elements of HBT to better influence healthy eating behavior. This may be accomplished by creating

  7. Color degradation of acrylic resin denture teeth as a function of liquid diet: ultraviolet-visible reflection analysis.

    PubMed

    Hipólito, Ana Carolina; Barão, Valentim A; Faverani, Leonardo P; Ferreira, Mayara B; Assunção, Wirley G

    2013-10-01

    The effect of different beverages on acrylic resin denture teeth color degradation is evaluated. Ten acrylic resin denture teeth brands were evaluated: Art Plus (AP), Biolux (BX), Biotone IPN (BI), Magister (MG), Mondial 6 (MD), Premium 6 (PR), SR Vivodent PE (SR), Trilux (TR), Trubyte Biotone (TB), and Vipi Dent Plus (VP). Teeth were immersed in staining solutions (coffee, cola, and orange juice) or artificial saliva (control) (n=6) for 1, 7, 15, or 30 days. Specimen colors were evaluated spectrophotometrically based on the Commission Internationale d'Eclairage L*a*b* system. Color differences (ΔE) were calculated between the baseline and post-staining results. Data were evaluated by analysis of variance and Tukey test (α = 0.05). BI (1.82 ± 0.95) and TR (1.78 ± 0.72) teeth exhibited the greatest ΔE values, while BX (0.88 ± 0.43) and MD (1.09 ± 0.44) teeth were the lowest, regardless of solution and measurement period, and were different from BI and TR teeth (P < 0.05). Cola and coffee promoted higher denture teeth color alterations than orange juice and saliva (P < 0.05). Saliva generated the lowest denture teeth color alterations. Greater immersion times caused higher denture teeth color changes. The lifespan of removable dentures and the aesthetic satisfaction of several edentulous patients may be increased with the use of stain-resistant artificial denture teeth.

  8. Malnutrition and brain development: an analysis of the effects of inadequate diet during different stages of life in rat.

    PubMed

    Alamy, Meryem; Bengelloun, Wail A

    2012-07-01

    Protein malnutrition or undernutrition can result in abnormal development of the brain. Depending on type, age at onset and duration, different structural and functional deficits can be observed. In the present review, we discuss the neuroanatomical, behavioral, neurochemical and oxidative status changes associated with protein malnutrition or undernutrition at different ages during prenatal and immediately postnatal periods as well as in adult rat. Analysis of all data suggests that protein malnutrition as well as undernutrition induced impaired learning and retention when imposed during the immediately postnatal period and in adulthood, whereas hyperactivity including increased impulsiveness and greater reactivity to aversive stimuli occurred when malnutrition or undernutrition was imposed either pre or postnatally. This general state of hyperreactivity may be linked essentially to an alteration in dopaminergic system. Hence, the present review shows that in spite of the attention devoted in the literature to prenatal effects, cognitive deficits are more serious following malnutrition or undernutrition after birth. We thus clearly establish a special vulnerability to malnutrition after weaning in rats.

  9. Can a CNN recognize Catalan diet?

    NASA Astrophysics Data System (ADS)

    Herruzo, P.; Bolaños, M.; Radeva, P.

    2016-10-01

    Nowadays, we can find several diseases related to the unhealthy diet habits of the population, such as diabetes, obesity, anemia, bulimia and anorexia. In many cases, these diseases are related to the food consumption of people. Mediterranean diet is scientifically known as a healthy diet that helps to prevent many metabolic diseases. In particular, our work focuses on the recognition of Mediterranean food and dishes. The development of this methodology would allow to analise the daily habits of users with wearable cameras, within the topic of lifelogging. By using automatic mechanisms we could build an objective tool for the analysis of the patient's behavior, allowing specialists to discover unhealthy food patterns and understand the user's lifestyle. With the aim to automatically recognize a complete diet, we introduce a challenging multi-labeled dataset related to Mediter-ranean diet called FoodCAT. The first type of label provided consists of 115 food classes with an average of 400 images per dish, and the second one consists of 12 food categories with an average of 3800 pictures per class. This dataset will serve as a basis for the development of automatic diet recognition. In this context, deep learning and more specifically, Convolutional Neural Networks (CNNs), currently are state-of-the-art methods for automatic food recognition. In our work, we compare several architectures for image classification, with the purpose of diet recognition. Applying the best model for recognising food categories, we achieve a top-1 accuracy of 72.29%, and top-5 of 97.07%. In a complete diet recognition of dishes from Mediterranean diet, enlarged with the Food-101 dataset for international dishes recognition, we achieve a top-1 accuracy of 68.07%, and top-5 of 89.53%, for a total of 115+101 food classes.

  10. [Breastfeeding and vegan diet].

    PubMed

    Wagnon, J; Cagnard, B; Bridoux-Henno, L; Tourtelier, Y; Grall, J-Y; Dabadie, A

    2005-10-01

    Vegan diet in lactating women can induce vitamin B12 deficiency for their children with risk of an impaired neurological development. A 9.5-month-old girl presented with impaired growth and severe hypotonia. She had a macrocytic anemia secondary to vitamin B12 deficiency. MRI showed cerebral atrophy. She was exclusively breastfed. Her mother was also vitamin B12 deficient, secondary to a vegan diet. She had a macrocytic anemia when discharged from the maternity. Vegan diet is a totally inadequate regimen for pregnant and lactating women, especially for their children. Prevention is based on screening, information and vitamin supplementation.

  11. DNA vs. mirror-image DNA: a universal approach to tune the absolute configuration in DNA-based asymmetric catalysis.

    PubMed

    Wang, Jocelyn; Benedetti, Erica; Bethge, Lucas; Vonhoff, Stefan; Klussmann, Sven; Vasseur, Jean-Jacques; Cossy, Janine; Smietana, Michael; Arseniyadis, Stellios

    2013-10-25

    Mirror mirror on the wall: By taking advantage of the unique structural features of L-DNA, the first examples of left-helical enantioselective induction in the field of DNA-based asymmetric catalysis were realized. Most importantly, this approach is the only one that allows a reliable and predictable access to both enantiomers for any given reaction.

  12. Potential for DNA-based identification of Great Lakes fauna: Match and mismatch between taxa inventories and DNA barcode libraries

    EPA Science Inventory

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However, the abi...

  13. Isothermal titration calorimetry studies on the binding of DNA bases and PNA base monomers to gold nanoparticles.

    PubMed

    Gourishankar, A; Shukla, Sourabh; Ganesh, Krishna N; Sastry, Murali

    2004-10-20

    An isothermal titration calorimetric (ITC) investigation of the interaction of DNA bases and PNA base monomers with gold nanoparticles is described revealing a binding sequence in the order C > G > A > T. Direct measurement of the strength of interaction of ligands with nanogold by ITC has important implications in surface modification strategies for biomedical, catalysis, and nanoarchitecture applications.

  14. Estimating the effect of human base excision repair protein variants on the repair of oxidative DNA base damage.

    PubMed

    Sokhansanj, Bahrad A; Wilson, David M

    2006-05-01

    Epidemiologic studies have revealed a complex association between human genetic variance and cancer risk. Quantitative biological modeling based on experimental data can play a critical role in interpreting the effect of genetic variation on biochemical pathways relevant to cancer development and progression. Defects in human DNA base excision repair (BER) proteins can reduce cellular tolerance to oxidative DNA base damage caused by endogenous and exogenous sources, such as exposure to toxins and ionizing radiation. If not repaired, DNA base damage leads to cell dysfunction and mutagenesis, consequently leading to cancer, disease, and aging. Population screens have identified numerous single-nucleotide polymorphism variants in many BER proteins and some have been purified and found to exhibit mild kinetic defects. Epidemiologic studies have led to conflicting conclusions on the association between single-nucleotide polymorphism variants in BER proteins and cancer risk. Using experimental data for cellular concentration and the kinetics of normal and variant BER proteins, we apply a previously developed and tested human BER pathway model to (i) estimate the effect of mild variants on BER of abasic sites and 8-oxoguanine, a prominent oxidative DNA base modification, (ii) identify ranges of variation associated with substantial BER capacity loss, and (iii) reveal nonintuitive consequences of multiple simultaneous variants. Our findings support previous work suggesting that mild BER variants have a minimal effect on pathway capacity whereas more severe defects and simultaneous variation in several BER proteins can lead to inefficient repair and potentially deleterious consequences of cellular damage.

  15. Perceived and objective diet quality in US adults: a cross-sectional analysis of the National Health and Nutrition Examination Survey (NHANES)

    PubMed Central

    Powell-Wiley, Tiffany M; Miller, Paige E; Agyemang, Priscilla; Agurs-Collins, Tanya; Reedy, Jill

    2014-01-01

    Objective The Dietary Approaches to Stop Hypertension (DASH) dietary pattern has been shown to reduce cardiometabolic risk. Little is understood about the relationship between objective diet quality and perceived diet quality (PDQ), a potential psychosocial barrier to appropriate dietary intake. We compared PDQ and diet quality measured by a nutrient-based DASH index score in the USA. Design Cross-sectional study. Participants in the 2005–2006 National Health and Nutrition Examination Survey (NHANES) rated diet quality on a 5-point Likert scale and PDQ scores were generated (low, medium, high). A single 24 h dietary recall was used to estimate DASH index scores (range 0–9 points) by assigning 0, 0·5 or 1 point (optimal) for nine target nutrients: total fat, saturated fat, protein, cholesterol, fibre, Ca, Mg, K and Na. Setting Nationally representative sample of the US population. Subjects Adults aged ≥19 years in 2005–2006 NHANES (n 4419). Results Participants with high PDQ (33%) had higher DASH index scores (mean 3·0 (sd 0·07)) than those with low PDQ (mean 2·5 (sd 0·06), P < 0·001), but average scores did not align with targets for intermediate or optimal DASH accordance. Adults with high PDQ reported higher total fat, saturated fat and Na intakes compared with optimal DASH nutrient goals. Differences between those with high υ. low PDQ were similar for Whites and Blacks, but there was no difference between PDQ groups for Mexican Americans. Conclusions Among Whites and Blacks, but not Mexican Americans, high PDQ may be associated with higher diet quality, but not necessarily a diet meeting DASH nutrient goals. This disconnect between PDQ and actual diet quality may serve as a target in obesity prevention. PMID:24636343

  16. Horses for courses: a DNA-based test for race distance aptitude in thoroughbred racehorses.

    PubMed

    Hill, Emmeline W; Ryan, Donal P; MacHugh, David E

    2012-12-01

    Variation at the myostatin (MSTN) gene locus has been shown to influence racing phenotypes in Thoroughbred horses, and in particular, early skeletal muscle development and the aptitude for racing at short distances. Specifically, a single nucleotide polymorphism (SNP) in the first intron of MSTN (g.66493737C/T) is highly predictive of best race distance among Flat racing Thoroughbreds: homozygous C/C horses are best suited to short distance races, heterozygous C/T horses are best suited to middle distance races, and homozygous T/T horses are best suited to longer distance races. Patent applications for this gene marker association, and other linked markers, have been filed. The information contained within the patent applications is exclusively licensed to the commercial biotechnology company Equinome Ltd, which provides a DNA-based test to the international Thoroughbred horse racing and breeding industry. The application of this information in the industry enables informed decision making in breeding and racing and can be used to assist selection to accelerate the rate of change of genetic types among distinct populations (Case Study 1) and within individual breeding operations (Case Study 2).

  17. Fast and highly specific DNA-based multiplex detection on a solid support.

    PubMed

    Barišić, Ivan; Kamleithner, Verena; Schönthaler, Silvia; Wiesinger-Mayr, Herbert

    2015-01-01

    Highly specific and fast multiplex detection methods are essential to conduct reasonable DNA-based diagnostics and are especially important to characterise infectious diseases. More than 1000 genetic targets such as antibiotic resistance genes, virulence factors and phylogenetic markers have to be identified as fast as possible to facilitate the correct treatment of a patient. In the present work, we developed a novel ligation-based DNA probe concept that was combined with the microarray technology and used it for the detection of bacterial pathogens. The novel linear chain (LNC) probes identified all tested species correctly within 1 h based on their 16S rRNA gene in a 25-multiplex reaction. Genomic DNA was used directly as template in the ligation reaction identifying as little as 10(7) cells without any pre-amplification. The high specificity was further demonstrated characterising a single nucleotide polymorphism leading to no false positive fluorescence signals of the untargeted single nucleotide polymorphism (SNP) variants. In comparison to conventional microarray probes, the sensitivity of the novel LNC3 probes was higher by a factor of 10 or more. In summary, we present a fast, simple, highly specific and sensitive multiplex detection method adaptable for a wide range of applications.

  18. Challenges of DNA-based mark-recapture studies of American black bears

    USGS Publications Warehouse

    Settlage, K.E.; Van Manen, F.T.; Clark, J.D.; King, T.L.

    2008-01-01

    We explored whether genetic sampling would be feasible to provide a region-wide population estimate for American black bears (Ursus americanus) in the southern Appalachians, USA. Specifically, we determined whether adequate capture probabilities (p >0.20) and population estimates with a low coefficient of variation (CV <20%) could be achieved given typical agency budget and personnel constraints. We extracted DNA from hair collected from baited barbed-wire enclosures sampled over a 10-week period on 2 study areas: a high-density black bear population in a portion of Great Smoky Mountains National Park and a lower density population on National Forest lands in North Carolina, South Carolina, and Georgia. We identified individual bears by their unique genotypes obtained from 9 microsatellite loci. We sampled 129 and 60 different bears in the National Park and National Forest study areas, respectively, and applied closed mark–recapture models to estimate population abundance. Capture probabilities and precision of the population estimates were acceptable only for sampling scenarios for which we pooled weekly sampling periods. We detected capture heterogeneity biases, probably because of inadequate spatial coverage by the hair-trapping grid. The logistical challenges of establishing and checking a sufficiently high density of hair traps make DNA-based estimates of black bears impractical for the southern Appalachian region. Alternatives are to estimate population size for smaller areas, estimate population growth rates or survival using mark–recapture methods, or use independent marking and recapturing techniques to reduce capture heterogeneity.

  19. High-affinity DNA base analogs as supramolecular, nanoscale promoters of macroscopic adhesion.

    PubMed

    Anderson, Cyrus A; Jones, Amanda R; Briggs, Ellen M; Novitsky, Eric J; Kuykendall, Darrell W; Sottos, Nancy R; Zimmerman, Steven C

    2013-05-15

    Adhesion phenomena are essential to many biological processes and to synthetic adhesives and manufactured coatings and composites. Supramolecular interactions are often implicated in various adhesion mechanisms. Recently, supramolecular building blocks, such as synthetic DNA base-pair mimics, have drawn attention in the context of molecular recognition, self-assembly, and supramolecular polymers. These reversible, hydrogen-bonding interactions have been studied extensively for their adhesive capabilities at the nano- and microscale, however, much less is known about their utility for practical adhesion in macroscopic systems. Herein, we report the preparation and evaluation of supramolecular coupling agents based on high-affinity, high-fidelity quadruple hydrogen-bonding units (e.g., DAN·DeUG, Kassoc = 10(8) M(-1) in chloroform). Macroscopic adhesion between polystyrene films and glass surfaces modified with 2,7-diamidonaphthyridine (DAN) and ureido-7-deazaguanine (DeUG) units was evaluated by mechanical testing. Structure-property relationships indicate that the designed supramolecular interaction at the nanoscale plays a key role in the observed macroscopic adhesive response. Experiments probing reversible adhesion or self-healing properties of bulk samples indicate that significant recovery of initial strength can be realized after failure but that the designed noncovalent interaction does not lead to healing during the process of adhesion loss.

  20. Use of H19 Gene Regulatory Sequences in DNA-Based Therapy for Pancreatic Cancer

    PubMed Central

    Scaiewicz, V.; Sorin, V.; Fellig, Y.; Birman, T.; Mizrahi, A.; Galula, J.; Abu-lail, R.; Shneider, T.; Ohana, P.; Buscail, L.; Hochberg, A.; Czerniak, A.

    2010-01-01

    Pancreatic cancer is the eighth most common cause of death from cancer in the world, for which palliative treatments are not effective and frequently accompanied by severe side effects. We propose a DNA-based therapy for pancreatic cancer using a nonviral vector, expressing the diphtheria toxin A chain under the control of the H19 gene regulatory sequences. The H19 gene is an oncofetal RNA expressed during embryo development and in several types of cancer. We tested the expression of H19 gene in patients, and found that 65% of human pancreatic tumors analyzed showed moderated to strong expression of the gene. In vitro experiments showed that the vector was effective in reducing Luciferase protein activity on pancreatic carcinoma cell lines. In vivo experiment results revealed tumor growth arrest in different animal models for pancreatic cancer. Differences in tumor size between control and treated groups reached a 75% in the heterotopic model (P = .037) and 50% in the orthotopic model (P = .007). In addition, no visible metastases were found in the treated group of the orthotopic model. These results indicate that the treatment with the vector DTA-H19 might be a viable new therapeutic option for patients with unresectable pancreatic cancer. PMID:21052499

  1. DNA-based identification of Brassica vegetable species for the juice industry.

    PubMed

    Etoh, Kazumi; Niijima, Noritaka; Yokoshita, Masahiko; Fukuoka, Shin-Ichi

    2003-10-01

    Since kale (Brassica oleracea var. acephala), a cruciferous vegetable with a high level of vitamins and functional compounds beneficial to health and wellness, has become widely used in the juice industry, a precise method for quality control of vegetable species is necessary. We describe here a DNA-based identification method to distinguish kale from cabbage (Brassica oleracea var. capitata), a closely related species, which can be inadvertently mixed with kale during the manufacturing process. Using genomic DNA from these vegetables and combinatory sets of nucleotide primers, we screened for random amplified polymorphic DNA (RAPD) fragments and found three cabbage-specific fragments. These RAPD fragments, with lengths of 1.4, 0.5, and 1.5 kb, were purified, subcloned, and sequenced. Based on sequence-tagged sites (STS), we designed sets of primers to detect cabbage-specific identification (CAI) DNA markers. Utilizing the CAI markers, we successfully distinguished more than 10 different local cabbage accessions from 20 kale accessions, and identified kale juices experimentally spiked with different amounts of cabbage.

  2. DNA-Based Synthesis and Assembly of Organized Iron Oxide Nanostructures

    NASA Astrophysics Data System (ADS)

    Khomutov, Gennady B.

    Organized bio-inorganic and hybrid bio-organic-inorganic nanostructures consisting of iron oxide nanoparticles and DNA complexes have been formed using methods based on biomineralization, interfacial and bulk phase assembly, ligand exchange and substitution, Langmuir-Blodgett technique, DNA templating and scaffolding. Interfacially formed planar DNA complexes with water-insoluble amphiphilic polycation or intercalator Langmuir monolayers were prepared and deposited on solid substrates to form immobilized DNA complexes. Those complexes were then used for the synthesis of organized DNA-based iron oxide nanostructures. Planar net-like and circular nanostructures of magnetic Fe3O4 nanoparticles were obtained via interaction of cationic colloid magnetite nanoparticles with preformed immobilized DNA/amphiphilic polycation complexes of net-like and toroidal morphologies. The processes of the generation of iron oxide nanoparticles in immobilized DNA complexes via redox synthesis with various iron sources of biological (ferritin) and artificial (FeCl3) nature have been studied. Bulk-phase complexes of magnetite nanoparticles with biomolecular ligands (DNA, spermine) were formed and studied. Novel nano-scale organized bio-inorganic nanostructures - free-floating sheet-like spermine/magnetite nanoparticle complexes and DNA/spermine/magnetite nanoparticle complexes were synthesized in bulk aqueous phase and the effect of DNA molecules on the structure of complexes was discovered.

  3. Excited-State Energies and Electronic Couplings of DNA Base Dimers

    SciTech Connect

    Kozak, Christopher R.; Kistler, Kurt A.; Lu, Zhen; Matsika, Spiridoula

    2010-02-04

    The singlet excited electronic states of two π-stacked thymine molecules and their splittings due to electronic coupling have been investigated with a variety of computational methods. Focus has been given on the effect of intermolecular distance on these energies and couplings. Single-reference methods, CIS, CIS(2), EOMCCSD, TDDFT, and the multireference method CASSCF, have been used, and their performance has been compared. It is found that the excited-state energies are very sensitive to the applied method but the couplings are not as sensitive. Inclusion of diffuse functions in the basis set also affects the excitation energies significantly but not the couplings. TDDFT is inadequate in describing the states and their coupling, while CIS(2) gives results very similar to EOM-CCSD. Excited states of cytosine and adenine π-stacked dimers were also obtained and compared with those of thymine dimers to gain a more general picture of excited states in π-stacked DNA base dimers. The coupling is very sensitive to the relative position and orientation of the bases, indicating great variation in the degree of delocalization of the excited states between stacked bases in natural DNA as it fluctuates.

  4. A resettable and reprogrammable DNA-based security system to identify multiple users with hierarchy.

    PubMed

    Li, Hailong; Hong, Wei; Dong, Shaojun; Liu, Yaqing; Wang, Erkang

    2014-03-25

    Molecular-level security devices have raised ever-increasing interest in recent years to protect data and information from illegal invasion. Prior molecular keypad locks have an output signal dependent upon not only the appropriate combination but also the exact sequence of inputs, but it cannot be reset or reprogrammed. Here, a DNA-based security system with reset and never-reported reprogram function is successfully developed in proof-of-principle, with which one can change the password in case that the system is cracked. The previous password becomes invalid in the reprogrammed security system. Interestingly, more than one password is designed to permit multiple users to access. By harnessing the intrinsic merit of the different passwords, the system can distinguish different user who is endowed with prior authority. The intelligent device is addressed on solid support and facilitates electronic processes, avoiding chemical accumulation in the system by simple removal of the electrode from the input solution and indicating a main avenue for its further development.

  5. Functional protein expression from a DNA based wheat germ cell-free system.

    PubMed

    Zhao, Kate Qin; Hurst, Robin; Slater, Michael R; Bulleit, Robert F

    2007-12-01

    Wheat germ based eukaryotic cell-free systems have been shown to be applicable for both functional and structural analyses of proteins. However, the existing methods might require specialized instrumentation and/or a separate mRNA synthesis step. We have developed a DNA based, highly productive, coupled transcription/translation wheat germ cell-free system that incorporates the normally separate mRNA synthesis step and does not require specialized instrumentation. Using a small-volume batch reaction with fluorescence labeling, DNA templates predicted to encode proteins could be quickly screened for their ability to direct the expression of proteins of the appropriate size. Protein yield can be increased as much as 2 to 4-fold in this system using a dialysis reaction, reaching approximately 200-440 microg/ml in 10-20 h. Furthermore, enzyme activities can be assayed directly in the extract without further purification. Simple purification with affinity tags can be achieved in one-step and with minor modifications, efficient SeMet and [U-15N] labeling of >95% can be accomplished in this system. Thus, this efficient cell-free expression system can facilitate both functional and structural proteomics.

  6. Single-Molecule Force Spectroscopy of DNA-Based Reversible Polymer Bridges: Surface Robustness and Homogeneity

    PubMed Central

    Serpe, Michael J.; Whitehead, Jason R.; Rivera, Monica; Clark, Robert L.; Craig, Stephen L.

    2011-01-01

    Single-molecule force spectroscopy, as implemented in an atomic force microscope, provides a rarely-used method by which to monitor dynamic processes that occur near surfaces. Here, a methodology is presented and characterized that facilitates the study of polymer bridging across nanometer-sized gaps. The model system employed is that of DNA-based reversible polymers, and an automated procedure is introduced that allows the AFM tip-surface contact point to be automatically determined, and the distance d between opposing surfaces to be actively controlled. Using this methodology, the importance of several experimental parameters was systematically studied, e.g. the frequency of repeated tip/surface contacts, the area of the substrate surface sampled by the AFM, and the use of multiple AFM tips and substrates. Experiments revealed the surfaces to be robust throughout pulling experiments, so that multiple touches and pulls could be carried out on a single spot with no measurable affect on the results. Differences in observed bridging probabilities were observed, both on different spots on the same surface and, more dramatically, from one day to another. Data normalization via a reference measurement allows data from multiple days to be directly compared. PMID:21966095

  7. Detection of Variation in Long-Term Micropropagated Mature Pistachio via DNA-Based Molecular Markers.

    PubMed

    Akdemir, Hülya; Suzerer, Veysel; Tilkat, Engin; Onay, Ahmet; Çiftçi, Yelda Ozden

    2016-12-01

    Determination of genetic stability of in vitro-grown plantlets is needed for safe and large-scale production of mature trees. In this study, genetic variation of long-term micropropagated mature pistachio developed through direct shoot bud regeneration using apical buds (protocol A) and in vitro-derived leaves (protocol B) was assessed via DNA-based molecular markers. Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) were employed, and the obtained PIC values from RAPD (0.226), ISSR (0.220), and AFLP (0.241) showed that micropropagation of pistachio for different periods of time resulted in "reasonable polymorphism" among donor plant and its 18 clones. Mantel's test showed a consistence polymorphism level between marker systems based on similarity matrices. In conclusion, this is the first study on occurrence of genetic variability in long-term micropropagated mature pistachio plantlets. The obtained results clearly indicated that different marker approaches used in this study are reliable for assessing tissue culture-induced variations in long-term cultured pistachio plantlets.

  8. DNA-based digital tension probes reveal integrin forces during early cell adhesion

    PubMed Central

    Zhang, Yun; Ge, Chenghao; Zhu, Cheng; Salaita, Khalid

    2014-01-01

    Mechanical stimuli profoundly alter cell fate, yet the mechanisms underlying mechanotransduction remain obscure due to a lack of methods for molecular force imaging. Here, to address this need, we develop a new class of molecular tension probes that function as a switch to generate a 20–30-fold increase in fluorescence upon experiencing a threshold piconewton force. The probes employ immobilized DNA-hairpins with tunable force response thresholds, ligands, and fluorescence reporters. Quantitative imaging reveals that integrin tension is highly dynamic and increases with an increasing integrin density during adhesion formation. Mixtures of fluorophore-encoded probes show integrin mechanical preference for cyclized-RGD over linear-RGD peptides. Multiplexed probes with variable guanine-cytosine content within their hairpins reveal integrin preference for the more stable probes at the leading tip of growing adhesions near the cell edge. DNA-based tension probes are among the most sensitive optical force reporters to date, overcoming the force and spatial-resolution limitations of traction force microscopy. PMID:25342432

  9. Activation of cellular signaling by 8-oxoguanine DNA glycosylase-1-initiated DNA base excision repair.

    PubMed

    German, Peter; Szaniszlo, Peter; Hajas, Gyorgy; Radak, Zsolt; Bacsi, Attila; Hazra, Tapas K; Hegde, Muralidhar L; Ba, Xueqing; Boldogh, Istvan

    2013-10-01

    Accumulation of 8-oxo-7,8-dihydroguanine (8-oxoG) in the DNA results in genetic instability and mutagenesis, and is believed to contribute to carcinogenesis, aging processes and various aging-related diseases. 8-OxoG is removed from the DNA via DNA base excision repair (BER), initiated by 8-oxoguanine DNA glycosylase-1 (OGG1). Our recent studies have shown that OGG1 binds its repair product 8-oxoG base with high affinity at a site independent from its DNA lesion-recognizing catalytic site and the OGG1•8-oxoG complex physically interacts with canonical Ras family members. Furthermore, exogenously added 8-oxoG base enters the cells and activates Ras GTPases; however, a link has not yet been established between cell signaling and DNA BER, which is the endogenous source of the 8-oxoG base. In this study, we utilized KG-1 cells expressing a temperature-sensitive mutant OGG1, siRNA ablation of gene expression, and a variety of molecular biological assays to define a link between OGG1-BER and cellular signaling. The results show that due to activation of OGG1-BER, 8-oxoG base is released from the genome in sufficient quantities for activation of Ras GTPase and resulting in phosphorylation of the downstream Ras targets Raf1, MEK1,2 and ERK1,2. These results demonstrate a previously unrecognized mechanism for cellular responses to OGG1-initiated DNA BER.

  10. Sensitive determination of DNA based on the interaction between prulifloxacin-terbium(III) complex and DNA.

    PubMed

    Wu, Ting; Fang, Biyun; Chang, Lin; Liu, Min; Chen, Fang

    2013-01-01

    A simple spectrofluorimetric method is described for the determination of DNA, based on its enhancement of the fluorescence intensity of prulifloxacin (PUFX)-Tb(3+). The luminescence intensity of the PUFX-Tb(3+) complex increased up to 10-fold after adding DNA. The excitation and emission wavelengths were 345 and 545 nm, respectively. Under optimum conditions, variations in the fluorescence intensity showed a good linear relationship with the concentration of hsDNA in the range of 3.0 × 10(-9) to 1.0 × 10(-6) g/mL, with a correlation coefficient (R) of 0.997, and the detection limit was 2.1 × 10(-9) g/mL. The method was successfully applied to the determination of DNA in synthetic samples, and recoveries were in the range 97.3-102.0%. The mechanism of fluorescence enhancement of the PUFX-Tb(3+) complex by DNA is also discussed. The mechanism may involve formation of a ternary complex mainly by intercalation binding together with weak electrostatic interaction, which will increase the energy transition from ligand to Tb(3+), increasing the rigidity of the complex, and decreasing the radiationless energy loss through O-H vibration of the H2O molecule in the PUFX-Tb(3+) complex. Compared with the previous DNA probes, the proposed method is not only more robust and friendly to the environment, but also of relatively higher sensitivity.

  11. Is a large-scale DNA-based inventory of ancient life possible?

    PubMed

    Lambert, D M; Baker, A; Huynen, L; Haddrath, O; Hebert, P D N; Millar, C D

    2005-01-01

    A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.

  12. DNA base detection using a single-layer MoS2.

    PubMed

    Farimani, Amir Barati; Min, Kyoungmin; Aluru, Narayana R

    2014-08-26

    Nanopore-based DNA sequencing has led to fast and high-resolution recognition and detection of DNA bases. Solid-state and biological nanopores have low signal-to-noise ratio (SNR) (< 10) and are generally too thick (> 5 nm) to be able to read at single-base resolution. A nanopore in graphene, a 2-D material with sub-nanometer thickness, has a SNR of ∼3 under DNA ionic current. In this report, using atomistic and quantum simulations, we find that a single-layer MoS2 is an extraordinary material (with a SNR > 15) for DNA sequencing by two competing technologies (i.e., nanopore and nanochannel). A MoS2 nanopore shows four distinct ionic current signals for single-nucleobase detection with low noise. In addition, a single-layer MoS2 shows a characteristic change/response in the total density of states for each base. The band gap of MoS2 is significantly changed compared to other nanomaterials (e.g., graphene, h-BN, and silicon nanowire) when bases are placed on top of the pristine MoS2 and armchair MoS2 nanoribbon, thus making MoS2 a promising material for base detection via transverse current tunneling measurement. MoS2 nanopore benefits from a craftable pore architecture (combination of Mo and S atoms at the edge) which can be engineered to obtain the optimum sequencing signals.

  13. Species identification in the genus Saprolegnia (Oomycetes): defining DNA-based molecular operational taxonomic units.

    PubMed

    Sandoval-Sierra, Jose Vladimir; Martín, María P; Diéguez-Uribeondo, Javier

    2014-07-01

    The lack of a robust taxonomy in the genus Saprolegnia is leading to the presence of incorrectly named isolates in culture collections and of an increasing number of misassigned sequences in DNA databases. Accurate species delimitation is critical for most biological disciplines. A recently proposed approach to solve species delimitation (taxonomic diagnosis system) of difficult organisms is the definition of molecular operational taxonomic units (MOTUs). We have used 961 sequences of nrDNA ITS from culture collections (461 sequences) and GenBank (500 sequences), to perform phylogenetic and clustering optimization analyses. As result, we have identified 29 DNA-based MOTUs in agreement with phylogenetic studies. The resulting molecular clusters support the validity of 18 species of Saprolegnia and identify 11 potential new ones. We have also listed a number of incorrectly named isolates in culture collections, misassigned species names to GenBank sequences, and reference sequences for the species. We conclude that GenBank represents the main source of errors for identifying Saprolegnia species since it possesses sequences with misassigned names and also sequencing errors. The presented taxonomic diagnosis system might help setting the basis for a suitable identification of species in this economically important genus.

  14. Proton tunneling in the A∙T Watson-Crick DNA base pair: myth or reality?

    PubMed

    Brovarets', Ol'ha O; Hovorun, Dmytro M

    2015-01-01

    The results and conclusions reached by Godbeer et al. in their recent work, that proton tunneling in the A∙T(WC) Watson-Crick (WC) DNA base pair occurs according to the Löwdin's (L) model, but with a small (~10(-9)) probability were critically analyzed. Here, it was shown that this finding overestimates the possibility of the proton tunneling at the A∙T(WC)↔A*∙T*(L) tautomerization, because this process cannot be implemented as a chemical reaction. Furthermore, it was outlined those biologically important nucleobase mispairs (A∙A*↔A*∙A, G∙G*↔G*∙G, T∙T*↔T*∙T, C∙C*↔C*∙C, H∙H*↔H*∙H (H - hypoxanthine)) - the players in the field of the spontaneous point mutagenesis - where the tunneling of protons is expected and for which the application of the model proposed by Godbeer et al. can be productive.

  15. DNA Base Pair Resolution Measurements Using Resonance Energy Transfer Efficiency in Lanthanide Doped Nanoparticles

    PubMed Central

    Delplanque, Aleksandra; Wawrzynczyk, Dominika; Jaworski, Pawel; Matczyszyn, Katarzyna; Pawlik, Krzysztof; Buckle, Malcolm; Nyk, Marcin; Nogues, Claude; Samoc, Marek

    2015-01-01

    Lanthanide-doped nanoparticles are of considerable interest for biodetection and bioimaging techniques thanks to their unique chemical and optical properties. As a sensitive luminescence material, they can be used as (bio) probes in Förster Resonance Energy Transfer (FRET) where trivalent lanthanide ions (La3+) act as energy donors. In this paper we present an efficient method to transfer ultrasmall (ca. 8 nm) NaYF4 nanoparticles dispersed in organic solvent to an aqueous solution via oxidation of the oleic acid ligand. Nanoparticles were then functionalized with single strand DNA oligomers (ssDNA) by inducing covalent bonds between surface carboxylic groups and a 5’ amine modified-ssDNA. Hybridization with the 5’ fluorophore (Cy5) modified complementary ssDNA strand demonstrated the specificity of binding and allowed the fine control over the distance between Eu3+ ions doped nanoparticle and the fluorophore by varying the number of the dsDNA base pairs. First, our results confirmed nonradiative resonance energy transfer and demonstrate the dependence of its efficiency on the distance between the donor (Eu3+) and the acceptor (Cy5) with sensitivity at a nanometre scale. PMID:25748446

  16. DNA base excision repair of uracil residues in reconstituted nucleosome core particles

    PubMed Central

    Nilsen, Hilde; Lindahl, Tomas; Verreault, Alain

    2002-01-01

    The human base excision repair machinery must locate and repair DNA base damage present in chromatin, of which the nucleosome core particle is the basic repeating unit. Here, we have utilized fragments of the Lytechinus variegatus 5S rRNA gene containing site-specific U:A base pairs to investigate the base excision repair pathway in reconstituted nucleosome core particles in vitro. The human uracil-DNA glycosylases, UNG2 and SMUG1, were able to remove uracil from nucleosomes. Efficiency of uracil excision from nucleosomes was reduced 3- to 9-fold when compared with naked DNA, and was essentially uniform along the length of the DNA substrate irrespective of rotational position on the core particle. Furthermore, we demonstrate that the excision repair pathway of an abasic site can be reconstituted on core particles using the known repair enzymes, AP-endonuclease 1, DNA polymerase β and DNA ligase III. Thus, base excision repair can proceed in nucleosome core particles in vitro, but the repair efficiency is limited by the reduced activity of the uracil-DNA glycosylases and DNA polymerase β on nucleosome cores. PMID:12411511

  17. Poisonous or non-poisonous plants? DNA-based tools and applications for accurate identification.

    PubMed

    Mezzasalma, Valerio; Ganopoulos, Ioannis; Galimberti, Andrea; Cornara, Laura; Ferri, Emanuele; Labra, Massimo

    2017-01-01

    Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.

  18. A Constant Rate of Spontaneous Mutation in DNA-Based Microbes

    NASA Astrophysics Data System (ADS)

    Drake, John W.

    1991-08-01

    In terms of evolution and fitness, the most significant spontaneous mutation rate is likely to be that for the entire genome (or its nonfrivolous fraction). Information is now available to calculate this rate for several DNA-based haploid microbes, including bacteriophages with single- or double-stranded DNA, a bacterium, a yeast, and a filamentous fungus. Their genome sizes vary by ≈6500-fold. Their average mutation rates per base pair vary by ≈16,000-fold, whereas their mutation rates per genome vary by only ≈2.5-fold, apparently randomly, around a mean value of 0.0033 per DNA replication. The average mutation rate per base pair is inversely proportional to genome size. Therefore, a nearly invariant microbial mutation rate appears to have evolved. Because this rate is uniform in such diverse organisms, it is likely to be determined by deep general forces, perhaps by a balance between the usually deleterious effects of mutation and the physiological costs of further reducing mutation rates.

  19. Molecular dynamics simulation of DNA base-pair opening by sharp bending

    NASA Astrophysics Data System (ADS)

    Cong, Peiwen; Dai, Liang; van der Maarel, Johan R. C.; Yan, Jie

    2013-03-01

    Many biological processes require sharp bending of DNA. According to worm-like chain model, the bending energy dominates the free energy cost of those processes containing DNA loops shorter than 40 nm, such as DNA wrapping around histones, Lac repressor looping and virus DNA packaging. However, several recent experimental observations suggest that the WLC model s not applicable under tight bending conditions. In full atom molecular dynamics simulations, a double stranded, 20 base-pairs DNA fragment is forced to bend by an external spring. It is found that one or two AT-rich regions are disrupted for sufficiently small end-to-end distance. The disrupted DNA base-pairs separate and usually stack with the neighbouring base-pairs to form a defect. It is shown that these defects are more bendable than the bending rigidity of the duplex in the regular B-form. The simulation suggests a curvature dependent, non-harmonic bending elasticity of the DNA backbone is necessary to describe the DNA conformation under tight bending conditions.

  20. Diet and cancer

    MedlinePlus

    Fiber and cancer; Cancer and fiber; Nitrates and cancer; Cancer and nitrates ... DIET AND BREAST CANCER The link between nutrition and breast cancer has been well studied. To reduce risk of breast cancer the American ...

  1. Diet - clear liquid

    MedlinePlus

    ... Group. Clear liquid diet. In: Morrison. Manual of Clinical Nutrition Management. Updated 2013. bscn2k15.weebly.com/uploads/1/2/9/2/12924787/manual_of_clinical_nutrition2013.pdf . Accessed August 20, 2016. Schattner MA, ...

  2. Protein in diet

    MedlinePlus

    ... basic structure of protein is a chain of amino acids. You need protein in your diet to help ... Protein foods are broken down into parts called amino acids during digestion. The human body needs a number ...

  3. Diet and Exercise

    MedlinePlus

    ... Types Risk Factors Prevention & Early Detection Diet And Exercise Transplant recipients need to be aware of the ... help arrange for counseling and other support services. Exercise After a Transplant Most people are weak after ...

  4. Diets that Work

    MedlinePlus

    ... non-vegetarians. A vegetarian diet can help fight heart disease and high blood pressure. Sample Dinner Menus Vegetarian Spaghetti with Mushroom-Tomato-Asiago Cheese Sauce Steamed Green Beans with Pine Nuts Fruit Salad Vegan Roasted Vegetables with Whole ...

  5. Low-Carb Diet

    MedlinePlus

    ... Your body needs carbohydrates as a source of fuel (energy). If you don’t eat enough carbs, your body will use stored energy from muscle or fat cells to fuel itself. In low-carb diets, only 15% to ...

  6. Are Detox Diets Safe?

    MedlinePlus

    ... avoided if you are pregnant or have an eating disorder . Detox diets can be addicting. That's because there's ... addiction that leads to health problems, including serious eating disorders, heart problems, and even death. Detox supplements can ...

  7. A changing Hausa diet.

    PubMed

    Ross, P J; Etkin, N L; Muazzamu, I

    1996-12-01

    We report results of a longitudinal study of shifting patterns of food consumption in a rural Hausa-Fulani village in northern Nigeria. While the broad outlines of diet did not change over the 12 years between two dietary surveys, important shifts occurred: a decline in the consumption of local cultigens, with a corresponding decrease in total caloric intake, as well as an embellishment of diet through the introduction of new foods. We suggest that this is best understood through the growing participation of this village in the wider economy. We juxtapose these dietary shifts to a model of disease risk that suggests, for the early period, that the coincidence of dietary elaboration and the periodicity of disease risk offered some degree of protection against malaria infection. For the more recent period, diet was no longer marked by conspicuous seasonal changes. To what extent these differences in diet patterns have affected the disease experience of this population is not yet clear.

  8. Selenium in diet

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/002414.htm Selenium in diet To use the sharing features on this page, please enable JavaScript. Selenium is an essential trace mineral. This means your ...

  9. Are Detox Diets Safe?

    MedlinePlus

    ... toxins hang around in our digestive, lymph, and gastrointestinal systems as well as in our skin and hair ... cause dehydration, mineral imbalances, and problems with the digestive system. Detox diets don't help people lose fat. ...

  10. Gastric Bypass Diet

    MedlinePlus

    ... changes you can make to your diet. References Bariatric surgery for severe obesity. National Institute on Diabetes and ... com/home. Accessed Jan. 19, 2015. Hamad G. Bariatric surgery: Postoperative and long-term management of the uncomplicated ...

  11. Diet and Health

    PubMed Central

    Gotto, Antonio M.; Scott, Lynne W.; Foreyt, John P.

    1984-01-01

    The role of diet in personal health maintenance is important whether a person is trying to stay healthy or to treat diet-related diseases such as hypercholesterolemia, hypertension, diabetes mellitus or obesity. Dietary recommendations include limiting fat to 30% and protein to 20% of total calories, with the remaining 50% coming from carbohydrate. Maintaining dietary changes for long periods is very difficult for many persons. Specific self-management skills may ease the task. PMID:6523862

  12. Specific Carbohydrate Diet: Does It Work?

    MedlinePlus

    ... Specific Carbohydrate Diet (SCD) Go Back The Specific Carbohydrate Diet (SCD) Email Print + Share There is no ... diet that has received attention is the Specific Carbohydrate Diet. This diet limits poorly digestible carbohydrates to ...

  13. Popular weight reduction diets.

    PubMed

    Volpe, Stella Lucia

    2006-01-01

    The percentage of people who are overweight and obese has increased tremendously over the last 30 years. It has become a worldwide epidemic. This is evident by the number of children are being diagnosed with a body mass index >85th percentile, and the number of children begin diagnosed with type 2 diabetes mellitus, a disease previously reserved for adults. The weight loss industry has also gained from this epidemic; it is a billion dollar industry. People pay large sums of money on diet pills, remedies, and books, with the hope of losing weight permanently. Despite these efforts, the number of individuals who are overweight or obese continues to increase. Obesity is a complex, multifactorial disorder. It would be impossible to address all aspects of diet, exercise, and weight loss in this review. Therefore, this article will review popular weight loss diets, with particular attention given to comparing low fat diets with low carbohydrate diets. In addition, the role that the environment plays on both diet and exercise and how they impact obesity will be addressed. Finally, the National Weight Control Registry will be discussed.

  14. Vegan diets and hypothyroidism.

    PubMed

    Tonstad, Serena; Nathan, Edward; Oda, Keiji; Fraser, Gary

    2013-11-20

    Diets eliminating animal products have rarely been associated with hypothyroidism but may protect against autoimmune disease. Thus, we investigated whether risk of hypothyroidism was associated with vegetarian compared to omnivorous dietary patterns. The Adventist Health Study-2 was conducted among church members in North America who provided data in a self-administered questionnaire. Hypothyroidism was queried at baseline in 2002 and at follow-up to 2008. Diet was examined as a determinant of prevalent (n = 4237 of 65,981 [6.4%]) and incident cases (1184 of 41,212 [2.9%]) in multivariate logistic regression models, controlled for demographics and salt use. In the prevalence study, in addition to demographic characterstics, overweight and obesity increased the odds (OR 1.32, 95% CI: 1.22-1.42 and 1.78, 95% CI: 1.64-1.93, respectively). Vegan versus omnivorous diets tended to be associated with reduced risk (OR 0.89, 95% CI: 0.78-1.01, not statistically significant) while a lacto-ovo diet was associated with increased risk (OR 1.09, 95% CI: 1.01-1.18). In the incidence study, female gender, white ethnicity, higher education and BMI were predictors of hypothyroidism. Following a vegan diet tended to be protective (OR 0.78, 95% CI: 0.59-1.03, not statistically significant). In conclusion, a vegan diet tended to be associated with lower, not higher, risk of hypothyroid disease.

  15. Benefits and challenges to using DNA-based identification methods: An example study of larval fish from nearshore areas of Lake Superior

    EPA Science Inventory

    DNA-based identification methods could increase the ability of aquatic resource managers to track patterns of invasive species, especially for taxa that are difficult to identify morphologically. Nonetheless, use of DNA-based identification methods in aquatic surveys is still unc...

  16. Tree nut consumption improves nutrient intake and diet quality in US adults: an analysis of National Health and Nutrition Examination Survey (NHANES) 1999-2004.

    PubMed

    O'Neil, Carol E; Keast, Debra R; Fulgoni, Victor L; Nicklas, Theresa A

    2010-01-01

    Recent epidemiologic studies assessing tree nut (almonds, Brazil nuts, cashews, hazelnuts, macadamia nuts, pecans, pine nuts, pistachios, and walnuts) consumption and the association with nutrient intake and diet quality are lacking. This study determined the association of tree nut consumption and nutrient intake and diet quality using a nationally representative sample of adults. Adults 19+ years (y) (n=13,292) participating in the 1999-2004 National Health and Nutrition Examination Survey were used. Intake was determined from 24-hour diet recalls; tree nut consumers were defined as those consuming > or =(1/4) ounce/day (7.09 g). Means, standard errors, and ANOVA (adjusted for covariates) were determined using appropriate sample weights. Diet quality was measured using the Healthy Eating Index-2005. Among consumers, mean intake of tree nuts/tree nut butters was 1.19 +/- 0.04 oz/d versus 0.01 +/- 0.00 oz/d for non-consumers. In this study, 5.5 +/- 0.3 % of individuals 19-50 y (n=7,049) and 8.4 +/- 0.6 % of individuals 51+ y (n=6,243) consumed tree nuts/tree nut butters. Mean differences (p<0.01) between tree nut consumers and non-consumers of adult shortfall nutrients were: fiber (+5.0 g/d), vitamin E (+3.7 mg AT/d), calcium (+73 mg/d), magnesium (+95 mg/d), and potassium (+260 mg/d). Tree nut consumers had lower sodium intake (-157 mg/d, p<0.01). Diet quality was significantly higher in tree nut consumers (58.0+/-0.4 vs. 48.5+/-0.3, p<0.01). Tree nut consumption was associated with a higher overall diet quality score and improved nutrient intakes. Specific dietary recommendations for nut consumption should be provided for consumers.

  17. DNA-based prediction of human externally visible characteristics in forensics: motivations, scientific challenges, and ethical considerations.

    PubMed

    Kayser, Manfred; Schneider, Peter M

    2009-06-01

    There will always be criminal cases, where the evidence DNA sample will not match either a suspect's DNA profile, or any in a criminal DNA database. In the absence of DNA-based mass intelligence screenings, including familial searching (both of which may be restricted by legislation), there is only one option to potentially avoid or retrospectively solve "cold cases": the DNA-based prediction of human externally visible characteristics of an unknown person based on the crime scene sample left behind. Predictive DNA markers are expected to be available for some group-specific appearance traits in the near future; although it is unlikely that we will soon be able to understand the biological complexity of individual-specific appearance. In suspect-less cases reliable DNA-based prediction of broader externally visible characteristics from crime scene samples are expected to reduce the potential pool of suspects by allowing police investigations to concentrate on specific groups of people. Here, we aim to describe the forensic motivations for DNA-based prediction of human externally visible traits as well as the scientific challenges of finding predictive DNA markers, and will discuss examples with promising (e.g. sex, eye color and hair color), as well as less promising expectations (e.g. adult body height), in the foreseen future. Despite the complex ethical and legal implications arising from DNA-based prediction of externally visible characteristics, we argue that their use does not lead to a violation of privacy. We suggest that likelihood-based results, rather than DNA data itself, should be provided to the police for investigative purposes avoiding data protection issues. Furthermore, we note that the risk of exacerbating social pressure on minority groups due to DNA-based prediction of externally visible traits in crime cases may be reduced rather than increased compared to a conventional eyewitness testimony. A firm legal basis will need to be established for

  18. Ionization Cross Sections and Dissociation Channels of DNA Bases by Electron Collisions

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

    Free secondary electrons are the most abundant secondary species in ionizing radiation. Their role in DNA damage, both direct and indirect, is an active area of research. While indirect damage by free radicals, particularly by the hydroxyl radical generated by electron collision with water. is relatively well studied, damage by direct electron collision with DNA is less well understood. Only recently Boudaiffa et al. demonstrated that electrons at energies well below ionization thresholds can induce substantial yields of single- and double-strand breaks in DNA by a resonant, dissociative attachment process. This study attracted renewed interest in electron collisions with DNA, especially in the low energy region. At higher energies ionization becomes important. While Monte Carlo track simulations of radiation damage always include ionization, the probability of dissociative ionization, i.e., simultaneous ionization and dissociation, is ignored. Just like dissociative attachment, dissociative ionization may be an important contributor to double-strand breaks since the radicals and ions produced by dissociative ionization, located in the vicinity of the DNA coil, can readily interact with other parts of the DNA. Using the improved binary-encounter dipole (iBED) formulation, we calculated the ionization cross sections of the four DNA bases, adenine, cytosine, guanine, and thymine, by electrons at energies from threshold to 1 KeV. The present calculation gives cross sections approximately 20% lower than the results by Bemhardt and Paretzke using the Deutsch-Mark and Binary-Encounter-Bethe (BEB) formalisms. The difference is most likely due to the lack of a shielding term in the dipole potential used in the Deutsch-Mark and BEB formalisms. The dissociation channels of ionization for the bases are currently being studied.

  19. Comparison of the long-term effects of high-fat v. low-fat diet consumption on cardiometabolic risk factors in subjects with abnormal glucose metabolism: a systematic review and meta-analysis.

    PubMed

    Schwingshackl, Lukas; Hoffmann, Georg

    2014-06-28

    The aim of the present systematic review and meta-analysis was to examine the long-term effects (≥ 12 months) of high-fat (HF) v. low-fat (LF) diet consumption on the indicators of glycaemic control as well as cardiovascular risk factors in pre-diabetic and diabetic individuals. Literature search was carried out using the electronic databases MEDLINE, Embase and the Cochrane Trial Register until November 2013. Study-specific weighted mean differences (MD) were pooled using a random-effects model of the Cochrane software package Review Manager 5.1 and Stata 12.0 was used for meta-regressions. A total of fourteen trials met the inclusion criteria and a maximum of 1753 subjects were included in the meta-analysis. HF regimens were found to result in a significant decrease in TAG levels (MD -0·19 mmol/l, 95 % CI -0·23, -0·14, P< 0·001; I² = 0 %, P= 0·58) and diastolic blood pressure (MD -1·30 mmHg, 95 % CI -1·73, -0·87, P< 0·001; I² = 0 %, P= 0·60) and a significant increase in HDL-cholesterol levels (MD 0·05 mmol/l, 95 % CI 0·01, 0·08, P= 0·01; I² = 57 %, P= 0·01). In addition, MD in the reductions of fasting glucose levels (-0·41 mmol/l, 95 % CI -0·74, -0·08, P= 0·01; I² = 56 %, P= 0·02) were significantly high in patients with type 2 diabetes adhering to a HF diet. HF and LF diets might not be of equal value in the management of either pre-diabetes or type 2 diabetes, leading to emphasis being placed on the recommendations of HF diets.

  20. Diet and physical performance.

    PubMed

    Montain, Scott J; Young, Andrew J

    2003-06-01

    This paper provides a historical summary of military nutrition research into the role of diet for sustaining soldier physical performance. Studies of underfeeding document that physical performance is preserved during several days of underfeeding provided sufficient carbohydrate and minerals are consumed to minimize the diuresis associated with semi-starvation diets and serial intake of carbohydrate is available to support metabolism during prolonged work. The Military Recommended Dietary Allowances, AR 40-25, currently recommends that when restricted rations are required, that the ration contain at least 1,100-1,500 kcal, 50-70 g of protein, and a minimum of 100 g of carbohydrate on a daily basis. This low energy diet, however, is not recommended for subsistence for longer than 10 consecutive days. Dietary carbohydrate intakes of approximately 300-400 g will more closely match the quantity of carbohydrate oxidized to meet daily energy requirements during field operations. Research into the potential advantages of dietary supplements has generally not proved advantageous when compared to eating a well balanced diet. Future investigations of the role of diet for sustaining soldier health and performance should be directed toward a better understanding of the influence of energy intake and macro-nutrient composition for preserving lean body mass, reducing susceptibility to illness and injury and enhancing recovery during and after sustained operations.

  1. Tree nut consumption improves nutrient intake and diet quality in US adults: an analysis of National Health and Nutrition Examination Survey (NHANES) 1999-2004

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent epidemiologic studies assessing tree nut (almonds, Brazil nuts, cashews, hazelnuts, macadamia nuts, pecans, pine nuts, pistachios, and walnuts) consumption and the association with nutrient intake and diet quality are lacking. This study determined the association of tree nut consumption and ...

  2. Comparison of aerobic exercise, diet or both on lipids and lipoproteins in adults: a meta-analysis of randomized controlled trials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Given that previous studies have reached conflicting conclusions regarding the effects of diet (D), aerobic exercise (E) or both (DE) on blood lipid and lipoprotein concentrations in adults, the meta-analytic approach was used to address this issue. Data Sources: Nine electronic databases, cross-ref...

  3. 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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 US and European cohort studies comprising 51,289 persons without diabetes to test whether...

  4. Nutrigenomics in Arma chinensis: Transcriptome Analysis of Arma chinensis Fed on Artificial Diet and Chinese Oak Silk Moth Antheraea pernyi Pupae

    PubMed Central

    Zou, Deyu; Coudron, Thomas A.; Liu, Chenxi; Zhang, Lisheng; Wang, Mengqing; Chen, Hongyin

    2013-01-01

    Background The insect predator, Arma chinensis, is capable of effectively controlling many pests, such as Colorado potato beetle, cotton bollworm, and mirid bugs. Our previous study demonstrated several life history parameters were diminished for A. chinensis reared on an artificial diet compared to a natural food source like the Chinese oak silk moth pupae. The molecular mechanisms underlying the nutritive impact of the artificial diet on A. chinensis health are unclear. So we utilized transcriptome information to better understand the impact of the artificial diet on A. chinensis at the molecular level. Methodology/Principal Findings Illumina HiSeq2000 was used to sequence 4.79 and 4.70 Gb of the transcriptome from pupae-fed and artificial diet-fed A. chinensis libraries, respectively, and a de novo transcriptome assembly was performed (Trinity short read assembler). This resulted in 112,029 and 98,724 contigs, clustered into 54,083 and 54,169 unigenes for pupae-fed and diet-fed A. chinensis, respectively. Unigenes from each sample’s assembly underwent sequence splicing and redundancy removal to acquire non-redundant unigenes. We obtained 55,189 unigenes of A. chinensis, including 12,046 distinct clusters and 43,143 distinct singletons. Unigene sequences were aligned by BLASTx to nr, Swiss-Prot, KEGG and COG (E-value <10−5), and further aligned by BLASTn to nt (E-value <10−5), retrieving proteins of highest sequence similarity with the given unigenes along with their protein functional annotations. Totally, 22,964, 7,898, 18,069, 15,416, 8,066 and 5,341 unigenes were annotated in nr, nt, Swiss-Prot, KEGG, COG and GO, respectively. We compared gene expression variations and found thousands of genes were differentially expressed between pupae-fed and diet-fed A. chinensis. Conclusions/Significance Our study provides abundant genomic data and offers comprehensive sequence information for studying A. chinensis. Additionally, the physiological roles of the

  5. Deciphering seasonal variations in the diet and drinking water of modern White-Tailed deer by in situ analysis of osteons in cortical bone

    NASA Astrophysics Data System (ADS)

    Larson, T. E.; Longstaffe, F. J.

    2007-12-01

    In situ carbon and oxygen isotope values for bioapatite were obtained from longitudinal slices of cortical bone from modern domesticated sheep and free-range White-Tailed deer. The analyses were obtained using an IR-laser coupled to a GC-IRMS interface. Ablation pits averaged 200 × 50 μm, making it possible to sample individual or small bundles of osteons. Cortical bone is remodeled along osteons throughout a mammal's life. Therefore, data at this scale can record seasonal variations in diet and drinking water during the adult stages of a mammal, whereas teeth provide may provide information about the juvenile years of a mammal. Average δ18O and δ13C values for the sheep from southwestern Ontario, Canada, were 14.0 and -16.1‰, respectively. No trend was observed in the isotopic composition of the sheep's osteons, consistent with its constant diet and water supply. The δ18O (14.2 to 16.6‰) and δ13C (-19.2 to -15.6‰) values of osteons from White-Tailed deer from nearby Pinery Provincial Park, however, varied systematically and were negatively correlated. Oxygen isotope values of the osteons correlated well with changes in the δ18O values of the main water source for these deer: winter average, -10.7‰; summer average, -8.6‰. The variation in δ13C values of the osteons reflects changes in diet; summer diet consisted mainly of leafy C3 vegetation (-28.4‰), whereas winter diet comprised bark (-25.6‰), C4 grasses (δ13C, -12.7‰), and corn stalks and husks (-11.3‰).

  6. Diet and Dermatology

    PubMed Central

    Desai, Samir P.

    2014-01-01

    For decades, it was thought that many common dermatological conditions had no relationship to diet. Studies from recent years, however, have made it clear that diet may influence outcome. In this review, the authors focus on conditions for which the role of diet has traditionally been an underappreciated aspect of therapy. In some cases, dietary interventions may influence the course of the skin disease, as in acne. In others, dietary change may serve as one aspect of prevention, such as in skin cancer and aging of the skin. In others, dermatological disease may be linked to systemic disease, and dietary changes may affect health outcomes, as in psoriasis. Lastly, systemic medications prescribed for dermatological disease, such as steroids, are known to raise the risk of other diseases, and dietary change may reduce this risk. PMID:25053983

  7. Fast DNA-based identification of the black truffle Tuber melanosporum with direct PCR and species-specific primers.

    PubMed

    Bonito, Gregory

    2009-12-01

    Abstract A quick and sensitive DNA-based assay for identifying the black truffle species Tuber melanosporum is presented. Both direct PCR and species-specific primers are used to amplify a phylogenetically informative region of T. melanosporum rDNA. This method was successfully used to screen fresh and frozen T. melanosporum fruitbodies, and could be modified for the molecular detection of other truffle and mushroom species.

  8. The effect of CP concentration in the diet on urea kinetics and microbial usage of recycled urea in cattle: a meta-analysis.

    PubMed

    Batista, E D; Detmann, E; Valadares Filho, S C; Titgemeyer, E C; Valadares, R F D

    2017-01-10

    In ruminants, urea recycling is considered an evolutionary advantage. The amount of urea recycled mainly depends of the nitrogen (N) intake and the amount of organic matter (OM) digested in the rumen. Because recycled N contributes to meeting microbial N requirements, accurate estimates of urea recycling can improve the understanding of efficiency of N utilization and N losses to the environment. The objective of this study was to evaluate urea kinetics and microbial usage of recycled urea N in ruminants using a meta-analytical approach. Treatment mean values were compiled from 25 studies with ruminants (beef cattle, dairy cows and sheep) which were published from 2001 to 2016, totalling 107 treatment means. The data set was analyzed according to meta-analysis techniques using linear or non-linear mixed models, taking into account the random variations among experiments. Urea N synthesized in the liver (UER) and urea N recycled to the gut (GER) linearly increased (P<0.001) as N intake (g/BW0.75) increased, with increases corresponding to 71.5% and 35.2% of N intake, respectively. The UER was positively associated (P<0.05) with dietary CP concentration and the ratio of CP to digestible OM (CP:DOM). Maximum curvature analyses identified 17% dietary CP as the point where there was a prominent increase in hepatic synthesis of urea N, likely due to an excess of dietary N leading to greater ammonia absorption. The GER:UER decreased with increasing dietary CP concentration (P<0.05). At dietary CP⩾19%, GER:UER reached near minimal values. The fraction of UER eliminated as urinary urea N and the contribution of urea N to total urinary N were positively associated with dietary CP (P<0.05), both reaching values near the plateau when dietary CP was 17%. The fractions of GER excreted in the feces and utilized for anabolism decreased, whereas the fraction of GER returned to the ornithine cycle increased with dietary CP concentration (P<0.05). Recycled urea N assimilated by

  9. Road Traffic and Railway Noise Exposures and Adiposity in Adults: A Cross-Sectional Analysis of the Danish Diet, Cancer, and Health Cohort

    PubMed Central

    Christensen, Jeppe Schultz; Raaschou-Nielsen, Ole; Tjønneland, Anne; Overvad, Kim; Nordsborg, Rikke B.; Ketzel, Matthias; Sørensen, Thorkild IA; Sørensen, Mette

    2015-01-01

    Background Traffic noise has been associated with cardiovascular and metabolic disorders. Potential modes of action are through stress and sleep disturbance, which may lead to endocrine dysregulation and overweight. Objectives We aimed to investigate the relationship between residential traffic and railway noise and adiposity. Methods In this cross-sectional study of 57,053 middle-aged people, height, weight, waist circumference, and bioelectrical impedance were measured at enrollment (1993–1997). Body mass index (BMI), body fat mass index (BFMI), and lean body mass index (LBMI) were calculated. Residential exposure to road and railway traffic noise exposure was calculated using the Nordic prediction method. Associations between traffic noise and anthropometric measures at enrollment were analyzed using general linear models and logistic regression adjusted for demographic and lifestyle factors. Results Linear regression models adjusted for age, sex, and socioeconomic factors showed that 5-year mean road traffic noise exposure preceding enrollment was associated with a 0.35-cm wider waist circumference (95% CI: 0.21, 0.50) and a 0.18-point higher BMI (95% CI: 0.12, 0.23) per 10 dB. Small, significant increases were also found for BFMI and LBMI. All associations followed linear exposure–response relationships. Exposure to railway noise was not linearly associated with adiposity measures. However, exposure > 60 dB was associated with a 0.71-cm wider waist circumference (95% CI: 0.23, 1.19) and a 0.19-point higher BMI (95% CI: 0.0072, 0.37) compared with unexposed participants (0–20 dB). Conclusions The present study finds positive associations between residential exposure to road traffic and railway noise and adiposity. Citation Christensen JS, Raaschou-Nielsen O, Tjønneland A, Overvad K, Nordsborg RB, Ketzel M, Sørensen TI, Sørensen M. 2016. Road traffic and railway noise exposures and adiposity in adults: a cross-sectional analysis of the Danish Diet

  10. Spontaneous germline excision of Tol1, a DNA-based transposable element naturally occurring in the medaka fish genome.

    PubMed

    Watanabe, Kohei; Koga, Hajime; Nakamura, Kodai; Fujita, Akiko; Hattori, Akimasa; Matsuda, Masaru; Koga, Akihiko

    2014-04-01

    DNA-based transposable elements are ubiquitous constituents of eukaryotic genomes. Vertebrates are, however, exceptional in that most of their DNA-based elements appear to be inactivated. The Tol1 element of the medaka fish, Oryzias latipes, is one of the few elements for which copies containing an undamaged gene have been found. Spontaneous transposition of this element in somatic cells has previously been demonstrated, but there is only indirect evidence for its germline transposition. Here, we show direct evidence of spontaneous excision in the germline. Tyrosinase is the key enzyme in melanin biosynthesis. In an albino laboratory strain of medaka fish, which is homozygous for a mutant tyrosinase gene in which a Tol1 copy is inserted, we identified de novo reversion mutations related to melanin pigmentation. The gamete-based reversion rate was as high as 0.4%. The revertant fish carried the tyrosinase gene from which the Tol1 copy had been excised. We previously reported the germline transposition of Tol2, another DNA-based element that is thought to be a recent invader of the medaka fish genome. Tol1 is an ancient resident of the genome. Our results indicate that even an old element can contribute to genetic variation in the host genome as a natural mutator.

  11. DNA-based small molecules for hole charge injection and channel passivation in organic heptazole field effect transistors

    NASA Astrophysics Data System (ADS)

    Cho, Youngsuk; Lee, Junyeong; Lim, June Yeong; Yu, Sanghyuck; Yi, Yeonjin; Im, Seongil

    2017-02-01

    DNA-based small molecules of guanine, cytosine, thymine and adenine are adopted for the charge injection layer between the Au electrodes and organic semiconductor, heptazole (C26H16N2). The heptazole-channel organic field effect transistors (OFETs) with a DNA-based small molecule charge injection layer showed higher hole mobility (maximum 0.12 cm2 V-1 s-1) than that of a pristine device (0.09 cm2 V-1 s-1). We characterized the contact resistance of each device by a transfer length method (TLM) and found that the guanine layer among all DNA-based materials performs best as a hole injection layer leading to the lowest contact resistance. Since the guanine layer is also known to be a proper channel passivation layer coupled with a thin conformal Al2O3 layer protecting the channel from bias stress and ambient molecules, we could realize ultra-stable OFETs utilizing guanine/Au contact and guanine/Al2O3 bilayer on the organic channel.

  12. High protein diets and diabetes.

    PubMed

    Carapetis, Melissa; Phillips, Patrick J

    2006-06-01

    Higher protein diets are currently 'hot'. The CSIRO total wellbeing diet book has been on the bestseller list in Australia and internationally. Various other high protein diets have also had, or are getting, media attention. However, high protein diets, particularly for people with diabetes, are controversial. There are questions about effectiveness and safety, especially in the long term. As a general practitioner people will look to you for advice about what to eat. This article summarises the pros and cons of two of the popular higher protein diets--the Atkins diet and the CSIRO total wellbeing.

  13. Cadmium contamination in cereal-based diets and diet ingredients

    SciTech Connect

    Siitonen, P.H.; Thompson, H.C. Jr. )

    1990-11-01

    Cereal-based diet and/or diet ingredient cadmium levels were determined by graphite furnace AAS. Cadmium contamination was 88.3 and 447 ppb in two cereal-based diets, 44.6 and 48.9 ppb in two purified diets, and ranged from less than 1.1 to 22,900 ppb in the ingredients of one cereal-based diet. The major source of cadmium contamination was attributed to the calcium supplement used for diet formulation. Comparative analyses of two purified diet samples and one cereal-based diet by the National Institute of Standards and Technology (NIST, formerly the National Bureau of Standards) and the National Center for Toxicological Research (NCTR) gave virtually identical results for Cd. A comparative study of Cd levels determined by flame and furnace AAS was also made by the NCTR and the NIST.

  14. Use and Knowledge of Diet Pills among Female College Students.

    ERIC Educational Resources Information Center

    Dorociak, Jeffery D.; Vincent, Murray L.

    1985-01-01

    A survey was conducted in an attempt to assess the use and knowledge of diet pills and dietary patterns of female college students. Analysis of the data indicated that, while many students used diet pills, their knowledge of the effects of the pills was minimal. Conclusions are presented. (MT)

  15. Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production.

    PubMed

    Wallenhammar, Ann-Charlotte; Gunnarson, Albin; Hansson, Fredrik; Jonsson, Anders

    2016-04-22

    Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR) in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to planting, P. brassicae DNA was detected in 60% of 45 fields on 10 of 18 farms. In 2014, P. brassicae DNA was detected in 44% of 59 fields in 14 of 36 farms, in the main winter OSR producing region in southern Sweden. P. brassicae was present indicative of a risk for >10% yield loss with susceptible cultivars (>1300 DNA copies g soil(-1)) in 47% and 44% of fields in 2013 and 2014 respectively. Furthermore, P. brassicae DNA was indicative of sites at risk of complete crop failure if susceptible cultivars were grown (>50 000 copies g(-1) soil) in 14% and 8% of fields in 2013 and 2014, respectively. A survey of all fields at Lanna research station in western Sweden showed that P. brassicae was spread throughout the farm, as only three of the fields (20%) showed infection levels below the detection limit for P.brassicae DNA, while the level was >50,000 DNA copies g(-1) soil in 20% of the fields. Soil-borne spread is of critical importance and soil scraped off footwear showed levels of up to 682 million spores g(-1) soil. Soil testing is an important tool for determining the presence of P. brassicae and providing an indication of potential yield loss, e.g., in advisory work on planning for a sustainable OSR crop rotation. This soil test is gaining acceptance as a tool that increases the likelihood of success in precision agriculture and in applied research conducted in commercial oilseed fields and at research stations. The present application highlights the importance of prevention of

  16. Sensitivity to lytic agents and DNA base composition of several aerobic spore-bearing bacilli.

    PubMed

    Candeli, A; Mastrandrea, V; Cenci, G; De Bartolomeo, A

    1978-01-01

    The authors studied the possible relationship between a genetic characteristic, like DNA base composition, and certain phenotypic characteristics, i.e., sensitivity to lytic agents, morphology of colonies, and biochemical reactions in 34 strains of spore-bearing bacilli. From the results obtained two groups of bacilli have been identified. The first group includes the species B. subtilis, B. pumilus, B. licheniformis, and B. firmus and one strain of B. megaterium. The mean value of the GC% of the DNA is 44.22 +/- 1.76. All the strains examined are highly sensitive to lysozyme and resistant to sodium lauryl sulphate (S.L.S.); the surface colonies have a "rhizoid" appearance and the microcolonies on slide microculture are star-shaped. The second group includes the species B. cereus, B. cereus var. mycoides, B. anthracis, and B. thuringiensis. The mean value of the GC% of the DNA is 33.65 +/- 0.59. All the strains belonging to this group are resistant to both lysozyme and S.L.S., and the surface macro-colonies and the microcolonies have a "medusae head" appearance. The two groups also have certain different biochemical reactions; e.g., anaerobic growth and the egg yolk reaction, with few exception, are negative for the first group and positive for the second; furthermore, the strains in the first group (with rare exceptions) cause fermentation in the three carbohydrates, glucose, arabinose, and xylose, while glucose only is fermented by all strains with one exception in the second group. The position of B. megaterium is not yet clear, although one strain may certainly be included in the first group. Lysis by lipase is extremely variable and does not correlate with any of the other characteristics studied. The other species studied in relation to the characteristics, considered in our research (B. coagulans, B. macerans, B. polymyxa, B. laterosporus, B. alvei, B. circulans, B. stearothermophilus, and B. brevis), are not susceptible to grouping, either in the first, or

  17. Probing heterobivalent binding to the endocytic AP-2 adaptor complex by DNA-based spatial screening.

    PubMed

    Diezmann, F; von Kleist, L; Haucke, V; Seitz, O

    2015-08-07

    The double helical DNA scaffold offers a unique set of properties, which are particularly useful for studies of multivalency in biomolecular interactions: (i) multivalent ligand displays can be formed upon nucleic acid hybridization in a self-assembly process, which facilitates spatial screening (ii) valency and spatial arrangement of the ligand display can be precisely controlled and (iii) the flexibility of the ligand display can be adjusted by integrating nick sites and unpaired template regions. Herein we describe the use of DNA-based spatial screening for the characterization of the adaptor complex 2 (AP-2), a central interaction hub within the endocytic protein network in clathrin-mediated endocytosis. AP-2 is comprised of a core domain and two, so-called appendage domains, the α- and the β2-ear, which associate with cytoplasmatic proteins required for the formation or maturation of clathrin/AP-2 coated pits. Each appendage domain has two binding grooves which recognize distinct peptide motives with micromolar affinity. This provides opportunities for enhanced interactions with protein molecules that contain two (or more) different peptide motives. To determine whether a particular, spatial arrangement of binding motifs is required for high affinity binding we probed the distance-affinity relationships by means of DNA-programmed spatial screening with self-assembled peptide-DNA complexes. By using trimolecular and tetramolecular assemblies two different peptides were positioned in 2-22 nucleotide distance. The binding data obtained with both recombinant protein in well-defined buffer systems and native AP-2 in brain extract suggests that the two binding sites of the AP-2 α-appendage can cooperate to provide up to 40-fold enhancement of affinity compared to the monovalent interaction. The distance between the two recognized peptide motives was less important provided that the DNA duplex segments were connected by flexible, single strand segments. By

  18. Short communication: Diet-induced variations in milk fatty acid composition have minor effects on the estimated melting point of milk fat in cows, goats, and ewes: Insights from a meta-analysis.

    PubMed

    Toral, P G; Bernard, L; Chilliard, Y; Glasser, F

    2013-02-01

    In ruminants, the ability to maintain milk fat melting point within physiological values could play a role in the regulation of milk fat secretion when milk fatty acid (FA) composition varies, such as in response to feeding factors. However, the relationship between milk fat fluidity and changes in milk FA composition is difficult to study experimentally. A meta-analysis was therefore conducted to compare the magnitude of diet-induced variations in milk FA composition and the calculated melting point of milk FA (used as a proxy to estimate the variations in the melting point of milk fat) in 3 dairy ruminant species (cow, goat, and sheep). The coefficient of variation (CV), a scale-free measure of statistical dispersion, was used to compare the variability of criteria differing in their order of magnitude. The analysis of a database of milk FA profiles from cows, goats, and sheep fed different dietary treatments (unsupplemented diets and diets supplemented with lipids rich in oleic acid, linoleic acid, linolenic acid, or C20-22 polyunsaturated FA) revealed that the variability of the calculated melting point of milk FA was narrow (CV of 5%) compared with the variability of milk FA percentages (CV of 18 to 72%). The regulation of the melting point of milk fat is thus probably involved in the control of diet-induced variations in milk fat secretion. The calculated melting point of ewe milk FA was approximately 3°C lower than that of goats or cows across all types of diets, which might be linked to differences in milk fat content (higher in sheep) or the structure of milk triacylglycerides among these species. Lipid supplementation increased the calculated melting point of C18 FA in milk, whereas that of total FA was significantly reduced by supplements rich in oleic, linoleic, and linolenic acids but not C20-22 polyunsaturated FA. However, the slight effects of dietary treatments on the calculated melting point of milk FA did not differ between cows, goats, and ewes.

  19. Dieting and Gallstones

    MedlinePlus

    ... slowly. Some ways of treating obesity, such as weight-loss surgery and very low-calorie diets (VLCDs), may increase ... of developing gallstones by promoting rapid weight loss. Weight-loss surgery is an operation on the stomach and/or ...

  20. Is Dieting OK for Kids?

    MedlinePlus

    ... Dictionary of Medical Words En Español What Other Kids Are Reading Taking Care of Your Ears Taking ... Getting an X-ray Is Dieting OK for Kids? KidsHealth > For Kids > Is Dieting OK for Kids? ...

  1. Diet Choices to Prevent Cancer

    MedlinePlus

    ... Pets and Animals myhealthfinder Food and Nutrition Healthy Food Choices Weight Loss and Diet Plans Nutrients and Nutritional ... Pets and Animals myhealthfinder Food and Nutrition Healthy Food Choices Weight Loss and Diet Plans Nutrients and Nutritional ...

  2. Cereal foods are the major source of betaine in the Western diet--analysis of betaine and free choline in cereal foods and updated assessments of betaine intake.

    PubMed

    Ross, Alastair B; Zangger, Alicia; Guiraud, Seu Ping

    2014-02-15

    Betaine and its precursor choline are important components of one-carbon metabolism, remethylating homocysteine into methionine and providing methyl groups for DNA methylation. Cereals are the main source of betaine in the diet, though there is little literature available on the content of betaine in cereal products, nor on betaine intake from cereals. Betaine and free-choline concentrations were measured by liquid-chromatography with tandem mass spectrometry in a wide range of commercially available cereal foods and cereal fractions. Whole grain wheat and related fractions were the best overall common source of betaine, while the pseudocereal quinoa had the highest amount of betaine measured (3900 μg/g). Based on estimates of dietary intake data cereal foods provide approximately 60-67% of betaine in Western diets, and 20-40% of betaine in South-East Asian diets. Average intake of betaine was 131 mg/d, well below those used in intervention studies using betaine to lower blood homocysteine.

  3. Effects of low glycaemic index/low glycaemic load vs. high glycaemic index/ high glycaemic load diets on overweight/obesity and associated risk factors in children and adolescents: a systematic review and meta-analysis.

    PubMed

    Schwingshackl, Lukas; Hobl, Lisa Patricia; Hoffmann, Georg

    2015-08-25

    The objective of the present systematic review and meta-analysis was to synthesize the available literature data investigating the effects of low glycaemic index/low glycamic load dietary regimens on anthropometric parameters, blood lipid profiles, and indicators of glucose metabolism in children and adolescents. Literature search was performed using the electronic databases MEDLINE, EMBASE, and the Cochrane Central Register of trials with restrictions to randomized controlled trials, but no limitations concerning language and publication date. Parameters taken into account were: body weight, body mass index, z-score of body mass index, fat mass, fat-free mass, height, waist cicrumference, hip circumference, waist-to-hip ratio, total cholesterol, LDL-cholesterol, HDL-cholesterol, triglycerides, diastolic and systolic blood pressure, fasting serum glucose, fasting serum insulin, HOMA-index, glycosylated haemoglobin, and C-reactive protein. Meta-analyses were performed for each parameter to assess pooled effect in terms of weighted mean differences between the post-intervention (or differences in means) of the low glycaemic index diets and the respective high glycaemic index counterparts. Data analysis was performed using the Review Manager 5.3. software. Nine studies enrolling 1.065 children or adolescents met the inclusion criteria. Compared to diets providing a high gylcaemic index, low glycaemic index protocols resulted in significantly more pronounced decreases in serum triglycerides [mean differences -15.14 mg/dl, 95%-CI (-26.26, -4.00)] and HOMA-index [mean difference -0.70, 95%-CI (-1.37, -0.04), fixed-effects model only]. Other parameters under investigation were not affected by either low or high glycaemic indices. The present systematic review and meta-analysis provides evidence of a beneficial effect of a low glycaemic index/load diet in children and adolescents being either overweight or obese. Regarding the limitations of this analysis, further studies

  4. Aluminium in foodstuffs and diets in Sweden.

    PubMed

    Jorhem, L; Haegglund, G

    1992-01-01

    The levels of aluminium have been determined in a number of individual foodstuffs on the Swedish market and in 24 h duplicate diets collected by women living in the Stockholm area. The results show that the levels in most foods are very low and that the level in vegetables can vary by a factor 10. Beverages from aluminium cans were found to have aluminium levels not markedly different from those in glass bottles. Based on the results of the analysis of individual foods, the average Swedish daily diet was calculated to contain about 0.6 mg aluminium, whereas the mean content of the collected duplicate diets was 13 mg. A cake made from a mix containing aluminium phosphate in the baking soda was identified as the most important contributor of aluminium to the duplicate diets. Tea and aluminium utensils were estimated to increase the aluminium content of the diets by approximately 4 and 2 mg/day, respectively. The results also indicate that a considerable amount of aluminium must be introduced from other sources.

  5. Eating, Diet, and Nutrition for Constipation

    MedlinePlus

    ... Treatment Eating, Diet, & Nutrition Clinical Trials Eating, Diet, & Nutrition for Constipation How can your diet help prevent ... Management Liver Disease Urologic Diseases Endocrine Diseases Diet & Nutrition Blood Diseases Diagnostic Tests La información de la ...

  6. Is a healthy diet an environmentally sustainable diet?

    PubMed

    Macdiarmid, Jennie I

    2013-02-01

    The concept of a healthy and environmentally sustainable diet is not new, but with increasing concern about future global food security and climate change there is a renewed interest in this topic. Dietary intakes in UK accounts for approximately 20-30% of total annual greenhouse gas emissions (GHGE), with the greatest contributions coming from high intakes of meat and dairy products. Dietary proposals to help mitigate climate change (i.e. reduce GHGE) have focused on reducing consumption of meat and dairy products, but this must be considered in the context of the whole diet, alongside any possible nutritional consequences for health. Bringing together health and environmental impact of the diet raises the question of whether a healthy diet can also be an environmentally sustainable diet. While recent research showed that it is possible to achieve a realistic diet that meets dietary requirement for health and has lower GHGE, it cannot be assumed that a healthy diet will always have lower GHGE. With different combinations of food it is possible to consume a diet that meets dietary requirements for health, but has high GHGE. It is important to understand what constitutes a sustainable diet, but this then needs to be communicated effectively to try and change well-established dietary intakes of the population. Studies show that understanding of sustainable diets is poor and there are many misconceptions (e.g. the overestimation of the protein requirements for a healthy diet), which could contribute to the barriers towards changing dietary intakes.

  7. Diet quality on meatless days: National Health and Nutrition Examination Survey (NHANES), 2007-2012

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objective: To compare diet quality scores between adult non-meat eaters and meat eaters, and to compare the consumption of diet components across quintiles of diet quality. Design: Cross-sectional analysis. Healthy Eating Index-2010 (HEI-2010) and Alternative Healthy Eating Index-2010 (AHEI-2010) we...

  8. The Choice of Diet for Young Children and Its Relation to Children's Growth.

    ERIC Educational Resources Information Center

    Chernichovsky, Dov; Coate, Douglas

    1980-01-01

    Results of an ongoing analysis of the household's choice of diet for its children under three years and how that diet relates to the child's growth. Focuses on the extent to which family income and mother's education are obstacles to the provision of adequate diets for children in poor American families. (CT)

  9. Protein and vegetarian diets.

    PubMed

    Marsh, Kate A; Munn, Elizabeth A; Baines, Surinder K

    2013-08-19

    A vegetarian diet can easily meet human dietary protein requirements as long as energy needs are met and a variety of foods are eaten. Vegetarians should obtain protein from a variety of plant sources, including legumes, soy products, grains, nuts and seeds. Eggs and dairy products also provide protein for those following a lacto-ovo-vegetarian diet. There is no need to consciously combine different plant proteins at each meal as long as a variety of foods are eaten from day to day, because the human body maintains a pool of amino acids which can be used to complement dietary protein. The consumption of plant proteins rather than animal proteins by vegetarians may contribute to their reduced risk of chronic diseases such as diabetes and heart disease.

  10. [Controversies around diet proteins].

    PubMed

    Cichosz, Grazyna; Czeczot, Hanna

    2013-12-01

    Critical theories regarding proteins of anima origin are still and still popularized, though they are ungrounded from scientific point of view. Predominance of soya proteins over the animal ones in relation to their influence on calcium metabolism, bone break risk or risk of osteoporosis morbidity has not been confirmed in any honest, reliable research experiment. Statement, that sulphur amino acids influence disadvantageously on calcium metabolism of human organism and bone status, is completely groundless, the more so as presence of sulphur amino acids in diet (animal proteins are their best source) is the condition of endogenic synthesis of glutathione, the key antioxidant of the organism, and taurine stimulating brain functioning. Deficiency of proteins in the diet produce weakness of intellectual effectiveness and immune response. There is no doubt that limitation of consumption of animal proteins of standard value is not good for health.

  11. Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting

    PubMed Central

    Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G.

    2006-01-01

    Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS

  12. Estimation of endogenous protein and amino acid ileal losses in weaned piglets by regression analysis using diets with graded levels of casein

    PubMed Central

    2013-01-01

    Background Many studies have investigated endogenous loss of proteins and amino acids (AAs) at the ileal level in growing pigs. However, only a few studies have researched this subject in piglets. Knowledge regarding AA ileal digestibility in piglets would be helpful during the formulation of diets for weaning piglets, rather than just using coefficients obtained in growing pigs. Therefore, in this study, we sought to estimate endogenous protein and AA ileal losses in piglets. Furthermore, apparent and true ileal digestibility (AID and TID) of protein and AAs from casein were measured. Results The average flow of protein was 20.8 g/kg of dry matter intake (DMI). Basal protein loss, as estimated by regression, was 16.9 g/kg DMI. Glutamic acid, arginine, and aspartic acid (2.2, 1.4, and 1.2 g/kg DMI, respectively) were the AAs for which greater losses were seen. The AID of protein and AAs increased as the protein level in the diet increased. A higher increment in AID was observed between diets with 80 and160 g CP/kg of feed; this finding was mainly attributable to increases in glycine and arginine (46.1% and 18%, respectively). The TID of protein was 97.8, and the TID of AAs varied from 93.9 for histidine to 100.2 for phenylalanine. Conclusions The basal endogenous protein loss in piglets was 16.9 g/kg DMI. Endogenous protein was rich in glutamic acid, aspartic acid, and arginine, which represented 32.7% of endogenous protein loss in weaning piglets. The TID of casein was high and varied from 93.0 for histidine to 100.2 for phenylalanine. PMID:24053636

  13. A Comparative Analysis of the Contents Of Iron, Zinc, Copper, Manganese, and Calcium in the Collective Diet Of Preschool Children in the Northwestern Region of Bosnia.

    PubMed

    Đermanović, Mirjana; Miletić, Ivanka; Pavlović, Zoran

    2017-01-01

    Researches conducted worldwide indicate a frequent deficiency in mineral matters. Due to the increased need during the period of accelerated growth and development, children belong to the group that is exposed to the highest risk of mineral matter deficiency. Our objectives were to determine the iron, zinc, copper, manganese, and calcium intake in the collective diet of the preschool population in the in the northwestern region of Bosnia- in the Republic of Srpska and to estimate the adequacy of the application of the international food composition tables for nutrition planning relating to mineral matters. Samples of food intended for children's diet were collected in the preschool institution "Radost" (a kindergarten), in the city of Prijedor. In daily portions, Fe, Zn, Cu, Mn, and Ca contents were determined by flame atomic absorption spectrophotometry. Contents of mineral matters in daily meals were also calculated by the food composition tables. An average daily meal contained 2.86 mg of Fe, 1.71 mg of Zn, 0.19 mg of Cu, 0.21 mg of Mn, and 83.5 mg of Ca. With calculation method, contents of all minerals are significantly higher than the experimental data for all used food composition tables. The obtained results indicate a significant deficiency in mineral matters in the collective diet of the preschool population in the Republic of Srpska, a certain non-compliance with the applicable recommendations, and also suggest a need to create food composition tables for food being consumed in our region.

  14. [Diet low in potassium].

    PubMed

    Sáez Rodríguez, Loreto; Meizoso Ameneiro, Ana; Pérez Paz, Ma Jesús; Valiño Pazos, Cristina

    2011-11-01

    After confirming the high prevalence rates in our hemodialysis unit of the following nursing diagnoses: nutritional imbalances--both excesses and shortages, willingness to improve nutrition and fear related to the consequences of excessive intake of potassium and manifested by the inhibition in some people towards the enjoyment of food, we decided to plan an educational strategy which later resulted in a nursing intervention for these diagnoses, with the objective of providing adequate resources for the monitoring of balanced diets with a restriction of potassium. Inspired by dietary rations, as well as recognized dietary programs of learning by points, we decided to incorporate these ideas to design an educational tool to facilitate advice to our patients on how to follow diet plans as well as the choice of appropriate foods. The result was a set of cards incorporating nutritional information of various kinds, aimed at our patients covering different aspects of the diet appropriate food rations using household measurements, promoting good food preparation, appropriate dietary advice for different chronic diseases and a scoring system of foods according to their potassium content. Together they form a board game available during the hemodialysis sessions that also takes into consideration other issues of importance related to conditions such as cognitive stimulation, coping with the disease, improving the therapeutic performance or resources to increase patient motivation. Although initially it was only an educational exercise, the result has turned out to be both enjoyable and entertaining.

  15. Plants, diet, and health.

    PubMed

    Martin, Cathie; Zhang, Yang; Tonelli, Chiara; Petroni, Katia

    2013-01-01

    Chronic disease is a major social challenge of the twenty-first century. In this review, we examine the evidence for discordance between modern diets and those on which humankind evolved as the cause of the increasing incidence of chronic diseases, and the evidence supporting consumption of plant foods as a way to reduce the risk of chronic disease. We also examine the evidence for avoiding certain components of plant-based foods that are enriched in Western diets, and review the mechanisms by which different phytonutrients are thought to reduce the risk of chronic disease. This body of evidence strongly suggests that consuming more fruits and vegetables could contribute both to medical nutrition therapies, as part of a package of treatments for conditions like type 2 diabetes, heart disease, cancer, and obesity, and to the prevention of these diseases. Plant science should be directed toward improving the quality of plant-based foods by building on our improved understanding of the complex relationships between plants, our diet, and our health.

  16. Group-specific primers for DNA-based detection of springtails (Hexapoda: Collembola) within predator gut contents.

    PubMed

    Kuusk, A K; Agustí, N

    2008-05-01

    Group-specific, degenerate polymerase chain reaction primers for DNA-based detection of springtails (Hexapoda: Collembola) within predator gut contents have been developed for the first time. Primers were designed from 18S rDNA and amplified fragments of 272 bp and 177 bp from 17 springtail species collected in agricultural habitats. Specificity tests against 41 nontarget species revealed no cross-reactivity. Group-specific polymerase chain reaction is advantageous when working in species-rich habitats and these primers could facilitate studies of trophic links between springtails and generalist arthropod predators worldwide.

  17. Meta-Analysis of Early Nutrition: The Benefits of Enteral Feeding Compared to a Nil Per Os Diet Not Only in Severe, but Also in Mild and Moderate Acute Pancreatitis

    PubMed Central

    Márta, Katalin; Farkas, Nelli; Szabó, Imre; Illés, Anita; Vincze, Áron; Pár, Gabriella; Sarlós, Patrícia; Bajor, Judit; Szűcs, Ákos; Czimmer, József; Mosztbacher, Dóra; Párniczky, Andrea; Szemes, Kata; Pécsi, Dániel; Hegyi, Péter

    2016-01-01

    The recently published guidelines for acute pancreatitis (AP) suggest that enteral nutrition (EN) should be the primary therapy in patients suffering from severe acute pancreatitis (SAP); however, none of the guidelines have recommendations on mild and moderate AP (MAP). A meta-analysis was performed using the preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P). The following PICO (problem, intervention, comparison, outcome) was applied: P: nutrition in AP; I: enteral nutrition (EN); C: nil per os diet (NPO); and O: outcome. There were 717 articles found in Embase, 831 in PubMed, and 10 in the Cochrane database. Altogether, seven SAP and six MAP articles were suitable for analyses. In SAP, forest plots were used to illustrate three primary endpoints (mortality, multiorgan failure, and intervention). In MAP, 14 additional secondary endpoints were analyzed (such as CRP (C-reactive protein), WCC (white cell count), complications, etc.). After pooling the data, the Mann–Whitney U test was used to detect significant differences. Funnel plots were created for testing heterogeneity. All of the primary endpoints investigated showed that EN is beneficial vs. NPO in SAP. In MAP, all of the six articles found merit in EN. Analyses of the primary endpoints did not show significant differences between the groups; however, analyzing the 17 endpoints together showed a significant difference in favor of EN vs. NPO. EN is beneficial compared to a nil per os diet not only in severe, but also in mild and moderate AP. PMID:27775609

  18. Fatty acid signatures of stomach oil and adipose tissue of northern fulmars (Fulmarus glacialis) in Alaska: Implications for diet analysis of Procellariiform birds

    USGS Publications Warehouse

    Wang, S.W.; Iverson, S.J.; Springer, A.M.; Hatch, Shyla A.

    2007-01-01

    Procellariiforms are unique among seabirds in storing dietary lipids in both adipose tissue and stomach oil. Thus, both lipid sources are potentially useful for trophic studies using fatty acid (FA) signatures. However, little is known about the relationship between FA signatures in stomach oil and adipose tissue of individuals or whether these signatures provide similar information about diet and physiology. We compared the FA composition of stomach oil and adipose tissue biopsies of individual northern fulmars (N = 101) breeding at three major colonies in Alaska. Fatty acid signatures differed significantly between the two lipid sources, reflecting differences in dietary time scales, metabolic processing, or both. However, these signatures exhibited a relatively consistent relationship between individuals, such that the two lipid sources provided a similar ability to distinguish foraging differences among individuals and colonies. Our results, including the exclusive presence of dietary wax esters in stomach oil but not adipose tissue, are consistent with the notion that stomach oil FA signatures represent lipids retained from prey consumed during recent foraging and reflect little metabolic processing, whereas adipose tissue FA signatures represent a longer-term integration of dietary intake. Our study illustrates the potential for elucidating short- versus longer-term diet information in Procellariiform birds using different lipid sources. ?? 2007 Springer-Verlag.

  19. How much of the data published in observational studies of the association between diet and prostate or bladder cancer is usable for meta-analysis?

    PubMed

    Bekkering, Geertruida E; Harris, Ross J; Thomas, Steve; Mayer, Anne-Marie B; Beynon, Rebecca; Ness, Andrew R; Harbord, Roger M; Bain, Chris; Smith, George Davey; Sterne, Jonathan A C

    2008-05-01

    Epidemiologic investigations often report dose-response associations, which may be combined in meta-analyses. The authors examined how often the log odds, risk, or hazard ratio per unit increase in exposure, and its standard error, can be estimated from results reported from observational studies of diet and prostate or bladder cancer so that results are usable in meta-analyses estimating dose-response associations. Eight electronic databases were searched for studies reporting on the association of diet, nutrition, or physical activity with these cancers. A total of 767 papers reported 3,284 results; 1,999 (61%) results, reported in 545 (71%) papers, were usable in dose-response meta-analyses. The most important reason that results were not usable was the absence of sufficient information on exposure levels in the different groups. The proportion of results usable in "high-low" meta-analyses (comparisons of extreme categories) was similar (62%). Results that showed evidence of an association were more likely to be usable than results that found no such evidence. Insufficient detail in reporting of results of observational studies can lead to exclusion of these results from meta-analyses and is an important threat to the validity of systematic reviews of such research. Results providing evidence of associations may be overrepresented in meta-analyses of observational studies.

  20. The environmental cost of subsistence: Optimizing diets to minimize footprints.

    PubMed

    Gephart, Jessica A; Davis, Kyle F; Emery, Kyle A; Leach, Allison M; Galloway, James N; Pace, Michael L

    2016-05-15

    The question of how to minimize monetary cost while meeting basic nutrient requirements (a subsistence diet) was posed by George Stigler in 1945. The problem, known as Stigler's diet problem, was famously solved using the simplex algorithm. Today, we are not only concerned with the monetary cost of food, but also the environmental cost. Efforts to quantify environmental impacts led to the development of footprint (FP) indicators. The environmental footprints of food production span multiple dimensions, including greenhouse gas emissions (carbon footprint), nitrogen release (nitrogen footprint), water use (blue and green water footprint) and land use (land footprint), and a diet minimizing one of these impacts could result in higher impacts in another dimension. In this study based on nutritional and population data for the United States, we identify diets that minimize each of these four footprints subject to nutrient constraints. We then calculate tradeoffs by taking the composition of each footprint's minimum diet and calculating the other three footprints. We find that diets for the minimized footprints tend to be similar for the four footprints, suggesting there are generally synergies, rather than tradeoffs, among low footprint diets. Plant-based food and seafood (fish and other aquatic foods) commonly appear in minimized diets and tend to most efficiently supply macronutrients and micronutrients, respectively. Livestock products rarely appear in minimized diets, suggesting these foods tend to be less efficient from an environmental perspective, even when nutrient content is considered. The results' emphasis on seafood is complicated by the environmental impacts of aquaculture versus capture fisheries, increasing in aquaculture, and shifting compositions of aquaculture feeds. While this analysis does not make specific diet recommendations, our approach demonstrates potential environmental synergies of plant- and seafood-based diets. As a result, this study

  1. The development and validation of the Dieting Intentions Scale (DIS).

    PubMed

    Cruwys, Tegan; Platow, Michael J; Rieger, Elizabeth; Byrne, Don G

    2013-03-01

    This article presents information on the psychometric properties of the Dieting Intentions Scale (DIS), a new scale of dieting that predicts future behavioral efforts to lose weight. We begin by reviewing recent research indicating theoretical and empirical problems with traditional approaches to measuring dieting. The DIS addresses several of these problems by (a) focusing on naturalistic dieting behavior and (b) being future-oriented. Four validation studies are presented with a total of 741 participants. We demonstrate that the DIS has predictive utility for dieting behaviors and is positively correlated with other measures related to eating, weight, and shape. Furthermore, the DIS demonstrates discriminant validity by not being related to constructs such as self-esteem and social desirability. The DIS also has high internal consistency, with a 1-factor solution replicated with confirmatory factor analysis. The potential uses of the scale in both research and clinical settings are considered.

  2. Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries.

    PubMed

    Trebitz, Anett S; Hoffman, Joel C; Grant, George W; Billehus, Tyler M; Pilgrim, Erik M

    2015-07-22

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections.

  3. Coupling a DNA-Based Machine with Glucometer Readouts for Amplified Detection of Telomerase Activity in Cancer Cells

    PubMed Central

    Wang, Wenjing; Huang, Shan; Li, Jingjing; Rui, Kai; Zhang, Jian-Rong; Zhu, Jun-Jie

    2016-01-01

    The strong correlation between cancer and telomerase activity has inspired the development of new strategies to evaluate telomerase activity. Here, a personal glucose meter (PGM) system that uses DNA-based machine amplification to detect telomerase in cancer cells is reported. In this assay, telomerase elongation products are amplified in the form of another type of product by a DNA-based machine. This process can only be activated by the hybridization of the extended telomerase substrate (TS) probe and the complementary primer in the presence of telomerase. The obtained products are then transformed to glucose-related signals via a three-component assay, which enables the simple use of a PGM to indirectly quantify the telomerase activity. The proposed method realizes sensitive telomerase activity detection down to 20 HeLa cells with a significantly enhanced dynamic range. Additionally, short telomerase elongation products, such as telomerase substrate probes with two repetitive sequences, that cannot be detected using the most widely used telomeric repeat amplification protocol assay were detected. PMID:27009555

  4. A reversible adsorption-desorption interface of DNA based on nano-sized zirconia and its application.

    PubMed

    Liu, Shou-Qing; Xu, Jing-Juan; Chen, Hong-Yuan

    2004-08-01

    It is essential for the information storage in