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

    PubMed Central

    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. PMID:23785258

  8. 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...

  9. 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...

  10. Electronic structure simulations of DNA base recognition and vibrational property analysis of polyanionic hydrides

    NASA Astrophysics Data System (ADS)

    Lee, Myeong Hwa

    This thesis presents electronic structure simulations of electron transport across DNA base-pairs for base recognition and analysis of vibrational properties for polyanionic hydrides. The work on DNA base recognition is motivated by a recent experiment to sequence DNA by measuring tunnel conductance when a single stranded DNA molecule passes through a nanopore. An electric circuit is completed when a DNA base and the phosphate backbone form hydrogen bonds with the reader nucleobase and a guanidinium ion, respectively, tethered to either side of metal electrodes. The tunnel conductance has been obtained across DNA base-pairs, across nucleoside-base pairs, and for a complete circuit containing deoxycytidine-monophosphate (dCMP) by computing the complex bandstructure, Fermi level alignment, and current-voltage curve. The results indicate that a complete dCMP circuit has a very low conductance (on the order of fS) while the base-pair has a moderate conductance (on the order of tens of nS). An alternate base readout scheme, which uses a shorter tunneling path, is explored. Electron transport through other organic single molecules is also examined. Examples include the effects of torsion angle between rings, oxidation states, and stretching on the electron transport properties of polyaniline molecules and the effects of molecule-metal contact geometries in alkanedithiol molecules. Additionally, an analysis of vibrational properties is presented to understand the bonding of hydrogen in aluminum and gallium hydrides by computing phonon dispersion curve. Both Al-H and Ga-H stretching mode frequencies are found to be low compared to other hydrides. The weak Al(Ga)-H bond is balanced by Sr(Ba)-H interactions. Finally, the electronic and the vibrational property changes are examined when superconducting MAlSi (M = Ca, Sr, Ba) absorbs hydrogen and forms semiconducting hydrides MAlSiH with hydrogen attached to Al exclusively. While only a minor rearrangement of the metal atoms

  11. Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

    PubMed

    Deagle, Bruce E; Thomas, Austen C; Shaffer, Amanda K; Trites, Andrew W; Jarman, Simon N

    2013-07-01

    A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis. © 2013 John Wiley & Sons Ltd.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. Overcoming PCR Inhibition During DNA-Based Gut Content Analysis of Ants.

    PubMed

    Penn, Hannah J; Chapman, Eric G; Harwood, James D

    2016-10-01

    Generalist predators play an important role in many terrestrial systems, especially within agricultural settings, and ants (Hymenoptera: Formicidae) often constitute important linkages of these food webs, as they are abundant and influential in these ecosystems. Molecular gut content analysis provides a means of delineating food web linkages of ants based on the presence of prey DNA within their guts. Although this method can provide insight, its use on ants has been limited, potentially due to inhibition when amplifying gut content DNA. We designed a series of experiments to determine those ant organs responsible for inhibition and identified variation in inhibition among three species (Tetramorium caespitum (L.), Solenopsis invicta Buren, and Camponotus floridanus (Buckley)). No body segment, other than the gaster, caused significant inhibition. Following dissection, we determined that within the gaster, the digestive tract and crop cause significant levels of inhibition. We found significant differences in the frequency of inhibition between the three species tested, with inhibition most evident in T. caespitum The most effective method to prevent inhibition before DNA extraction was to exude crop contents and crop structures onto UV-sterilized tissue. However, if extracted samples exhibit inhibition, addition of bovine serum albumin to PCR reagents will overcome this problem. These methods will circumvent gut content inhibition within selected species of ants, thereby allowing more detailed and reliable studies of ant food webs. As little is known about the prevalence of this inhibition in other species, it is recommended that the protocols in this study are used until otherwise shown to be unnecessary. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. Computerized Diet Analysis: Friend or Foe?

    ERIC Educational Resources Information Center

    Sevenhuysen, Gustaaf P.

    1984-01-01

    This paper considers some advantages of manual nutrient calculation over computerized calculations, pointing out especially some pitfalls of using computers. It also discusses proper uses of computers in nutritional calculation, such as in computerized diet analysis. (JB)

  4. DNA-based human karyotype

    SciTech Connect

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

    1984-01-01

    Image cytometry and computer analysis are used to determine the relative DNA content and the DNA-based centromeric index of the 24 chromosomes of the human karyotype. A two-step procedure is used. Chromosomes of cells in metaphase first are stained with quinacrine and identified visually by their fluorescent Q-band patterns. They then are stained for DNA using gallocyanin-chrome alum. The chromosome images are scanned and recorded as digital values of optical density by an CYDAC image cytometric microscope system, CYDAC. The digital images are processed by computer to measure for each chromosome the relative DNA stain contents of the whole chromosome and of the p and q arms and the DNA-based centromeric index. About ten cells are analyzed for each of the donors, who are phenotypically normal men and women. The chromosome measurements are pooled by chromosome type for each donor and are compared among donors. The means of the chromosome measurements give the DNA-based human karyotype. Analysis of the DNA-based data shows that some chromosomes or portions of chromosomes vary significantly among donors. These variants do not correlate with detectable morphologic polymorphisms, such as Q- or C-band variants; thus they represent new and otherwise undetectable chromosome polymorphisms whose genetic basis and clinical significance are yet to be determined. 54 references, 1 figure, 3 tables.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus).

    PubMed

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

    2007-09-05

    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. 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. 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.

  10. 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.

  11. DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches

    PubMed Central

    Murray, Dáithí C.; Bunce, Michael; Cannell, Belinda L.; Oliver, Rebecca; Houston, Jayne; White, Nicole E.; Barrero, Roberto A.; Bellgard, Matthew I.; Haile, James

    2011-01-01

    The genetic analysis of faecal material represents a relatively non-invasive way to study animal diet and has been widely adopted in ecological research. Due to the heterogeneous nature of faecal material the primary obstacle, common to all genetic approaches, is a means to dissect the constituent DNA sequences. Traditionally, bacterial cloning of PCR amplified products was employed; less common has been the use of species-specific quantitative PCR (qPCR) assays. Currently, with the advent of High-Throughput Sequencing (HTS) technologies and indexed primers it has become possible to conduct genetic audits of faecal material to a much greater depth than previously possible. To date, no studies have systematically compared the estimates obtained by HTS with that of qPCR. What are the relative strengths and weaknesses of each technique and how quantitative are deep-sequencing approaches that employ universal primers? Using the locally threatened Little Penguin (Eudyptula minor) as a model organism, it is shown here that both qPCR and HTS techniques are highly correlated and produce strikingly similar quantitative estimates of fish DNA in faecal material, with no statistical difference. By designing four species-specific fish qPCR assays and comparing the data to the same four fish in the HTS data it was possible to directly compare the strengths and weaknesses of both techniques. To obtain reproducible quantitative data one of the key, and often overlooked, steps common to both approaches is ensuring that efficient DNA isolation methods are employed and that extracts are free of inhibitors. Taken together, the methodology chosen for long-term faecal monitoring programs is largely dependent on the complexity of the prey species present and the level of accuracy that is desired. Importantly, these methods should not be thought of as mutually exclusive, as the use of both HTS and qPCR in tandem will generate datasets with the highest fidelity. PMID:21998697

  12. 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.

  13. 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.

  14. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis.

    PubMed

    Mackie, F L; Hemming, K; Allen, S; Morris, R K; Kilby, M D

    2017-01-01

    Cell-free fetal DNA (cffDNA) non-invasive prenatal testing (NIPT) is rapidly expanding, and is being introduced at varying rates depending on country and condition. Determine accuracy of cffDNA-based NIPT for all conditions. Evaluate influence of other factors on test performance. Medline, Embase, CINAHL, Cochrane Library, from 1997 to April 2015. Cohort studies reporting cffDNA-based NIPT performance in singleton pregnancies. Bivariate or univariate meta-analysis and subgroup analysis performed to explore influence of test type and population risk. A total of 117 studies were included that analysed 18 conditions. Bivariate meta-analysis demonstrated sensitivities and specificities, respectively, for: fetal sex, 0.989 (95% CI 0.980-0.994) and 0.996 (95% CI 0.989-0.998), 11 179 tests; rhesus D, 0.993 (95% CI 0.982-0.997) and 0.984 (95% CI 0.964-0.993), 10 290 tests; trisomy 21, 0.994 (95% CI 0.983-0.998) and 0.999 (95% CI 0.999-1.000), 148 344 tests; trisomy 18, 0.977 (95% CI 0.952-0.989) and 0.999 (95% CI 0.998-1.000), 146 940 tests; monosomy X, 0.929 (95% CI 0.741-0.984) and 0.999 (95% CI 0.995-0.999), 6712 tests. Trisomy 13 was analysed by univariate meta-analysis, with a summary sensitivity of 0.906 (95% CI 0.823-0.958) and specificity of 1.00 (95% CI 0.999-0.100), from 134 691 tests. False and inconclusive results were poorly reported across all conditions. Although the test type affected both sensitivity and specificity, there was no evidence that population risk had any effect. Performance of cffDNA-based NIPT is affected by condition under investigation. For fetal sex and rhesus D status, NIPT can be considered diagnostic. For trisomy 21, 18, and 13, the lower sensitivity, specificity, and disease prevalence, combined with the biological influence of confined placental mosaicism, designates it a screening test. These factors must be considered when counselling patients and assessing the cost of introduction into routine care

  15. DNA-based machines.

    PubMed

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

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

  16. Diagnostic value of immunohistochemistry for the detection of the BRAF(V600E) mutation in papillary thyroid carcinoma: comparative analysis with three DNA-based assays.

    PubMed

    Ilie, Marius I; Lassalle, Sandra; Long-Mira, Elodie; Bonnetaud, Christelle; Bordone, Olivier; Lespinet, Virginie; Lamy, Aude; Sabourin, Jean-Christophe; Haudebourg, Juliette; Butori, Catherine; Guevara, Nicolas; Peyrottes, Isabelle; Sadoul, Jean-Louis; Bozec, Alexandre; Santini, José; Capper, David; von Deimling, Andreas; Emile, Jean-François; Hofman, Véronique; Hofman, Paul

    2014-05-01

    The aim of this study was to compare the detection of BRAF(V600E) by immunohistochemistry (IHC) using a mutation-specific antibody with molecular biology methods for evaluation of papillary thyroid carcinoma (PTC) patients. This study concerned 198 consecutive conventional PTC patients, of which the majority were women (133/198; 67%), with a mean age of 56 years (range 19-79 years). BRAF mutation analysis was performed using DNA-based (direct sequencing, pyrosequencing, and SNaPshot) and IHC (VE1 antibody) methods. The sensitivity and specificity of IHC for BRAF(V600E) was compared with the molecular biology data. A BRAF mutational result was obtained in 194 cases. A BRAF(V600E) mutation was detected in 153/194 (79%) cases of PTC when using at least one molecular method, and in 151/194 (78%) cases with IHC. No false positive results were noted using IHC to detect the BRAF(V600E) mutation. Besides this mutation, other rare BRAF mutations (BRAF(V600K) and BRAF(K601E)), used as negative controls, were consistently negative with IHC. The sensitivity and specificity of IHC for the detection of this mutation were 98.7% and 100% respectively. The IHC test demonstrated excellent performance at a level equivalent to two DNA-based counterparts (pyrosequencing and SNaPshot). Failure to achieve a result was more frequent with the direct sequencing method than with the three other methods. IHC using the VE1 antibody is a specific and sensitive method for the detection of the BRAF(V600E) mutation in PTC. IHC may be an alternative to molecular biology approaches for the routine detection of this mutation in PTC patients.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  18. Lactic acid bacteria associated with vacuum-packed cooked meat product spoilage: population analysis by rDNA-based methods.

    PubMed

    Chenoll, E; Macián, M C; Elizaquível, P; Aznar, R

    2007-02-01

    To determine the lactic acid bacteria (LAB) implicated in bloating spoilage of vacuum-packed and refrigerated meat products. A total of 18 samples corresponding to four types of meat products, with and without spoilage symptoms, were studied. In all, 387 colonies growing on de Man, Rogosa and Sharpe, yeast glucose lactose peptone and trypticase soy yeast extract plates were identified by internal spacer region (ISR), ISR-restriction fragment length polymorphism and rapid amplified ribosomal DNA restriction analysis profiles as Lactobacillus (37%), Leuconostoc (43%), Carnobacterium (11%), Enterococcus (4%) and Lactococcus (2%). Leuconostoc mesenteroides dominated the microbial population of spoiled products and was always present at the moment bloating occurred. Lactobacillus sakei, Lactobacillus plantarum and Lactobacillus curvatus were found in decreasing order of abundance. The analysis of two meat products, 'morcilla' and 'fiambre de magro adobado' obtained from production lines revealed a common succession pattern in LAB populations in both products and showed that Leuc. mesenteroides became the main species during storage, despite being below the detection level of culture methods after packing. Our results pointed to Leuc. mesenteroides as the main species responsible for bloating spoilage in vacuum-packed meat products. Prevention of bloating spoilage in vacuum-packed cooked meat products requires the sensitive detection of Leuc. mesenteroides (i.e. by PCR).

  19. 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.

  20. 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.

  1. 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

    2017-02-01

    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. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. 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.

  3. 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. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  4. Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan.

    PubMed

    Shehzad, Wasim; Riaz, Tiayyba; Nawaz, Muhammad A; Miquel, Christian; Poillot, Carole; Shah, Safdar A; Pompanon, François; Coissac, Eric; Taberlet, Pierre

    2012-04-01

    Diet analysis is a prerequisite to fully understand the biology of a species and the functioning of ecosystems. For carnivores, traditional diet analyses mostly rely upon the morphological identification of undigested remains in the faeces. Here, we developed a methodology for carnivore diet analyses based on the next-generation sequencing. We applied this approach to the analysis of the vertebrate component of leopard cat diet in two ecologically distinct regions in northern Pakistan. Despite being a relatively common species with a wide distribution in Asia, little is known about this elusive predator. We analysed a total of 38 leopard cat faeces. After a classical DNA extraction, the DNA extracts were amplified using primers for vertebrates targeting about 100 bp of the mitochondrial 12S rRNA gene, with and without a blocking oligonucleotide specific to the predator sequence. The amplification products were then sequenced on a next-generation sequencer. We identified a total of 18 prey taxa, including eight mammals, eight birds, one amphibian and one fish. In general, our results confirmed that the leopard cat has a very eclectic diet and feeds mainly on rodents and particularly on the Muridae family. The DNA-based approach we propose here represents a valuable complement to current conventional methods. It can be applied to other carnivore species with only a slight adjustment relating to the design of the blocking oligonucleotide. It is robust and simple to implement and allows the possibility of very large-scale analyses.

  5. Choosing a Diet Analysis System for Classroom Use.

    ERIC Educational Resources Information Center

    Murphy, Suzanne P.; And Others

    1984-01-01

    Presents experiences with, and recommendations for, choosing a diet analysis system for use in a high school or college classroom. Software considerations, hardware considerations, and decisions based on relationship between these considerations are addressed. (JN)

  6. 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]. © 2014 John Wiley & Sons Ltd.

  7. 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.

  8. Communication: Electron ionization of DNA bases.

    PubMed

    Rahman, M A; Krishnakumar, E

    2016-04-28

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

  9. Chimpanzee diet: phytolithic analysis of feces.

    PubMed

    Phillips, Caroline; Lancelotti, Carla

    2014-08-01

    Most primate populations remain unobservable; therefore, researchers depend on the analyses of indirect evidence encountered at a study-site in order to understand their behavioral ecology. Diet can be determined through the analyses of scats or feeding remains encountered on-site. This allows aspects of their dietary repertoire to be established, which has implications both for conservation efforts (by locating food resources), and for understanding the evolution of hominin diet (if used as referential models). Macroscopic inspection of fecal samples is a common method applied to ascertain a primate population's diet. However, new approaches are required to identify food-items unrecognizable at this level. We applied a dry ash extraction method to fecal samples (N=50) collected from 10 adult chimpanzees in Kanyawara, Kibale National Park, Uganda and also to plant parts (N=66) from 34 species known to be included in the diet of this community of apes. We recovered phytoliths in 26 of the 34 plant species. Fifteen phytolith morphotypes were only detected in 14 plant species (termed "distinct" phytoliths). We used these distinct phytoliths to identify plant foods (i.e., that they were associated with) in fecal samples. We then validated findings by checking if the 10 chimpanzees had eaten parts of these plants ∼24 hr prior to fecal sample collection; six plant species associated with five distinct phytoliths had been eaten. Finally, we compared plant foods identified in fecal samples from phytolith analyses with plants that had been identified from macroscopic inspection of the same fecal samples. Findings from phytolith analyses corroborate with those from macroscopic inspection by expanding the total number of plant species identified per fecal sample (i.e., we identified certain plant parts that remained unrecognizable at macroscopic level). This study highlights the potential of phytolith analyses of feces to increase our knowledgebase of the dietary

  10. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. 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.

  12. 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.

  13. Vegetarian diets and blood pressure: a meta-analysis.

    PubMed

    Yokoyama, Yoko; Nishimura, Kunihiro; Barnard, Neal D; Takegami, Misa; Watanabe, Makoto; Sekikawa, Akira; Okamura, Tomonori; Miyamoto, Yoshihiro

    2014-04-01

    IMPORTANCE Previous studies have suggested an association between vegetarian diets and lower blood pressure (BP), but the relationship is not well established. OBJECTIVE To conduct a systematic review and meta-analysis of controlled clinical trials and observational studies that have examined the association between vegetarian diets and BP. DATA SOURCES MEDLINE and Web of Science were searched for articles published in English from 1946 to October 2013 and from 1900 to November 2013, respectively. STUDY SELECTION All studies met the inclusion criteria of the use of (1) participants older than 20 years, (2) vegetarian diets as an exposure or intervention, (3) mean difference in BP as an outcome, and (4) a controlled trial or observational study design. In addition, none met the exclusion criteria of (1) use of twin participants, (2) use of multiple interventions, (3) reporting only categorical BP data, or (4) reliance on case series or case reports. DATA EXTRACTION AND SYNTHESIS Data collected included study design, baseline characteristics of the study population, dietary data, and outcomes. The data were pooled using a random-effects model. MAIN OUTCOMES AND MEASURES Net differences in systolic and diastolic BP associated with the consumption of vegetarian diets were assessed. RESULTS Of the 258 studies identified, 7 clinical trials and 32 observational studies met the inclusion criteria. In the 7 controlled trials (a total of 311 participants; mean age, 44.5 years), consumption of vegetarian diets was associated with a reduction in mean systolic BP (-4.8 mm Hg; 95% CI, -6.6 to -3.1; P < .001; I2 = 0; P = .45 for heterogeneity) and diastolic BP (-2.2 mm Hg; 95% CI, -3.5 to -1.0; P < .001; I2 = 0; P = .43 for heterogeneity) compared with the consumption of omnivorous diets. In the 32 observational studies (a total of 21,604 participants; mean age, 46.6 years), consumption of vegetarian diets was associated with lower mean systolic BP (-6

  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. 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.

  16. Chiroplasmonic DNA-based nanostructures

    NASA Astrophysics Data System (ADS)

    Cecconello, Alessandro; Besteiro, Lucas V.; Govorov, Alexander O.; Willner, Itamar

    2017-09-01

    Chiroplasmonic properties of nanoparticles, organized using DNA-based nanostructures, have attracted both theoretical and experimental interest. Theory suggests that the circular dichroism spectra accompanying chiroplasmonic nanoparticle assemblies are controlled by the sizes, shapes, geometries and interparticle distances of the nanoparticles. In this Review, we present different methods to assemble chiroplasmonic nanoparticle or nanorod systems using DNA scaffolds, and we discuss the operations of dynamically reconfigurable chiroplasmonic nanostructures. The chiroplasmonic properties of the different systems are characterized by circular dichroism and further supported by high-resolution transmission electron microscopy or cryo-transmission electron microscopy imaging and theoretical modelling. We also outline the applications of chiroplasmonic assemblies, including their use as DNA-sensing platforms and as functional systems for information processing and storage. Finally, future perspectives in applying chiroplasmonic nanoparticles as waveguides for selective information transfer and their use as ensembles for chiroselective synthesis are discussed. Specifically, we highlight the upscaling of the systems to device-like configurations.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  18. 16S rDNA-based metagenomic analysis of bacterial diversity associated with two populations of the kleptoplastic sea slug Elysia chlorotica and its algal prey Vaucheria litorea.

    PubMed

    Devine, Susan P; Pelletreau, Karen N; Rumpho, Mary E

    2012-08-01

    The molluscan sea slug Elysia chlorotica is best known for its obligate endosymbiosis with chloroplasts (= kleptoplasty) from its algal prey Vaucheria litorea and its ability to sustain itself photoautotrophically for several months. This unusual photosynthetic sea slug also harbors an array of undescribed bacteria, which may contribute to the long-term success of the symbiosis. Here, we utilized 16S rDNA-based metagenomic analyses to characterize the microbial diversity associated with two populations of E. chlorotica from Halifax, Nova Scotia, Canada, and from Martha's Vineyard, Massachusetts, USA. Animals were examined immediately after collection from their native environments, after being starved of their algal prey for several months, and after being bred in the laboratory (second-generation sea slugs) to characterize the effect of varying environmental and culturing conditions on the associated bacteria. Additionally, the microbiome of the algal prey, laboratory-cultured V. litorea, was analyzed to determine whether the laboratory-bred sea slugs obtained bacteria from their algal food source during development. Bacterial profiles varied between populations and among all conditions except for the F2 laboratory-bred samples, which were similar in diversity and abundance, but not to the algal microbiome. Alpha-, beta-, and gamma-proteobacteria dominated all of the samples along with Actinobacteria, Bacilli, Flavobacteria, and Sphingobacteria. Bacteria capable of polysaccharide digestion and photosynthesis, as well as putative nitrogen fixation, vitamin B(12) production, and natural product biosynthesis were associated with the sea slug and algal samples.

  19. Graphene oxide-DNA based sensors.

    PubMed

    Gao, Li; Lian, Chaoqun; Zhou, Yang; Yan, Lirong; Li, Qin; Zhang, Chunxia; Chen, Liang; Chen, Keping

    2014-10-15

    Since graphene oxide (GO) is readily available and exhibits exceptional optical, electrical, mechanical and chemical properties, it has attracted increasing interests for use in GO-DNA based sensors. This paper reviews the advances in GO-DNA based sensors using DNA as recognition elements. In solution, GO is as an excellent acceptor of fluorescence resonance energy transfer (FRET) to quench the fluorescence in dye labeled DNA sequences. This review discusses the emerging GO-DNA based sensors related to FRET for use in the detection of DNA, proteins, metal ions, cysteine (Cys), and others. The application of the electrochemical GO-DNA based sensors is also summarized because GO possesses exceptional electrochemical properties. The detection mechanisms and the advantages of GO are also revealed and discussed. GO-DNA based sensors perform well at low cost, and high sensitivity, and provide low detection limits. Additionally, GO-DNA based sensors should appear in the near future as scientists explore their usefulness and properties. Finally, future perspectives and possible challenges in this area are outlined. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2014-01-01

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

  1. 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.

  2. [Analysis of the fatty acid profile of vegetarian and non-vegetarian diet in the context of some diet-related diseases prevention].

    PubMed

    Kornek, Agata; Kucharska, Alicja; Kamela, Katarzyna

    2016-01-01

    Research increasingly provide evidence that vegetarian diet can have a positive impact on health. The aim of this study was to analyze the fatty acid profile of vegetarian and non-vegetarian diet and prove which of them is more optimal in the context of some diet-related diseases prevention. The study involved 83 women (47 vegetarians and 36 non-vegetarians). Estimates of the supply of individual fatty acids in the diet was based on analysis of 3-day dietary records (calculations in a computer program DIETA 5). Found: - in vegan diet significantly lower percentage of energy from SFA than in lactoovovegetarian diet and non-vegetarian diet (5,2% vs 11,2% i 11,9%), - in vegan and lactoovovegetarian diet - significantly higher percentage of energy from PUFA than in non-vegetarian diet (9,2% i 7,8% vs 5,0%), - in vegan and lactoovovegetarian diet - significantly higher percentage of energy from LA than in non-vegetarian diet (6,7% i 5,5% vs 3,9%), - in vegan and lactoovovegetarian diet - significantly higher percentage of energy from ALA than in non-vegetarian diet (1,3% i 1,2% vs. 0,8%) - in vegan and lactoovovegetarian diet - significantly lower intake of EPA+DHA than in non-vegetarian diet (0 mg i 15 mg vs 76 mg), - only 25% of non-vegetarian diets fulfilled recommendations on the content of EPA + DHA Conclusions: Vegetarian, particularly vegan, nutrition may promote good balancing of the fatty acids in the diet, except for the long chain polyunsaturated omega-3, which are also deficient in the case of conventional diet.

  3. [Analysis of the fatty acid profile of vegetarian and non-vegetarian diet in the context of some diet-related diseases prevention].

    PubMed

    Kornek, Agata; Kucharska, Alicja; Kamela, Katarzyna

    Research increasingly provide evidence that vegetarian diet can have a positive impact on health. The aim of this study was to analyze the fatty acid profile of vegetarian and non-vegetarian diet and prove which of them is more optimal in the context of some diet-related diseases prevention. The study involved 83 women (47 vegetarians and 36 non-vegetarians). Estimates of the supply of individual fatty acids in the diet was based on analysis of 3-day dietary records (calculations in a computer program DIETA 5). Found: - in vegan diet significantly lower percentage of energy from SFA than in lactoovovegetarian diet and non-vegetarian diet (5,2% vs 11,2% i 11,9%), - in vegan and lactoovovegetarian diet - significantly higher percentage of energy from PUFA than in non-vegetarian diet (9,2% i 7,8% vs 5,0%), - in vegan and lactoovovegetarian diet - significantly higher percentage of energy from LA than in non-vegetarian diet (6,7% i 5,5% vs 3,9%), - in vegan and lactoovovegetarian diet - significantly higher percentage of energy from ALA than in non-vegetarian diet (1,3% i 1,2% vs. 0,8%) - in vegan and lactoovovegetarian diet - significantly lower intake of EPA+DHA than in non-vegetarian diet (0 mg i 15 mg vs 76 mg), - only 25% of non-vegetarian diets fulfilled recommendations on the content of EPA + DHA Conclusions: Vegetarian, particularly vegan, nutrition may promote good balancing of the fatty acids in the diet, except for the long chain polyunsaturated omega-3, which are also deficient in the case of conventional diet.

  4. 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.

  5. 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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Theoretical study on the relationship between Rp-phosphorothioation and base-step in S-DNA: based on energetic and structural analysis.

    PubMed

    Chen, Limeng; Wang, Xiao-Lei; Shi, Ting; Wu, Tingting; Deng, Zixin; Zhao, Yi-Lei

    2015-01-15

    Phosphorothioation (PT), previously used in synthetic antisense drugs to arrest the transcription or translation process, is also a novel physiological modification in bacteria DNAs. In the previous study, we reported that Rp-phosphorothioation (Rp-PT) destabilizes B-type helix significantly, using a quantum-mechanics-based energy scoring function developed with a dinucleotide model ( Zhang et al. J. Phys. Chem. B , 2012 , 116 , 10639 - 10648 ). A consequent question surfaces in the field of the phosphorothioated DNA (S-DNA) research: does the endogenous chemical modification interact with the base sequence in the bacterial genomes, e.g., in terms of the most common structure of the B-type helix? In this work, we carried out further energetic analysis on the backbone relative energies calculated with the scoring function according to 16 groups of base-step classifications. Moreover, we conducted molecular dynamics simulations of the B-helical structure with the different base-pair steps, to investigate the detailed structural changes upon the O-/S-substitution. As a result, the Rp-PT modification definitively enhances the stiffness of the backbone and differentiates backbone stability as an interaction with base-steps. Furthermore, certain exceptional sequences such as GT and CC were highlighted in the structural analysis of the sulfur local contacts and relative orientation of double strands, indicating that Rp-PT can cross-talk with particular base-steps. The special effects between the phosphorothioation and base-step may be related to the conservative consensus observed highly frequently in bacterial genomes.

  7. Liver Ischemic Preconditioning (IPC) Improves Intestinal Microbiota Following Liver Transplantation in Rats through 16s rDNA-Based Analysis of Microbial Structure Shift

    PubMed Central

    Lu, Haifeng; Chen, Xinhua; Jiang, Jianwen; Liu, Hui; He, Yong; Ding, Songming; Hu, Zhenhua; Wang, Weilin; Zheng, Shusen

    2013-01-01

    Background Ischemia-reperfusion (I/R) injury is associated with intestinal microbial dysbiosis. The “gut-liver axis” closely links gut function and liver function in health and disease. Ischemic preconditioning (IPC) has been proven to reduce I/R injury in the surgery. This study aims to explore the effect of IPC on intestinal microbiota and to analyze characteristics of microbial structure shift following liver transplantation (LT). Methods The LT animal models of liver and gut IPC were established. Hepatic graft function was assessed by histology and serum ALT/AST. Intestinal barrier function was evaluated by mucosal ultrastructure, serum endotoxin, bacterial translocation, fecal sIgA content and serum TNF-α. Intestinal bacterial populations were determined by quantitative PCR. Microbial composition was characterized by DGGE and specific bacterial species were determined by sequence analysis. Principal Findings Liver IPC improved hepatic graft function expressed as ameliorated graft structure and reduced ALT/AST levels. After administration of liver IPC, intestinal mucosal ultrastructure improved, serum endotoxin and bacterial translocation mildly decreased, fecal sIgA content increased, and serum TNF-α decreased. Moreover, liver IPC promoted microbial restorations mainly through restoring Bifidobacterium spp., Clostridium clusters XI and Clostridium cluster XIVab on bacterial genus level. DGGE profiles indicated that liver IPC increased microbial diversity and species richness, and cluster analysis demonstrated that microbial structures were similar and clustered together between the NC group and Liver-IPC group. Furthermore, the phylogenetic tree of band sequences showed key bacteria corresponding to 10 key band classes of microbial structure shift induced by liver IPC, most of which were assigned to Bacteroidetes phylum. Conclusion Liver IPC cannot only improve hepatic graft function and intestinal barrier function, but also promote restorations of

  8. 16S rDNA-based metagenomic analysis of dental plaque and lung bacteria in patients with severe acute exacerbations of chronic obstructive pulmonary disease.

    PubMed

    Tan, L; Wang, H; Li, C; Pan, Y

    2014-12-01

    Acute exacerbations of chronic obstructive pulmonary disease (AE-COPD) are leading causes of mortality in hospital intensive care units. We sought to determine whether dental plaque biofilms might harbor pathogenic bacteria that can eventually cause lung infections in patients with severe AE-COPD. Paired samples of subgingival plaque biofilm and tracheal aspirate were collected from 53 patients with severe AE-COPD. Total bacterial DNA was extracted from each sample individually for polymerase chain reaction amplification and/or generation of bacterial 16S rDNA sequences and cDNA libraries. We used a metagenomic approach, based on bacterial 16S rDNA sequences, to compare the distribution of species present in dental plaque and lung. Analysis of 1060 sequences (20 clones per patient) revealed a wide range of aerobic, anaerobic, pathogenic, opportunistic, novel and uncultivable bacterial species. Species indistinguishable between the paired subgingival plaque and tracheal aspirate samples (97-100% similarity in 16S rDNA sequence) were dental plaque pathogens (Aggregatibacter actinomycetemcomitans, Capnocytophaga sputigena, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola) and lung pathogens (Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Streptococcus pneumoniae). Real-time polymerase chain reaction of 16S rDNA indicated lower levels of Pseudomonas aeruginosa and Porphyromonas gingivalis colonizing the dental plaques compared with the paired tracheal aspirate samples. These results support the hypothesis that dental bacteria may contribute to the pathology of severe AE-COPD. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. 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

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

    2006-04-01

    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.

  10. 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

  11. Analysis of Endophytic Bacterial Communities of Potato by Plating and Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rDNA Based PCR Fragments.

    PubMed

    Garbeva, P.; Overbeek, L.S.; Vuurde, J.W.L.; Elsas, J.D.

    2001-02-01

    The diversity of endophytic bacterial populations of potato (Solanum tuberosum cv Desirée) was assessed using a combination of dilution plating of plant macerates followed by isolation and characterization of isolates, and direct PCR-DGGE on the basis of DNA extracted from plants. The culturable endophytic bacterial communities detected in potato stem bases as well as in roots were in most cases on the order 103 to 105 CFU g?1 of fresh plant tissue. Dilution plating revealed that a range of bacterial types dominated these populations. Dominant isolates fell into the a and g subgroups of the Proteobacteria, as well as in the Flavobacterium/Cytophaga group. Different representatives of the Firmicutes were also found. The most frequently isolated strains (>5% of the total) were characterized as different Pseudomonas spp. (including P. aureofaciens, P. corrugata, and P. putida), Agrobacterium radiobacter, Stenotrophomonas maltophilia, and Flavobacterium resinovorans, using fatty acid methyl ester (FAME) analysis and/or sequencing of their partial 16S ribosomal RNA genes. Other Proteobacteria or Firmicutes were also found, albeit infrequently, and mainly in potato stem tissue. The fate of three putative potato endophytes, Stenotrophomonas maltophilia, Bacillus sp., and Sphingomonas paucimobilis, was monitored following their release into potato plants via injection, via root dipping, or via the soil. Following stem injection, the S. maltophilia and Bacillus inoculants could be tracked over time periods of, respectively, 22 and 1 day(s) by dilution plating as well as via PCR-DGGE. However, only S. maltophilia was able to colonize, and persist in, plant tissue from soil or dipped roots. S. paucimobilis was never recovered from the plant irrespective of the mode of introduction. The diversity of the indigenous bacterial flora associated with potato was then monitored via PCR-DGGE. The patterns obtained revealed the existence of bacterial communities of limited complexity

  12. 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

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

    PubMed

    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

  14. 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.

  15. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  17. 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 ...

  18. 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 ...

  19. Comparison of vegetarian diets and omnivorous diets on plasma level of HDL-c: a meta-analysis.

    PubMed

    Zhang, Zili; Wang, Jian; Chen, Sifan; Wei, Zhaoyu; Li, Zhengtu; Zhao, Siwen; Lu, Wenju

    2014-01-01

    Low plasma level of high density lipoprotein cholesterol (HDL-c) was an independent risk factor for cardio vascular disorder, and associated with poor outcomes in pulmonary arterial hypertension. To compare the effects of vegetarian diets and omnivorous diets on HDL-c in plasma, we identified cross-sectional and cohort studies related to HDL-c listed on PubMed and ISI Web of Knowledge as well as the corresponding references (until Nov, 2013). Twelve studies with a total of 4177 individuals were selected for meta-analysis. This meta-analysis indicates that vegetarian diets did not alter plasma HDL-c concentrations, as it wasn't initially expected by the authors [Standardized Mean Difference (SMD) = 0.02 mmol/l; 95% confidence interval (CI): -0.19 to 0.22 mmol/l]. In Asia and Latin America countries, no significant differences in HDL-c levels between vegetarians and omnivores were found (SMD = -0.09 mmol/l; 95% CI: -0.43 to 0.25 mmol/l). In Europe and North America countries, the plasma level of HDL-c was also not different between the two diets (SMD = 0.09 mmol/l; 95% CI: -0.19 to 0.36 mmol/l). In light of this meta-analysis, we conclude that there is no evidence that plasma HDL-c levels differs in vegetarians and omnivores, even after adjusting for cultural circumstances.

  20. Comparison of Vegetarian Diets and Omnivorous Diets on Plasma Level of HDL-c: A Meta-Analysis

    PubMed Central

    Chen, Sifan; Wei, Zhaoyu; Li, Zhengtu; Zhao, Siwen; Lu, Wenju

    2014-01-01

    Low plasma level of high density lipoprotein cholesterol (HDL-c) was an independent risk factor for cardio vascular disorder, and associated with poor outcomes in pulmonary arterial hypertension. To compare the effects of vegetarian diets and omnivorous diets on HDL-c in plasma, we identified cross-sectional and cohort studies related to HDL-c listed on PubMed and ISI Web of Knowledge as well as the corresponding references (until Nov, 2013). Twelve studies with a total of 4177 individuals were selected for meta-analysis. This meta-analysis indicates that vegetarian diets did not alter plasma HDL-c concentrations, as it wasn’t initially expected by the authors [Standardized Mean Difference (SMD) = 0.02 mmol/l; 95% confidence interval (CI): −0.19 to 0.22 mmol/l]. In Asia and Latin America countries, no significant differences in HDL-c levels between vegetarians and omnivores were found (SMD = −0.09 mmol/l; 95% CI: −0.43 to 0.25 mmol/l). In Europe and North America countries, the plasma level of HDL-c was also not different between the two diets (SMD = 0.09 mmol/l; 95% CI: −0.19 to 0.36 mmol/l). In light of this meta-analysis, we conclude that there is no evidence that plasma HDL-c levels differs in vegetarians and omnivores, even after adjusting for cultural circumstances. PMID:24671216

  1. DNA-Based Applications in Nanobiotechnology

    PubMed Central

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

    2010-01-01

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

  2. 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.

  3. A mini me?: exploring early childhood diet with stable isotope ratio analysis using primary teeth dentin.

    PubMed

    Burt, Nicole M; Amin, Maryam

    2014-11-01

    Reconstruct childhood diet using teeth collected in Edmonton in a collaborative effort between the Departments of Dentistry and Anthropology at the University of Alberta. Deciduous teeth needing extraction were collected from 33 children for stable isotope ratio analysis of diet. Tooth dentin was microsampled in three locations using a newly developed technique to reconstruct the changing pattern of participants' diet through early childhood including breastfeeding practices. The microsampling method can reconstruct diet with tiny samples (0.3 mg). The results reconstruct fetal isotope ratios, which showed significant variation. δ(15)N values indicate some children were being breastfed (7/17), while others were likely bottle fed (10/17). Surprisingly, the early childhood results do not show the range of diets expected in adults based on known eating habits. Toddler diets form a tight cluster implying diets of similar isotopic composition in almost all of the households despite potential cultural and class distinctions (δ(15)N values 11-11.5‰, δ(13)C values around -18‰). The δ(13)C values show a strong C₃ dependence for most children, a two outliers show C₄ (-12‰) dependence indicating a possible corn based diet. Microsampling can potentially track each child's diet through early childhood. For this group of children, both breastfeeding and bottle feeding was practiced. However, the percent of breastfed infants was less than reported Canadian rates. Surprisingly, the choice to breastfeed or to bottle feed was not linked to the choice of toddler diet. All toddler diets were narrower in scope than adult diets. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. 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.

  5. 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

  6. Analysis of Diet Tonic Water Using Capillary Electrophoresis. An Undergraduate Instrumental Analysis Experiment

    NASA Astrophysics Data System (ADS)

    Herman, Harvey B.; Jezorek, John R.; Tang, Zhe

    2000-06-01

    An experiment for instrumental analysis is described in which components of diet tonic water are determined using capillary electrophoresis. Separation of quinine, saccharin, and benzoate in pH 7 phosphate buffer, with phenol as internal standard, is accomplished in about 12 minutes. The equipment requirements are modest: UV detection on an unmodified column. One of the components, quinine, is quantitated using a four-point standard addition calibration curve.

  7. Evaluation of methodologies for assessing the overall diet: dietary quality scores and dietary pattern analysis.

    PubMed

    Ocké, Marga C

    2013-05-01

    This paper aims to describe different approaches for studying the overall diet with advantages and limitations. Studies of the overall diet have emerged because the relationship between dietary intake and health is very complex with all kinds of interactions. These cannot be captured well by studying single dietary components. Three main approaches to study the overall diet can be distinguished. The first method is researcher-defined scores or indices of diet quality. These are usually based on guidelines for a healthy diet or on diets known to be healthy. The second approach, using principal component or cluster analysis, is driven by the underlying dietary data. In principal component analysis, scales are derived based on the underlying relationships between food groups, whereas in cluster analysis, subgroups of the population are created with people that cluster together based on their dietary intake. A third approach includes methods that are driven by a combination of biological pathways and the underlying dietary data. Reduced rank regression defines linear combinations of food intakes that maximally explain nutrient intakes or intermediate markers of disease. Decision tree analysis identifies subgroups of a population whose members share dietary characteristics that influence (intermediate markers of) disease. It is concluded that all approaches have advantages and limitations and essentially answer different questions. The third approach is still more in an exploration phase, but seems to have great potential with complementary value. More insight into the utility of conducting studies on the overall diet can be gained if more attention is given to methodological issues.

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

    PubMed

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

    2015-01-20

    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. 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). 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. 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, were energy .56, .01

  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. Comparison of diets for Largemouth and Smallmouth Bass in Eastern Lake Ontario using DNA barcoding and stable isotope analysis

    PubMed Central

    Holden, Jeremy; Eves, Robert; Tufts, Bruce

    2017-01-01

    Largemouth (LMB: Micropterus salmoides) and Smallmouth Bass (SMB: Micropterus dolomieu) are important species in the recreational fisheries of the Laurentian Great Lakes. The invasion of the Round Goby (Neogobius melanostomus) into these lakes has changed several facets of black bass biology, but there is still much to learn about the relationship between these species. Previous dietary analyses have shown Round Goby to be important prey for bass, but have been limited by low visual identification rates of dissected stomach items. Within the present study, DNA barcoding and stable isotope analysis improve prey identification and provide a more quantitative dietary analysis of adult black bass in Lake Ontario, comparing the importance of Round Goby as prey between these two species. Eighty-four LMB (406mm fork length ±4mm SEM) and two hundred sixty-four SMB (422mm ±2mm) obtained as tournament mortalities had prey identified using DNA-based methods. Round Goby was the most prevalent prey species for both predators. The diet of LMB was three times more diverse than that of SMB, which almost entirely consists of Round Goby. Our results provide further support that recent increases in the size of Lake Ontario bass are a result of Round Goby consumption, and that the effects of this dietary shift on body condition are greater for SMB. Techniques developed in this study include reverse-oriented dual priming oligonucleotides used as blocking primers for predator DNA, and an automated design approach of restriction fragment length polymorphism tests for identifying prey DNA barcodes. PMID:28771612

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Diet reconstruction in antebellum Baltimore: Insights from dental microwear analysis.

    PubMed

    Ma, Peter H; Teaford, Mark F

    2010-04-01

    Construction in the City of Baltimore during 1996 led to the recovery of human skeletal remains dating from 1792 to 1856. Historical research indicates that the skeletal remains come from two adjacent graveyards: Christ's Church Episcopalian Cemetery and the Potters Field East. The different socioeconomic status of the internees in each cemetery suggests the possibility of marked contrasts in lifestyle, health, and diet. To shed further light on these possibilities, analyses of microscopic wear patterns on teeth, or dental microwear analyses, were undertaken. A sample from Spanish Florida was used to help interpret the results. Epoxy casts of incisor and molar teeth were placed in an SEM and photomicrographs of clean wear facets were taken. The photomicrographs were digitized using the software package Microware 4.02. Statistical analyses of rank transformed data consisted of single-factor ANOVA, followed by post hoc tests. No significant differences were found between Christ's Church and Potters Field East samples for any of the variables examined in either molar or incisor teeth. However, differences between each Baltimore sample and the La Florida samples give suggestions of possible diet differences in antebellum Baltimore. The mosaic of differences between the Baltimore and La Florida samples probably reflects the wide variety of foods available to antebellum Baltimoreans as well as the relative lack of abrasives in their diet. (c) 2009 Wiley-Liss, Inc.

  17. Inferring pterosaur diets through quantitative 3D textural analysis of tooth microwear in extant analogues

    NASA Astrophysics Data System (ADS)

    Bestwick, Jordan; Unwin, David; Butler, Richard; Henderson, Don; Purnell, Mark

    2017-04-01

    Pterosaurs (Pterosauria) were a successful group of Mesozoic flying reptiles. For 150 million years they were integral components of terrestrial and coastal ecosystems, yet their feeding ecology remains poorly constrained. Postulated pterosaur diets include insectivory, piscivory and/or carnivory, but many dietary hypotheses are speculative and/or based on little evidence, highlighting the need for alternative approaches to provide robust data. One method involves quantitative analysis of the micron-scale 3D textures of worn pterosaur tooth surfaces - dental microwear texture analysis. Microwear is produced as scratches and chips generated by food items create characteristic tooth surface textures. Microwear analysis has never been applied to pterosaurs, but we might expect microwear textures to differ between pterosaurs with different diets. An important step in investigating pterosaur microwear is to examine microwear from extant organisms with known diets to provide a comparative data set. This has been achieved through analysis of non-occlusal microwear textures in extant bats, crocodilians and monitor lizards, clades within which species exhibit insectivorous, piscivorous and carnivorous diets. The results - the first test of the hypothesis that non-occlusal microwear textures in these extant clades vary with diet - provide the context for the first robust quantitative tests of pterosaur diets.

  18. [Situation and adequacy analysis of dysphagia diets at a regional hospital].

    PubMed

    Moreno, C; García, M J; Martinez, C

    2006-01-01

    The study aims at confirming the adequacy of diets prescribed for dysphagia during hospitalization through a specific questionnaire to identify, give advice, and manage dysphagia. To compare and analyze the diet for dysphagia offered at our Hospital with the recommendations for a dysphagia diet published in recent nutritional literature. From the results obtained, to establish diet improvements (if necessary) and nursing working tools aimed at early detection of swallowing problems and decreasing the risk for Hyponutrition, dehydration and aspiration. A cross-sectional study among patients from our hospital with a prescription for a dysphagia diet is performed, assessing the diet usefulness, the characteristics of the 30 patients admitted at the Hospital Complex of Segovia, in several nursing units and with an established diet for dysphagia for two months and with different pathologies. Ages were comprised between 68-85 years. The questionnaire was analyzed and we verified that all patients had a swallowing impairment. The nutritional analysis showed an inadequate adaptation of hospital diet to dysphagia patients with regards to consistency of some dishes and the poor energy intake was significant (x 1339 kcal), poor protein intake (58 g), and a deficiency in some minerals (iron and calcium), and vitamins (vitamin C). Dysphagia is a problem that affects a considerable number of patients in our Hospital (10-15%). The diet provided by the Hospital was inadequate before the study. A more adequate diet has been designed with regards to nutritional value and consistency, its indication is broaden, as well as interventional measures and previous patient assessment. The Nutrition Unit has implemented improvements in nutritional content.

  19. 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

  20. 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.

  1. 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.

  2. Mediterranean Diet, Retinopathy, Nephropathy, and Microvascular Diabetes Complications: A Post Hoc Analysis of a Randomized Trial.

    PubMed

    Díaz-López, Andrés; Babio, Nancy; Martínez-González, Miguel A; Corella, Dolores; Amor, Antonio J; Fitó, Montse; Estruch, Ramon; Arós, Fernando; Gómez-Gracia, Enrique; Fiol, Miquel; Lapetra, José; Serra-Majem, Lluís; Basora, Josep; Basterra-Gortari, F Javier; Zanon-Moreno, Vicente; Muñoz, Miguel Ángel; Salas-Salvadó, Jordi

    2015-11-01

    To date no clinical trials have evaluated the role of dietary patterns on the incidence of microvascular diabetes complications. We hypothesized that a nutritional intervention based on the Mediterranean diet (MedDiet) would have greater protective effect on diabetic retinopathy and nephropathy than a low-fat control diet. This was a post hoc analysis of a cohort of patients with type 2 diabetes participating in the PREvención con DIeta MEDiterránea (PREDIMED) study, a multicenter randomized nutritional intervention trial conducted in a population at high cardiovascular risk. Individuals with type 2 diabetes who were free of microvascular complications at enrollment (n = 3,614, aged 55-80 years) were randomly assigned to one of three dietary interventions: MedDiet supplemented with extravirgin olive oil (MedDiet+EVOO), MedDiet supplemented with mixed nuts (MedDiet+Nuts), or a low-fat control diet. Two independent outcomes were considered: new onset of diabetic retinopathy and nephropathy. Hazard ratios (HRs) were calculated using multivariable-adjusted Cox regression. During a median follow-up of 6.0 years, we identified 74 new cases of retinopathy and 168 of nephropathy. Compared with the control diet, multivariable-adjusted HRs for diabetic retinopathy were 0.56 (95% CI 0.32-0.97) for the MedDiet+EVOO and 0.63 (0.35-1.11) for the MedDiet+Nuts. No between-group differences were found for nephropathy. When the yearly updated information on adherence to the MedDiet was considered, the HR for retinopathy in the highest versus the lowest quintile was 0.34 (0.13-0.89; P = 0.001 for trend). No significant associations were found for nephropathy. A MedDiet enriched with EVOO may protect against diabetic retinopathy but not diabetic nephropathy. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  3. 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.

  4. 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.

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

    USGS Publications Warehouse

    Deloria-Sheffield, Christie M.; Millenbah, Kelly F.; Bocetti, Carol 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%).

  6. Adherence to a Mediterranean-style diet and incident fractures: pooled analysis of observational evidence.

    PubMed

    Kunutsor, Setor K; Laukkanen, Jari A; Whitehouse, Michael R; Blom, Ashley W

    2017-03-22

    The Mediterranean diet is associated with decreased morbidity and mortality from various chronic diseases. Adherence to a Mediterranean-style diet has been suggested to have protective effects on bone health and decreases the incidence of bone fractures, but the evidence is not clear. We conducted a systematic review and meta-analysis of available observational studies to quantify the association between adherence to a Mediterranean-style diet, as assessed by the Mediterranean Diet Score (MDS), and the risk of fractures in the general population. Relevant studies were identified in a literature search of MEDLINE, EMBASE, Web of Science, and reference lists of relevant studies to October 2016. Relative risks (RRS) with 95% confidence intervals (CIs) were aggregated using random-effects models. Five observational studies with data on 353,076 non-overlapping participants and 33,576 total fractures (including 6,881 hip fractures) were included. The pooled fully adjusted RR (95% CI) for hip fractures per 2-point increment in adherence to the MDS was 0.82 (0.71-0.96). Adherence to the MDS was not associated with the risk of any or total fractures based on pooled analysis of only two studies. Limited observational evidence supports a beneficial effect of adherence to a Mediterranean-style diet on the incidence of hip fractures. Well-designed intervention studies are needed to elucidate the relationship between adherence to a Mediterranean-style diet and the risk of adverse bone health outcomes such as fractures.

  7. Effects of Low-Carbohydrate Diets Versus Low-Fat Diets on Metabolic Risk Factors: A Meta-Analysis of Randomized Controlled Clinical Trials

    PubMed Central

    Hu, Tian; Mills, Katherine T.; Yao, Lu; Demanelis, Kathryn; Eloustaz, Mohamed; Yancy, William S.; Kelly, Tanika N.; He, Jiang; Bazzano, Lydia A.

    2012-01-01

    The effects of low-carbohydrate diets (≤45% of energy from carbohydrates) versus low-fat diets (≤30% of energy from fat) on metabolic risk factors were compared in a meta-analysis of randomized controlled trials. Twenty-three trials from multiple countries with a total of 2,788 participants met the predetermined eligibility criteria (from January 1, 1966 to June 20, 2011) and were included in the analyses. Data abstraction was conducted in duplicate by independent investigators. Both low-carbohydrate and low-fat diets lowered weight and improved metabolic risk factors. Compared with participants on low-fat diets, persons on low-carbohydrate diets experienced a slightly but statistically significantly lower reduction in total cholesterol (2.7 mg/dL; 95% confidence interval: 0.8, 4.6), and low density lipoprotein cholesterol (3.7 mg/dL; 95% confidence interval: 1.0, 6.4), but a greater increase in high density lipoprotein cholesterol (3.3 mg/dL; 95% confidence interval: 1.9, 4.7) and a greater decrease in triglycerides (−14.0 mg/dL; 95% confidence interval: −19.4, −8.7). Reductions in body weight, waist circumference and other metabolic risk factors were not significantly different between the 2 diets. These findings suggest that low-carbohydrate diets are at least as effective as low-fat diets at reducing weight and improving metabolic risk factors. Low-carbohydrate diets could be recommended to obese persons with abnormal metabolic risk factors for the purpose of weight loss. Studies demonstrating long-term effects of low-carbohydrate diets on cardiovascular events were warranted. PMID:23035144

  8. 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...

  9. 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...

  10. [Analysis of antioxidant status and actual diet of students].

    PubMed

    Kolesnikova, L I; Darenskaya, M A; Grebenkina, L A; Osipova, E V; Dolgikh, M I; Semenova, N V

    2015-01-01

    The study of the features of the antioxidant status and dietary intake of students is highly relevant, since this population cohort is the future labor potential of society. 40 female students (mean age--22.4 +/- 0.6 years) living in hostel dormitories (n=20) and rented apartments (n=20) were surveyed. To assess the nutrition the method of questioning within 5 days, including weekends has been used. Personal energy consumption per diem has been calculated by table-keeping method. It was found that, retinol blood serum content (measured spectrofluorimetrically) in students living in dormitories was 1.45 fold lower than that in students living in rented apartments (1.28 +/- 0.66 vs. 1.86 +/- 0.17 mmol/l, p<0.001). When analyzing the changes of the integral parameter of antioxidant defense system (the total antioxidant activity assessed using as a model system a suspension of egg yolks lipoprotein) a decrease of this parameter with respect to standards for the majority of the surveyed women (65% of students living in dorms and 80% of students living in rented apartments) has been noted. The energy value of the daily ration for girls in both groups (1375 +/- 626 kcal--in a dormitory and 1731 +/- 547 kcal--in a rented apartment) was lower than energy expenditure (1789 +/- 202 and 1808 +/- 234 kcal/day, respectively), with higher energy value in students living in rented apartments (p<0.001). Carbohydrates prevailed in the diet of students living in dormitories (417 +/- 207 g/day vs. 289 +/- 131 g/day in female students living in rented apartments, p<0.0001) while in the diet of the students living in rented apartments fats (110.5 +/- 55.7 g/day, compared with that of the students living in the hostel--66.1 +/- 50.8 g/day, p<0.0001) and proteins (99.1 +/- 47.9 vs. 81.6 +/- 42.7 g/day, p<0.001) prevailed. Thus, the high-risk group with regard to adaptive capacity and unbalanced diet are students living in dormitories, with a crucial role played by low material support.

  11. Efficacy of and patient compliance with a ketogenic diet in adults with intractable epilepsy: a meta-analysis.

    PubMed

    Ye, Fang; Li, Xiao-Jia; Jiang, Wan-Lin; Sun, Hong-Bin; Liu, Jie

    2015-01-01

    Despite the successful use of a ketogenic diet in pediatric epilepsy, its application in adults has been limited. The aim of this meta-analysis was to summarize the findings of relevant published studies in order to identify the efficacy of and compliance with a ketogenic diet and its main subtypes (i.e., classic ketogenic diet and modified Atkins diet) in adults with intractable epilepsy, and to provide useful information for clinical practice. Electronic searches of PubMed, EMBASE, Google Scholar, and the ISI Web of Science were conducted to identify studies of the efficacy of and patient compliance with a ketogenic diet in adults with intractable epilepsy; the included studies were reviewed. Meta-analyses were performed using STATA to determine combined efficacy rates and combined rates of compliance with the ketogenic diet and its main subtypes. In total, 12 studies qualified for inclusion, and data from 270 patients were evaluated.The results of the meta-analysis revealed combined efficacy rates of all types of ketogenic diet, a classical ketogenic diet, and a modified Atkins diet were 42%, 52%, and 34%, respectively; the corresponding combined compliance rates were 45%, 38%, and 56%. The results indicate that a ketogenic diet is a promising complementary therapy in adult intractable epilepsy, and that while a classical ketogenic diet may be more effective, adult patients are likely to be less compliant with it than with a modified Atkins diet.

  12. Efficacy of and Patient Compliance with a Ketogenic Diet in Adults with Intractable Epilepsy: A Meta-Analysis

    PubMed Central

    Ye, Fang; Li, Xiao-Jia; Jiang, Wan-Lin

    2015-01-01

    Background and Purpose Despite the successful use of a ketogenic diet in pediatric epilepsy, its application in adults has been limited. The aim of this meta-analysis was to summarize the findings of relevant published studies in order to identify the efficacy of and compliance with a ketogenic diet and its main subtypes (i.e., classic ketogenic diet and modified Atkins diet) in adults with intractable epilepsy, and to provide useful information for clinical practice. Methods Electronic searches of PubMed, EMBASE, Google Scholar, and the ISI Web of Science were conducted to identify studies of the efficacy of and patient compliance with a ketogenic diet in adults with intractable epilepsy; the included studies were reviewed. Meta-analyses were performed using STATA to determine combined efficacy rates and combined rates of compliance with the ketogenic diet and its main subtypes. Results In total, 12 studies qualified for inclusion, and data from 270 patients were evaluated.The results of the meta-analysis revealed combined efficacy rates of all types of ketogenic diet, a classical ketogenic diet, and a modified Atkins diet were 42%, 52%, and 34%, respectively; the corresponding combined compliance rates were 45%, 38%, and 56%. Conclusions The results indicate that a ketogenic diet is a promising complementary therapy in adult intractable epilepsy, and that while a classical ketogenic diet may be more effective, adult patients are likely to be less compliant with it than with a modified Atkins diet. PMID:25628734

  13. 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.

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

    PubMed

    El Zaatari, Sireen; Hublin, Jean-Jacques

    2014-04-01

    This article presents the results of the occlusal molar microwear texture analysis of 32 adult Upper Paleolithic modern humans from a total of 21 European sites dating to marine isotope stages 3 and 2. The occlusal molar microwear textures of these specimens were analyzed with the aim of examining the effects of the climatic, as well as the cultural, changes on the diets of the Upper Paleolithic modern humans. The results of this analysis do not reveal any environmentally driven dietary shifts for the Upper Paleolithic hominins indicating that the climatic and their associated paleoecological changes did not force these humans to significantly alter their diets in order to survive. However, the microwear texture analysis does detect culturally related changes in the Upper Paleolithic humans' diets. Specifically, significant differences in diet were found between the earlier Upper Paleolithic individuals, i.e., those belonging to the Aurignacian and Gravettian contexts, and the later Magdalenian ones, such that the diet of the latter group was more varied and included more abrasive foods compared with those of the former. Copyright © 2014 Wiley Periodicals, Inc.

  15. 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.

  16. 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

  17. 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.

  18. Diet after gastric banding

    MedlinePlus

    Gastric banding surgery - your diet; Obesity - diet after banding; Weight loss - diet after banding ... al. Bariatric surgery versus non-surgical treatment for obesity: a systematic review and meta-analysis of randomised ...

  19. 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

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

    PubMed

    Darmon, Nicole; Drewnowski, Adam

    2015-10-01

    It is well established in the literature that healthier diets cost more than unhealthy diets. The aim of this review was to examine the contribution of food prices and diet cost to socioeconomic inequalities in diet quality. A systematic literature search of the PubMed, Google Scholar, and Web of Science databases was performed. Publications linking food prices, dietary quality, and socioeconomic status were selected. Where possible, review conclusions were illustrated using a French national database of commonly consumed foods and their mean retail prices. 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. 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. © The Author(s) 2015. Published by Oxford University Press on behalf of the International Life Sciences Institute.

  1. Vegetarian Diets and Weight Reduction: a Meta-Analysis of Randomized Controlled Trials.

    PubMed

    Huang, Ru-Yi; Huang, Chuan-Chin; Hu, Frank B; Chavarro, Jorge E

    2016-01-01

    Vegetarian diets may promote weight loss, but evidence remains inconclusive. PubMed, EMBASE and UpToDate databases were searched through September 22, 2014, and investigators extracted data regarding study characteristics and assessed study quality among selected randomized clinical trials. Population size, demographic (i.e., gender and age) and anthropometric (i.e., body mass index) characteristics, types of interventions, follow-up periods, and trial quality (Jadad score) were recorded. The net changes in body weight of subjects were analyzed and pooled after assessing heterogeneity with a random effects model. Subgroup analysis was performed based on type of vegetarian diet, type of energy restriction, study population, and follow-up period. Twelve randomized controlled trials were included, involving a total of 1151 subjects who received the intervention over a median duration of 18 weeks. Overall, individuals assigned to the vegetarian diet groups lost significantly more weight than those assigned to the non-vegetarian diet groups (weighted mean difference, -2.02 kg; 95 % confidence interval [CI]: -2.80 to -1.23). Subgroup analysis detected significant weight reduction in subjects consuming a vegan diet (-2.52 kg; 95 % CI: -3.02 to -1.98) and, to a lesser extent, in those given lacto-ovo-vegetarian diets (-1.48 kg; 95 % CI: -3.43 to 0.47). Studies on subjects consuming vegetarian diets with energy restriction (ER) revealed a significantly greater weight reduction (-2.21 kg; 95 % CI: -3.31 to -1.12) than those without ER (-1.66 kg; 95 % CI: -2.85 to -0.48). The weight loss for subjects with follow-up of <1 year was greater (-2.05 kg; 95 % CI: -2.85 to -1.25) than those with follow-up of ≥1 year (-1.13 kg; 95 % CI: -2.04 to -0.21). Vegetarian diets appeared to have significant benefits on weight reduction compared to non-vegetarian diets. Further long-term trials are needed to investigate the effects of vegetarian diets on body weight control.

  2. 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.

  3. DNA based computing for understanding complex shapes.

    PubMed

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

    2014-03-01

    This study deals with a computing method called DNA based computing (DBC) that takes inspiration from the Central Dogma of Molecular Biology. The proposed DBC uses a set of user-defined rules to create a DNA-like sequence from a given piece of problem-relevant information (e.g., image data) in a dry-media (i.e., in an ordinary computer). It then uses another set of user-defined rules to create an mRNA-like sequence from the DNA. Finally, it uses the genetic code to translate the mRNA (or directly the DNA) to a protein-like sequence (a sequence of amino acids). The informational characteristics of the protein (entropy, absence, presence, abundance of some selected amino acids, and relationships among their likelihoods) can be used to solve problems (e.g., to understand complex shapes from their image data). Two case studies ((1) fractal geometry generated shape of a fern-leaf and (2) machining experiment generated shape of the worn-zones of a cutting tool) are presented elucidating the shape understanding ability of the proposed DBC in the presence of a great deal of variability in the image data of the respective shapes. The implication of the proposed DBC from the context of Internet-aided manufacturing system is also described. Further study can be carried out in solving other complex computational problems by using the proposed DBC and its derivatives. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  4. Programmable DNA-Based Finite Automata

    NASA Astrophysics Data System (ADS)

    Ratner, Tamar; Keinan, Ehud

    Computation using DNA has many advantages, including the potential for massive parallelism that allows for large number of operations per second, the direct interface between the computation process and a biological output, and the miniaturization of the computing devices to a molecular scale. In 2001, we reported on the first DNA-based, programmable finite automaton (2-symbol-2-state) capable of computing autonomously with all its hardware, software, input, and output being soluble biomolecules mixed in solution. Later, using similar principles, we developed advanced 3-symbol-3-state automata. We have also shown that real-time detection of the output signal, as well as real-time monitoring of all the computation intermediates, can be achieved by the use of surface plasmon resonance (SPR) technology. More recently, we have shown that it is possible to achieve a biologically relevant output, such as specific gene expression, by using a reporter-gene as an output-readout. We cloned the input into circular plasmids, and thereby achieved control over gene expression by a programmable sequence of computation events. Further efforts are currently directed to immobilization of the input molecules onto a solid chip to enable parallel computation, where the location of the input on the chip represents specific tagging.

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

    PubMed

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

    2014-10-01

    Previous studies have suggested an association between vegetarian diets and improvements in glycemic control in diabetes, although this relationship is not well established. No meta-analysis of these studies has been performed. To conduct a systematic review and meta-analysis of controlled clinical trials examining the association between vegetarian diets and glycemic control in type 2 diabetes. The electronic databases Medline, Web of Science, Excerpta Medica Database (EMBASE), and Cochrane Central Register of Controlled Trials were searched for articles published in any language through December 9, 2013. The following criteria were used for study inclusion: (I) age of participants >20 years; (II) vegetarian diet as intervention; (III) mean difference in hemoglobin A1c (HbA1c) and/or fasting blood glucose levels used as outcomes; and (IV) controlled trials, duration ≥4 weeks. Exclusion criteria were: (I) not an original investigation; (II) duplicate samples; (III) diabetes other than type 2; (IV) multiple interventions; and (V) uncontrolled studies. The data collected included study design, baseline population characteristics, dietary data, and outcomes. Data were pooled using a random-effects model. Differences in HbA1c and fasting blood glucose levels associated with vegetarian diets were assessed. Of 477 studies identified, six met the inclusion criteria (n=255, mean age 42.5 years). Consumption of vegetarian diets was associated with a significant reduction in HbA1c [-0.39 percentage point; 95% confidence interval (CI), -0.62 to -0.15; P=0.001; I(2)=3.0; P for heterogeneity =0.389], and a non-significant reduction in fasting blood glucose concentration (-0.36 mmol/L; 95% CI, -1.04 to 0.32; P=0.301; I(2)=0; P for heterogeneity =0.710), compared with consumption of comparator diets. Consumption of vegetarian diets is associated with improved glycemic control in type 2 diabetes. PROSPERO registration number is CRD42013004370.

  6. 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

  7. 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.

  8. 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.

  9. 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.

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

    PubMed

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

    2016-10-01

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

  11. Special diets in modern America: Analysis of the 2012 National Health Interview Survey data.

    PubMed

    Leung, Brenda; Lauche, Romy; Leach, Matthew; Zhang, Yan; Cramer, Holger; Sibbritt, David

    2017-01-01

    Special diets are frequently used by the public but reasons for use and characteristics of users remain unclear. To determine prevalence of the use of special diets, the individual characteristics associated with their use and reasons for use. The secondary analysis used data from the 2012 National Health Interview Survey (NHIS), a cross-sectional household interview survey of a nationally representative sample of non-hospitalized US adult populations ( n = 34,525). The dependent variables in this secondary analysis were the use of a special diet (vegetarian, macrobiotic, Atkins, Pritikin, and Ornish) ever and during the past 12 months. Independent variables included sociodemographic, clinical and behavioral variables. Prevalence of special diet use and reasons for use were analyzed descriptively. Associations between independent and dependent variables were analyzed using Chi-square tests and logistic regression. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. Lifetime and 12-month prevalence of using special diets were 7.5% (weighted n = 17.7 million) and 2.9% (weighted n = 6.9 million), respectively. Individuals using special diets in the past 12 months were more likely female (OR = 1.45; 95% CI = 1.21-1.74), not married (OR = 0.76; 95% CI = 0.63-0.91), college-educated (OR = 1.98; 95% CI = 1.25-3.11) and depressed (OR = 1.50; 95% CI = 1.14-1.98). They more likely also used herbal products (OR = 2.35; 95%CI = 1.84-2.99), non-vitamin (OR = 1.82; 95% CI = 1.45-2.27) and vitamin supplements (OR = 1.57; 95% CI = 1.24-1.99). Diets were mainly used to improve overall health (76.7%) or for general wellness/prevention (70.4%). Special diets are mainly used for unspecific health reasons by those who are females, have a college degree or with depression, and commonly used in conjunction with herbs and dietary supplements.

  12. DNA-Based Methods in the Immunohematology Reference Laboratory

    PubMed Central

    Denomme, Gregory A

    2010-01-01

    Although hemagglutination serves the immunohematology reference laboratory well, when used alone, it has limited capability to resolve complex problems. This overview discusses how molecular approaches can be used in the immunohematology reference laboratory. In order to apply molecular approaches to immunohematology, knowledge of genes, DNA-based methods, and the molecular bases of blood groups are required. When applied correctly, DNA-based methods can predict blood groups to resolve ABO/Rh discrepancies, identify variant alleles, and screen donors for antigen-negative units. DNA-based testing in immunohematology is a valuable tool used to resolve blood group incompatibilities and to support patients in their transfusion needs. PMID:21257350

  13. Meta-analysis of studies of a specific delivery mode for a modified-carbohydrate diet.

    PubMed

    Shikany, J M; Desmond, R; McCubrey, R; Allison, D B

    2011-12-01

    Obesity is highly prevalent throughout the world. Although modified-carbohydrate diets (MCDs) comprise one popular approach, questions remain about their utility for weight loss. The objective of the present study was to conduct a meta-analysis of randomised controlled trials (RCTs) of a specific MCD compared with various control diets on weight loss. Data from four RCTs (three obtained from the sponsor and one indentified through literature searches) were included. Intent-to-treat analyses were conducted using multiple imputation to handle missing data, where possible. Because inter-study heterogeneity was demonstrated with fixed-effects meta-analysis, a random-effects meta-analysis also was conducted. When considered separately, all four studies showed greater reduction in body weight with the MCD compared to control diets at 12-week follow-up; the results at 24 weeks (available for three of the studies) were not as consistent. Results for body mass index (BMI) were similar. Greater reductions in waist circumference with the MCD were seen at either time point in only one study. When fixed-effects meta-analysis was applied, significantly greater reductions in weight, BMI and waist circumference with the MCD at both 12 weeks (1.66 kg, 0.53 kg m(-2) and 1.02 cm, respectively) and 24 weeks (1.20 kg, 0.43 kg m(-2) and 0.69 cm, respectively) were evident. Random-effects meta-analysis revealed similar results; however, the 24-week difference for a reduction in waist circumference was no longer statistically significant. Meta-analysis of individual RCT results demonstrated consistent benefits of this MCD compared to control diets on weight loss up to 24 weeks and waist circumference up to 12 weeks. © 2011 The Authors. Journal of Human Nutrition and Dietetics © 2011 The British Dietetic Association Ltd.

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

    PubMed Central

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

    2014-01-01

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

  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. Therapeutic Success of the Ketogenic Diet as a Treatment Option for Epilepsy: a Meta-analysis

    PubMed Central

    Li, Hai-feng; Zou, Yan; Ding, Gangqiang

    2013-01-01

    Objective To systematically evaluate therapeutic success of the ketogenic diet (KD) as a treatment option for epilepsy. Methods Using MEDLINE and Google Scholar search, we searched for studies investigating the therapeutic success of ketogenic diet for epilepsy. We estimated therapeutic success rate for ketogenic diet as a treatment option for epilepsy and its 95% CIs using generic inverse variance method. Findings A total of 38 studies met the inclusion criteria. In retrospective studies, the weighted success rate of the patients who take the KD as a treatment option for epilepsy was 58.4% (95% confidence interval (95%CI)=48.7% – 69.9%) at 3 months (n=336); 42.8% (95%CI =36.3% – 50.3%) at 6 months (n=492), and 30.1% (95%CI =24.3% – 37.2%) at 12 months (n=387); in prospective studies, weighted success rate was 53.9% (95%CI 45.5% – 63.8%) at 3 months (n=474); 53.2% (95%CI =44.0% – 64.2%) at 6 months (n=321), and 55.0% (95%CI =45.9% – 65.9%) at 12 months (n=347). Conclusion This meta-analysis provides formal statistical support for the efficacy of the ketogenic diet in the treatment of epileptic patients. PMID:24910737

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. Dental microwear texture analysis shows within-species diet variability in fossil hominins.

    PubMed

    Scott, Robert S; Ungar, Peter S; Bergstrom, Torbjorn S; Brown, Christopher A; Grine, Frederick E; Teaford, Mark F; Walker, Alan

    2005-08-04

    Reconstructing the diets of extinct hominins is essential to understanding the paleobiology and evolutionary history of our lineage. Dental microwear, the study of microscopic tooth-wear resulting from use, provides direct evidence of what an individual ate in the past. Unfortunately, established methods of studying microwear are plagued with low repeatability and high observer error. Here we apply an objective, repeatable approach for studying three-dimensional microwear surface texture to extinct South African hominins. Scanning confocal microscopy together with scale-sensitive fractal analysis are used to characterize the complexity and anisotropy of microwear. Results for living primates show that this approach can distinguish among diets characterized by different fracture properties. When applied to hominins, microwear texture analysis indicates that Australopithecus africanus microwear is more anisotropic, but also more variable in anisotropy than Paranthropus robustus. This latter species has more complex microwear textures, but is also more variable in complexity than A. africanus. This suggests that A. africanus ate more tough foods and P. robustus consumed more hard and brittle items, but that both had variable and overlapping diets.

  5. Proteomic analysis of mice fed methionine and choline deficient diet reveals marker proteins associated with steatohepatitis.

    PubMed

    Lee, Su Jin; Kang, Jeong Han; Iqbal, Waqas; Kwon, Oh-Shin

    2015-01-01

    The mechanisms underlying the progression of simple steatosis to steatohepatitis are yet to be elucidated. To identify the proteins involved in the development of liver tissue inflammation, we performed comparative proteomic analysis of non-alcoholic steatohepatitis (NASH). Mice fed a methionine and choline deficient diet (MCD) developed hepatic steatosis characterized by increased free fatty acid (FFA) and triglyceride levels as well as alpha-SMA. Two-dimensional proteomic analysis revealed that the change from the normal diet to the MCD diet affected the expressions of 50 proteins. The most-pronounced changes were observed in the expression of proteins involved in Met metabolism and oxidative stress, most of which were significantly downregulated in NASH model animals. Peroxiredoxin (Prx) is the most interesting among the modulated proteins identified in this study. In particular, cross-regulated Prx1 and Prx6 are likely to participate in cellular defense against the development of hepatitis. Thus, these Prx isoforms may be a useful new marker for early stage steatohepatitis. Moreover, curcumin treatment results in alleviation of the severity of hepatic inflammation in steatohepatitis. Notably, curcumin administration in MCD-fed mice dramatically reduced CYP2E1 as well as Prx1 expression, while upregulating Prx6 expression. These findings suggest that curcumin may have a protective role against MCD fed-induced oxidative stress.

  6. Qualitative analysis of factors affecting adherence to the phenylketonuria diet in adolescents.

    PubMed

    Sharman, Rachael; Mulgrew, Kate; Katsikitis, Mary

    2013-01-01

    Phenylketonuria (PKU) is an inborn error of metabolism that is primarily treated with a severely restricted, low-protein diet to prevent permanent neurological damage. Despite the recognition of the importance of strict dietary adherence in the prevention of intellectual impairment in individuals with PKU, apathy and attrition from diet, especially during adolescence, remain a threat to normal development in this population. This study's aim was to examine adolescents' perception of factors that encourage or inhibit their dietary adherence. This was a qualitative study, with the authors using thematic analysis to interpret the findings. The study was conducted as part of a Metabolic Disorders Association conference. Eight adolescents with PKU were recruited through convenience sampling. A focus group was conducted with the adolescents to gather information about factors that encourage and discourage dietary adherence. Thematic analysis revealed that the adolescents encountered problems explaining the nature and food requirements of their condition to other people. Friends, family, and wanting to maintain "normal" cognitive abilities were identified as factors that encouraged dietary adherence. Adolescents with PKU appear to share several barriers and incentives for maintaining the strict dietary regimen. Considering such perceptions may aid future interventions aiming to reduce diet attrition rates among adolescents.

  7. Molecular diet analysis of phyllosoma larvae of the Japanese spiny lobster Panulirus japonicus (Decapoda: Crustacea).

    PubMed

    Suzuki, Nobuaki; Hoshino, Kouichi; Murakami, Keisuke; Takeyama, Haruko; Chow, Seinen

    2008-01-01

    To clarify the natural diet of phyllosoma larvae of the Japanese spiny lobster Panulirus japonicus, the sources of 18S rDNA clones obtained from the hepatopancreas were investigated. Of a total of 1537 clones examined, 160 had different restriction profiles from the host larvae, in which 21 restriction types were observed. Nucleotide sequences of 16 of 21 restriction types were successfully determined and their assignments were investigated by homology search and phylogenetic analysis. From seven late-stage larvae collected in spring to early summer, eukaryote DNA molecules of Teleostei, Oomycetes, Mycetozoa, and Fungi were identified. Exogenous DNA from four younger phyllosoma larvae collected in late autumn could not be recovered. A previous study identified DNAs of cnidarians and urochordates in late-stage phyllosoma larvae of a closely related species collected in winter. This indicates that the phyllosoma larvae are opportunistic carnivores, whose diets correlate with the relative abundance of prey organisms in the ambient water.

  8. 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

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

    PubMed

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

    1999-01-29

    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

  10. NIST physical standards for DNA-based medical testing.

    PubMed

    Barker, Peter E; Watson, Michael S; Ticehurst, John R; Colbert, Jennifer C; O'Connell, Catherine D

    2002-01-01

    As DNA and RNA become major targets for clinical laboratory analysis, benchmark reagents will play an increasingly important role in standardization. Reliable national and international nucleic acid standards promote automation and third-party reimbursement for clinical testing. Furthermore, nucleic acid standards provide materials for quality assurance and quality control (QA/QC), and proficiency testing. Standard methods and training initially evolved from consensus guidelines endorsed by professional societies and governmental agencies. The National Institute of Standards and Technology (NIST), a nonregulatory agency of the U.S. Department of Commerce, develops and certifies physical and chemical standards in support of national commerce, manufacturing, and science. In its role supporting U.S. science and industry, the NIST responds to specific standards needs, most recently for medically and biologically important analytes. Broad-based consensus developed through interdisciplinary NIST workshops initiated development of NIST-certified DNA standards. Such materials serve the diagnostic community and help manufacturers benchmark a variety of DNA diagnostic testing platforms. Here we summarize the NIST experience and programs for development of national standards for DNA-based medical diagnostic testing. Copyright 2002 Wiley-Liss, Inc.

  11. DNA based random key generation and management for OTP encryption.

    PubMed

    Zhang, Yunpeng; Liu, Xin; Sun, Manhui

    2017-09-01

    One-time pad (OTP) is a principle of key generation applied to the stream ciphering method which offers total privacy. The OTP encryption scheme has proved to be unbreakable in theory, but difficult to realize in practical applications. Because OTP encryption specially requires the absolute randomness of the key, its development has suffered from dense constraints. DNA cryptography is a new and promising technology in the field of information security. DNA chromosomes storing capabilities can be used as one-time pad structures with pseudo-random number generation and indexing in order to encrypt the plaintext messages. In this paper, we present a feasible solution to the OTP symmetric key generation and transmission problem with DNA at the molecular level. Through recombinant DNA technology, by using only sender-receiver known restriction enzymes to combine the secure key represented by DNA sequence and the T vector, we generate the DNA bio-hiding secure key and then place the recombinant plasmid in implanted bacteria for secure key transmission. The designed bio experiments and simulation results show that the security of the transmission of the key is further improved and the environmental requirements of key transmission are reduced. Analysis has demonstrated that the proposed DNA-based random key generation and management solutions are marked by high security and usability. Published by Elsevier B.V.

  12. 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.

  13. 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.

  14. Diet analysis in piscivorous birds: What can the addition of molecular tools offer?

    PubMed

    Oehm, Johannes; Thalinger, Bettina; Eisenkölbl, Stephanie; Traugott, Michael

    2017-03-01

    In trophic studies on piscivorous birds, it is vital to know which kind of dietary sample provides the information of interest and how the prey can be identified reliably and efficiently. Often, noninvasively obtained dietary samples such as regurgitated pellets, feces, and regurgitated fish samples are the preferred source of information. Fish prey has usually been identified via morphological analysis of undigested hard parts, but molecular approaches are being increasingly used for this purpose. What remains unknown, however, is which dietary sample type is best suited for molecular diet analysis and how the molecular results compare to those obtained by morphological analysis. Pellets, feces, and regurgitated fish samples of Great Cormorants (Phalacrocorax carbo sinensis) were examined for prey using both morphological hard part analysis and molecular prey identification. The sample types and methods were compared regarding number of species detected (overall and per sample) as well as the prey species composition and its variability among individual samples. Via molecular analysis, significantly higher numbers of prey species were detected in pellets, feces, and fish samples. Of the three sample types, pellets contained the most comprehensive trophic information and could be obtained with the lowest sampling effort. Contrastingly, dietary information obtained from feces was least informative and most variable. For all sample types, the molecular approach outperformed morphological hard part identification regarding the detectable prey spectrum and prey species composition. We recommend the use of pellets in combination with molecular prey identification to study the diet of piscivorous birds.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. Pregnant women's diet composition and transitional milk fatty acids: factor analysis.

    PubMed

    Bobiński, Rafał; Mikulska, Monika; Mojska, Hanna; Ulman-Włodarz, Izabela; Sodowska, Patrycja

    2015-02-01

    The variation in the nutrients contained in the milk is the result of changes to the breast metabolism, placenta metabolism and the diet of pregnant women. Various factors influence fatty acid composition which are one of the major components of woman's breast milk. In our research, we wanted to determine the relationship between the components of the diet of and the transitional milk fatty acid composition mothers who delivered healthy full-term babies, preterm and small for gestational age neonates. The study group comprised of 95 healthy women who were divided into three sub-groups: mothers of appropriate for gestational age (AGA) neonates (group A); mothers of preterm neonates (group B); and mothers who gave birth to small for gestational age (SGA) babies (Group C). The women's elements diet and the content of biochemical components were estimated based on the dietary questionnaire. The FAs in the mother's milk were analyzed using GCMS chromatography. The results of the studies of the dietary components and fatty acids of the milk underwent factor analysis. In group A, 10 correlations (5 positive and 5 negative) were found between the components of the mother's diet and the FAs in the milk (correlation varying from 0.285-0.366). In group B, only negative correlations were observed and these had higher absolute correlation values (0.354-0.500). The most correlations between dietary components and FAs in the milk were found in group C (0.537-0.800). Nature of the correlations between the variables examined in groups A, B and C are different.

  20. 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.

  1. 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.

  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. 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.

  4. 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

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

    PubMed

    Zaidan, Sarah; Roehrer, Erin

    2016-07-11

    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. 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. 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. 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. The analysis has shown that ease of use, reminder, bar code scanning, motivation, usable for all, and synchronization are significant attributes

  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. 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.

  8. [Cost-effectiveness analysis and diet quality index applied to the WHO Global Strategy].

    PubMed

    Machado, Flávia Mori Sarti; Simões, Arlete Naresse

    2008-02-01

    To test the use of cost-effectiveness analysis as a decision making tool in the production of meals for the inclusion of the recommendations published in the World Health Organization's Global Strategy. Five alternative options for breakfast menu were assessed previously to their adoption in a food service at a university in the state of Sao Paulo, Southeastern Brazil, in 2006. Costs of the different options were based on market prices of food items (direct cost). Health benefits were estimated based on adaptation of the Diet Quality Index (DQI). Cost-effectiveness ratios were estimated by dividing benefits by costs and incremental cost-effectiveness ratios were estimated as cost differential per unit of additional benefit. The meal choice was based on health benefit units associated to direct production cost as well as incremental effectiveness per unit of differential cost. The analysis showed the most simple option with the addition of a fruit (DQI = 64 / cost = R$ 1.58) as the best alternative. Higher effectiveness was seen in the options with a fruit portion (DQI1=64 / DQI3=58 / DQI5=72) compared to the others (DQI2=48 / DQI4=58). The estimate of cost-effectiveness ratio allowed to identifying the best breakfast option based on cost-effectiveness analysis and Diet Quality Index. These instruments allow easy application easiness and objective evaluation which are key to the process of inclusion of public or private institutions under the Global Strategy directives.

  9. Meta-analysis of the quantity of calcium excretion associated with the net acid excretion of the modern diet under the acid-ash diet hypothesis.

    PubMed

    Fenton, Tanis R; Eliasziw, Michael; Lyon, Andrew W; Tough, Suzanne C; Hanley, David A

    2008-10-01

    The acid-ash diet hypothesis of osteoporosis suggests that acid from the modern diet causes a demineralization of the skeleton, and mobilized bone calcium is excreted. A systematic approach has not been used to summarize the findings of the numerous studies about the hypothesis. The purpose of this meta-analysis was to estimate the quantity of net acid excretion and calciuria associated with the modern diet, to assess the association between acid excretion and calcium excretion, and to assess the influence of urine preservatives on calcium measurement. We systematically searched for trials of the acid-ash hypothesis and conducted a meta-analysis. Twenty-five of 105 studies met the inclusion criteria. The estimated quantity of net acid excretion from the weighted average of the control diets from 11 studies was 47 mEq/d. The increase in urinary calcium with a change in renal net acid excretion depended on whether the urine was acidic or alkaline (P < 0.001). A significant linear relation was observed between net acid excretion and calcium excretion for both acidic and alkaline urine (P < 0.001). The estimated change in urine calcium associated with a change of 47 mEq of net acid excretion in acidic urine was 1.6 mmol/d (66 mg/d) of calcium. Evidence suggests a linear association between changes in calcium excretion in response to experimental changes in net acid excretion. However, this finding is not evidence that the source of the excreted calcium is bone or that this calciuria contributes to the development of osteoporosis.

  10. Long term weight maintenance after advice to consume low carbohydrate, higher protein diets--a systematic review and meta analysis.

    PubMed

    Clifton, P M; Condo, D; Keogh, J B

    2014-03-01

    Meta analysis of short term trials indicates that a higher protein, lower carbohydrate weight loss diet enhances fat mass loss and limits lean mass loss compared with a normal protein weight loss diet. Whether this benefit persists long term is not clear. We selected weight loss studies in adults with at least a 12 month follow up in which a higher percentage protein/lower carbohydrate diet was either planned or would be expected for either weight loss or weight maintenance. Studies were selected regardless of the success of the advice but difference in absolute and percentage protein intake at 12 months was used as a moderator in the analysis. Data was analysed using Comprehensive Meta analysis V2 using a random effects analysis. As many as 32 studies with 3492 individuals were analysed with data on fat and lean mass, glucose and insulin from 18 to 22 studies and lipids from 28 studies. A recommendation to consume a lower carbohydrate, higher protein diet in mostly short term intensive interventions with long term follow up was associated with better weight and fat loss but the effect size was small-standardised means of 0.14 and 0.22, p = 0.008 and p < 0.001 respectively (equivalent to 0.4 kg for both). A difference of 5% or greater in percentage protein between diets at 12 mo was associated with a 3 fold greater effect size compared with <5% (p = 0.038) in fat mass (0.9 vs. 0.3 kg). Fasting triglyceride and insulin were also lower with high protein diets with effect sizes of 0.17 and 0.22, p = 0.003 and p = 0.042 respectively. Other lipids and glucose were not different. The short term benefit of higher protein diets appears to persist to a small degree long term. Benefits are greater with better compliance to the diet. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. 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

  12. 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.

  13. 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

  14. 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

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

    PubMed

    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

    2015-05-01

    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.

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

    PubMed

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

    2014-09-04

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

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

    PubMed Central

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

    1998-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  19. 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. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  20. 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. © 2013 Society of Chemical Industry.

  1. The effects of various diets on glycemic outcomes during pregnancy: A systematic review and network meta-analysis

    PubMed Central

    Ha, Vanessa; Bonner, Ashley J.; Jadoo, Jaynendr K.; Beyene, Joseph; Anand, Sonia S.

    2017-01-01

    Aims Evidence to support dietary modifications to improve glycemia during pregnancy is limited, and the benefits of diet beyond limiting gestational weight gain is unclear. Therefore, a systematic review and network meta-analysis of randomized trials was conducted to compare the effects of various common diets, stratified by the addition of gestational weight gain advice, on fasting glucose and insulin, hemoglobin A1c (HbA1c), and homeostatic model assessment for insulin resistance (HOMA-IR) in pregnant women. Methods MEDLINE, EMBASE, Cochrane database, and reference lists of published studies were searched through April 2017. Randomized trials directly comparing two or more diets for ≥2-weeks were eligible. Bayesian network meta-analysis was performed for fasting glucose. Owing to a lack of similar dietary comparisons, a standard pairwise meta-analysis for the other glycemic outcomes was performed. The certainty of the pooled effect estimates was assessed using the GRADE tool. Results Twenty-one trials (1,865 participants) were included. In general, when given alongside gestational weight gain advice, fasting glucose improved in most diets compared to diets that gave gestational weight gain advice only. However, fasting glucose increased in high unsaturated or monounsaturated fatty acids diets. In the absence of gestational weight gain advice, fasting glucose improved in DASH-style diets compared to standard of care. Although most were non-significant, similar trends were observed for these same diets for the other glycemic outcomes. Dietary comparisons ranged from moderate to very low in quality of evidence. Conclusion/Interpretation Alongside with gestational weight gain advice, most diets, with the exception of a high unsaturated or a high monounsaturated fatty acid diet, demonstrated a fasting glucose improvement compared with gestational weight gain advice only. When gestational weight gain advice was not given, the DASH-style diet appeared optimal on

  2. 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

  3. Molecular analysis of intestinal bacterial microbiota of broiler chickens fed diets containing fermented cottonseed meal.

    PubMed

    Sun, H; Tang, J W; Fang, C L; Yao, X H; Wu, Y F; Wang, X; Feng, J

    2013-02-01

    The study was conducted to investigate the effects of dietary inclusion of fermented cottonseed meal (FCM) on the ileal and cecal bacterial microbiota of broiler chickens. A total of 300 newborn yellow-feathered broiler chickens were randomly divided into 2 treatments with 3 replicates each (50 birds per replicate): control and 80 g/kg of FCM group. The feeding trial lasted for 42 d. Ileal and cecal digesta samples were collected from 8 chicks per replicate at 21 and 42 d of age to determine the composition of bacterial microbiota using denaturing gradient gel electrophoresis, cloning, sequencing, and real-time quantitative PCR analysis. The results demonstrated that the microbial composition in the ileum and cecum were considerably affected by the diet. The similarity dendrogram of banding profiles showed a more rapid stabilization of intestinal bacterial microbiota in broilers fed diets supplemented with FCM, compared with that of the birds fed the control diet. No significant difference was observed in total number of bands and Shannon-Weaver index, indicating that FCM had no effects on bacterial diversity. However, enumeration of bacteria in the ileal and cecal contents by quantitative PCR showed an increased (P < 0.05) population of lactobacilli, as well as a decreased (P < 0.05) Escherichia coli number by the dietary inclusion of FCM. In summary, dietary inclusion of FCM did not affect the intestinal microbial diversity but shifted intestinal microbiota, with a more homogenous population and an increased colonization of lactobacilli. The results also support the concept that dietary FCM inclusion could promote the beneficial bacteria in the intestinal tract.

  4. Impact of avocado-enriched diets on plasma lipoproteins: A meta-analysis.

    PubMed

    Peou, Sokunthea; Milliard-Hasting, Brittany; Shah, Sachin A

    2016-01-01

    Optimizing plasma lipoproteins is the primary goal of pharmacotherapy and diet interventions in people at risk for cardiovascular diseases. Avocados offer a rich source of monounsaturated fat and may pose beneficial effects on the lipid profile. We aimed to perform a meta-analysis of randomized clinical trials assessing the impact of avocados on TC, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and/or triglycerides (TG). We searched PUBMED, Cumulative Index to Nursing and Allied Health Literature, Index to Nursing and Allied Health Literature, and the Cochrane Database of Systemic Reviews from their inception to February 2015. The weighted mean difference from baseline was calculated for all endpoints. Subgroup analyses were performed to assess heterogeneity, and funnel plots inspected to assess publication bias. Ten unique studies (n = 229) were included. Avocado consumption significantly reduced TC, LDL-C, and TG by -18.80 mg/dL (95% confidence interval [CI], -24.56 to -13.05; I(2), 46.9%), -16.50 mg/dL (95% CI, -22.91 to -10.10; I(2), 72.5%), -27.20 mg/dL (95% CI, -44.41 to -9.99; I(2), 91.1%) respectively. High-density lipoprotein cholesterol decreased nonsignificantly by -0.18 mg/dL (95% CI, -3.23 to 2.88; I(2), 84.8%). Avocado-substituted diets significantly decrease TC, LDL-C, and TG levels. Substituting dietary fats with avocados versus adding to the free diet should be the primary recommendation strategy. Larger trials looking at the impact of avocados on major adverse cardiovascular events are warranted. Copyright © 2016 National Lipid Association. All rights reserved.

  5. 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

  6. 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

  7. 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

  8. Effect of low-fat diet interventions versus other diet interventions on long-term weight change in adults: a systematic review and meta-analysis.

    PubMed

    Tobias, Deirdre K; Chen, Mu; Manson, JoAnn E; Ludwig, David S; Willett, Walter; Hu, Frank B

    2015-12-01

    The effectiveness of low-fat diets for long-term weight loss has been debated for decades, with many randomised controlled trials (RCTs) and recent reviews giving mixed results. We aimed to summarise the large body of evidence from RCTs to determine whether low-fat diets contribute to greater weight loss than participants' usual diet, low-carbohydrate diets, and other higher-fat dietary interventions. We did a systematic review and random effects meta-analysis of RCTs comparing the long-term effect (≥1 year) of low-fat and higher-fat dietary interventions on weight loss by searching MEDLINE, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), and Cochrane Database of Systematic Reviews to identify eligible trials published from database inception up until July 31, 2014. We excluded trials if one intervention group included a non-dietary weight loss component but the other did not, and trials of dietary supplements or meal replacement drink interventions. Data including the main outcome measure of mean difference in weight change between interventions, and whether interventions were intended to lead to weight loss, weight maintenance, or neither, were extracted from published reports. We estimated the pooled weighted mean difference (WMD) with a DerSimonian and Laird random effects method. 3517 citations were identified by the search and 53 studies met our inclusion criteria, including 68 128 participants (69 comparisons). In weight loss trials, low-carbohydrate interventions led to significantly greater weight loss than did low-fat interventions (18 comparisons; WMD 1·15 kg [95% CI 0·52 to 1·79]; I(2)=10%). Low-fat interventions did not lead to differences in weight change compared with other higher-fat weight loss interventions (19 comparisons; WMD 0·36 kg [-0·66 to 1·37; I(2)=82%), and led to a greater weight decrease only when compared with a usual diet (eight comparisons; -5·41 kg [-7·29 to -3·54]; I(2)=68%). Similarly, results of non

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

    PubMed

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

    2016-06-01

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

  10. 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 ...

  11. The Effect of the Mediterranean Diet on Hypertension: A Systematic Review and Meta-Analysis.

    PubMed

    Nissensohn, Mariela; Román-Viñas, Blanca; Sánchez-Villegas, Almudena; Piscopo, Suzanne; Serra-Majem, Lluis

    2016-01-01

    The adoption of a Mediterranean diet (MD) pattern of eating is often described as a strategy to help prevent or manage hypertension. However, this dietary regimen has not been reviewed systematically for its efficacy against hypertension. Therefore, the purpose of this study was to analyze the effect of interventions of at least 1 year duration on blood pressure (BP) values through a systematic review and meta-analysis. The focus was on interventions comparing an MD with a low-fat diet. The authors accessed and searched PubMed and Scopus databases up to March, 2015. Randomized control trials comparing MD vs low-fat diet were included. The researchers assessed the methodological quality, extracted the valid data, and conducted the meta-analysis following Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Six trials (more than 7,000 individuals) were identified. Meta-analysis showed that interventions aiming at adopting an MD pattern for at least 1 year reduced both the systolic BP and diastolic BP levels in individuals with normal BP or mild hypertension. The effect was higher for the systolic BP (-1.44 mm Hg) but also consistent for the diastolic BP (-0.70 mm Hg). However, the results have to be interpreted with caution owing to the reduced number of studies eligible for inclusion in this meta-analysis. This situation limited the statistical power of the analyses. Furthermore, in all analyses, the pooled effect estimation showed a high evidence of heterogeneity, which compromises the validity of the pooled estimates. A positive and significant association was found between the MD and BP in adults. However, in all cases the magnitude of the effect was small. Based on this limited group of studies and their heterogeneity, the authors found insufficient convincing evidence to suggest that the MD decreased BP. Further standardized research is urgently needed to reach evidence-based conclusions to clarify the role of MD in BP management

  12. 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.

  13. Reconstructing diet in Napoleon's Grand Army using stable carbon and nitrogen isotope analysis.

    PubMed

    Holder, Sammantha; Dupras, Tosha L; Jankauskas, Rimantas; Williams, Lana; Schultz, John

    2017-05-01

    Historical evidence has provided information regarding disease and mortality in Napoleon Bonaparte's Grand Army, but dietary information beyond individual soldier accounts remains scarce. The purpose of this research is to reconstruct the diets of Napoleon's multiethnic army who were associated with the Russian Campaign of 1812. We conducted stable carbon and nitrogen isotope ratio analysis on femoral bone collagen of 78 individuals recovered from a salvage excavation at the mass gravesite of Šiaurės miestelis in Vilnius, Lithuania. These individuals were later discovered to be Napoleonic soldiers and camp followers who participated in the 1812 Russian Campaign. Stable carbon isotope ratios range from -19.2‰ to -11.8‰, with a mean of -17.8‰ ± 1.5‰ (1 σ). Stable nitrogen isotope ratios range from 7.1‰ to 13.6‰, with a mean of 10.5‰ ± 1.4‰ (1 σ). Both δ(13) C and δ(15) N values show a wide range of variation. Stable isotope data indicate considerable dietary variation in this population associated with a multiethnic and socially stratified military population. Diets ranged from predominantly C3 -based to predominantly C4 -based, with varying inputs of terrestrial, freshwater, and marine animal protein. Comparison with other European populations further denotes the exceptional range of dietary variation of soldiers and camp followers in Napoleon's army. © 2017 Wiley Periodicals, Inc.

  14. 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.

  15. Impact of Diet and/or Exercise Intervention on Infrapatellar Fat Pad Morphology: Secondary Analysis from the Intensive Diet and Exercise for Arthritis (IDEA) Trial.

    PubMed

    Pogacnik Murillo, Aarón Leonardo; Eckstein, Felix; Wirth, Wolfgang; Beavers, Daniel; Loeser, Richard F; Nicklas, Barbara J; Mihalko, Shannon L; Miller, Gary D; Hunter, David J; Messier, Stephen P

    2017-01-01

    The infrapatellar fat pad (IPFP) represents intra-articular adipose tissue that may contribute to intra-articular inflammation and pain by secretion of proinflammatory cytokines. Here we examined the impact of weight loss by diet and/or exercise interventions on the IPFP volume. Intensive Diet and Exercise for Arthritis (IDEA) was a single-blinded, single-center, 18-month, prospective, randomized controlled trial that enrolled 454 overweight and obese older adults with knee pain and radiographic osteoarthritis. Participants were randomized to 1 of 3 groups: exercise-only control (E), diet-induced weight loss (D), and diet-induced weight loss + exercise (D+E). In a subsample (n = 106; E: n = 36, D: n = 35, and D+E: n = 35), magnetic resonance images were acquired at baseline and at the 18-month follow-up, from which we analyzed IPFP volume, surface areas, and thickness in this secondary analysis. The average weight loss amounted to 1.0% in the E group, 10.5% in the D group, and 13.0% in the D+E group. A significant (p < 0.01) reduction in IPFP volume was observed in the E (2.1%), D (4.0%), and D+E (5.2%) groups. The IPFP volume loss in the D+E group was significantly greater than that in the E group (p < 0.05) when not adjusting for parallel comparisons. Across intervention groups, there were significant correlations between IPFP volume change, individual weight loss (r = 0.40), and change in total body fat mass (dual-energy X-ray absorptiometry; r = 0.44, n = 88) and in subcutaneous thigh fat area (computed tomography; r = 0.32, n = 82). As a potential link between obesity and knee osteoarthritis, the IPFP was sensitive to intervention by diet and/or exercise, and its reduction was correlated with changes in weight and body fat. © 2017 S. Karger AG, Basel.

  16. Effect of restricted protein diet supplemented with keto analogues in chronic kidney disease: a systematic review and meta-analysis.

    PubMed

    Jiang, Zheng; Zhang, Xiaoyan; Yang, Lichuan; Li, Zi; Qin, Wei

    2016-03-01

    To evaluate the efficacy and safety of the restricted protein diet (low or very low protein diet) supplemented with keto analogues in the treatment of chronic kidney disease (CKD). The Cochrane library, PubMed, Embase, CBM and CENTRAL databases were searched and reviewed up to April 2015. Clinical trials were analyzed using RevMan 5.3 software. Seven random control trials, one cross-over trial and one non-randomized concurrent control trial were selected and included in this study according to our inclusion and exclusion criteria. The changes of eGFR, BUN, Scr, albumin, PTH, triglyceride, cholesterol, calcium, phosphorus and nutrition indexes (BMI, lean body mass and mid-arm muscular circumference) before and after treatment were analyzed. The meta-analysis results indicated that, comparing with normal protein diet, low protein diet (LPD) or very low protein diet (vLPD) supplemented with keto analogues (s(v)LPD) could significantly prevent the deterioration of eGFR (P < 0.001), hyperparathyroidism (P = 0.04), hypertension (P < 0.01) and hyperphosphatemia (P < 0.001). No differences in BUN, Scr, Albumin, triglyceride, cholesterol, hemoglobin, calcium and nutrition indexes were observed between different protein intake groups. Restricted protein diet supplemented with keto analogues (s(v)LPD) could delay the progression of CKD effectively without causing malnutrition.

  17. 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

  18. 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.

  19. A universal DNA-based protein detection system.

    PubMed

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

    2013-09-25

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

  20. Effect of low-protein diet on kidney function in diabetic nephropathy: meta-analysis of randomised controlled trials.

    PubMed

    Nezu, Uru; Kamiyama, Hiroshi; Kondo, Yoshinobu; Sakuma, Mio; Morimoto, Takeshi; Ueda, Shinichiro

    2013-05-28

    To evaluate the effect of low-protein diet on kidney function in patients with diabetic nephropathy. A systematic review and a meta-analysis of randomised controlled trials. MEDLINE, EMBASE, Cochrane Library, ClinicalTrials.gov, International Standard Randomised Controlled Trial Number (ISRCTN) Register and University Hospital Medical Information Network-Clinical Trials Registry (UMIN-CTR) from inception to 10 December 2012. Internet searches were also carried out with general search engines (Google and Google Scholar). Randomised controlled trials that compared low-protein diet versus control diet and assessed the effects on kidney function, proteinuria, glycaemic control or nutritional status. The primary outcome was a change in the glomerular filtration rate (GFR). The secondary outcomes were changes in proteinuria, post-treatment value of glycated haemoglobin A1C (HbA1c) and post-treatment value of serum albumin. The results were summarised as the mean difference for continuous outcomes and pooled by the random effects model. Subgroup analyses and sensitivity analyses were conducted regarding patient characteristics, intervention period, methodological quality and assessment of diet compliance. The assessment of diet compliance was performed based on the actual protein intake ratio (APIR) of the low-protein diet group to the control group. We identified 13 randomised controlled trials enrolling 779 patients. A low-protein diet was associated with a significant improvement in GFR (5.82 ml/min/1.73 m(2), 95% CI 2.30 to 9.33, I(2)=92%; n=624). This effect was consistent across the subgroups of type of diabetes, stages of nephropathy and intervention period. However, GFR was improved only when diet compliance was fair (8.92, 95% CI 2.75 to 15.09, I(2)=92% for APIR <0.9 and 0.03, 95% CI -1.49 to 1.56, I(2)=90% for APIR ≥0.9). Proteinuria and serum albumin were not differed between the groups. HbA1c was slightly but significantly decreased in the low-protein diet

  1. 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.

  2. DNA Based Electrolyte/Separator for Lithium Battery Application (Postprint)

    DTIC Science & Technology

    2015-10-07

    electronics to hybrid and electric vehicles . Two general categories of secondary batteries are mainly explored: the first are liquid electrolyte metal-ion...AFRL-RX-WP-JA-2016-0302 DNA BASED ELECTROLYTE/SEPARATOR FOR LITHIUM BATTERY APPLICATION (POSTPRINT) Jitendra Kumar1, Fahima...BASED ELECTROLYTE/SEPARATOR FOR LITHIUM BATTERY APPLICATION (POSTPRINT) 5a. CONTRACT NUMBER FA8650-15-D-5405-0001 5b. GRANT NUMBER 5c. PROGRAM

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. DNA-Based Random Number Generation in Security Circuitry

    PubMed Central

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

    2010-01-01

    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. PMID:20303385

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

    PubMed

    Carberry, Ciara A; Kenny, David A; Kelly, Alan K; Waters, Sinéad M

    2014-01-01

    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. 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. 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.

  14. Health advantages and disadvantages of weight-reducing diets: a computer analysis and critical review.

    PubMed

    Anderson, J W; Konz, E C; Jenkins, D J

    2000-10-01

    Some weight-loss diets are nutritionally sound and consistent with recommendations for healthy eating while others are "fad" diets encouraging irrational and, sometimes, unsafe practices. The purpose of the study was to compare several weight loss diets and assess their potential long-term effects. Eight popular weight-loss diets were selected (Atkins, Protein Power, Sugar Busters, Zone, ADA Exchange, High-Fiber Fitness, Pritikin and Omish) to be non-clinically analyzed by means of a computer to predict their relative benefits/potential harm. A summary description, menu plan and recommended snacks were developed for each diet. The nutrient composition of each diet was determined using computer software, and a Food Pyramid Score was calculated to compare diets. The Mensink, Hegsted and other formulae were applied to estimate coronary heart disease risk factors. Higher fat diets are higher in saturated fats and cholesterol than current dietary guidelines and their long-term use would increase serum cholesterol levels and risk for CHD. Diets restricted in sugar intake would lower serum cholesterol levels and long-term risk for CHD; however, higher carbohydrate, higher fiber, lower fat diets would have the greatest effect in decreasing serum cholesterol concentrations and risk of CHD. While high fat diets may promote short-term weight loss, the potential hazards for worsening risk for progression of atherosclerosis override the short-term benefits. Individuals derive the greatest health benefits from diets low in saturated fat and high in carbohydrate and fiber: these increase sensitivity to insulin and lower risk for CHD.

  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. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2016-01-01

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

  18. Nutritional analysis and microbiological evaluation of commercially available enteral diets for cats.

    PubMed

    Prantil, Lori R; Markovich, Jessica E; Heinze, Cailin R; Linder, Deborah E; Tams, Todd R; Freeman, Lisa M

    2016-01-01

    To determine the prevalence of nutrients less than or greater than accepted standards in commercially available enteral diets for cats, and to identify contamination incidence in enteral diets for cats. Prospective cross-sectional study. University teaching hospital. Seven commercial enteral diets for cats. Labels were evaluated to determine if diets were intended to be nutritionally complete and balanced. One diet under storage techniques partially representative of clinical conditions was sampled on days 0, 1, 3, 5, and 7 of storage for aerobic bacterial culture. All 7 diets were analyzed for key nutrients and results were compared to Association of American Feed Control Officials (AAFCO) Nutrient Profiles for Adult Cats for maintenance and National Research Council recommended allowance (NRC-RA). From label information, 4 diets were classified as complete and balanced and 3 diets were classified as not complete and balanced. All 7 diets had at least 1 nutrient less than the AAFCO minimums and the NRC-RA. The total number of nutrients less than AAFCO minimums ranged from 3 to 9 (median = 4), with iron, potassium, and manganese being the most common. Concentrations of some nutrients were undetectable. None of the samples tested had a positive aerobic culture at baseline (day 0) or on subsequent samples from days 1, 3, 5, and 7 under any storage condition. None of the diets analyzed met all of the minimum nutrient concentrations. While short-term feeding may not be of concern for an individual patient, clinicians should be aware of potential nutritional limitations when feeding enteral diets to ill or injured cats. © Veterinary Emergency and Critical Care Society 2015.

  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. 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.

  1. 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.

  2. 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.

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

    PubMed Central

    Kadoya, Taku; Osada, Yutaka; Takimoto, Gaku

    2012-01-01

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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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…

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

    PubMed

    Poyraz, Ismail

    2016-01-01

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

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

    PubMed

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

    2014-03-01

    The macrobiotic, Ma-Pi 2 diet (12% protein, 18% fat and 70% carbohydrate), has shown benefit in adults with type 2 diabetes mellitus (T2DM). This pooled analysis aims to confirm results from four, 21-day intervention studies with the Ma-Pi 2 diet, carried out in Cuba, China, Ghana and Italy. Baseline and end of study biochemical, body composition and blood pressure data, were compared using multivariate statistical methods and assessment of the Cohen effect size (d). Results showed that all measured indicators demonstrated significant changes (p < 0.001); most of them with a very high (d ≥ 1.30), or high (d = 0.80-1.29) effect size. The global effect size of the diet was Italy (1.96), China (1.79), Cuba (1.38) and Ghana (0.98). The magnitude of the individual effect on each variable by country, and the global effect by country, was independent of the sample size (p > 0.05). Similarly, glycemia and glycemic profiles in all four studies were independent of the sample size (p = 0.237). The Ma-Pi diet 2 significantly reduced glycemia, serum lipids, uremia and cardiovascular risk in adults with T2DM. These results suggest that the Ma-Pi 2 diet could be a valid alternative treatment for patients with T2DM and point to the need for further clinical studies. Mechanisms related to its benefits as a functional diet are discussed. © 2013 The Authors. Diabetes/Metabolism Research and Reviews published by John Wiley & Sons, Ltd.

  15. 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.

  16. 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.

  17. Effects of Vegetarian Diets on Blood Lipids: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

    PubMed

    Wang, Fenglei; Zheng, Jusheng; Yang, Bo; Jiang, Jiajing; Fu, Yuanqing; Li, Duo

    2015-10-27

    Vegetarian diets exclude all animal flesh and are being widely adopted by an increasing number of people; however, effects on blood lipid concentrations remain unclear. This meta-analysis aimed to quantitatively assess the overall effects of vegetarian diets on blood lipids. We searched PubMed, Scopus, Embase, ISI Web of Knowledge, and the Cochrane Library through March 2015. Studies were included if they described the effectiveness of vegetarian diets on blood lipids (total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, and triglyceride). Weighted mean effect sizes were calculated for net changes by using a random-effects model. We performed subgroup and univariate meta-regression analyses to explore sources of heterogeneity. Eleven trials were included in the meta-analysis. Vegetarian diets significantly lowered blood concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, and non-high-density lipoprotein cholesterol, and the pooled estimated changes were -0.36 mmol/L (95% CI -0.55 to -0.17; P<0.001), -0.34 mmol/L (95% CI -0.57 to -0.11; P<0.001), -0.10 mmol/L (95% CI -0.14 to -0.06; P<0.001), and -0.30 mmol/L (95% CI -0.50 to -0.10; P=0.04), respectively. Vegetarian diets did not significantly affect blood triglyceride concentrations, with a pooled estimated mean difference of 0.04 mmol/L (95% CI -0.05 to 0.13; P=0.40). This systematic review and meta-analysis provides evidence that vegetarian diets effectively lower blood concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, and non-high-density lipoprotein cholesterol. Such diets could be a useful nonpharmaceutical means of managing dyslipidemia, especially hypercholesterolemia. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

  18. 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.

  19. Analysis of health consumers' behavior using self-tracker for activity, sleep, and diet.

    PubMed

    Kim, Jeongeun

    2014-06-01

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

  20. Determination of allergenic egg proteins in food by protein-, mass spectrometry-, and DNA-based methods.

    PubMed

    Lee, Ji-Yun; Kim, Chang Jong

    2010-01-01

    Egg allergy is one of the most common food allergies in both adults and children, and foods including eggs and their byproducts should be declared under food allergen labeling policies in industrial countries. Therefore, to develop and validate a sensitive and specific method to detect hidden egg allergens in foods, we compared immunochemical, DNA-based, and proteomic methods for detecting egg allergens in foods using egg allergen standards such as egg whole protein, egg white protein, egg yolk protein, ovomucoid, ovalbumin, ovotransferrin, lysozyme, and alpha-livetin. Protein-based immunochemical methods, including ELISA as an initial screening quantitative analysis and immunoblotting as a final confirmatory qualitative analysis, were very sensitive and specific in detecting potentially allergenic egg residues in processed foods in trace amounts. In contrast, the proteomics-based, matrix-assisted laser desorption/ionization time-of-flight MS and LC-tandem quadrupole time-of-flight MS methods were not able to detect some egg allergens, such as ovomucoid, because of its nondenaturing property under urea and trypsin. The DNA-based PCR method could not distinguish between egg and chicken meat because it is tissue-nonspecific. In further studies for the feasibility of these immunochemical methods on 100 real raw dietary samples, four food samples without listed egg ingredients produced a positive response by ELISA, but exhibited negative results by immunoblotting.

  1. DNA-Based Identification of Forensically Important Blow Flies (Diptera: Calliphoridae) From India.

    PubMed

    Bharti, Meenakshi; Singh, Baneshwar

    2017-09-01

    Correct species identification is the first and the most important criteria in entomological evidence-based postmortem interval (PMI) estimation. Although morphological keys are available for species identification of adult blow flies, keys for immature stages are either lacking or are incomplete. In this study, cytochrome oxidase subunit 1 (COI) reference data were developed from nine species (belonging to three subfamilies, namely, Calliphorinae, Luciliinae, and Chrysomyinae) of blow flies from India. Seven of the nine species included in this study were found suitable for DNA-based identification using COI gene, because they showed nonoverlapping intra- (0.0-0.3%) and inter-(1.96-18.14%) specific diversity, and formed well-supported monophyletic clade in phylogenetic analysis. The remaining two species (i.e., Chrysomya megacephala (Fabricius) and Chrysomya chani Kurahashi) cannot be distinguished reliably using our database because they had a very low interspecific diversity (0.11%), and Ch. megacephala was paraphyletic with respect to Ch. chani in the phylogenetic analysis. We conclude that the COI gene is a useful marker for DNA-based identification of blow flies from India. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

    USGS Publications Warehouse

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

    2002-01-01

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

  3. Analysis of fatty acid composition revealed differences in the diets of tadpoles of two amphibian species.

    PubMed

    Dgebuadze, Yu Yu; Sushchik, N N; Bashinskiy, I V; Makhutova, O N; Kalacheva, G S; Osipov, V V; Gladyshev, M I

    2017-01-01

    The study of the composition of fatty acid markers of tadpoles of cohabiting amphibian species for the first time revealed differences in their diets: the moor frog Rana arvalis prefers bacteria not associated with plant detritus, whereas the diet of the common spadefoot Pelobates fuscus is based on cyanobacteria, green algae, diatoms, and possibly higher plants. Major differences in the fatty acid composition are determined by the difference in the percentage of eicosapentaenoic and myristic acids.

  4. 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

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

    PubMed

    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.

  6. Diet influenced tooth erosion prevalence in children and adolescents: Results of a meta-analysis and meta-regression.

    PubMed

    Salas, M M S; Nascimento, G G; Vargas-Ferreira, F; Tarquinio, S B C; Huysmans, M C D N J M; Demarco, F F

    2015-08-01

    The aim of the present study was to assess the influence of diet in tooth erosion presence in children and adolescents by meta-analysis and meta-regression. Two reviewers independently performed the selection process and the quality of studies was assessed. Studies published until May 2014 were identified in electronic databases: Pubmed, EBSHost, Scopus, Science direct, Web of Science and Scielo, using keywords. Criteria used included: observational studies, tooth erosion and diet, subject age range 8-19 years old, permanent dentition and index. Meta-analysis was performed and in case of heterogeneity a random-effects model was used. Thirteen studies that fulfilled the inclusion criteria were selected. Higher consumption of carbonated drinks (p=0.001) or acid snacks/sweets (p=0.01 and for acid fruit juices (p=0.03)) increased the odds for tooth erosion, while higher intake of milk (p=0.028) and yogurt (p=0.002) reduced the erosion occurrence. Heterogeneity was observed in soft drinks, confectionary and snacks and acidic fruit juices models. Methodological issues regarding the questionnaires administration and the inclusion of other variables, such as food groups and tooth brushing, explained partially the heterogeneity observed. Some dietary components (carbonated drinks, acid snacks/sweets and natural acidic fruits juice) increased erosion occurrence while milk and yogurt had a protective effect. Methods to assess diet could influence the homogeneity of the studies and should be considered during the study design. The method to assess diet should be carefully considered and well conducted as part of the clinical assessment of tooth erosion, since diet could influence the occurrence of tooth erosion. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. 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

  8. Vegetarian, vegan diets and multiple health outcomes: A systematic review with meta-analysis of observational studies.

    PubMed

    Dinu, Monica; Abbate, Rosanna; Gensini, Gian Franco; Casini, Alessandro; Sofi, Francesco

    2017-11-22

    Beneficial effects of vegetarian and vegan diets on health outcomes have been supposed in previous studies. Aim of this study was to clarify the association between vegetarian, vegan diets, risk factors for chronic diseases, risk of all-cause mortality, incidence, and mortality from cardio-cerebrovascular diseases, total cancer and specific type of cancer (colorectal, breast, prostate and lung), through meta-analysis. A comprehensive search of Medline, EMBASE, Scopus, The Cochrane Library, and Google Scholar was conducted. Eighty-six cross-sectional and 10 cohort prospective studies were included. The overall analysis among cross-sectional studies reported significant reduced levels of body mass index, total cholesterol, LDL-cholesterol, and glucose levels in vegetarians and vegans versus omnivores. With regard to prospective cohort studies, the analysis showed a significant reduced risk of incidence and/or mortality from ischemic heart disease (RR 0.75; 95% CI, 0.68 to 0.82) and incidence of total cancer (RR 0.92; 95% CI 0.87 to 0.98) but not of total cardiovascular and cerebrovascular diseases, all-cause mortality and mortality from cancer. No significant association was evidenced when specific types of cancer were analyzed. The analysis conducted among vegans reported significant association with the risk of incidence from total cancer (RR 0.85; 95% CI, 0.75 to 0.95), despite obtained only in a limited number of studies. This comprehensive meta-analysis reports a significant protective effect of a vegetarian diet versus the incidence and/or mortality from ischemic heart disease (-25%) and incidence from total cancer (-8%). Vegan diet conferred a significant reduced risk (-15%) of incidence from total cancer.

  9. Fluorescence of size-expanded DNA bases: reporting on DNA sequence and structure with an unnatural genetic set.

    PubMed

    Krueger, Andrew T; Kool, Eric T

    2008-03-26

    We recently described the synthesis and helix assembly properties of expanded DNA (xDNA), which contains base pairs 2.4 A larger than natural DNA pairs. This designed genetic set is under study with the goals of mimicking the functions of the natural DNA-based genetic system and of developing useful research tools. Here, we study the fluorescence properties of the four expanded bases of xDNA (xA, xC, xG, xT) and evaluate how their emission varies with changes in oligomer length, composition, and hybridization. Experiments were carried out with short oligomers of xDNA nucleosides conjugated to a DNA oligonucleotide, and we investigated the effects of hybridizing these fluorescent oligomers to short complementary DNAs with varied bases opposite the xDNA bases. As monomer nucleosides, the xDNA bases absorb light in two bands: one at approximately 260 nm (similar to DNA) and one at longer wavelength ( approximately 330 nm). All are efficient violet-blue fluorophores with emission maxima at approximately 380-410 nm and quantum yields (Phifl) of 0.30-0.52. Short homo-oligomers of the xDNA bases (length 1-4 monomers) showed moderate self-quenching except xC, which showed enhancement of Phifl with increasing length. Interestingly, multimers of xA emitted at longer wavelengths (520 nm) as an apparent excimer. Hybridization of an oligonucleotide to the DNA adjacent to the xDNA bases (with the xDNA portion overhanging) resulted in no change in fluorescence. However, addition of one, two, or more DNA bases in these duplexes opposite the xDNA portion resulted in a number of significant fluorescence responses, including wavelength shifts, enhancements, or quenching. The strongest responses were the enhancement of (xG)n emission by hybridization of one or more adenines opposite them, and the quenching of (xT)n and (xC)n emission by guanines opposite. The data suggest multiple ways in which the xDNA bases, both alone and in oligomers, may be useful as tools in biophysical analysis

  10. Commercial diet induced hypothyroidism due to high iodine. A histological and radiological analysis.

    PubMed

    Castillo, V A; Pisarev, M A; Lalia, J C; Rodriguez, M S; Cabrini, R L; Márquez, G

    2001-11-01

    A number of puppies of the School Hospital of the Faculty of Veterinary Science-UBA showed bone changes. Measurement of the iodine content of the commercial diet showed a significant increase in its content. Iodine excess causes alterations in thyroid function and morphology, and its hormones have a direct action on bone formation. Three groups of puppies were fed on different diets: a home-prepared diet, a commercial diet (containing 5.6 mg potassium iodide/kg dry food), and a home-prepared diet supplemented with 5.6 mg potassium iodide/kg dry food. Groups B and C developed hypothyroidism. A significant decrease (p<0.05) in the styloid apophyseal surface was found in groups B and C vs. A, determined by radiography. Histologically, the hypertrophied cartilage was shorter in groups B and C than in group A (p<0.0001). The present results suggest that commercial diets with a high iodine content may cause hypothyroidism and changes in bone metabolism.

  11. 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

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

    PubMed

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

    2013-01-01

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

  13. 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

  14. An analysis of the ruminal bacterial microbiota in West African Dwarf sheep fed grass- and tree-based diets.

    PubMed

    Omoniyi, L A; Jewell, K A; Isah, O A; Neumann, A P; Onwuka, C F I; Onagbesan, O M; Suen, G

    2014-05-01

    To measure the impact of supplementing a forage diet with tree-based browse on the ruminal bacterial communities of Nigerian West African Dwarf (WAD) sheep. Fifteen WAD sheep were fed a control diet of forage (Panicum maximum), with 12 animals shifted in groups of three to one of four browse-supplemented diets (Albizia saman, Bridelia micrantha, Ficus sur, or Gmelina arborea). These browse plants were shown in a concurrent but separate study to be reasonably nutritious (based on chemical composition and fibre constituents) and nontoxic (based on tannin, phytate, saponin, alkaloid and oxalate levels). Rumen liquids and solids for DNA extraction were collected via intubation from two animals in each group before and after dietary shift. Bacterial 16S rRNA gene regions V6-V8 were sequenced by 454 pyrosequencing. All communities were highly diverse and dominated by the phyla Firmicutes, Bacteroidetes, Tenericutes, Actinobacteria and Proteobacteria. All communities shared members of the genera Butryivibrio, Prevotella and Ruminococcus. Our analysis defined a core sets of bacteria shared by all animals, forage-fed animals and browse-fed animals. Community structure shifted dramatically in animals fed A. saman or G. arborea. The impact of tree-based browse on the ruminal bacterial community of Nigerian WAD sheep varies by browse species, likely due to differences in browse composition. Our study describes the first neotropical small ruminant bacterial microbiome and supports diet supplementation with specific tree-based browse for WAD sheep. © 2014 The Society for Applied Microbiology.

  15. Low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet improves symptoms in adults suffering from irritable bowel syndrome (IBS) compared to standard IBS diet: A meta-analysis of clinical studies

    PubMed Central

    Varjú, Péter; Farkas, Nelli; Hegyi, Péter; Garami, András; Szabó, Imre; Illés, Anita; Solymár, Margit; Vincze, Áron; Balaskó, Márta; Pár, Gabriella; Bajor, Judit; Szűcs, Ákos; Huszár, Orsolya; Pécsi, Dániel

    2017-01-01

    Background Irritable bowel syndrome (IBS) and functional digestive tract disorders, e.g. functional bloating, carbohydrate maldigestion and intolerances, are very common disorders frequently causing significant symptoms that challenge health care systems. A low Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAP) diet is one of the possible therapeutic approaches for decreasing abdominal symptoms and improving quality of life. Objectives We aimed to meta-analyze data on the therapeutic effect of a low-FODMAP diet on symptoms of IBS and quality of life and compare its effectiveness to a regular, standard IBS diet with high FODMAP content, using a common scoring system, the IBS Symptom Severity Score (IBS-SSS). Methods A systematic literature search was conducted in PubMed, EMBASE and the Cochrane Library as well as in the references in a recent meta-analysis. Adult patients diagnosed with IBS according to the Rome II, Rome III, Rome IV or NICE criteria were included in the analysis. Statistical methods Mean differences with 95% confidence intervals were calculated from studies that contained means, standard deviation (SD) or mean differences and SD of differences and p-values. A random effect model was used because of the heterogeneity (Q test (χ2) and I2 indicator). A p-value of less than 0.05 was chosen to indicate a significant difference. Results The literature search yielded 902 publications, but only 10 were eligible for our meta-analysis. Both regular and low-FODMAP diets proved to be effective in IBS, but post-diet IBS-SSS values were significantly lower (p = 0.002) in the low-FODMAP group. The low-FODMAP diet showed a correlation with the improvement of general symptoms (by IBS-SSS) in patients with IBS. Conclusions This meta-analysis provides high-grade evidence of an improved general symptom score among patients with irritable bowel syndrome who have maintained a low-FODMAP diet compared to those on a traditional IBS diet

  16. Analysis of bacterial community shifts in the gastrointestinal tract of pigs fed diets supplemented with β-glucan from Laminaria digitata, Laminaria hyperborea and Saccharomyces cerevisiae.

    PubMed

    Murphy, P; Dal Bello, F; O'Doherty, J; Arendt, E K; Sweeney, T; Coffey, A

    2013-07-01

    This study was designed to evaluate the effects of algal and yeast β-glucans on the porcine gastrointestinal microbiota, specifically the community of Lactobacillus, Bifidobacterium and coliforms. A total of 48 pigs were fed four diets over a 28-day period to determine the effect that each had on these communities. The control diet consisted of wheat and soya bean meal. The remaining three diets contained wheat and soya bean meal supplemented with β-glucan at 250 g/tonne from Laminaria digitata, Laminaria hyperborea or Saccharomyces cerevisiae. Faecal samples were collected from animals before feeding each diet and after the feeding period. The animals were slaughtered the following day and samples were collected from the stomach, ileum, caecum, proximal colon and distal colon. Alterations in Lactobacillus in the gastrointestinal tract (GIT) were analysed using denaturing gradient gel electrophoresis (DGGE) profiles generated by group-specific 16S rRNA gene PCR amplicons. Plate count analysis was also performed to quantify total coliforms. DGGE profiles indicated that all β-glucan diets provoked the emergence of a richer community of Lactobacillus. The richest community of lactobacilli emerged after feeding L. digitata (LD β-glucan). Plate count analysis revealed that the L. hyperborea (LH β-glucan) diet had a statistically significant effect on the coliform counts in the proximal colon in comparison with the control diet. β-glucan from L. digitata and S. cerevisiae also generally reduced coliforms but to a lesser extent. Nevertheless, the β-glucan diets did not significantly reduce levels of Lactobacillus or Bifidobacterium. DGGE analysis of GIT samples indicated that the three β-glucan diets generally promoted the establishment of a more varied range of Lactobacillus species in the caecum, proximal and distal colon. The LH β-glucan had the most profound reducing effect on coliform counts when compared with the control diet and diets supplemented with L

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  20. 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.

  1. Effects of moderate (MF) versus lower fat (LF) diets on lipids and lipoproteins: a meta-analysis of clinical trials in subjects with and without diabetes.

    PubMed

    Cao, Yumei; Mauger, David T; Pelkman, Christine L; Zhao, Guixiang; Townsend, Stacie M; Kris-Etherton, Penny M

    2009-02-01

    Dyslipidemia increases coronary heart disease (CHD) risk and often presents in diabetes, which amplifies risk of CHD. Lower fat (LF) diets increase triglyceride (TG) and decrease high-density lipoprotein cholesterol (HDL-C); moderate fat (MF) diets decrease TG and lower HDL-C less. To quantify the magnitude of lipid and lipoprotein responses to MF versus LF cholesterol-lowering weight maintenance diets in subjects with and without diabetes. A meta-analysis of 30 controlled-feeding studies (n = 1213 subjects) was conducted to evaluate LF versus MF diets on lipids and lipoproteins in subjects with and without diabetes. In all subjects, MF and LF diets decreased low-density lipoprotein cholesterol (LDL-C) similarly. MF diets decreased HDL-C less versus LF diets. The estimated increase in HDL-C after MF diets versus LF diets was 2.28 mg/dL (95% confidence interval 1.66 to 2.90 mg/dL, P < .0001). MF diets decreased TG, whereas LF diets increased TG. The decrease in TG was -9.36 mg/dL (-12.16 to -6.08 mg/dL, P < .00001) for MF versus LF diets. In subjects with diabetes, there was a similar increase in HDL-C (2.28 mg/dL) versus subjects without diabetes; however, there was a greater reduction in TG (-24.79 mg/dL, P < .05) on the MF diet. Subjects with diabetes had greater reductions in the total cholesterol (TC) to HDL-C ratio (TC:HDL-C) (-0.62, P < .0001) and non-HDL-C (-5.39 %, P < .06) after MF versus LF diets. Both men and women had greater estimated reductions (6.37% and 9.34%, respectively) in predicted CHD risk after MF diets compared to LF diets. Moreover, based on greater reductions in TG, the TC:HDL-C ratio and non-HDL-C in subjects with diabetes, the CHD risk reduction would be greater for a MF versus a LF weight maintenance, cholesterol-lowering diet.

  2. Ab initio study of naphtho-homologated DNA bases.

    PubMed

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

    2008-02-21

    Naphtho-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 naphtho-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 forms of naphtho-thymine (yyT) and naphtho-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 naphtho-guanine (yyG) and naphtho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphtho-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 naphtho-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.

  3. 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.

  4. 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

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

    PubMed

    Amara, Suneetha; Tiriveedhi, Venkataswarup

    2017-03-17

    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.

  6. 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.

  7. 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

  8. FTO genotype and weight loss in diet and lifestyle interventions: a systematic review and meta-analysis.

    PubMed

    Xiang, Lingwei; Wu, Hongyu; Pan, An; Patel, Bhakti; Xiang, Guangda; Qi, Lu; Kaplan, Robert C; Hu, Frank; Wylie-Rosett, Judith; Qi, Qibin

    2016-04-01

    Studies have suggested that the fat mass and obesity-associated (FTO) genotype is associated with individual variability in weight loss in response to diet/lifestyle interventions, but results are inconsistent. We aimed to provide a summary of the literature evaluating the relation between the FTO genotype and weight loss in response to diet/lifestyle interventions. A search of English-language articles in the PubMed and Embase databases (through 30 April 2015) was performed. Eligible studies were diet/lifestyle weight-loss intervention studies conducted in adults that reported changes in body weight or body mass index (BMI) by the FTO variant rs9939609 (or its proxy). Differences in weight loss between FTO genotypes across studies were pooled with the use of fixed-effect models. A meta-analysis of 10 studies (comprising 6951 participants) that reported the results of additive genetic models showed that individuals with the FTO TA genotype and AA genotype (those with the obesity-predisposing A allele) had 0.18-kg (95% CI: -0.09-, 0.45-kg;P= 0.19; NS) and 0.44-kg (95% CI: 0.09-, 0.79-kg;P= 0.015) greater weight loss, respectively, than those with the TT genotype. A meta-analysis of 14 studies (comprising 7700 participants) that reported the results of dominant genetic models indicated a 0.20-kg (-0.43-, 0.04-kg) greater weight loss in the TA/AA genotype than in the TT genotype (P= 0.10). In addition, differences in weight loss between the AA genotype and TT genotype were significant in studies with a diet intervention only, adjustment for baseline BMI or body weight, and several other subgroups. However, the relatively small number of studies limited these stratified analyses, and there was no statistically significant difference between subgroups. This meta-analysis suggests that individuals carrying the homozygous FTO obesity-predisposing allele may lose more weight through diet/lifestyle interventions than noncarriers. Our data provide evidence for genetic

  9. Low carbohydrate versus isoenergetic balanced diets for reducing weight and cardiovascular risk: a systematic review and meta-analysis.

    PubMed

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

    2014-01-01

    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. 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. 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 diets.

  10. 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.

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

    PubMed

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

    2016-09-01

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

  12. 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

  13. 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.

  14. 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.

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

    PubMed

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

    2014-10-01

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

  16. 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

  17. Utilization of stomach content DNA to determine diet diversity in piscivorous fishes.

    PubMed

    Carreon-Martinez, L; Johnson, T B; Ludsin, S A; Heath, D D

    2011-04-01

    The objective of the study was to validate and apply DNA-based approaches to describe fish diets. Laboratory experiments were performed to determine the number of hours after ingestion that DNA could be reliably isolated from stomach content residues, particularly with small prey fishes (c. 1 cm, <0·75 g). Additionally, experiments were conducted at different temperatures to resolve temperature effects on digestion rate and DNA viability. The molecular protocol of cloning and sequencing was then applied to the analysis of stomach contents of wild fishes collected from the western basin of Lake Erie, Canada-U.S.A. The results showed that molecular techniques were more precise than traditional visual inspection and could provide insight into diet preferences for even highly digested prey that have lost all physical characteristics. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

  18. Comparison of the hypoglycemic effect of acarbose monotherapy in patients with type 2 diabetes mellitus consuming an Eastern or Western diet: a systematic meta-analysis.

    PubMed

    Zhu, Qibo; Tong, Yuzhen; Wu, Taixiang; Li, Jieqing; Tong, Nanwei

    2013-06-01

    Because of its mechanism of action, the starch content of a diet might alter the hypoglycemic effect of acarbose. We aimed to determine whether differences in this hypoglycemic effect existed between individuals consuming Eastern and Western diets with significantly different starch contents, a systematic meta-analysis of studies comparing acarbose with placebo or other hypoglycemic agents in patients with type 2 diabetes mellitus (T2DM) was performed. Records were retrieved from the Cochrane clinical controlled trials, MEDLINE, EMBASE, Wanfang, Chinese Technical Periodicals, and ongoing trials databases, and full texts and reference lists were screened. Because no study has directly compared patients consuming different types of diet, fixed- and random-effect models were used to indirectly compare the hypoglycemic effect of acarbose monotherapy with that of placebo and/or comparator drugs in patients with T2DM consuming an Eastern (Eastern Asia) or Western (including Europe and North America) diet. A total of 46 studies were included in the meta-analysis. The results revealed that, compared with placebo, hemoglobin A1c (HbA1c) levels were reduced to a significantly greater extent (1.02%) in the Eastern diet (mean [SD], 1.54% [2.00%]) than in the Western diet (mean [SD], 0.52% [1.20%]) P < 0.00001). The ability of acarbose to reduce HbA1c levels in the Eastern (P = 0.20) and Western (P = 0.10) diet groups was similar to that of sulfonylureas, and HbA1c levels were reduced significantly more (0.39%; P < 0.00001) in the Eastern than in the Western diet group. The ability of acarbose to reduce HbA1c levels was similar to those of metformin and nateglinide/repaglinide, but a comparison of its efficacy with different diets was difficult because of the inclusion of few studies in these categories. Analysis of all included studies revealed that acarbose achieved a greater absolute reduction of HbA1c levels in the Eastern diet (mean [SD], 1.26% [1.20%]) than in the Western

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

    PubMed

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

    2015-06-01

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

  20. Assessment of helminth biodiversity in wild rats using 18S rDNA based metagenomics.

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  2. 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.

  3. Adherence to a Vegetarian Diet and Diabetes Risk: A Systematic Review and Meta-Analysis of Observational Studies

    PubMed Central

    Lee, Yujin; Park, Kyong

    2017-01-01

    We quantitatively assessed the association between a vegetarian diet and diabetes risk using pooled estimates from observational studies. Electronic database searches for articles published from January 1980 to May 2016 were independently performed by two investigators, and 13 articles (14 studies) were identified. The pooled odds ratio (OR) for diabetes in vegetarians vs. non-vegetarians was 0.726 (95% confidence interval (CI): 0.608, 0.867). In the subgroup analyses, this inverse association was stronger for the studies conducted in the Western Pacific region (OR 0.514, 95% CI: 0.304, 0.871) and Europe/North America (OR 0.756, 95% CI: 0.589, 0.971) than studies conducted in Southeast Asia (OR 0.888, 95% CI: 0.718, 1.099). No study had a substantial effect on the pooled effect size in the influence analysis, and the Egger’s (p = 0.465) and Begg’s tests (p = 0.584) revealed no publication bias. This meta-analysis indicates that a vegetarian diet is inversely associated with diabetes risk. Our results support the need for further investigations into the effects of the motivations for vegetarianism, the duration of the adherence to a vegetarian diet, and type of vegetarian on diabetes risk. PMID:28613258

  4. Adherence to a Vegetarian Diet and Diabetes Risk: A Systematic Review and Meta-Analysis of Observational Studies.

    PubMed

    Lee, Yujin; Park, Kyong

    2017-06-14

    We quantitatively assessed the association between a vegetarian diet and diabetes risk using pooled estimates from observational studies. Electronic database searches for articles published from January 1980 to May 2016 were independently performed by two investigators, and 13 articles (14 studies) were identified. The pooled odds ratio (OR) for diabetes in vegetarians vs. non-vegetarians was 0.726 (95% confidence interval (CI): 0.608, 0.867). In the subgroup analyses, this inverse association was stronger for the studies conducted in the Western Pacific region (OR 0.514, 95% CI: 0.304, 0.871) and Europe/North America (OR 0.756, 95% CI: 0.589, 0.971) than studies conducted in Southeast Asia (OR 0.888, 95% CI: 0.718, 1.099). No study had a substantial effect on the pooled effect size in the influence analysis, and the Egger's (p = 0.465) and Begg's tests (p = 0.584) revealed no publication bias. This meta-analysis indicates that a vegetarian diet is inversely associated with diabetes risk. Our results support the need for further investigations into the effects of the motivations for vegetarianism, the duration of the adherence to a vegetarian diet, and type of vegetarian on diabetes risk.

  5. 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

    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. The databases Pubmed, Scopus, Embase, and Cochrane CentralRegister 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. A total of 27 cross-sectional studies and three 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. 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 as type 2 diabetes, it is

  6. Vegetarian diet, Seventh Day Adventists and risk of cardiovascular mortality: a systematic review and meta-analysis.

    PubMed

    Kwok, Chun Shing; Umar, Saadia; Myint, Phyo K; Mamas, Mamas A; Loke, Yoon K

    2014-10-20

    Dietary interventions are an important component of cardiovascular risk factor management although their impact on cardiovascular risk and mortality remains uncertain. We have studied influence of a vegetarian diet on cardiovascular risk and mortality. We searched MEDLINE and EMBASE for comparative studies that evaluated clinical outcomes associated with vegetarian diet as compared to non-vegetarian controls or the general population. Relevant studies were pooled using random effects meta-analysis for risk of death, ischaemic heart disease (IHD) and cerebrovascular disease. We conducted subgroup analysis according to specific type of cohort (e.g. Seventh Day Adventist [SDA]) and gender. Eight studies met the inclusion criteria with 183,321 participants (n=183,321). There was significant heterogeneity in all the meta-analyses, particularly evident with the studies of SDA. In all instances, we found that SDA studies showed greater effect size as compared to non-SDA studies: death (RR 0.68 95% CI 0.45-1.02 vs RR 1.04 95% CI 0.98-1.10), ischaemic heart disease (IHD) (RR 0.60 95% CI 0.43-0.80 vs RR 0.84 95% CI 0.74-0.96) and cerebrovascular disease (RR 0.71 95% CI 0.41-1.20 vs RR 1.05 95% CI 0.89-1.24). Sex specific analyses showed that IHD was significantly reduced in both genders but risk of death and cerebrovascular disease was only significantly reduced in men. Data from observational studies indicates that there is modest cardiovascular benefit, but no clear reduction in overall mortality associated with a vegetarian diet. This evidence of benefit is driven mainly by studies in SDA, whereas the effect of vegetarian diet in other cohorts remains unproven. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  7. Low-residue versus clear liquid diet before colonoscopy: a meta-analysis of randomized, controlled trials.

    PubMed

    Nguyen, Douglas L; Jamal, M Mazen; Nguyen, Emily T; Puli, Srinivas R; Bechtold, Matthew L

    2016-03-01

    Colonoscopy is extremely important for the identification and removal of precancerous polyps. Bowel preparation before colonoscopy is essential for adequate visualization. Traditionally, patients have been instructed to consume only clear liquids the day before a colonoscopy. However, recent studies have suggested using a low-residue diet, with varying results. We evaluated the outcomes of patients undergoing colonoscopy who consumed a clear liquid diet (CLD) versus low-residue diet (LRD) on the day before colonoscopy by a meta-analysis. Scopus, PubMed/MEDLINE, Cochrane databases, and CINAHL were searched (February 2015). Studies involving adult patients undergoing colonoscopy examination and comparing LRD with CLD on the day before colonoscopy were included. The analysis was conducted by using the Mantel-Haenszel or DerSimonian and Laird models with the odds ratio (OR) to assess adequate bowel preparations, tolerability, willingness to repeat diet and preparation, and adverse effects. Nine studies (1686 patients) were included. Patients consuming an LRD compared with a CLD demonstrated significantly higher odds of tolerability (OR 1.92; 95% CI, 1.36-2.70; P < .01) and willingness to repeat preparation (OR 1.86; 95% CI, 1.34-2.59; P < .01) with no differences in adequate bowel preparations (OR 1.21; 95% CI, 0.64-2.28; P = .58) or adverse effects (OR 0.88; 95% CI, 0.58-1.35; P = .57). An LRD before colonoscopy resulted in improved tolerability by patients and willingness to repeat preparation with no differences in preparation quality and adverse effects. Copyright © 2016 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

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

    PubMed

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

    2005-02-10

    The relapsing nature and varying geographical prevalence of ulcerative colitis (UC) implicates environmental factors such as diet in its aetiology. 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. 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). The dietary analysis method described provides a new tool for establishing relationships between diet and disease and indicates a potentially

  9. The Self-Assembled Behavior of DNA Bases on the Interface

    PubMed Central

    Liu, Lei; Xia, Dan; Klausen, Lasse H.; Dong, Mingdong

    2014-01-01

    A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface. PMID:24473140

  10. 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...

  11. 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.

  12. 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.

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

    PubMed

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

    2015-12-15

    Numerous studies have been focused on the replacement of fish meal by other alternative protein sources. However, little is currently known about the molecular mechanism of utilization of diets with different protein sources in fish. Grass carp is a typical herbivorous fish. To elucidate the relationship between gene expression and utilization of animal and plant diets, transcriptome sequencing was performed in grass carp fed with chironomid larvae and duckweed. Grass carp fed with duckweed had significantly higher relative length of gut than those fed with chironomid larvae. 4435 differentially expressed genes were identified between grass carp fed with chironomid larvae and duckweed in brain, liver and gut, involved in cell proliferation and differentiation, appetite control, circadian rhythm, digestion and metabolism pathways. These pathways might play important roles in utilization of diets with different protein sources in grass carp. And the findings could provide a new insight into the replacement of fish meal in artificial diets. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. 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...

  15. 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...

  16. 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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  19. Teaching a Nutrition Unit Utilizing A Computerized Analysis of Students' Diets.

    ERIC Educational Resources Information Center

    Nickel, Stanley L.

    1982-01-01

    A three-lecture unit is described in which fourth-year undergraduate pharmacy students at the University of Toledo are taught basic nutrition principles. Students participate in lecture preparation through a nutrition attitude and knowledge survey and a 10-day diet inventory that is analyzed by computer program. (MSE)

  20. IBS Diet

    MedlinePlus

    ... and Diarrhea Foods that Cause Gas and Bloating Dietary Fiber 12 Week Elimination Diet for IBS Rice Based ... and Diarrhea Foods that Cause Gas and Bloating Dietary Fiber 12 Week Elimination Diet for IBS Rice-Based ...

  1. Diet & Nutrition

    MedlinePlus

    ... Nutrition Share this page Facebook Twitter Email Diet & Nutrition Eating healthy to take charge of your health. Shelly Diagnosed in 2006 Diet & Nutrition Take Control of Your Weight Portion Control Low ...

  2. Vegetarian Diet

    MedlinePlus

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

  3. 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.

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

    PubMed

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

    2015-05-07

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

  5. 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.

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

    USGS Publications Warehouse

    Haramis, G.M.; Jorde, Dennis 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 δ13C and δ15N 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 δ13C 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 δ13C 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.

  7. Sociodemographic determinants of diet quality of the EU elderly: a comparative analysis in four countries.

    PubMed

    Irz, Xavier; Fratiglioni, Laura; Kuosmanen, Nataliya; Mazzocchi, Mario; Modugno, Lucia; Nocella, Giuseppe; Shakersain, Behnaz; Traill, W Bruce; Xu, Weili; Zanello, Giacomo

    2014-05-01

    To investigate the sociodemographic determinants of diet quality of the elderly in four EU countries. Cross-sectional study. For each country, a regression was performed of a multidimensional index of dietary quality v. sociodemographic variables. In Finland, Finnish Household Budget Survey (1998 and 2006); in Sweden, SNAC-K (2001-2004); in the UK, Expenditure & Food Survey (2006-07); in Italy, Multi-purpose Survey of Daily Life (2009). One- and two-person households of over-50s (Finland, n 2994; UK, n 4749); over-50 s living alone or in two-person households (Italy, n 7564); over-60 s (Sweden, n 2023). Diet quality among the EU elderly is both low on average and heterogeneous across individuals. The regression models explained a small but significant part of the observed heterogeneity in diet quality. Resource availability was associated with diet quality either negatively (Finland and UK) or in a non-linear or non-statistically significant manner (Italy and Sweden), as was the preference for food parameter. Education, not living alone and female gender were characteristics positively associated with diet quality with consistency across the four countries, unlike socio-professional status, age and seasonality. Regional differences within countries persisted even after controlling for the other sociodemographic variables. Poor dietary choices among the EU elderly were not caused by insufficient resources and informational measures could be successful in promoting healthy eating for healthy ageing. On the other hand, food habits appeared largely set in the latter part of life, with age and retirement having little influence on the healthiness of dietary choices.

  8. 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

  9. 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.

  10. Reduced tobacco consumption, improved diet and life expectancy for 1988-1998: analysis of New Zealand and OECD data.

    PubMed

    Laugesen, Murray; Grace, Randolph C

    2017-06-02

    We compared changes in tobacco consumption and diet in relation to changes in life expectancy in 1988-1998 in 22 OECD (Organisation for Economic Cooperation and Development) countries. Between 1985 and 1995 using regression analysis we estimated differences in tobacco consumption per adult and the differences in the sum of atherogenic and thrombogenic indices against life expectancy. Each index was derived from the various fats per gram of food from standard texts, and from the annual measurements of fat in the food balance sheets of each country. In 1985-1995, New Zealand showed the largest decrease in tobacco consumption per adult (41%) and the greatest decrease (except for Switzerland) in the sum of atherogenic and thrombogenic indices (17%) as a measure of diet. New Zealand ranked first for life expectancy increases from 1988-1998 for men (3.2 years), women (2.8 years) and both sexes combined. Regression analyses revealed that increases in life expectancy across the OECD for males, but not females, were strongly associated with decreases in tobacco consumption, with a weaker effect of diet improvement. These results suggest that reduced tobacco consumption in 1985-1995 likely contributed to New Zealand's gains in life expectancy from 1988-1998.

  11. Electron accommodation dynamics in the DNA base thymine

    SciTech Connect

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

    2015-07-14

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

  12. Electron accommodation dynamics in the DNA base thymine

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    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-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-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-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.

  13. 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

  14. 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.

  15. 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

  16. Adherence to Mediterranean Diet and Risk of Cancer: An Updated Systematic Review and Meta-Analysis.

    PubMed

    Schwingshackl, Lukas; Schwedhelm, Carolina; Galbete, Cecilia; Hoffmann, Georg

    2017-09-26

    The aim of the present systematic review and meta-analysis was to gain further insight into the effects of adherence to Mediterranean Diet (MedD) on risk of overall cancer mortality, risk of different types of cancer, and cancer mortality and recurrence risk in cancer survivors. Literature search was performed using the electronic databases PubMed, and Scopus until 25 August 2017. We included randomized trials (RCTs), cohort (for specific tumors only incidence cases were used) studies, and case-control studies. Study-specific risk ratios, hazard ratios, and odds ratios (RR/HR/OR) were pooled using a random effects model. Observational studies (cohort and case-control studies), and intervention trials were meta-analyzed separately. The updated review process showed 27 studies that were not included in the previous meta-analysis (total number of studies evaluated: 83 studies). An overall population of 2,130,753 subjects was included in the present update. The highest adherence score to a MedD was inversely associated with a lower risk of cancer mortality (RRcohort: 0.86, 95% CI 0.81 to 0.91, I² = 82%; n = 14 studies), colorectal cancer (RRobservational: 0.82, 95% CI 0.75 to 0.88, I² = 73%; n = 11 studies), breast cancer (RRRCT: 0.43, 95% CI 0.21 to 0.88, n = 1 study) (RRobservational: 0.92, 95% CI 0.87 to 0.96, I² = 22%, n = 16 studies), gastric cancer (RRobservational: 0.72, 95% CI 0.60 to 0.86, I² = 55%; n = 4 studies), liver cancer (RRobservational: 0.58, 95% CI 0.46 to 0.73, I² = 0%; n = 2 studies), head and neck cancer (RRobservational: 0.49, 95% CI 0.37 to 0.66, I² = 87%; n = 7 studies), and prostate cancer (RRobservational: 0.96, 95% CI 0.92 to 1.00, I² = 0%; n = 6 studies). Among cancer survivors, the association between the adherence to the highest MedD category and risk of cancer mortality, and cancer recurrence was not statistically significant. Pooled analyses of individual components of the MedD revealed that the protective effects appear to be

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

    PubMed

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

    2014-08-01

    Knowledge of the dietary choices and trophic niches of organisms is the key to understanding their roles in ecosystems. In seabird diet studies, prey identification is a difficult challenge, often yielding results with technique-specific biases. Additionally, sampling efforts are often not extensive enough to reveal intrapopulational variation. Immature animals, which may constitute up to 50% of a population, may occupy a significantly different trophic niche to more experienced birds, but this remains largely unexplored. We investigated the diet of Cory's shearwater (Calonectris diomedea) from Selvagem Grande, an island located off the northwest African coast, collecting a total of 698 regurgitate samples over three consecutive breeding seasons. The diet was assessed using two complementary approaches for prey identification: conventional morphological analysis (using fish vertebrae, otoliths and cephalopod beaks) and DNA barcoding of the 16S rRNA mitochondrial gene, in cases where a positive identification could not be retrieved. Species assignments employed BLAST and distance-based methods, as well as direct optimization of the tree length based on unaligned sequences in POY. This method resulted in robust tree estimates and species assignments, showing its potential for DNA barcoding of stomach contents using hypervariable markers such as the 16S. The molecular approach increased taxonomic resolution and revealed an additional 17 taxa. Diet differed significantly according to breeding status, sex, breeding phase (prelaying and chick rearing) and year. Such direct evidence of trophic segregation within the same population has rarely been shown in seabirds and highlights the importance of including such variables in ecosystem-based management approaches. © 2014 John Wiley & Sons Ltd.

  18. 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.

  19. 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.

  20. Little appetite for obesity: meta-analysis of the effects of maternal obesogenic diets on offspring food intake and body mass in rodents.

    PubMed

    Lagisz, M; Blair, H; Kenyon, P; Uller, T; Raubenheimer, D; Nakagawa, S

    2015-12-01

    There is increasing recognition that maternal effects contribute to variation in individual food intake and metabolism. For example, many experimental studies on model animals have reported the effect of a maternal obesogenic diet during pregnancy on the appetite of offspring. However, the consistency of effects and the causes of variation among studies remain poorly understood. After a systematic search for relevant publications, we selected 53 studies on rats and mice for a meta-analysis. We extracted and analysed data on the differences in food intake and body weight between offspring of dams fed obesogenic diets and dams fed standard diets during gestation. We used meta-regression to study predictors of the strength and direction of the effect sizes. We found that experimental offspring tended to eat more than control offspring but this difference was small and not statistically significant (0.198, 95% highest posterior density (HPD)=-0.118-0.627). However, offspring from dams on obesogenic diets were significantly heavier than offspring of control dams (0.591, 95% HPD=0.052-1.056). Meta-regression analysis revealed no significant influences of tested predictor variables (for example, use of choice vs no-choice maternal diet, offspring sex) on differences in offspring appetite. Dietary manipulations that extended into lactation had the largest effect on body weight. Subgroup analysis revealed that high protein to non-protein ratio of the maternal diet may promote increased body weight in experimental offspring in comparison with control offspring; low protein content in the maternal chow can have opposite effect. Exposure to maternal obesogenic diets in early life is not likely to result in a substantial change in offspring appetite. Nevertheless, we found an effect on offspring body weight, consistent with permanent alterations of offspring metabolism in response to maternal diet. Additionally, it appears that protein content of the obesogenic diet and timing

  1. Behavioral analysis of Wistar rats fed with a flaxseed based diet added to an environmental enrichment.

    PubMed

    Azevedo de Meneses, J; Junqueira Lopes, C A; Coca Velarde, L G; Teles Boaventura, G

    2011-01-01

    Flaxseed has a high content of n-3 fatty acids and its intake associated with an environmental enrichment may promote distinct behavioral results upon habituation and animal behavior. This work aimed to evaluating animal behavior under the use of these two tools in the Open Field Test. Thirty-six male Wistar rats were divided into 6 groups (n = 6): FEEG, receiving chow made up of flaxseed and kept in enriched environment; FSEG, receiving flaxseed based diet and kept in a standard environment; CEEG, receiving casein based diet and kept in enriched environment; CSEG, receiving casein based chow and kept in standard environment; MCEEG, receiving chow made up of casein but modified so as to provide the same content of fibers and lipids found in flaxseed diet and kept in enriched environment; MCSEG, receiving modified casein based diet and kept in standard environment. All animals were kept under controlled temperature, collective cages and dark/light cycle, receiving chow and water ad libitum, except for MCEEG and MCSEG, which were pair fed with FEEG and FSEG, respectively. Chow intake and animal body weight were evaluated twice in a week. Animals were maintained in these groups from the first until the second month of life, by the time when 3 day tests in Open Field Test began. Finishing the tests, animals were sacrificed and their brains were obtained in order to calculate the relative brain weight. Our results show an interplay between flaxseed and environmental enrichment in habituation to a new environment, making the animals more manageable and less stressed.

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

    PubMed Central

    2014-01-01

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

  3. 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.

  4. 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.

  5. 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

  6. Comparative proteomic and bioinformatic analysis of the effects of a high-grain diet on the hepatic metabolism in lactating dairy goats.

    PubMed

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

    2013-01-01

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

  7. 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. © 2016 World Obesity.

  8. 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.

  9. 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

  10. Using cumulative diet data and stable isotope analysis to determine trophic position of walleye Sander vitreus in a large, complex system

    USGS Publications Warehouse

    Fincel, Mark J.; James, Daniel A.; Chipps, Steven R.; Davis, Blake A.

    2014-01-01

    Diet studies have traditionally been used to determine prey use and food web dynamics, while stable isotope analysis provides for a time-integrated approach to evaluate food web dynamics and characterize energy flow in aquatic systems. Direct comparison of the two techniques is rare and difficult to conduct in large, species rich systems. We compared changes in walleye Sander vitreus trophic position (TP) derived from paired diet content and stable isotope analysis. Individual diet-derived TP estimates were dissimilar to stable isotope-derived TP estimates. However, cumulative diet-derived TP estimates integrated from May 2001 to May 2002 corresponded to May 2002 isotope-derived estimates of TP. Average walleye TP estimates from the spring season appear representative of feeding throughout the entire previous year.

  11. Probing the nature of hydrogen bonds in DNA base pairs.

    PubMed

    Mo, Yirong

    2006-07-01

    Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler-London, polarization, electron-transfer and dispersion-energy terms, where the Heitler-London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson-Crick adenine-thymine (AT), guanine-cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (-25.4 kcal mol(-1) at the MP2/6-31G** level) twice that of the AT (-12.4 kcal mol(-1)) and H-AT (-12.8 kcal mol(-1)) pairs, compared with three conventional N-H...O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the pi-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that pi-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology "resonance-assisted hydrogen bonding (RHAB)" may be replaced with "resonance-assisted binding" which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea).

    PubMed

    Berry, Tina E; Osterrieder, Sylvia K; Murray, Dáithí C; Coghlan, Megan L; Richardson, Anthony J; Grealy, Alicia K; Stat, Michael; Bejder, Lars; Bunce, Michael

    2017-07-01

    The analysis of apex predator diet has the ability to deliver valuable insights into ecosystem health, and the potential impacts a predator might have on commercially relevant species. The Australian sea lion (Neophoca cinerea) is an endemic apex predator and one of the world's most endangered pinnipeds. Given that prey availability is vital to the survival of top predators, this study set out to understand what dietary information DNA metabarcoding could yield from 36 sea lion scats collected across 1,500 km of its distribution in southwest Western Australia. A combination of PCR assays were designed to target a variety of potential sea lion prey, including mammals, fish, crustaceans, cephalopods, and birds. Over 1.2 million metabarcodes identified six classes from three phyla, together representing over 80 taxa. The results confirm that the Australian sea lion is a wide-ranging opportunistic predator that consumes an array of mainly demersal fauna. Further, the important commercial species Sepioteuthis australis (southern calamari squid) and Panulirus cygnus (western rock lobster) were detected, but were present in <25% of samples. Some of the taxa identified, such as fish, sharks and rays, clarify previous knowledge of sea lion prey, and some, such as eel taxa and two gastropod species, represent new dietary insights. Even with modest sample sizes, a spatial analysis of taxa and operational taxonomic units found within the scat shows significant differences in diet between many of the sample locations and identifies the primary taxa that are driving this variance. This study provides new insights into the diet of this endangered predator and confirms the efficacy of DNA metabarcoding of scat as a noninvasive tool to more broadly define regional biodiversity.

  17. Maternal low glycaemic index diet, fat intake and postprandial glucose influences neonatal adiposity – secondary analysis from the ROLO study

    PubMed Central

    2014-01-01

    Background The in utero environment is known to affect fetal development however many of the mechanisms by which this occurs remain unknown. The aim of this study was to examine the association between maternal dietary macronutrient intake and lifestyle throughout pregnancy and neonatal weight and adiposity. Methods This was an analysis of 542 mother and infant pairs from the ROLO study (Randomised cOntrol trial of LOw glycaemic index diet versus no dietary intervention to prevent recurrence of fetal macrosomia). Food diaries as well as food frequency and lifestyle and physical activity questionnaires were completed during pregnancy. Maternal anthropometry was measured throughout pregnancy and neonatal anthropometry was measured at birth. Results Multiple linear regression analysis revealed the main maternal factor associated with increased birth weight was greater gestational weight gain R2adj23.3% (F = 11.547, p < 0.001). The main maternal factor associated with increased birth length was non-smoking status R2adj27.8% (F = 6.193, p < 0.001). Neonatal central adiposity (determined using waist:length ratio) was negatively associated with maternal age, and positively associated with the following parameters: smoking status, maternal pre-pregnancy arm circumference, percentage energy from saturated fat in late pregnancy, postprandial glucose at 28 weeks gestation and membership of the control group with a positive trend towards association with trimester 2 glycaemic load R2adj 38.1% (F = 8.000, p < 0.001). Conclusions Several maternal diet and lifestyle factors were associated with neonatal anthropometry . Low glycaemic index dietary intervention in pregnancy was found to have a beneficial effect on neonatal central adiposity. Additionally, central adiposity was positively associated with maternal dietary fat intake and postprandial glucose highlighting the important role of healthy diet in pregnancy in promoting normal neonatal adiposity

  18. Maternal low glycaemic index diet, fat intake and postprandial glucose influences neonatal adiposity--secondary analysis from the ROLO study.

    PubMed

    Horan, Mary K; McGowan, Ciara A; Gibney, Eileen R; Donnelly, Jean M; McAuliffe, Fionnuala M

    2014-08-01

    The in utero environment is known to affect fetal development however many of the mechanisms by which this occurs remain unknown. The aim of this study was to examine the association between maternal dietary macronutrient intake and lifestyle throughout pregnancy and neonatal weight and adiposity. This was an analysis of 542 mother and infant pairs from the ROLO study (Randomised cOntrol trial of LOw glycaemic index diet versus no dietary intervention to prevent recurrence of fetal macrosomia). Food diaries as well as food frequency and lifestyle and physical activity questionnaires were completed during pregnancy. Maternal anthropometry was measured throughout pregnancy and neonatal anthropometry was measured at birth. Multiple linear regression analysis revealed the main maternal factor associated with increased birth weight was greater gestational weight gain R2adj 23.3% (F = 11.547, p < 0.001). The main maternal factor associated with increased birth length was non-smoking status R2adj 27.8% (F = 6.193, p < 0.001). Neonatal central adiposity (determined using waist:length ratio) was negatively associated with maternal age, and positively associated with the following parameters: smoking status, maternal pre-pregnancy arm circumference, percentage energy from saturated fat in late pregnancy, postprandial glucose at 28 weeks gestation and membership of the control group with a positive trend towards association with trimester 2 glycaemic load R2adj 38.1% (F = 8.000, p < 0.001). Several maternal diet and lifestyle factors were associated with neonatal anthropometry . Low glycaemic index dietary intervention in pregnancy was found to have a beneficial effect on neonatal central adiposity. Additionally, central adiposity was positively associated with maternal dietary fat intake and postprandial glucose highlighting the important role of healthy diet in pregnancy in promoting normal neonatal adiposity. Current Controlled Trials ISRCTN54392969.

  19. 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

  20. 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

  1. 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.

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

    PubMed Central

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

    2013-01-01

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

  3. 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.

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

    USGS Publications Warehouse

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

    2006-01-01

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

  5. 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

  6. 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

  7. Perceptions of genetic testing for personalized nutrition: a randomized trial of DNA-based dietary advice.

    PubMed

    Nielsen, Daiva E; Shih, Sarah; El-Sohemy, Ahmed

    2014-01-01

    Direct-to-consumer (DTC) genetic tests have facilitated easy access to personal genetic information related to health and nutrition; however, consumer perceptions of the nutritional information provided by these tests have not been evaluated. The objectives of this study were to assess individual perceptions of personalized nutrition and genetic testing and to determine whether a personalized nutrition intervention modifies perceptions. A double-blind, parallel-group, randomized controlled trial was conducted among healthy men and women aged 20-35 years (n = 138). Participants in the intervention group (n = 92) were given a report of DNA-based dietary advice and those in the control group (n = 46) were given a general dietary advice report. A survey was completed at baseline and 3 and 12 months after distributing the reports to assess perceptions between the two groups. No significant differences in perceptions of personalized nutrition and genetic testing were observed between the intervention and control group, so responses of both groups were combined. As compared to baseline, participant responses increased significantly toward the positive end of a Likert scale at 3 months for the statement 'I am interested in the relationship between diet and genetics' (mean change ± SD: 0.28 ± 0.99, p = 0.0002). The majority of participants indicated that a university research lab (47%) or health care professional (41%) were the best sources for obtaining accurate personal genetic information, while a DTC genetic testing company received the fewest selections (12%). Most participants (56%) considered dietitians to be the best source of personalized nutrition followed by medical doctors (27%), naturopaths (8%) and nurses (6%). These results suggest that perceptions of personalized nutrition changed over the course of the intervention. Individuals view a research lab or health care professional as better providers of genetic information than a DTC genetic testing company

  8. 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.

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

    PubMed Central

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

    2015-01-01

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

  10. 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

  11. 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

    2017-09-01

    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. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. 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.

  13. Vegetarian diets.

    PubMed

    Sutnick, M R

    1975-06-01

    A growing number of Americans are choosing to follow vegetarian diets. These diets can meet the nutritional needs of individuals of all ages. Vegetarians who eat eggs and/or milk and dairy products have no special problems in obtaining adequate nutrients. Pure vegetarians, who avoid all animal products, should pay particular attention to sources of protein, calcium, and riboflavin. Supplementation of vitamin B12 is indicated in these individuals. Guidelines for both good normal nutrition and therapeutic diets can be adapted for use with a vegetarian diet.

  14. Association of maternal and index child's diet with subsequent leukemia risk: A systematic review and meta analysis.

    PubMed

    Dessypris, Nick; Karalexi, Maria A; Ntouvelis, Evangelos; Diamantaras, Andreas-Antonios; Papadakis, Vassilios; Baka, Margarita; Hatzipantelis, Emmanuel; Kourti, Maria; Moschovi, Maria; Polychronopoulou, Sophia; Sidi, Vasiliki; Stiakaki, Eftichia; Petridou, Eleni Th

    2017-04-01

    Exploring the effect of maternal and/or childhood diet on offspring leukemogenesis is challenging, given differences in food group categories, their potentially variable impact depending on time window of exposure and the multiple leukemia subtypes. We opted to quantitatively synthesize published data on the association of maternal/child diet with leukemia risk. Medline was searched until June 30th, 2016 for eligible articles on the association of childhood leukemia with consumption of (i) food groups, excluding alcoholic and non-alcoholic beverages, and (ii) specific dietary supplements before/during index pregnancy and childhood. Eighteen studies of case-control design (N=11,720 cases/18,721 controls) were included, of which nine assessed maternal dietary components, five index child's and four both, mainly focusing on acute lymphoblastic leukemia (ALL). Statistically significant inverse estimates for ALL were found (2 studies, 413 cases, 490 controls) for fruit (OR: 0.81, 95% CI: 0.67, 0.99); vegetables (OR: 0.51, 95% CI: 0.28, 0.94); legumes (OR: 0.76, 95% CI: 0.62, 0.94); fish (OR: 0.27, 95% CI: 0.14, 0.53, among the 0-4year old; 2 studies 215 cases, 215 controls); preconception folic acid supplementation (OR: 0.69, 95%CI: 0.50-0.95; published meta analysis plus 2 studies, 3511 cases, 6816 controls); and use of vitamins during pregnancy (OR: 0.81, 95%CI: 0.74-0.88; published meta analysis plus one study, 5967 cases, 8876 controls). The associations (2 studies) of the remaining food groups and maternal dietary supplements consumption during pregnancy as well as of childhood diet and supplements intake (2-4 studies) were non significant. Maternal consumption of specific food groups comprising"healthy" items of the Mediterranean diet, preconception use of folic acid and intake of vitamins during pregnancy were associated with decreased ALL risk. Further research is needed, however preferably with homogeneous dietary information and data on immunophenotypic

  15. 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

  16. Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations.

    PubMed

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

    2014-08-12

    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. The increased availability of high-throughput sequencing data has positioned the gut microbiota as a major new focal point for biomedical research. However, despite the expenditure of huge efforts and resources, sequencing-based analysis of the microbiome has uncovered mostly associative relationships between human health and diet, rather than a causal, mechanistic one. In order to utilize the full potential of systems biology approaches, one must first characterize the metabolic requirements of gut bacteria, specifically, the degradation of glycans, which are their primary nutritional source. We developed a computational framework called GlyDeR for integrating expert knowledge along with high-throughput data to uncover important new relationships within glycan metabolism

  17. Intermolecular magnetic interactions in stacked DNA base pairs.

    PubMed

    Martínez, Fernando A; Aucar, Gustavo A

    2017-10-09

    The influence of pi-stacking on the magnetic properties of atoms that belong to adenine-thymine and guanine-cytosine pairs in sequences of three and five layers of DNA base pairs was analysed. As probes we used NMR spectroscopic parameters, which are among the most useful tools to learn about the transmission of magnetic interactions in molecules. Four DFT functionals were employed: B3LYP, BHANDLYP, KT2 and KT3, together with the SOPPA method. Besides, given that the number of non-hydrogen atoms of the supramolecular systems studied here is larger than 50 we applied a locally dense basis set scheme. Our results show that the piling up of a few Watson-Crick base pairs above and below a given pair modifies its NMR spectroscopic parameters by an amount that may be measurable and the percentage of variation does not depend on dispersion. We found that magnetic shieldings are more sensitive than J-couplings, and also that some atoms are more sensitive than others. Stacking affects the shielding of non-hydrogen atoms like nitrogens, that are donors in hydrogen bonds, HBs, and the carbons bonded to them. The amount of variation of these shieldings was found to be from 2% to 5% when the pairs are considered first as isolated, and then, placed in the middle of a sequence of three layers of base pairs. Such a variation becomes vanishingly small when the sequence contains more than three layers, showing that the stacking effect on NMR spectroscopic parameters has a local nature. We have also found a pattern for shieldings. First, equivalent atoms of similar monomers (thymine and adenine, or guanine and cytosine) have similar values of absolute shieldings in isolated pairs, and the amount of variation from isolated pairs to aggregates of a few pairs is also similar, meaning that equivalent atoms are affected in a similar manner by pi-stacking. Second, the hydrogen atoms which belong to hydrogen bonds are more sensitive to the piling up than the non-hydrogen atoms.

  18. 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.

  19. Phytolith analysis on dental calculus, enamel surface, and burial soil: information about diet and paleoenvironment.

    PubMed

    Fox, C L; Juan, J; Albert, R M

    1996-09-01

    Silica phytoliths (microscopic remains originating in plant tissues) have been identified on the enamel surface and dental calculus of a sample of teeth selected from well preserved skeletons from a Late Roman necropolis in Tarragona (Spain). Phytoliths were observed by scanning electron microscopy (SEM) and their siliceous nature was confirmed by X-ray microanalysis. The phytoliths were compared to those of soil samples from both the areas of the tombs corresponding to the abdomen and the periphery of the skeletons, and were classified taxonomically by comparison with a large collection of silica particles from modern plants in the Mediterranean area. Most of the phytoliths identified on the enamel and the dental calculus belong to the family of Poaceae, while the phytoliths from the abdominal area belong to Poaceae, Leguminosae, Cyperaceae, and Chenopodiaceae. Results are concordant with archaeological, ecological, and historical data from the same site, and with the human Mediterranean diet. If done properly, the study of phytoliths can provide direct information about the vegetable diet of past human populations, and could be applied to the study of human fossils.

  20. 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.

  1. [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.

  2. Effects of anti-obesity drugs, diet, and exercise on weight-loss maintenance after a very-low-calorie diet or low-calorie diet: a systematic review and meta-analysis of randomized controlled trials123

    PubMed Central

    Neovius, Martin; Hemmingsson, Erik

    2014-01-01

    Background: Weight-loss maintenance remains a major challenge in obesity treatment. Objective: The objective was to evaluate the effects of anti-obesity drugs, diet, or exercise on weight-loss maintenance after an initial very-low-calorie diet (VLCD)/low-calorie diet (LCD) period (<1000 kcal/d). Design: We conducted a systematic review by using MEDLINE, the Cochrane Controlled Trial Register, and EMBASE from January 1981 to February 2013. We included randomized controlled trials that evaluated weight-loss maintenance strategies after a VLCD/LCD period. Two authors performed independent data extraction by using a predefined data template. All pooled analyses were based on random-effects models. Results: Twenty studies with a total of 27 intervention arms and 3017 participants were included with the following treatment categories: anti-obesity drugs (3 arms; n = 658), meal replacements (4 arms; n = 322), high-protein diets (6 arms; n = 865), dietary supplements (6 arms; n = 261), other diets (3 arms; n = 564), and exercise (5 arms; n = 347). During the VLCD/LCD period, the pooled mean weight change was −12.3 kg (median duration: 8 wk; range 3–16 wk). Compared with controls, anti-obesity drugs improved weight-loss maintenance by 3.5 kg [95% CI: 1.5, 5.5 kg; median duration: 18 mo (12–36 mo)], meal replacements by 3.9 kg [95% CI: 2.8, 5.0 kg; median duration: 12 mo (10–26 mo)], and high-protein diets by 1.5 kg [95% CI: 0.8, 2.1 kg; median duration: 5 mo (3–12 mo)]. Exercise [0.8 kg; 95% CI: −1.2, 2.8 kg; median duration: 10 mo (6–12 mo)] and dietary supplements [0.0 kg; 95% CI: −1.4, 1.4 kg; median duration: 3 mo (3–14 mo)] did not significantly improve weight-loss maintenance compared with control. Conclusion: Anti-obesity drugs, meal replacements, and high-protein diets were associated with improved weight-loss maintenance after a VLCD/LCD period, whereas no significant improvements were seen for dietary supplements and exercise. PMID:24172297

  3. Effects of anti-obesity drugs, diet, and exercise on weight-loss maintenance after a very-low-calorie diet or low-calorie diet: a systematic review and meta-analysis of randomized controlled trials.

    PubMed

    Johansson, Kari; Neovius, Martin; Hemmingsson, Erik

    2014-01-01

    Weight-loss maintenance remains a major challenge in obesity treatment. The objective was to evaluate the effects of anti-obesity drugs, diet, or exercise on weight-loss maintenance after an initial very-low-calorie diet (VLCD)/low-calorie diet (LCD) period (<1000 kcal/d). We conducted a systematic review by using MEDLINE, the Cochrane Controlled Trial Register, and EMBASE from January 1981 to February 2013. We included randomized controlled trials that evaluated weight-loss maintenance strategies after a VLCD/LCD period. Two authors performed independent data extraction by using a predefined data template. All pooled analyses were based on random-effects models. Twenty studies with a total of 27 intervention arms and 3017 participants were included with the following treatment categories: anti-obesity drugs (3 arms; n = 658), meal replacements (4 arms; n = 322), high-protein diets (6 arms; n = 865), dietary supplements (6 arms; n = 261), other diets (3 arms; n = 564), and exercise (5 arms; n = 347). During the VLCD/LCD period, the pooled mean weight change was -12.3 kg (median duration: 8 wk; range 3-16 wk). Compared with controls, anti-obesity drugs improved weight-loss maintenance by 3.5 kg [95% CI: 1.5, 5.5 kg; median duration: 18 mo (12-36 mo)], meal replacements by 3.9 kg [95% CI: 2.8, 5.0 kg; median duration: 12 mo (10-26 mo)], and high-protein diets by 1.5 kg [95% CI: 0.8, 2.1 kg; median duration: 5 mo (3-12 mo)]. Exercise [0.8 kg; 95% CI: -1.2, 2.8 kg; median duration: 10 mo (6-12 mo)] and dietary supplements [0.0 kg; 95% CI: -1.4, 1.4 kg; median duration: 3 mo (3-14 mo)] did not significantly improve weight-loss maintenance compared with control. Anti-obesity drugs, meal replacements, and high-protein diets were associated with improved weight-loss maintenance after a VLCD/LCD period, whereas no significant improvements were seen for dietary supplements and exercise.

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

    PubMed

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

    2012-07-01

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

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. Diet and Men's Sexual Health.

    PubMed

    La, Justin; Roberts, Natalie H; Yafi, Faysal A

    2017-08-01

    Male sexual dysfunctions are more prevalent with aging. With increasing evidence about the impact of various diets on chronic diseases, there is a growing interest in establishing an association between various diets and men's health and sexual dysfunction. To review the current literature examining diet and dietary patterns and male sexual health. A thorough literature search of peer-reviewed publications on the association between diet and dietary patterns and male sexual health (erectile dysfunction, hypogonadism, and infertility) was carried using the online PubMed database from 1977 through 2017 with the keywords diet, dietary patterns, erectile dysfunction, male hypogonadism, low testosterone, and male infertility. Summary of significant findings on erectile function, androgen levels, and semen analysis parameters in relation to diets or dietary patterns. Thirteen studies on diet and erectile dysfunction and 15 studies on diet and testosterone levels were reviewed, including observational studies and randomized controlled trials. Thirteen studies analyzing the relation between diet and semen analysis parameters were reviewed but consisted of only cross-sectional and case-control studies. Evidence exists demonstrating the association between various diets and men's sexual health. Erectile dysfunction appears to lessen in men adhering to the Mediterranean diet. Obese and overweight men who lose weight through low-fat, low-calorie diets seem to have improvements in their erectile function and testosterone levels. Furthermore, a Western diet is associated with lower semen quality. Future prospective and randomized controlled trials are necessary to establish the benefit of diet and dietary patterns on men's sexual health. La J, Roberts NH, Yafi FA. Diet and Men's Sexual Health. Sex Med Rev 2017;X:XXX-XXX. Copyright © 2017 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

  11. A DNA-based registry for all animal species: the barcode index number (BIN) system.

    PubMed

    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.

  12. 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

  13. Association of vegetarian diet with inflammatory biomarkers: a systematic review and meta-analysis of observational studies.

    PubMed

    Haghighatdoost, Fahimeh; Bellissimo, Nick; Totosy de Zepetnek, Julia O; Rouhani, Mohammad Hossein

    2017-10-01

    Vegetarian diets contain various anti-inflammatory components. We aimed to investigate the effects of vegetarianism on inflammatory biomarkers when compared with omnivores. Systematic review and meta-analysis. Literature search was conducted in Science Direct, Proquest, MEDLINE and Google Scholar up to June 2016. Summary estimates and corresponding 95 % CI were derived via the DerSimonian and Laird method using random effects, subgroup analyses were run to find the source of heterogeneity and a fixed-effect model examined between-subgroup heterogeneity. Studies were included if they evaluated effects of any type of vegetarianism compared with omnivores on circulating levels of inflammatory biomarkers. No restriction was made in terms of language or the date of study publications. Eighteen articles were included. Pooled effect size showed no difference in high-sensitivity C-reactive protein (hs-CRP) levels in vegetarians v. omnivores (Hedges' g=-0·15; 95 % CI -0·35, 0·05), with high heterogeneity (I 2=75·6 %, P<0·01). A subgroup analysis by minimum duration of vegetarianism showed that a minimum duration of 2 years vegetarianism was associated with lower hs-CRP levels v. omnivores (Hedges' g=-0·29; 95 % CI -0·59, 0·01), with moderate heterogeneity (I 2=68·9 %, P<0·01). No significant effect was found in studies using a minimum duration of 6 months of vegetarianism, with low heterogeneity. Vegetarianism was associated with increased IL-6 concentrations (0·21 pg/ml; 95 % CI 0·18, 0·25), with no heterogeneity (I 2=0·0 %, P=0·60). The meta-analysis provides evidence that vegetarianism is associated with lower serum concentrations of hs-CRP when individuals follow a vegetarian diet for at least 2 years. Further research is necessary to draw appropriate conclusions regarding potential associations between vegetarianism and IL-6 levels. A vegetarian diet might be a useful approach to manage inflammaging in the long term.

  14. A DNA-Based Encryption Method Based on Two Biological Axioms of DNA Chip and Polymerase Chain Reaction (PCR) Amplification Techniques.

    PubMed

    Zhang, Yunpeng; Wang, Zhiwen; Wang, Zhenzhen; Liu, Xin; Yuan, Xiaojing

    2017-09-27

    Researchers have gained a deeper understanding of DNA-based encryption and its effectiveness in enhancing information security in recent years. However, there are many theoretical and technical issues about DNA-based encryption that need to be addressed before it can be effectively used in the field of security. Currently, the most popular DNA-based encryption schemes are based on traditional cryptography and the integration of existing DNA technology. These schemes are not completely based on DNA computing and biotechnology. Herein, as inspired by nature, encryption based on DNA has been developed, which is, in turn, based on two fundamental biological axioms about DNA sequencing: 1) DNA sequencing is difficult under the conditions of not knowing the correct sequencing primers and probes, and 2) without knowing the correct probe, it is difficult to decipher precisely and sequence the information of unknown and mixed DNA/peptide nucleic acid (PNA) probes, which only differ in nucleotide sequence, arranged on DNA chips (microarrays). In essence, when creating DNA-based encryption by means of biological technologies, such as DNA chips and polymerase chain reaction (PCR) amplification, the encryption method discussed herein cannot be decrypted, unless the DNA/PNA probe or PCR amplification is known. The biological analysis, mathematical analysis, and simulation results demonstrate the feasibility of the method, which provides much stronger security and reliability than that of traditional encryption methods. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed Central

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

    1992-01-01

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

  16. 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 Central

    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.

    2013-01-01

    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 genotype and diet interact to influence FG or FI concentration. We constructed a diet score using study-specific quartile rankings for intakes of whole grains, fish, fruits, vegetables, and nuts/seeds (favorable) and red/processed meats, sweets, sugared beverages, and fried potatoes (unfavorable). We used linear regression within studies, followed by inverse-variance-weighted meta-analysis, to quantify 1) associations of diet score with FG and FI levels and 2) interactions of diet score with 16 FG-associated loci and 2 FI-associated loci. Diet score (per unit increase) was inversely associated with FG (β = −0.004 mmol/L, 95% confidence interval: −0.005, −0.003) and FI (β = −0.008 ln-pmol/L, 95% confidence interval: −0.009, −0.007) levels after adjustment for demographic factors, lifestyle, and body mass index. Genotype variation at the studied loci did not modify these associations. Healthier diets were associated with lower FG and FI concentrations regardless of genotype at previously replicated FG- and FI-associated loci. Studies focusing on genomic regions that do not yield highly statistically significant associations from main-effect genome-wide association studies may be more fruitful in identifying diet-gene interactions. PMID:23255780

  17. 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.

  18. 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

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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.

  4. 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

  5. Transcriptomic analysis of hepatic responses to testosterone deficiency in miniature pigs fed a high-cholesterol diet.

    PubMed

    Cai, Zhaowei; Jiang, Xiaoling; Pan, Yongming; Chen, Liang; Zhang, Lifan; Zhu, Keyan; Cai, Yueqin; Ling, Yun; Chen, Fangming; Xu, Xiaoping; Chen, Minli

    2015-02-06

    Recent studies have indicated that low serum testosterone levels are associated with increased risk of developing hepatic steatosis; however, the mechanisms mediating this phenomenon have not been fully elucidated. To gain insight into the role of testosterone in modulating hepatic steatosis, we investigated the effects of testosterone on the development of hepatic steatosis in pigs fed a high-fat and high-cholesterol (HFC) diet and profiled hepatic gene expression by RNA-Seq in HFC-fed intact male pigs (IM), castrated male pigs (CM), and castrated male pigs with testosterone replacement (CMT). Serum testosterone levels were significantly decreased in CM pigs, and testosterone replacement attenuated castration-induced testosterone deficiency. CM pigs showed increased liver injury accompanied by increased hepatocellular steatosis, inflammation, and elevated serum alanine aminotransferase levels compared with IM pigs. Moreover, serum levels of total cholesterol, low-density lipoprotein cholesterol, and triglycerides were markedly increased in CM pigs. Testosterone replacement decreased serum and hepatic lipid levels and improved liver injury in CM pigs. Compared to IM and CMT pigs, CM pigs had lower serum levels of superoxide dismutase but higher levels of malondialdehyde. Gene expression analysis revealed that upregulated genes in the livers of CM pigs were mainly enriched for genes mediating immune and inflammatory responses, oxidative stress, and apoptosis. Surprisingly, the downregulated genes mainly included those that regulate metabolism-related processes, including fatty acid oxidation, steroid biosynthesis, cholesterol and bile acid metabolism, and glucose metabolism. KEGG analysis showed that metabolic pathways, fatty acid degradation, pyruvate metabolism, the tricarboxylic acid cycle, and the nuclear factor-kappaB signaling pathway were the major pathways altered in CM pigs. This study demonstrated that testosterone deficiency aggravated

  6. Effects of diet and exercise on weight-related outcomes for breast cancer survivors and their adult daughters: an analysis of the DAMES trial.

    PubMed

    Tometich, Danielle B; Mosher, Catherine E; Winger, Joseph G; Badr, Hoda J; Snyder, Denise C; Sloane, Richard J; Demark-Wahnefried, Wendy

    2017-08-01

    Few trials have aimed to promote diet and exercise behaviors in both cancer survivors and their family members and examine their associations with weight-related outcomes. We conducted a secondary analysis to examine associations between change in diet and exercise behaviors and weight-related outcomes for overweight breast cancer survivors and their overweight adult daughters in the Daughters And MothErS Against Breast Cancer (DAMES) randomized trial. The DAMES trial assessed the impact of two iteratively tailored, mailed print diet and exercise interventions against standard brochures over a 12-month period. This analysis examined change in diet and exercise behaviors and weight-related variables from baseline to post-intervention for the 50 breast cancer survivors and their adult daughters randomized to the intervention arms. To reduce the potential for type II error in this pilot, p values <0.10 were considered statistically significant. For mothers, change in diet quality was uniquely related to change in BMI (β = -0.12, p = 0.082), weight (β = -0.12, p = 0.060), and waist circumference (β = -0.38, p = 0.001), whereas change in caloric intake was related to waist circumference (β = 0.21, p = 0.002). For daughters, change in caloric intake was related to change in waist circumference (β = 0.12, p = 0.055). However, change in diet quality was not associated with weight-related outcomes in daughters. Additionally, change in exercise was not associated with weight-related outcomes in mothers or daughters. Findings support mail-based and other tailored interventions for weight loss in this population, with an emphasis on diet quality for breast cancer survivors and caloric intake for their adult daughters.

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

    PubMed

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

    2014-02-12

    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. 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). 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 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. 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)). Social media may provide certain advantages for public health interventions; however, studies of social media interventions to date relating to healthy lifestyles tend to show low levels of participation and do not show significant differences between groups in key outcomes.

  8. 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.

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

    PubMed

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

    2015-01-21

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

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

    PubMed Central

    2014-01-01

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

  11. 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.

  12. 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.

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

    PubMed

    Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene

    2014-01-01

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

  14. Diet and the Risk of Head and Neck Cancer: A Pooled Analysis in the INHANCE Consortium

    PubMed Central

    Chuang, Shu-Chun; Jenab, Mazda; Heck, Julia E.; Bosetti, Cristina; Talamini, Renato; Matsuo, Keitaro; Castellsague, Xavier; Franceschi, Silvia; Herrero, Rolando; Winn, Deborah M.; La Vecchia, Carlo; Morgenstern, Hal; Zhang, Zuo-Feng; Levi, Fabio; Dal Maso, Luigino; Kelsey, Karl; McClean, Michael D.; Vaughan, Thomas; Lazarus, Philip; Muscat, Joshua; Ramroth, Heribert; Chen, Chu; Schwartz, Stephen M.; Eluf-Neto, Jose; Hayes, Richard B.; Purdue, Mark; Boccia, Stefania; Cadoni, Gabriella; Zaridze, David; Koifman, Sergio; Curado, Maria Paula; Ahrens, Wolfgang; Benhamou, Simone; Matos, Elena; Lagiou, Pagona; Szeszenia-Dabrowska, Neonilla; Olshan, Andrew F.; Fernandez, Leticia; Menezes, Ana; Agudo, Antonio; Daudt, Alexander W.; Merletti, Franco; Macfarlane, Gary J.; Kjaerheim, Kristina; Mates, Dana; Holcatova, Ivana; Schantz, Stimson; Yu, Guo-Pei; Simonato, Lorenzo; Brenner, Hermann; Mueller, Heiko; Conway, David I.; Thomson, Peter; Fabianova, Eleonora; Znaor, Ariana; Rudnai, Peter; Healy, Claire M.; Ferro, Gilles; Brennan, Paul; Boffetta, Paolo; Hashibe, Mia

    2013-01-01

    We investigated the association between diet and head and neck cancer (HNC) risk using data from the International Head and Neck Cancer Epidemiology (INHANCE) Consortium. The INHANCE pooled data included 22 case-control studies with 14,520 cases and 22,737 controls. Center-specific quartiles among the controls were used for food groups and frequencies per week were used for single food items. A dietary pattern score combining high fruit and vegetable intake and low red meat intake, was created. Odds ratios (OR) and 95% confidence intervals (CI) for the dietary items on the risk of HNC were estimated with a two-stage random effects logistic regression model. An inverse association was observed for higher frequency intake of fruit (4th vs. 1st quartile OR=0.52, 95% CI=0.43–0.62, ptrend<0.01) and vegetables (OR=0.66, 95% CI=0.49–0.90, ptrend=0.01). Intake of red meat (OR=1.40, 95% CI=1.13–1.74, ptrend=0.13) and processed meat (OR=1.37, 95% CI=1.14–1.65, ptrend<0.01) were positively associated with HNC risk. Higher dietary pattern scores, reflecting high fruit/vegetable and low red meat intake, were associated with reduced HNC risk (per score increment OR=0.90, 95% CI=0.84–0.97). PMID:22037906

  15. [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.

  16. 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

  17. Gout Diet

    MedlinePlus

    ... to lower levels of uric acid. A little history Gout has been associated for centuries with overindulgence ... nutrition-and-healthy-eating/in-depth/gout-diet/art-20048524 . Mayo Clinic Footer Legal Conditions and Terms ...

  18. 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 ...

  19. Effects of short-term hypocaloric diet on sympatho-vagal interaction assessed by spectral analysis of heart rate and blood pressure variability during stress tests in obese hypertensive patients.

    PubMed

    Ashida, Terunao; Ono, Chikako; Sugiyama, Takao

    2007-12-01

    We examined the effects of a short-term low-calorie diet on the activity of the autonomic nervous system during stress tests in obese patients with hypertension by analysis of heart rate and blood pressure variability. Eighteen obese inpatients with essential hypertension were given a regular-calorie diet (1,600 kcal, NaCl 7 g) for 4 days, and then a low-calorie diet (1,100 kcal, NaCl 7 g) for 11 days. During both the regular-calorie diet and low-calorie diet, power spectral analysis of heart rate and blood pressure variability at rest and during mental arithmetic test, deep breathing test, isometric handgrip test or cold pressor test was performed. Body weight and 24-h ambulatory blood pressure were significantly lower during the low-calorie diet than during the regular-calorie diet. Systolic and diastolic blood pressure significantly increased over the handgrip test and cold pressor test during both diets. The low frequency component (LF) of systolic blood pressure, a marker of sympathetic activity to the vasculature, during the deep breathing test and cold pressor test were significantly lower on the low-calorie diet than the regular-calorie diet. The blood leptin concentration was also significantly lower on the low-calorie diet than the regular-calorie diet. The decrease in body weight was positively correlated with the decrease in blood leptin concentration. The LF/high frequency component (HF) ratio of the RR interval at rest on the regular-calorie diet was negatively correlated with the decrease in blood leptin concentration. These results suggest that the autonomic nervous function assessed by analysis of heart rate and blood pressure variability during stress tests may be improved by weight loss due to a short-term low-calorie diet in obese patients with hypertension.

  20. Characterisation of UK diets according to degree of food processing and associations with socio-demographics and obesity: cross-sectional analysis of UK National Diet and Nutrition Survey (2008-12).

    PubMed

    Adams, Jean; White, Martin

    2015-12-18

    Food processing alters food from its natural state for safety, convenience, taste or palatability. Previous research suggests that industrially processed foods, and diets high in these products, tend to be less healthful. However, most previous work is based on household, rather than individual-level, data. Little has been reported on the relationship between processed food consumption and markers of health; or on socio-demographic correlates of processed food consumption. Our objective was to describe: the nutritional content of foods classified according to degree of processing; the nutritional content of diets with different relative intakes of processed foods; the socio-demographic characteristics of individuals with different relative intakes of processed foods; and the association between intake of processed foods and body weight. Secondary analysis of data from the UK National Diet and Nutrition Survey (2008-12), a large national cross-sectional study of diet. Dietary information was collected using four-day, unweighed, food-diaries. Foods were classified as: unprocessed or minimally processed (MPF; foods with no processing or mostly physical processes applied to single whole foods), processed ingredients (PI; extracted and purified components of single whole foods), or ultra-processed food products (UPF; products produced from industrial combining of MPF and PI). Two thousand one hundred seventy four adults were included. MPF and diets high in these foods, had the most healthful nutritional profile. UPF did not necessarily have the least healthful nutritional profile, but diets high in these foods did. Women, and older adults consumed more energy from MPF, and less from UPF. Those living in lower occupation social class households consumed less energy from MPF, but no more from UPF. Only higher intake of PI was consistently, inversely, associated with body weight. This is the first study to explore correlates of processed food consumption, using individual

  1. Contribution of diet to aggregate arsenic exposures—An analysis across populations

    PubMed Central

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

    2014-01-01

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

  2. FTO gene variation, macronutrient intake and coronary heart disease risk: a gene-diet interaction analysis.

    PubMed

    Gustavsson, Jaana; Mehlig, Kirsten; Leander, Karin; Berg, Christina; Tognon, Gianluca; Strandhagen, Elisabeth; Björck, Lena; Rosengren, Annika; Lissner, Lauren; Nyberg, Fredrik

    2016-02-01

    The fat mass and obesity-associated gene (FTO) is related to obesity and coronary heart disease (CHD). We studied interaction between macronutrient intake and FTO in association with CHD risk or body mass index (BMI). The pooled population-based case-control studies, SHEEP and INTERGENE, included 1,381 first-time CHD patients and 4,290 population controls genotyped for FTO rs9939609 (T/A). Diet data were collected in self-administered food frequency questionnaires. Macronutrients were dichotomized into low/high energy percentages (E%) by median levels in controls. Association of FTO genotype (TA/AA vs. TT) with CHD risk was analysed by multiple logistic regression, and with BMI by multiple linear regression. Interaction between FTO and macronutrient was assessed by introducing an interaction term FTO × macronutrient. Interaction on CHD as deviation from additive effects was assessed by calculating relative excess risk due to interaction. No statistically significant interaction was found between FTO genotype and any macronutrient on CHD risk or BMI on either the multiplicative or additive scale. However, FTO genotype (TA/AA vs. TT) was associated with significantly increased CHD risk only in subjects with low E% from fat (OR 1.36, 95% CI 1.11-1.66) or saturated fatty acids (OR 1.36, 95% CI 1.10-1.69), or in subjects with high E% from carbohydrate (OR 1.32, 95% CI 1.07-1.61) or protein (OR 1.41, 95% CI 1.13-1.75). Mean BMI was 0.3-0.6 kg/m(2) higher in control subjects with TA/AA compared to TT, regardless of macronutrient E%. We found no evidence of interactions between FTO genotype and macronutrient intake on CHD risk or BMI.

  3. 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.

  4. 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. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  5. Effectiveness of interventions to promote healthy diet in primary care: systematic review and meta-analysis of randomised controlled trials

    PubMed Central

    2013-01-01

    Background A diet rich in fruit, vegetables and dietary fibre and low in fat is associated with reduced risk of chronic disease. This review aimed to estimate the effectiveness of interventions to promote healthy diet for primary prevention among participants attending primary care. Methods A systematic review of trials using individual or cluster randomisation of interventions delivered in primary care to promote dietary change over 12 months in healthy participants free from chronic disease or defined high risk states. Outcomes were change in fruit and vegetable intake, consumption of total fat and fibre and changes in serum cholesterol concentration. Results Ten studies were included with 12,414 participants. The design and delivery of interventions were diverse with respect to grounding in behavioural theory and intervention intensity. A meta-analysis of three studies showed an increase in fruit consumption of 0.25 (0.01 to 0.49) servings per day, with an increase in vegetable consumption of 0.25 (0.06 to 0.44) serving per day. A further three studies that reported on fruit and vegetable consumption together showed a pooled increment of 0.50 (0.13 to 0.87) servings per day. The pooled effect on consumption of dietary fibre, from four studies, was estimated to be 1.97 (0.43 to 3.52) gm fibre per day. Data from five studies showed a mean decrease in total fat intake of 5.2% of total energy (1.5 to 8.8%). Data from three studies showed a mean decrease in serum cholesterol of 0.10 (-0.19 to 0.00) mmol/L. Conclusion Presently-reported interventions to promote healthy diet for primary prevention in primary care, which illustrate a diverse range of intervention methods, may yield small beneficial changes in consumption of fruit, vegetables, fibre and fat over 12 months. The present results do not exclude the possibility that more effective intervention strategies might be developed. PMID:24355095

  6. Physical activity, diet and BMI in children aged 6-8 years: a cross-sectional analysis.

    PubMed

    Basterfield, Laura; Jones, Angela R; Parkinson, Kathryn N; Reilly, Jessica; Pearce, Mark S; Reilly, John J; Adamson, Ashley J

    2014-06-05

    To assess relationships between current physical activity (PA), dietary intake and body mass index (BMI) in English children. Longitudinal birth cohort study in northeast England, cross-sectional analysis. 425 children (41% of the original cohort) aged 6-8 years (49% boys). PA over 7 days was measured objectively by an accelerometer; three categories of PA were created: 'active' ≥60 min/day moderate-to-vigorous-intensity PA (MVPA); 'moderately active' 30-59 min/day MVPA; 'inactive' <30 min/day MVPA. Dietary intake over 4 days was measured using a prospective dietary assessment tool which incorporated elements of the food diary and food frequency methods. Three diet categories were created: 'healthy', 'unhealthy' and 'mixed', according to the number of portions of different foods consumed. Adherence to the '5-a-day' recommendations for portions of fruit and vegetables was also assessed. Children were classified as 'healthy weight' or 'overweight or obese' (OW/OB) according to International Obesity Taskforce cutpoints for BMI. Associations between weight status and PA/diet categories were analysed using logistic regression. Few children met the UK-recommended guidelines for either MVPA or fruit and vegetable intake, with just 7% meeting the recommended amount of MVPA of 60 min/day, and 3% meeting the 5-a-day fruit and vegetable recommendation. Higher PA was associated with a lower OR for OW/OB in boys only (0.20, 95% CI 0.04 to 0.88). There was no association detected between dietary intake and OW/OB in either sex. Increasing MVPA may help to reduce OW/OB in boys; however, more research is required to examine this relationship in girls. Children are not meeting the UK guidelines for diet and PA, and more needs to be done to improve this situation. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  7. Analysis of electrocorticographic patterns in rats fed standard or hyperlipidic diets in a normal state or during status epilepticus.

    PubMed

    Pessoa, Daniella; Cruz, Raquel; Machado, Birajara; Tenorio, Bruno; Nogueira, Romildo

    2016-06-01

    The consumption of hyperlipidic diets has grown markedly in recent decades, and several studies have linked this consumption with the development of neurodegenerative diseases. Conversely, hyperlipidic diets have been used as an alternative therapy for refractory epilepsy. The purpose of this study was to evaluate the effects of a hyperlipidic diet on brain electrical activity before and during status epilepticus (SE) using computational and mathematical methods. Electrocorticogram (ECoG) was recorded in Wistar rats fed with standard and hyperlipidic diets. Each recording was obtained during 30-minute period (baseline), after this time, the SE was induced by pilocarpine, and recording was continued for another 30 minutes. The ECoG signals were analyzed by the following methods: power spectrum, Lempel-Ziv complexity (LZC), and fractal dimension of the phase space. Hyperlipidic diet in normal animals caused a decrease in the theta, alpha, and beta rhythm, and reduced the LZC of the brain electrical activity. However, when the animals were induced to SE, these differences between nutritional groups were not observed. SE caused in both dietary groups increase in theta, alpha, and beta rhythm values, and increase in the complexity of brain electrical activity. Hyperlipidic diet consumption attenuated the brain's electrical activity, suggesting that healthy individuals who habitually eat a hyperlipidic diet may develop dysfunctions such as cognitive decline and memory impairment. Furthermore, the antagonistic effect between hyperlipidic diet and SE suggests that this diet could protect against seizures.

  8. 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

  9. 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…

  10. 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…

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

    USDA-ARS?s Scientific Manuscript database

    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...

  12. 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

  13. Determining minimum food intake amounts for diet diversity scores to maximize associations with nutrient adequacy: an analysis of schoolchildren's diets in rural Kenya.

    PubMed

    Gewa, Constance A; Murphy, Suzanne P; Weiss, Robert E; Neumann, Charlotte G

    2014-12-01

    To explore multiple methods of calculating diet diversity scores (DDS) to maximize associations with predicted dietary micronutrient adequacy among schoolchildren in rural Kenya. Up to three 24 h recall interviews were administered for each child for a total of 1544 d of intake from all schoolchildren. Daily amounts of food consumed were assigned to one of eight food groups. Five DDS were developed based on various minimum intake amounts from each food group: (i) 1 g; (ii) 15 g; (iii) a variable minimum based on the content of a target nutrient for each group; (iv) the median intake level for each group; and (v) the 90th percentile intake level for each group. A diet was assigned 1 point towards the daily DDS if the food group intake was above the defined minimum level. Five scores were calculated for each child, and bivariate longitudinal random-effects models were used to assess the correlation between each DDS and the mean probability of adequacy for fourteen nutrients. Embu District, Kenya. Schoolchildren (n 529), mean age 7·00 (sd 1·41) years. Only DDS based on a 15 g minimum and DDS based on nutrient content were significantly associated with mean probability of adequacy after adjusting for energy intake (0·21 and 0·41, respectively). A DDS using minimum intakes based on nutrients contributed by a food group best predicted nutrient adequacy in this population. These analyses contribute to the continued search for simpler and more valid dietary quality indicators among low-income nations.

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

    PubMed

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

    2016-08-01

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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Ethanol fixation of sputum sediments for DNA-based detection of Mycobacterium tuberculosis.

    PubMed Central

    Williams, D L; Gillis, T P; Dupree, W G

    1995-01-01

    The effect of ethanol fixation on PCR detection and viability of Mycobacterium tuberculosis in human sputum sediments was evaluated. M. tuberculosis seeded into sputum sediments was efficiently killed when treated for 1 h with 50, 70, or 95% ethanol. PCR amplification of a 123-bp fragment of the M. tuberculosis-specific IS6110 was not affected in ethanol-treated samples even when fixation was extended to 24 h. Ethanol fixation of sputum sediments did not affect the PCR detection of M. tuberculosis in clinical samples. PCR results from ethanol-treated clinical samples containing M. tuberculosis (smear positive and smear negative) or other respiratory pathogens correlated directly with the results by conventional detection methods for M. tuberculosis. Our results show that ethanol fixation of human sputum sediments containing M. tuberculosis significantly reduces the potential exposure of workers to viable M. tuberculosis without affecting DNA analysis by PCR. Also, ethanol fixation of sputum sediments provides a simple and inexpensive way to store and transport clinical specimens identified for DNA-based diagnostics without refrigeration. PMID:7650186

  20. 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.

  1. From Pharmacognosia to DNA-Based Medicinal Plant Authentication - Pharmacognosy through the Centuries.

    PubMed

    Heinrich, Michael; Anagnostou, Sabine

    2017-10-01

    For centuries, pharmacognosy was essential for the identification, quality, purity, and, until the end of the 18th century, even for the efficacy of medicinal plants. Since the 19th century, it concentrated on authenticity, purity, quality and the analysis of active substances, and was established as an academic branch discipline within pharmacy and continuously developed into a modern, highly sophisticated science. Even though the paradigm in pharmacy changed in the 19th century with the discovery of morphine and concentrated on single substances that could be synthesized fast by the upcoming industry, medicinal plants always remained an important element of the Materia medica, and during the last decades, medicinal plants continue to be a source of remedies, and natural products are an inspiration for new medicine. In this research, pharmacognostic skills remain an essential element, both with regards to identity, quality assurance of botanicals (both herbal medicines and supplements), and the discovery and development of new medicines. Over the years, the specific pharmacognostical tools have changed dramatically, and most recently, DNA-based techniques have become another element of our spectrum of scientific methods. Georg Thieme Verlag KG Stuttgart · New York.

  2. 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.

  3. Effects of low-fat diet on serum lipids in premenopausal and postmenopausal women: a meta-analysis of randomized controlled trials.

    PubMed

    Wu, Liping; Ma, Di; Walton-Moss, Benita; He, Zhong

    2014-01-01

    This study aims to conduct a meta-analysis to evaluate the effects of a low-fat diet, in comparison with participants' usual diet, on serum lipids in premenopausal and postmenopausal women. Ten electronic databases were searched for relevant articles reporting randomized controlled trials through August 31, 2012, including PubMed/Medline, EMBASE, Cochrane Library, CINAHL, Web of Science, SCOPUS, ProQuest Dissertations and Theses, SinoMed, CNKI (Chinese database), and WanFang (Chinese database). This systematic review and meta-analysis, which evaluated the effects of a low-fat diet, in comparison with the participants' usual diet, was conducted according to the guidelines of the Cochrane Handbook for Systematic Reviews of Interventions. All analyses were performed using RevMan version 5 (Cochrane Collaboration). From 512 potentially relevant publication citations reviewed, 8 randomized clinical trials were included in the meta-analysis, representing 22 groups (11 intervention groups and 11 control groups). A total of 1,536 women (900 in the intervention group and 636 in the control group) met the inclusion criteria. Total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) values changed more favorably in participants randomized to low-fat diets than in participants randomized to their usual diets. Low-fat diet was found to induce significant reductions in TC (random-effects model: mean difference [MD], -0.49 mmol/L; 95% CI, -0.69 to -0.29; I = 42%; Peffect < 0.00001), HDL-C (MD, -0.12 mmol/L; 95% CI, -0.20 to -0.05; I = 49%; Peffect = 0.00006), and LDL-C (MD, -0.24 mmol/L; 95% CI, -0.38 to -0.09; I = 42%; Peffect = 0.001) for two groups. For subgroup analysis, low-fat diet was efficacious in reducing TC, HDL-C, and LDL-C in premenopausal women but did not significantly reduce the same outcomes in postmenopausal women. However, there were also no statistically significant differences in triglycerides (TG

  4. The effect of Mediterranean diet on the development of type 2 diabetes mellitus: a meta-analysis of 10 prospective studies and 136,846 participants.

    PubMed

    Koloverou, Efi; Esposito, Katherine; Giugliano, Dario; Panagiotakos, Demosthenes

    2014-07-01

    The purpose of this work was to meta-analyze prospective studies that have evaluated the effect of a Mediterranean diet on the development of type 2 diabetes. PubMed, Embase and the Cochrane Central Register of Controlled Trials databases were searched up to 20 November 2013. English language publications were allocated; 17 original research studies (1 clinical trial, 9 prospective and 7 cross-sectional) were identified. Primary analyses were limited to prospective studies and clinical trials, yielding to a sample of 136,846 participants. A systematic review and a random effects meta-analysis were conducted. Higher adherence to the Mediterranean diet was associated with 23% reduced risk of developing type 2 diabetes (combined relative risk for upper versus lowest available centile: 0.77; 95% CI: 0.66, 0.89). Subgroup analyses based on region, health status of participants and number of confounders controlling for, showed similar results. Limitations include variations in Mediterranean diet adherence assessment tools, confounders' adjustment, duration of follow up and number of events with diabetes. The presented results are of major public health importance, since no consensus exists concerning the best anti-diabetic diet. Mediterranean diet could, if appropriately adjusted to reflect local food availability and individual's needs, constitute a beneficial nutritional choice for the primary prevention of diabetes. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. 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

  6. Phosphate decreases urine calcium and increases calcium balance: A meta-analysis of the osteoporosis acid-ash diet hypothesis

    PubMed Central

    Fenton, Tanis R; Lyon, Andrew W; Eliasziw, Michael; Tough, Suzanne C; Hanley, David A

    2009-01-01

    Background The acid-ash hypothesis posits that increased excretion of "acidic" ions derived from the diet, such as phosphate, contributes to net acidic ion excretion, urine calcium excretion, demineralization of bone, and osteoporosis. The public is advised by various media to follow an alkaline diet to lower their acidic ion intakes. The objectives of this meta-analysis were to quantify the contribution of phosphate to bone loss in healthy adult subjects; specifically, a) to assess the effect of supplemental dietary phosphate on urine calcium, calcium balance, and markers of bone metabolism; and to assess whether these affects are altered by the b) level of calcium intake, c) the degree of protonation of the phosphate. Methods Literature was identified through computerized searches regarding phosphate with surrogate and/or direct markers of bone health, and was assessed for methodological quality. Multiple linear regression analyses, weighted for sample size, were used to combine the study results. Tests of interaction included stratification by calcium intake and degree of protonation of the phosphate supplement. Results Twelve studies including 30 intervention arms manipulated 269 subjects' phosphate intakes. Three studies reported net acid excretion. All of the meta-analyses demonstrated significant decreases in urine calcium excretion in response to phosphate supplements whether the calcium intake was high or low, regardless of the degree of protonation of the phosphate supplement. None of the meta-analyses revealed lower calcium balance in response to increased phosphate intakes, whether the calcium intake was high or low, or the composition of the phosphate supplement. Conclusion All of the findings from this meta-analysis were contrary to the acid ash hypothesis. Higher phosphate intakes were associated with decreased urine calcium and increased calcium retention. This meta-analysis did not find evidence that phosphate intake contributes to demineralization

  7. Phosphate decreases urine calcium and increases calcium balance: a meta-analysis of the osteoporosis acid-ash diet hypothesis.

    PubMed

    Fenton, Tanis R; Lyon, Andrew W; Eliasziw, Michael; Tough, Suzanne C; Hanley, David A

    2009-09-15

    The acid-ash hypothesis posits that increased excretion of "acidic" ions derived from the diet, such as phosphate, contributes to net acidic ion excretion, urine calcium excretion, demineralization of bone, and osteoporosis. The public is advised by various media to follow an alkaline diet to lower their acidic ion intakes. The objectives of this meta-analysis were to quantify the contribution of phosphate to bone loss in healthy adult subjects; specifically, a) to assess the effect of supplemental dietary phosphate on urine calcium, calcium balance, and markers of bone metabolism; and to assess whether these affects are altered by the b) level of calcium intake, c) the degree of protonation of the phosphate. Literature was identified through computerized searches regarding phosphate with surrogate and/or direct markers of bone health, and was assessed for methodological quality. Multiple linear regression analyses, weighted for sample size, were used to combine the study results. Tests of interaction included stratification by calcium intake and degree of protonation of the phosphate supplement. Twelve studies including 30 intervention arms manipulated 269 subjects' phosphate intakes. Three studies reported net acid excretion. All of the meta-analyses demonstrated significant decreases in urine calcium excretion in response to phosphate supplements whether the calcium intake was high or low, regardless of the degree of protonation of the phosphate supplement. None of the meta-analyses revealed lower calcium balance in response to increased phosphate intakes, whether the calcium intake was high or low, or the composition of the phosphate supplement. All of the findings from this meta-analysis were contrary to the acid ash hypothesis. Higher phosphate intakes were associated with decreased urine calcium and increased calcium retention. This meta-analysis did not find evidence that phosphate intake contributes to demineralization of bone or to bone calcium excretion

  8. Roux-en-Y gastric bypass compared with aggressive diet and exercise therapy for morbidly obese patients awaiting renal transplant: a decision analysis.

    PubMed

    Choudhury, Rashikh A; Murayama, Kenric M; Abt, Peter L; Glick, Henry A; Naji, Ali; Williams, Noel N; Dumon, Kristoffel R

    2014-01-01

    The optimal management of morbidly obese patients awaiting renal transplant is controversial and unknown. The objective of this study was to compare the impact of Roux-en-Y gastric bypass (RYGB) versus diet and exercise on the survival of morbidly obese patients with end-stage renal disease awaiting renal transplant. A decision analytic Markov state transition model was designed to simulate the life of morbidly obese patients with end-stage renal disease awaiting transplant. Life expectancy after RYGB and after 1 and 2 years of diet and exercise was estimated and compared in the framework of 2 clinical scenarios in which patients above a body mass index (BMI) of 35 kg/m(2) or above a BMI of 40 kg/m(2) were ineligible for transplantation, reflecting the BMI restrictions of many transplant centers. In addition to base case analysis (45 kg/m(2) BMI preintervention), sensitivity analysis of initial BMI was completed. Markov model parameters were extracted from the literature. RYGB improved survival compared with diet and exercise. Patients who underwent RYGB received transplants sooner and in higher frequency. Using 40 kg/m(2) as the upper limit for transplant eligibility, base case patients who underwent RYGB gained 5.4 years of life, whereas patients who underwent 1 and 2 years of diet and exercise gained 1.5 and 2.8 years of life, respectively. Using 35 kg/m(2) as the upper limit, RYGB base case patients gained 5.3 years of life, whereas patients who underwent 1 and 2 years of diet and exercise gained .7 and 1.5 years of life, respectively. In morbidly obese patients with end-stage renal disease, RYGB may be more effective than optimistic weight loss outcomes after diet and exercise, thereby improving access to renal transplantation. Copyright © 2014 American Society for Bariatric Surgery. Published by Elsevier Inc. All rights reserved.

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

    PubMed

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

    2001-01-01

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

  10. Diet and colorectal cancer: analysis of a candidate pathway using SNPS, haplotypes, and multi-gene assessment.

    PubMed

    Slattery, Martha L; Lundgreen, Abbie; Herrick, Jennifer S; Caan, Bette J; Potter, John D; Wolff, Roger K

    2011-11-01

    There is considerable biologic plausibility to the hypothesis that genetic variability in pathways involved in insulin signaling and energy homeostasis may modulate dietary risk associated with colorectal cancer. We utilized data from 2 population-based case-control studies of colon (n = 1,574 cases, 1,970 controls) and rectal (n = 791 cases, 999 controls) cancer to evaluate genetic variation in candidate SNPs identified from 9 genes in a candidate pathway: PDK1, RP6KA1, RPS6KA2, RPS6KB1, RPS6KB2, PTEN, FRAP1 (mTOR), TSC1, TSC2, Akt1, PIK3CA, and PRKAG2 with dietary intake of total energy, carbohydrates, fat, and fiber. We employed SNP, haplotype, and multiple-gene analysis to evaluate associations. PDK1 interacted with dietary fat for both colon and rectal cancer and with dietary carbohydrates for colon cancer. Statistically significant interaction with dietary carbohydrates and rectal cancer was detected by haplotype analysis of PDK1. Evaluation of dietary interactions with multiple genes in this candidate pathway showed several interactions with pairs of genes: Akt1 and PDK1, PDK1 and PTEN, PDK1 and TSC1, and PRKAG2 and PTEN. Analyses show that genetic variation influences risk of colorectal cancer associated with diet and illustrate the importance of evaluating dietary interactions beyond the level of single SNPs or haplotypes when a biologically relevant candidate pathway is examined.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  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. Alternative diets.

    PubMed

    Berschneider, Helen M

    2002-02-01

    As pet owners become more conscious of their own diets and the impact it has on their health, they naturally become more interested in what their animal companions are eating and how that might be affecting their pet's health. Many are exploring alternatives to standard commercial pet foods, and some are asking their veterinarians for advice. Small-animal nutrition is an ever-changing field. What veterinarians were taught 10 years ago may no longer be sound advice. This article explores some of the reasoning behind the development of both conventional commercial pet foods and the alternative foods and diets. It questions some of the conventional dogma as well as some of the trendy assumptions in the current marketplace. The intent is to provide the veterinarian with some balanced information on which to base nutritional advice to clients, and to begin forming new opinions or at least asking new questions. Guidelines on formulating a homemade diet for dogs are included.

  18. Effect of a high-fat Mediterranean diet on bodyweight and waist circumference: a prespecified secondary outcomes analysis of the PREDIMED randomised controlled trial.

    PubMed

    Estruch, Ramon; Martínez-González, Miguel Angel; Corella, Dolores; Salas-Salvadó, Jordi; Fitó, Montserrat; Chiva-Blanch, Gemma; Fiol, Miquel; Gómez-Gracia, Enrique; Arós, Fernando; Lapetra, José; Serra-Majem, Lluis; Pintó, Xavier; Buil-Cosiales, Pilar; Sorlí, José V; Muñoz, Miguel A; Basora-Gallisá, Josep; Lamuela-Raventós, Rosa María; Serra-Mir, Mercè; Ros, Emilio

    2016-08-01

    Because of the high density of fat, high-fat diets are perceived as likely to lead to increased bodyweight, hence health-care providers are reluctant to recommend them to overweight or obese individuals. We assessed the long-term effects of ad libitum, high-fat, high-vegetable-fat Mediterranean diets on bodyweight and waist circumference in older people at risk of cardiovascular disease, most of whom were overweight or obese. PREDIMED was a 5 year parallel-group, multicentre, randomised, controlled clinical trial done in primary care centres affiliated to 11 hospitals in Spain. 7447 asymptomatic men (aged 55-80 years) and women (aged 60-80 years) who had type 2 diabetes or three or more cardiovascular risk factors were randomly assigned (1:1:1) with a computer-generated number sequence to one of three interventions: Mediterranean diet supplemented with extra-virgin olive oil (n=2543); Mediterranean diet supplemented with nuts (n=2454); or a control diet (advice to reduce dietary fat; n=2450). Energy restriction was not advised, nor was physical activity promoted. In this analysis of the trial, we measured bodyweight and waist circumference at baseline and yearly for 5 years in the intention-to-treat population. The PREDIMED trial is registered with ISRCTN.com, number ISRCTN35739639. After a median 4·8 years (IQR 2·8-5·8) of follow-up, participants in all three groups had marginally reduced bodyweight and increased waist circumference. The adjusted difference in 5 year changes in bodyweight in the Mediterranean diet with olive oil group was -0·43 kg (95% CI -0·86 to -0·01; p=0·044) and in the nut group was -0·08 kg (-0·50 to 0·35; p=0·730), compared with the control group. The adjusted difference in 5 year changes in waist circumference was -0·55 cm (-1·16 to -0·06; p=0·048) in the Mediterranean diet with olive oil group and -0·94 cm (-1·60 to -0·27; p=0·006) in the nut group, compared with the control group. A long-term intervention with an

  19. Influence of Dietary Approaches to Stop Hypertension (DASH) diet on blood pressure: a systematic review and meta-analysis on randomized controlled trials.

    PubMed

    Saneei, P; Salehi-Abargouei, A; Esmaillzadeh, A; Azadbakht, L

    2014-12-01

    Findings were not consistent on the therapeutic effect of Dietary Approaches to Stop Hypertension (DASH) diet on blood pressure. We aimed to review systematically and perform a meta-analysis to assess the magnitude of the effect of the DASH diet on blood pressure in randomized controlled trials (RCTs) among adults. We conducted a systematic review and random effects meta-analysis of all RCTs which evaluated the effect of the DASH diet on blood pressure including published papers until June 2013, using PubMed, ISI Web of Science, Scopus and Google scholar database. Subgroup analysis and meta-regression were used to find out possible sources of between-study heterogeneity. Seventeen RCTs contributing 20 comparisons with 2561 participants were included. Meta-analysis showed that the DASH diet significantly reduced systolic blood pressure by 6.74 mmHg (95%CI: -8.25, -5.23, I(2) = 78.1%) and diastolic blood pressure by 3.54 mmHg (95%CI: -4.29, -2.79, I(2) = 56.7%). RCTs with the energy restriction and those with hypertensive subjects showed a significantly greater decrease in blood pressure. Meta-regression showed that mean baseline of SBP and DBP was explained 24% and 49% of the variance between studies for SBP and DBP, respectively. The results revealed the profitable reducing effect of the DASH-like diet on both systolic and diastolic blood pressure in adults; although there was a variation in the extent of the fall in blood pressure in different subgroups. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Social media interventions for diet and exercise behaviours: a systematic review and meta-ana