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Sample records for dna-based diet analysis

  1. DNA-Based Diet Analysis for Any Predator

    PubMed Central

    Dunshea, Glenn

    2009-01-01

    Background Prey DNA from diet samples can be used as a dietary marker; yet current methods for prey detection require a priori diet knowledge and/or are designed ad hoc, limiting their scope. I present a general approach to detect diverse prey in the feces or gut contents of predators. Methodology/Principal Findings In the example outlined, I take advantage of the restriction site for the endonuclease Pac I which is present in 16S mtDNA of most Odontoceti mammals, but absent from most other relevant non-mammalian chordates and invertebrates. Thus in DNA extracted from feces of these mammalian predators Pac I will cleave and exclude predator DNA from a small region targeted by novel universal primers, while most prey DNA remain intact allowing prey selective PCR. The method was optimized using scat samples from captive bottlenose dolphins (Tursiops truncatus) fed a diet of 6–10 prey species from three phlya. Up to five prey from two phyla were detected in a single scat and all but one minor prey item (2% of the overall diet) were detected across all samples. The same method was applied to scat samples from free-ranging bottlenose dolphins; up to seven prey taxa were detected in a single scat and 13 prey taxa from eight teleost families were identified in total. Conclusions/Significance Data and further examples are provided to facilitate rapid transfer of this approach to any predator. This methodology should prove useful to zoologists using DNA-based diet techniques in a wide variety of study systems. PMID:19390570

  2. Assessing morphological and DNA-based diet analysis techniques in a generalist predator, the arrow squid Nototodarus gouldi.

    PubMed

    Braley, Michelle; Goldsworthy, Simon D; Page, Brad; Steer, Mike; Austin, Jeremy J

    2010-05-01

    Establishing the diets of marine generalist consumers is difficult, with most studies limited to the use of morphological methods for prey identification. Such analyses rely on the preservation of diagnostic hard parts, which can limit taxonomic resolution and introduce biases. DNA-based analyses provide a method to assess the diets of marine species, potentially overcoming many of the limitations introduced by other techniques. This study compared the effectiveness of morphological and DNA-based analysis for determining the diet of a free-ranging generalist predator, the arrow squid (Nototodarus gouldi). A combined approach was more effective than using either of the methods in isolation. Nineteen unique prey taxa were identified, of which six were found by both methods, 10 were only detected using DNA and three were only identified using morphological methods. Morphological techniques only found 50% of the total number of identifiable prey taxa, whereas DNA-based techniques found 84%. This study highlights the benefits of using a combination of techniques to detect and identify prey of generalist marine consumers.

  3. 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.

  4. 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

  5. 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.

  6. 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...

  7. 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

  8. In depth analysis of the quenching of three fluorene-phenylene-based cationic conjugated polyelectrolytes by DNA and DNA bases.

    PubMed

    Davies, Matthew L; Douglas, Peter; Burrows, Hugh D; Martincigh, Bice; Miguel, Maria da Graça; Scherf, Ullrich; Mallavia, Ricardo; Douglas, Alastair

    2014-01-16

    The interaction of three cationic poly {9,9-bis[N,N-(trimethylammonium)hexyl]fluorene-co-1,4-phenylene} polymers with average chain lengths of ∼6, 12, and 100 repeat units (PFP-NR36(I),12(Br),100(Br)) with both double and single stranded, short and long, DNA and DNA bases have been studied by steady state and time-resolved fluorescence techniques. Fluorescence of PFP-NR3 polymers is quenched with high efficiency by DNA (both double and single stranded) and DNA bases. The resulting quenching plots are sigmoidal and are not accurately described by using a Stern-Volmer quenching mechanism. Here, the quenching mechanism is well modeled in terms of an equilibrium in which a PFP-NR3/DNA aggregate complex is formed which brings polymer chains into close enough proximity to allow interchain excitation energy migration and quenching at aggregate or DNA base traps. Such an analysis gives equilibrium constants of 8.4 × 10(6) (±1.2 × 10(6)) M(-1) for short-dsDNA and 8.6 × 10(6) (±1.7 × 10(6)) M(-1) for short-ssDNA with PFP-NR36(I).

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

    PubMed

    Li, Cuiping; Wang, Hailin

    2015-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

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

    PubMed

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

    2015-04-01

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

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

    PubMed

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

    2015-04-01

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

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. DNA-based machines.

    PubMed

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

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

  7. 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.

  8. Diets

    MedlinePlus

    ... fat-free or low-fat milk and milk products May include lean meats, poultry, fish, beans, eggs ... specific region. Others, like the DASH diet, were designed for people who have certain health problems. But ...

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

    PubMed

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

    2015-07-01

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

  10. 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].

  11. 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.

  12. 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.

  13. Communication: Electron ionization of DNA bases.

    PubMed

    Rahman, M A; Krishnakumar, E

    2016-04-28

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

  14. [Forced Oscillations of DNA Bases].

    PubMed

    Yakushevich, L V; Krasnobaeva, L A

    2016-01-01

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

  15. [Forced Oscillations of DNA Bases].

    PubMed

    Yakushevich, L V; Krasnobaeva, L A

    2016-01-01

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

  16. 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.

  17. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  19. 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.

  20. Subterranean Sympatry: An Investigation into Diet Using Stable Isotope Analysis

    PubMed Central

    Robb, Gillian N.; Woodborne, Stephan; Bennett, Nigel C.

    2012-01-01

    In the Western Cape three species of mole-rat occur in sympatry, however, little is known about differences in their dietary preferences. Dietary composition of the three species; the common mole-rat (Cryptomys hottentotus hottentotus), the Cape mole-rat (Georychus capensis) and the Cape dune mole-rat (Bathyergus suillus) were examined using stable isotope analysis. Blood, fur and claw samples were collected from 70 mole-rats, in addition to several potential food items, to assess food selection of the three species under natural conditions. Overall there was a significant difference in the isotopic composition (δ13C and δ15N) between all three species and significant differences in their diet composition. There were also significant differences between tissues in all three species suggesting temporal variation in diet. The small size and colonial lifestyle of C. h. hottentotus allows it to feed almost 100% on bulbs, while the solitary and larger species G. capensis and B. suillus fed to a greater extent on other resources such as grasses and clover. B. suillus, the largest of the species, had the most generalized diet. However, overall all species relied most heavily upon geophytes and consumed the same species suggesting competition for resources could exist. We also showed a high level of individual variation in diet choices. This was most pronounced in B. suillus and G. capensis and less so in C. h. hottentotus. We demonstrate that stable isotope analysis can successfully be applied to examine dietary patterns in subterranean mammals and provide insights into foraging patterns and dietary variation at both the inter and intra population level. PMID:23139795

  1. Characterization of the tunneling conductance across DNA bases.

    PubMed

    Zikic, Radomir; Krstić, Predrag S; Zhang, X-G; Fuentes-Cabrera, Miguel; Wells, Jack; Zhao, Xiongce

    2006-07-01

    Characterization of the electrical properties of the DNA bases (adenine, cytosine, guanine, and thymine), in addition to building the basic knowledge on these fundamental constituents of a DNA, is a crucial step in developing a DNA sequencing technology. We present a first-principles study of the current-voltage characteristics of nucleotidelike molecules of the DNA bases, placed in a 1.5 nm gap formed between gold nanoelectrodes. The quantum transport calculations in the tunneling regime are shown to vary strongly with the electrode-molecule geometry and the choice of the density-functional theory exchange-correlation functionals. Analysis of the results in the zero-bias limit indicates that distinguishable current-voltage characteristics of different DNA bases are dominated by the geometrical conformations of the bases and nanoelectrodes.

  2. Characterization of the tunneling conductance across DNA bases

    SciTech Connect

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

    2006-01-01

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

  3. Characterization of the tunneling conductance across DNA bases

    NASA Astrophysics Data System (ADS)

    Zikic, Radomir; Krstić, Predrag S.; Zhang, X.-G.; Fuentes-Cabrera, Miguel; Wells, Jack; Zhao, Xiongce

    2006-07-01

    Characterization of the electrical properties of the DNA bases (adenine, cytosine, guanine, and thymine), in addition to building the basic knowledge on these fundamental constituents of a DNA, is a crucial step in developing a DNA sequencing technology. We present a first-principles study of the current-voltage characteristics of nucleotidelike molecules of the DNA bases, placed in a 1.5nm gap formed between gold nanoelectrodes. The quantum transport calculations in the tunneling regime are shown to vary strongly with the electrode-molecule geometry and the choice of the density-functional theory exchange-correlation functionals. Analysis of the results in the zero-bias limit indicates that distinguishable current-voltage characteristics of different DNA bases are dominated by the geometrical conformations of the bases and nanoelectrodes.

  4. 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

  5. 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

  6. 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.

  7. Molecular analysis of RAPD DNA based markers: their potential use for the detection of genetic variability in jojoba (Simmondsia chinensis L Schneider).

    PubMed

    Amarger, V; Mercier, L

    1995-01-01

    We have applied the recently developed technique of random amplified polymorphic DNA (RAPD) for the discrimination between two jojoba clones at the genomic level. Among a set of 30 primers tested, a simple reproducible pattern with three distinct fragments for clone D and two distinct fragments for clone E was obtained with primer OPB08. Since RAPD products are the results of arbitrarily priming events and because a given primer can amplify a number of non-homologous sequences, we wondered whether or not RAPD bands, even those of similar size, were derived from different loci in the two clones. To answer this question, two complementary approaches were used: i) cloning and sequencing of the amplification products from clone E; and ii) complementary Southern analysis of RAPD gels using cloned or amplified fragments (directly recovered from agarose gels) as RFLP probes. The data reported here show that the RAPD reaction generates multiple amplified fragments. Some fragments, although resolved as a single band on agarose gels, contain different DNA species of the same size. Furthermore, it appears that the cloned RAPD products of known sequence that do not target repetitive DNA can be used as hybridization probes in RFLP to detect a polymorphism among individuals.

  8. 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 ...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. 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.

  11. Enzyme-Operated DNA-Based Nanodevices

    PubMed Central

    2015-01-01

    Functional molecular nanodevices and nanomachines have attracted a growing interest for their potential use in life science and nanomedicine. In particular, due to their versatility and modularity DNA-based nanodevices appear extremely promising. However, a limitation of such devices is represented by the limited number of molecular stimuli and cues that can be used to control and regulate their function. Here we demonstrate the possibility to rationally control and regulate DNA-based nanodevices using biocatalytic reactions catalyzed by different enzymes. To demonstrate the versatility of our approach, we have employed three model DNA-based systems and three different enzymes (belonging to several classes, i.e., transferases and hydrolases). The possibility to use enzymes and enzymatic substrates as possible cues to operate DNA-based molecular nanodevices will expand the available toolbox of molecular stimuli to be used in the field of DNA nanotechnology and could open the door to many applications including enzyme-induced drug delivery and enzyme-triggered nanostructures assembly. PMID:26600418

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. HLA Class I typing of volunteers for a bone marrow registry: QC analysis by DNA-based methodology identifies serological typing discrepancies in the assignment of HLA-A and B antigens.

    PubMed

    Gourley, I S; Kearns, J; McKeen, M; Birkos, S; Brown, M; Kamoun, Malek

    2002-03-01

    Until recently, the majority of newly recruited volunteer donors were typed for HLA-A and -B by serology onto the National Marrow Donor Program Registry. Quality control of this serological typing performed by contracted laboratories was carried out by retesting approximately 1% of each laboratory's test volume utilizing DNA-based techniques (SSOP). The criteria used for selection included samples presumed to be homozygotes, samples with split antigen specificities and samples with antigens considered to be difficult to define. Out of 1983 samples analyzed, 156 HLA-A (3.9%) and 265 HLA-B (6.7%) locus discrepancies were identified. Review of these discrepancies by both the serological and QC laboratory revealed that the majority of discrepancies were due to errors in serological typing. Serological discrepancies were categorized as follows: blank antigens identified (36.8%) and misassignments (63.2%). Misassignments were defined as either the incorrect assignment of antigens within a group ("wrong split"), or a complete misassignment. Antigens reported as blanks most frequently belonged to the A19 and A28 groups and to the B70, 46 and 40 groups. The most frequent misassignments within groups were the A19 and A10 groups, and the B40 and B15 groups. Other HLA-A misassignments included A2 vs A28 or A2 vs A69, while other HLA-B misassignments included B35 and B70. This QC analysis showed that serological typing of class I antigens for the purposes of NMDP registry typing is prone to a significant error rate. Careful evaluation and selection of contracted laboratories by the NMDP suggests methodological limitations rather than poor performance as the main cause of these observations.

  17. DNA-Based Vaccine Guards Against Zika in Monkey Study

    MedlinePlus

    ... page: https://medlineplus.gov/news/fullstory_161106.html DNA-Based Vaccine Guards Against Zika in Monkey Study ... THURSDAY, Sept. 22, 2016 (HealthDay News) -- An experimental DNA-based vaccine protected monkeys from infection with the ...

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

    PubMed

    English, Sinead; Uller, Tobias

    2016-09-01

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

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

    PubMed

    English, Sinead; Uller, Tobias

    2016-09-01

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

  20. Fatty acid analysis as a tool to infer the diet in Illinois river otters (Lontra canadensis).

    PubMed

    Satterthwaite-Phillips, Damian; Novakofski, Jan; Mateus-Pinilla, Nohra

    2014-01-01

    Fatty acids (FA) have recently been used in several studies to infer the diet in a number of species. While these studies have been largely successful, most have dealt with predators that have a fairly specialized diet. In this paper, we used FA analysis as a tool to infer the diet of the nearctic river otter (Lontra canadensis). The river otter is an opportunistic predator known to subsist on a wide variety of prey including, fishes, crayfish, molluscs, reptiles and amphibians, among others. We analyzed the principle components of 60 FA from otters and 25 potential prey species in Illinois, USA. Prey species came from 4 major taxonomic divisions: fishes, crayfish, molluscs and amphibians. Within each division, most, but not all, species had significantly different profiles. Using quantitative FA signature analysis, our results suggest that, by mass, fish species are the most significant component of Illinois River otters' diet (37.7 ± 1.0%). Molluscs ranked second (32.0 ± 0.8%), followed by amphibians (27.3 ± 4.3%), and finally, crayfish (3.0 ± 0.6%). Our analysis indicates that molluscs make up a larger portion of the otter diet than previously reported. Throughout much of the Midwest there have been numerous otter reintroduction efforts, many of which appear to be successful. In regions where mollusc species are endangered, these data are essential for management agencies to better understand the potential impact of otters on these species. Our analysis further suggests that quantitative FA signature analysis can be used to infer diet even when prey species are diverse, to the extent that their FA profiles differ. Better understanding of the otter's metabolism of FA would improve inferences of diet from FA analysis.

  1. Recent progress on DNA based walkers.

    PubMed

    Pan, Jing; Li, Feiran; Cha, Tae-Gon; Chen, Haorong; Choi, Jong Hyun

    2015-08-01

    DNA based synthetic molecular walkers are reminiscent of biological protein motors. They are powered by hybridization with fuel strands, environment induced conformational transitions, and covalent chemistry of oligonucleotides. Recent developments in experimental techniques enable direct observation of individual walkers with high temporal and spatial resolution. The functionalities of state-of-the-art DNA walker systems can thus be analyzed for various applications. Herein we review recent progress on DNA walker principles and characterization methods, and evaluate various aspects of their functions for future applications.

  2. 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.

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

    USGS Publications Warehouse

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

    2001-01-01

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

  4. 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

  5. Diet fermentability influences lactational performance responses to corn distillers grains: a meta-analysis.

    PubMed

    Hollmann, M; Allen, M S; Beede, D K

    2011-04-01

    Increasing supply of corn distillers grains (CDG) raises questions about the extent to which they can be used in diets of lactating dairy cows. A database of treatment means (n=44) reported in 16 peer-reviewed journal articles published from 1985 to 2008 was developed. The database included response (within study) to a CDG diet compared with the control (no CDG) for milk yield (MY), milk fat concentration and yield, CDG content of the diet, and dietary composition of control and CDG diets (% of dietary dry matter). Additionally, corn grain fermentability was classified as high moisture (n=7) or dry (n=37). Data from studies with diets including more than one grain source (n=8) had been eliminated from the analysis. Dietary concentrations of CDG ranged from 4.2 to 42% across studies. Dietary concentrations in diets containing CDG were 16.8±1.91% (mean±standard deviation) crude protein, 36±15.5% corn silage, 23±8.8% corn grain, and 28±5.8% starch. Responses to CDG were 0.5±2.10 kg/cow per day (mean±standard deviation) for MY, 0.05±0.178 percentage units for milk fat concentration, and 26±77.6 g/cow per day for milk fat yield. Only MY response was related to increasing concentrations of CDG in diets and peaked at 1.2 kg/cow per day for 21% CDG. Diet fermentability was associated with responses. The greatest MY response to CDG was with 24% corn silage or 23% starch, and concentrations greater than 47% corn silage or 32% starch resulted in negative MY responses. Responses in MY differed by level of MY and were often more evident in higher- (>30.0 kg MY/d) than in lower-producing cows. Milk fat concentration response was not related to dietary CDG, but was correlated linearly with milk fat concentration of cows fed the control diet. Milk fat concentration greater than 3.6% for the control treatment was related to a negative milk fat concentration response to CDG, regardless of dietary concentration of CDG. Partially replacing high-moisture corn with CDG

  6. 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...

  7. 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.

  8. [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

  9. [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.

  10. An analysis of cercopithecoid odontometrics. II. Relations between dental dimorphism, body size dimorphism and diet.

    PubMed

    Post, D; Goldstein, S; Melnick, D

    1978-11-01

    Odontometric, dietary, and body weight data were collected for a sample of 29 cercopithecoid species. Each species was assigned to one of three diet classes (frugivore, folivore, and omnivore) , and indices were constructed to estimate the extent of sexual dimorphism in body weight, postcanine area and incisor width in each of the species. Analysis proceeded by means of the analysis of covariance with the dental dimorphism indices as the dependent variables. Body weight dimorphism was not significantly related to either measure of dental dimorphism across the sample, and an analysis by diet alone revealed that omnivores show significantly higher dental dimorphism than do either of the other two diet classes. The relationship between this result and theories of sexual subniche differentiation is discussed.

  11. 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

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

    PubMed

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

    2014-07-01

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

  13. 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.

  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. PMID:24449141

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

    PubMed

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

    2016-01-01

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

  16. 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.

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

    PubMed Central

    Drewnowski, Adam

    2015-01-01

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

  18. Automated DNA Base Pair Calling Algorithm

    1999-07-07

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

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

    PubMed

    Wei, Jinhua; Heng, Weijun; Gao, Jianbo

    2016-05-01

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

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

    PubMed

    Wei, Jinhua; Heng, Weijun; Gao, Jianbo

    2016-05-01

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

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

    PubMed

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

    2016-10-01

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

  2. 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.

  3. DNA based computing for understanding complex shapes.

    PubMed

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

    2014-03-01

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

  4. 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. 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.

  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. 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.

  8. 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…

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

    PubMed

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

    2016-05-01

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

  10. 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

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

    PubMed

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

    2016-09-01

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

  12. 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.

  13. 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.

  14. Meta-analysis of the response of growing pigs to the isoleucine concentration in the diet.

    PubMed

    van Milgen, J; Gloaguen, M; Le Floc'h, N; Brossard, L; Primot, Y; Corrent, E

    2012-10-01

    The efficiency of nitrogen utilization will be highest when the amino acid (AA) supply approaches the requirement of the animal. With the availability of different crystalline AA, it is theoretically possible to formulate low-protein diets for growing pigs in which seven AA are co-limiting for performance. In such a diet, the concentration of Lys, Met, Met + Cys, Thr, Trp and Val and a seventh AA would exactly match the requirement. To determine the extent to which low-protein diets can be used, it is important to have reliable information about the requirements for these AA. Isoleucine is often considered the seventh-limiting AA in diets for growing pigs; however, information about the Ile requirement is limited and sometimes conflicting. The purpose of this study was to carry out a meta-analysis of the available literature information to determine the Ile requirement in growing pigs. A total of 46 Ile dose-response experiments were identified that used at least four concentrations of Ile in the diet. Because of differences in experimental design, both the Ile concentration and the response criteria were standardized. In 13 dose-response experiments, there was no indication of a response to an increasing Ile concentration. For the other 33 experiments, a response to the increasing Ile concentration was observed and the Ile requirement estimates ranged from 53% to 114% of that of the National Research Council (1998). An Ile concentration below the requirement resulted in important reductions in both feed intake and growth. A 10% reduction in the Ile concentration (below the requirement) resulted in a 15% reduction in feed intake and a 21% reduction in daily gain. The use of blood products in the diet was the main factor determining whether a response to the Ile concentration was observed or not. Blood meal and blood cells are protein sources with a very low Ile concentration, but with high or very high concentrations of Leu, Val, Phe and His. Some of these AA

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

    PubMed

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

    1998-09-01

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

  16. 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

  17. DNA-based methods in the immunohematology reference laboratory.

    PubMed

    Reid, Marion E; Denomme, Gregory A

    2011-02-01

    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.

  18. 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.

  19. 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

  20. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

    Meyer, Christopher P.; Mills, Suzanne C.

    2015-01-01

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

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

    SciTech Connect

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

    1999-02-01

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

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

    USGS Publications Warehouse

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

    2012-01-01

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

  5. 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

  6. 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

  7. 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.

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

    PubMed

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

    2012-07-01

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

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

    PubMed Central

    Roehrer, Erin

    2016-01-01

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

  10. 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

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

    PubMed

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

    2014-11-01

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

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Stable isotopic analysis of human diet in the Marianas Archipelago, western Pacific.

    PubMed

    Ambrose, S H; Butler, B M; Hanson, D B; Hunter-Anderson, R L; Krueger, H W

    1997-11-01

    Proportions of marine vs. terrestrial resources in prehistoric human diets in the southern Mariana Islands (Guam, Rota, Saipan), Micronesia, have been estimated by analysis of stable isotope ratios of carbon and nitrogen in bone collagen and of carbon in apatite. The isotopic composition of marine and terrestrial food resources from the Marianas have also been determined. Experimental evidence shows that collagen carbon isotopes mainly reflect those of dietary protein sources and thus overestimate the contribution of marine animal foods. Marine protein consumption apparently ranges from approximately 20% to approximately 50% on these islands. Experiments also demonstrate the carbon isotope ratio of bone apatite carbonate accurately reflects that of the whole diet. Carbonate carbon isotope data suggest some individuals consumed significant amounts of 13C-enriched (C4) plants or seaweeds. Sugar cane is an indigenous C4 crop and seaweeds are eaten throughout the Pacific, but they have not been considered by archaeologists to have been prehistoric dietary staples. Apatite carbon isotope analysis has apparently identified previously unrecognized prehistoric dietary adaptations in the Mariana Islands, but this must be confirmed by archaeobotanical evidence.

  17. 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.

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

    PubMed

    Ji, S

    1999-10-01

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

  19. DNA-based methods of geochemical prospecting

    DOEpatents

    Ashby, Matthew

    2011-12-06

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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

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

    PubMed

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

    2014-08-01

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

  6. Diet and status at Chalcatzingo: some empirical and technical aspects of strontium analysis.

    PubMed

    Schoeninger, M J

    1979-09-01

    Determination of the levels of particular trace elements preserved in bone provides a potential pathway for reconstructing the diet of extinct primate species and archaic human groups. Strontium is one of the most useful trace elements for dietary reconstruction but several empirical properties of strontium must be considered during the interpretation of results. (1) Strontium is distributed unevenly throughout the physical environment. (2) Plants, in general, do not discriminate against strontium. (3) During ionic transfer across biological membranes, strontium is discriminated against by terrestrial vertebrates. (4) It is unlikely that strontium would be selectively removed from bone mineral during diagenesis. A particular difficulty in trace element analysis is caused by interaction between analytical technique and sample matrix. To assess this problem the skeletal population from Chalcatzingo was analyzed by two techniques: atomic absorption spectrometry and neutron activation analysis. The results from the two techniques compared favorably indicating that the pattern of bone strontium levels could be accepted as an accurate reflection of the distribution of bone strontium within the population. After demonstrating the internal accuracy of the results, the bone strontium level and position of social rank within Chalcatzingo were compared. Ethnographic and archaeological evidence on chiefdoms and states indicate that dietary differences in the amount of meat consumed occur between social ranks. The relative social ranks were reconstructed by using a "pattern analysis" of the burial goods accompanying each individual. The individuals accompanied by jade had the lowest mean bone strontium level (X = 532). Those individuals buried with a shallow dish had a slightly higher level (X = 635). A third group, which had no grave goods, had the highest mean bone strontium level (X = 700) which suggests that their diet contained less meat than was available to the rest of

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

    PubMed Central

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

    2016-01-01

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

  8. 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

  9. 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.

  10. 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.

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

    PubMed

    Rao, R R; Chatt, A

    1991-07-01

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

  12. 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.

  13. 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

  14. Chlorophenols, chlorocatechols and chloroguaiacols induce DNA base oxidation in human lymphocytes (in vitro).

    PubMed

    Michałowicz, Jaromir; Majsterek, Ireneusz

    2010-02-01

    Phenolic compounds are strong environmental toxicants, which are found in food, drinking water as well as in the indoor and outdoor air environment. In this work we investigated the effect of low concentrations of 0.2, 1 and 5 microg/ml of 2,4,5-trichlorophenol (2,4,5-TCP), pentachlorophenol (PCP), 4,6-dichloroguaiacol (4,6-DCG), tetrachloroguaiacol (TeCG), 4,5-dichlorocatechol (4,5-DCC) and tetrachlorocatechol (TeCC) on DNA bases oxidation in human peripheral blood lymphocytes. The analysis was performed using alkaline single cell gel electrophoresis (the comet assay). To detect oxidized pyrimidynes and purines we used the repair enzymes such as endonuclease III and formamidopyrimidine-DNA glycosylase. DNA oxidation was expressed as a percentage of comet tail, which was formed after the xenobiotics treatment. The obtained results showed that all the compounds examined were able to oxidize DNA bases in human lymphocytes. It was also observed that pyrimidine bases were more strongly oxidized in comparison to purine ones. Finally, it was found that chlorinated catechols and TeCC in particular, revealed a higher oxidative potential in comparison to chlorophenols and chloroguaiacols, and a rise in the number of chlorine atoms in the compound from each group examined led to an increase in DNA bases damage.

  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. PMID:24630913

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

    PubMed Central

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

    2016-01-01

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

  18. 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.

  19. 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.

  20. 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.

  1. [DNA-based methods for identification of seafood species].

    PubMed

    Zhang, Li; Zhang, Liang; Liu, Shu-Cheng; Zhang, Yi-Jun; Han, Yi

    2010-06-01

    With the development of molecular biotechnology, methods for identification of seafood species are developed from protein to DNA. At present, the main DNA-based methods for species identification are FINS, PCR-RFLP, and specific-PCR, which have been used to identify the species of fresh, frozen, and pickled or canned seafood. However, qualitative and quantitative methods for identification of the mixed seafood species remain to be resolved. The gene databases play an important role in identifying species and are valuable information resources for identification of seafood species. In this paper, recent progresses of major DNA-based methods for identification of seafood species are reviewed and the perspectives of this field are discussed. PMID:20566458

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

    PubMed Central

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

    2015-01-01

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

  3. A dual input DNA-based molecular switch.

    PubMed

    Nesterova, Irina V; Elsiddieg, Siddieg O; Nesterov, Evgueni E

    2014-11-01

    We have designed and characterized a DNA-based molecular switch which processes two physiologically relevant inputs: pH (i.e. alkalinisation) and enzymatic activity, and generates a chemical output (in situ synthesized oligonucleotide). The design, based on allosteric interactions between i-motif and hairpin stem within the DNA molecule, addresses such critical physiological system parameters as molecular simplicity, tunability, orthogonality of the two input sensing domains, and compatibility with intracellular operation/delivery. PMID:25099914

  4. 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.

  5. Meta-analysis of studies on breast cancer risk and diet in Chinese women

    PubMed Central

    Wu, Ying-Chao; Zheng, Dong; Sun, Jin-Jie; Zou, Zhi-Kang; Ma, Zhong-Li

    2015-01-01

    Objective: A meta-analysis was carried out to summarize published data on the relationship between breast cancer and dietary factors. Methods: Databases in Chinese (China National Knowledge Infrastructure [CNKI], China Biology Medicine [CBM], WanFang, VIP) and in English (PubMed and Web of Science) were searched for articles analyzing vegetable, fruit, soy food and fat consumption and breast cancer risk published through June 30, 2013. Random effects models were used to estimate summary odds ratios (OR) based on high versus low intake, and subgroup analysis was conducted according to region, study design, paper quality and adjustment for confounding factors to detect the potential source of heterogeneity. Every study was screened according to the inclusion criteria and exclusion criteria, evaluated in accordance with the Newcastle-Ottawa Scale. RevMan 5.2 software was used for analysis. Results: Of 785 studies retrieved, 22 met inclusion criteria (13 in Chinese and 9 in English), representing 23,201 patients: 10,566 in the experimental group and 12,635 in the control group. Thirteen included studies showed vegetables consumption to be a relevant factor in breast cancer risk, OR = 0.77 (95% CI [confidence interval] 0.62-0.96). Eleven studies showed fruits consumption to be relevant, OR = 0.68 (95% CI 0.49-0.93). Significant differences were also found between those who consumed soy foods, OR = 0.68 (95% CI 0.50-0.93) and those who ate a high-fat diet, OR = 1.15 (95% CI 1.01-1.30). Conclusion: This analysis confirms the association between intake of vegetables, fruits, soy foods and fat and the risk of breast cancer from published sources. It’s suggested that high consumption of vegetables, fruits and soy foods may reduce the risk of breast cancer, while increasing fat consumption may increase the risk. PMID:25784976

  6. 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…

  7. 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. PMID:25199878

  8. 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

  9. 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.

  10. 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.

  11. 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.

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

    PubMed

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

    2013-07-01

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

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

    PubMed

    Suzuki, Shogo; Okada, Yukiko; Hirai, Shoji

    2003-08-01

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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

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

    PubMed

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

    2015-01-01

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

  20. 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.

  1. An image based vibration sensor for soft tissue modal analysis in a Digital Image Elasto Tomography (DIET) system.

    PubMed

    Feng, Sheng; Lotz, Thomas; Chase, J Geoffrey; Hann, Christopher E

    2010-01-01

    Digital Image Elasto Tomography (DIET) is a non-invasive elastographic breast cancer screening technology, based on image-based measurement of surface vibrations induced on a breast by mechanical actuation. Knowledge of frequency response characteristics of a breast prior to imaging is critical to maximize the imaging signal and diagnostic capability of the system. A feasibility analysis for a non-invasive image based modal analysis system is presented that is able to robustly and rapidly identify resonant frequencies in soft tissue. Three images per oscillation cycle are enough to capture the behavior at a given frequency. Thus, a sweep over critical frequency ranges can be performed prior to imaging to determine critical imaging settings of the DIET system to optimize its tumor detection performance.

  2. Diet History Questionnaire: Suggested Citations

    Cancer.gov

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    1994-09-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2016-09-01

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

  7. 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.

  8. 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

  9. 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 ...

  10. 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

  11. 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

  12. 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

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

    USGS Publications Warehouse

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

    2015-01-01

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

  14. Analysis of J Coupling-Induced Fat Suppression in DIET Imaging

    NASA Astrophysics Data System (ADS)

    Stables, L. A.; Kennan, R. P.; Anderson, A. W.; Constable, R. T.; Gore, J. C.

    1999-02-01

    The DIET (ordualintervalechotrain) sequence, a modification of thefastspinecho (FSE) sequence that selectively reduces signal from fat in MR images, has been investigated. The DIET sequence uses an initial echo spacing longer than that of a conventional FSE sequence, thus allowingJcoupling-induced dephasing to take effect. The sequence is evaluated theoretically, and its effectiveness on a hydrocarbon (1-pentene) is demonstrated numerically using density matrix calculations. The sequence is also evaluated experimentally usingin vitrosolutions andin vivoimaging. The efficacy of the sequence is compared for different lipid chemical structures, field strengths, and pulse sequence parameters.

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

    PubMed

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

    2013-10-01

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

  16. 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.

  17. 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...

  18. 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...

  19. 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.

  20. 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.

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

    PubMed

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

    2015-01-01

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

  2. 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.

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

    PubMed

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

    2015-05-01

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

  4. 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.

  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. 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.

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

    PubMed

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

    2005-04-22

    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.

  8. A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces.

    PubMed

    Corse, Emmanuel; Costedoat, Caroline; Chappaz, Rémi; Pech, Nicolas; Martin, Jean-François; Gilles, André

    2010-01-01

    The development of DNA barcoding from faeces represents a promising method for animal diet analysis. However, current studies mainly rely on prior knowledge of prey diversity for a specific predator rather than on a range of its potential prey species. Considering that the feeding behaviour of teleosts may evolve with their environment, it could prove difficult to establish an exhaustive listing of their prey. In this article, we extend the DNA barcoding approach to diet analysis to allow the inclusion of a wide taxonomic range of potential prey items. Thirty-four ecological clade-specific primer sets were designed to cover a large proportion of prey species found in European river ecosystems. Selected primers sets were tested on isolated animal, algal or plant tissues and thereafter on fish faeces using nested PCR to increase DNA detection sensitivity. The PCR products were sequenced and analysed to confirm the identity of the taxa and to validate the method. The methodology developed here was applied to a diet analysis of three freshwater cyprinid species that are assumed to have similar feeding behaviour [Chondrostoma toxostoma toxostoma (Vallot 1837), Chondrostoma nasus nasus (Linnaeus, 1758) and Barbus barbus, (Linneaus 1758)]. These three species were sampled in four different hydrographic basins. Principal Component Analysis based on prey proportions identified distinct perilithon grazer and benthophagous behaviours. Furthermore, our results were consistent with the available literature on feeding behaviour in these fish. The simplicity of the PCR-based method and its potential generalization to other freshwater organisms may open new perspectives in food web ecology. PMID:21564994

  9. A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces.

    PubMed

    Corse, Emmanuel; Costedoat, Caroline; Chappaz, Rémi; Pech, Nicolas; Martin, Jean-François; Gilles, André

    2010-01-01

    The development of DNA barcoding from faeces represents a promising method for animal diet analysis. However, current studies mainly rely on prior knowledge of prey diversity for a specific predator rather than on a range of its potential prey species. Considering that the feeding behaviour of teleosts may evolve with their environment, it could prove difficult to establish an exhaustive listing of their prey. In this article, we extend the DNA barcoding approach to diet analysis to allow the inclusion of a wide taxonomic range of potential prey items. Thirty-four ecological clade-specific primer sets were designed to cover a large proportion of prey species found in European river ecosystems. Selected primers sets were tested on isolated animal, algal or plant tissues and thereafter on fish faeces using nested PCR to increase DNA detection sensitivity. The PCR products were sequenced and analysed to confirm the identity of the taxa and to validate the method. The methodology developed here was applied to a diet analysis of three freshwater cyprinid species that are assumed to have similar feeding behaviour [Chondrostoma toxostoma toxostoma (Vallot 1837), Chondrostoma nasus nasus (Linnaeus, 1758) and Barbus barbus, (Linneaus 1758)]. These three species were sampled in four different hydrographic basins. Principal Component Analysis based on prey proportions identified distinct perilithon grazer and benthophagous behaviours. Furthermore, our results were consistent with the available literature on feeding behaviour in these fish. The simplicity of the PCR-based method and its potential generalization to other freshwater organisms may open new perspectives in food web ecology.

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

    PubMed

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

    2014-08-01

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

  11. 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.

  12. 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.

  13. 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.

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

    PubMed

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

    2014-01-01

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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. Use of hierarchical models for meta-analysis: experience in the metabolic ward studies of diet and blood cholesterol.

    PubMed

    Frost, C; Clarke, R; Beacon, H

    1999-07-15

    Overviews that combine single effect estimates from published studies generally use a summary statistic approach where the effect of interest is first estimated within each study and then averaged across studies in an appropriately weighted manner. Combining multiple regression coefficients from publications is more problematic, particularly when there are differences in study design and inconsistent reporting of effect sizes and standard errors. This paper describes the use of a hierarchical model in such circumstances. Its use is illustrated in a meta-analysis of the metabolic ward studies that have investigated the effect of changes in intake of various dietary lipids on blood cholesterol. These studies all reported average blood cholesterol for groups of individuals who were studied on one or more diets. Thirty-one studies had randomized cross-over designs, 12 had matched parallel group designs, 12 had non-randomized Latin square designs and 16 had other uncontrolled designs. The hierarchical model allowed the different types of comparison (within-group between-diet, between matched group) that were made in the various studies to each contribute to the overall estimates in an appropriately weighted manner by distinguishing between-study variation, within-study between-matched-group variation and within-group between-diet variation. The hierarchical models do not require consistent specification of effect sizes and standard errors and hence have particular utility in combining results from published studies where the relationships between a dependent variable and two or more predictors have been investigated using heterogeneous methods of analysis.

  1. 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.

  2. 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.

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

    PubMed Central

    Friedman, Joshua I.; Stivers, James T.

    2010-01-01

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

  4. Applications of nanoparticles for DNA based rabies vaccine.

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2010-05-01

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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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.

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

    PubMed

    Nardoto, Gabriela B; Silva, Steven; Kendall, Carol; Ehleringer, James R; Chesson, Lesley A; Ferraz, Epaminondas S B; Moreira, Marcelo Z; Ometto, Jean P H B; Martinelli, Luiz A

    2006-09-01

    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 delta13C values (mean +/- standard deviation) were -15.4 +/- 1.0 and -18.8 +/- 0.8 per thousand and delta15N values were 10.4 +/- 0.7 and 9.4 +/- 0.6 per thousand 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  13. Comparative assessment of DNA-based approaches for the quantification of food allergens.

    PubMed

    Luber, Florian; Demmel, Anja; Herbert, Denise; Hosken, Anne; Hupfer, Christine; Huber, Ingrid; Busch, Ulrich; Engel, Karl-Heinz

    2014-10-01

    Governments all over the world have implemented regulatory frameworks concerning food allergen labelling and established or discussed the implementation of thresholds. Therefore, quantitative methods are needed for their surveillance. DNA-based approaches using a matrix-adapted calibration, an internal standard material and a modified standard addition have been developed. In order to enable a comparative assessment of the available quantification methods, experimental framework conditions and uniform performance criteria were defined. For the evaluation of the experimental results using homogenous sample material, the recovery, repeatability and reproducibility were considered along with the limit of detection and the limit of quantification. In addition, muffin dough and muffins spiked with sesame were analysed to assess the suitability of the methods to quantify sesame in model foods. The modified standard addition emerged from the comparative assessment and the analysis of the model foods to be the most appropriate method to quantify traces of allergens in food.

  14. 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

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

    SciTech Connect

    Hobson, K.A.

    1995-12-31

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

  17. 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.

  18. 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.

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

    PubMed

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

    2015-10-10

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

  20. Monitoring Cooperative Binding Using Electrochemical DNA-Based Sensors

    PubMed Central

    2015-01-01

    Electrochemical DNA-based (E-DNA) sensors are utilized to detect a variety of targets including complementary DNA, small molecules, and proteins. These sensors typically employ surface-bound single-stranded oligonucleotides that are modified with a redox-active molecule on the distal 3′ terminus. Target-induced flexibility changes of the DNA probe alter the efficiency of electron transfer between the redox active methylene blue and the electrode surface, allowing for quantitative detection of target concentration. While numerous studies have utilized the specific and sensitive abilities of E-DNA sensors to quantify target concentration, no studies to date have demonstrated the ability of this class of collision-based sensors to elucidate biochemical-binding mechanisms such as cooperativity. In this study, we demonstrate that E-DNA sensors fabricated with various lengths of surface-bound oligodeoxythymidylate [(dT)n] sensing probes are able to quantitatively distinguish between cooperative and noncooperative binding of a single-stranded DNA-binding protein. Specifically, we demonstrate that oligo(dT) E-DNA sensors are able to quantitatively detect nM levels (50 nM–4 μM) of gene 32 protein (g32p). Furthermore, the sensors exhibit signal that is able to distinguish between the cooperative binding of the full-length g32p and the noncooperative binding of the core domain (*III) fragment to single-stranded DNA. Finally, we demonstrate that this binding is both probe-length- and ionic-strength-dependent. This study illustrates a new quantitative property of this powerful class of biosensor and represents a rapid and simple methodology for understanding protein–DNA binding mechanisms. PMID:25517392

  1. Monitoring cooperative binding using electrochemical DNA-based sensors.

    PubMed

    Macazo, Florika C; Karpel, Richard L; White, Ryan J

    2015-01-20

    Electrochemical DNA-based (E-DNA) sensors are utilized to detect a variety of targets including complementary DNA, small molecules, and proteins. These sensors typically employ surface-bound single-stranded oligonucleotides that are modified with a redox-active molecule on the distal 3' terminus. Target-induced flexibility changes of the DNA probe alter the efficiency of electron transfer between the redox active methylene blue and the electrode surface, allowing for quantitative detection of target concentration. While numerous studies have utilized the specific and sensitive abilities of E-DNA sensors to quantify target concentration, no studies to date have demonstrated the ability of this class of collision-based sensors to elucidate biochemical-binding mechanisms such as cooperativity. In this study, we demonstrate that E-DNA sensors fabricated with various lengths of surface-bound oligodeoxythymidylate [(dT)n] sensing probes are able to quantitatively distinguish between cooperative and noncooperative binding of a single-stranded DNA-binding protein. Specifically, we demonstrate that oligo(dT) E-DNA sensors are able to quantitatively detect nM levels (50 nM-4 μM) of gene 32 protein (g32p). Furthermore, the sensors exhibit signal that is able to distinguish between the cooperative binding of the full-length g32p and the noncooperative binding of the core domain (*III) fragment to single-stranded DNA. Finally, we demonstrate that this binding is both probe-length- and ionic-strength-dependent. This study illustrates a new quantitative property of this powerful class of biosensor and represents a rapid and simple methodology for understanding protein-DNA binding mechanisms.

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

    PubMed

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

    2015-01-01

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

  3. 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.

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

    PubMed Central

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

    2016-01-01

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

  5. 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

  6. Collinearity diagnosis for a relative risk regression analysis: an application to assessment of diet-cancer relationship in epidemiological studies.

    PubMed

    Wax, Y

    1992-07-01

    In epidemiologic studies, two forms of collinear relationships between the intake of major nutrients, high correlations, and the relative homogeneity of the diet, can yield unstable and not easily interpreted regression estimates for the effect of diet on disease risk. This paper presents tools for assessing the magnitude and source of the corresponding collinear relationships among the estimated coefficients for relative risk regression models. I show how to extend three tools (condition indices, variance decomposition proportions, and standard inflation factors) for diagnosing collinearity in standard regression models to likelihood and partial likelihood estimation for logistic and proportional hazards models. This extension is based on the analogue role of the information matrix in such analyses and the cross-product matrix in the standard linear model. I apply the methodology to relative risk models that relate crude intakes (on the log scale) and nutrient densities to breast cancer cases in the NHANES-I follow-up study. The three diagnostic tools provide complementary evidence of the existence of a strong collinearity in all models that is due largely to homogeneity of the population with respect to our risk scale for the crude intakes. The analysis suggests that the non-significant relative risks for the crude intakes in these models may be due to their involvement in collinear relationships, while the nonsignificant relative risks for the nutrient densities are far less affected by multicollinearity.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. Low-fiber diet

    MedlinePlus

    ... restricted diet; Crohn disease - low fiber diet; Ulcerative colitis - low fiber diet; Surgery - low fiber diet ... of: Irritable bowel syndrome Diverticulitis Crohn disease Ulcerative colitis Sometimes people are put on this diet after ...

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  14. Clinical evidence of growth hormone, glutamine and a modified diet for short bowel syndrome: meta-analysis of clinical trials.

    PubMed

    Zhou, Yong; Wu, Xiao-Ting; Yang, Gang; Zhuang, Wen; Wei, Mao-ling

    2005-01-01

    This study assessed the safety and efficacy of growth hormone (GH) and glutamine (GLN) combined with a modified (high-carbohydrate-low-fat, HCLF) diet in patients with short bowel syndrome. A meta-analysis of all the relevant clinical trials was performed. Clinical trials were identified from the following electronic databases: MEDLINE, EMBASE, the Cochrane Controlled Trials Register, Chinese Bio-medicine Database. The search was undertaken in May 2004. Language was restricted to Chinese and English. Literature references were checked at the same time. Clinical trials were extracted and evaluated by two reviewers independently of each other. The statistical analysis was performed by RevMan4.2 software which was provided by the Cochrane Collaboration. A P value of < 0.05 was considered statistically significant. Thirteen trials involving 258 patients were included. The combined results showed that GH, GLN and HCLF diet had positive treatment effect on body weight (weighted mean difference [WMD] = 2.44, 95%CI [1.62, 3.27], P<0.00001), stool output (WMD = -376.49, 95%CI [-600.35, -152.63], P=0.001), lean body mass (WMD = 2.16, 95%CI [0.91, 3.41], P=0.0007), absorption of carbohydrates (WMD = 6.21, 95%CI [5.27, 7.15], P< 0.00001), absorption of nitrogen (WMD = 10.83, 95%CI [5.22, 16.44], P=0.0002), absorption of D-xylose (WMD = 0.37, 95%CI [0.29, 0.44], P<0.00001), and off TPN (total parenteral nutrition) (odds ratios [OR] = 64.63, 95%CI [15.51, 269.22], P<0.00001). But there were no improvements in fat mass (WMD = -1.50, 95%CI [-3.48, 0.48], P=0.14), absorption of energy (WMD = 7.48, 95%CI [-7.22, 22.17], P=0.32), and absorption of fat (WMD = 7.16, 95%CI [-2.95, 17.28], P=0.17). Most patients had side effects that are known to occur during treatment with high doses (0.14 mg/kg/day) of GH. No serious adverse effects occurred during active treatment with low doses (< or =0.1 mg/kg/day) of GH. Treatment with a combination of low-dose GH, GLN and HCLF diet is effective

  15. 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

  16. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2014-12-01

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

  20. 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.

  1. 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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  4. 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

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  6. 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.

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

    USGS Publications Warehouse

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

    2009-01-01

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

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

    USGS Publications Warehouse

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

    2009-01-01

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

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

    USGS Publications Warehouse

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

    2013-01-01

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

  10. 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...

  11. 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...

  12. 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

  13. DNA-based identification of the eastern subterranean termite, Reticulitermes flavipes (Isoptera: Rhinotermitidae).

    PubMed

    Foster, Bart T; Cognato, Anthony I; Gold, Roger E

    2004-02-01

    A DNA-based system for the identification of Reticulitermes flavipes (Koller) was established based on the following criteria: adequate molecular variation, comprehensive specimen sampling, explicit morphological species identification, and cladistic analysis. Termite soldiers were identified by labral shape, and these specimens and associated pseudergates were used in subsequent molecular analyses. Mitochondrial DNA from the AT-rich region was sequenced for 173 R. flavipes, Reticulitermes hageni Banks and Reticulitermes virginicus (Banks) soldiers and pseudergates collected from several widely dispersed Texan localities. Cladistic analysis was performed after exploration of an optimal sequence alignment inclusive of DNA sequences from Texas and published sequences from Georgia and Canada. Among the Texan individuals, 29, 5, and 1 mitochondrial DNA haplotypes were identified respectively with R. flavipes, R. hageni, and R. virginicus. One haplotype from El Paso likely represented a different Reticulitermes species. Species were monophyletic; however, individual relationships were unresolved in a strict consensus of 700 most parsimonious trees. Texas haplotypes were isolated by distance, and a correlation between genetic and geographic distance was observed among the Texas, Georgia, and Canada haplotypes. These results suggest that the methods outlined in this study will allow for the identification of R. flavipes from localities between Texas and Canada. PMID:14998132

  14. DNA based classification of food associated Enterobacteriaceae previously identified by Biolog GN Microplates.

    PubMed

    Olsson, Crister; Ahrné, Siv; Pettersson, Bertil; Molin, Göran

    2004-03-01

    Enterobacteriaceae are frequently isolated from food products and it is essential to have methods for correct identification for both food hygiene and epidemiology reasons. Phenotypic methods are not always sufficient and have to be supplemented by DNA based methods. In the present study, 70 strains of Enterobacteriaceae derived from milk, fish and meat that had previously been identified by Biolog GN Microplates were genomically classified together with 15 representative type strains of species of Enterobacteriaceae. The field strains were dominated by Hafnia alvei, Serratia liquefaciens and Rahnella aquatilis. All strains were subjected to temporal temperature gel electrophoresis (TTGE) analysis using amplicons encompassing the V3, V4 and V9 variable regions of the 16S rRNA gene. Selected strains were analysed by ribotyping and partial 16S rDNA sequencing. The type strains were differentiated into 10 different TTGE groups. Two of the groups contained two type strains. Enterobacter aerogenes and Klebsiella planticola were not distinguished due to their identical sequences and Yersinia ruckeri and Citrobacter freundii showed the same migration pattern. The 70 food strains could be differentiated into 14 TTGE groups where 33 strains (47.1%) could be assigned to TTGE groups including type or reference strains. Rahnella strains were dispersed into three TTGE groups of which one group corresponded to Rahnella genomospecies 1 and one to genomospecies 3. The grouping of Rahnella strains was supported by ribotyping and phylogenetic analysis. TTGE can be a useful additional tool for identification on the species level of food related Enterobacteriaceae.

  15. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

  2. Nutrition and Diet

    MedlinePlus

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

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

    PubMed

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

    2010-09-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2013-01-01

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

  8. 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

  9. 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. PMID:21353670

  10. 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.

  11. What the largest tadpole feeds on? A detailed analysis of the diet composition of Pseudis minuta tadpoles (Hylidae, Dendropsophini).

    PubMed

    Huckembeck, Sônia; Alves, Lívia T; Loebmann, Daniel; Garcia, Alexandre M

    2016-09-01

    We analyzed the diet of 25 individuals of Pseudis minuta tadpoles which consisted in debris with more than 30%, follow by diatoms, euglenids, green algae, and desmids. With regard to the feeding strategy, P. minuta tadpoles are generalist consumer. The negative correlation between the abundance of items in the digestive tract and the mouth width indicate an effect of metamorphosis on the diet. PMID:27508992

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

    PubMed Central

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Lesnik, Julie J

    2014-06-01

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

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

    PubMed

    Lesnik, Julie J

    2014-06-01

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

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

    PubMed Central

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

    2013-01-01

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

  1. Induction of olfaction and cancer-related genes in mice fed a high-fat diet as assessed through the mode-of-action by network identification analysis.

    PubMed

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

    2013-01-01

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

  2. DNA based electrolyte/separator for lithium battery application

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  5. Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions.

    PubMed

    Deagle, B E; Tollit, D J; Jarman, S N; Hindell, M A; Trites, A W; Gales, N J

    2005-05-01

    The DNA of prey present in animal scats may provide a valuable source of information for dietary studies. We conducted a captive feeding trial to test whether prey DNA could be reliably detected in scat samples from Steller sea lions (Eumetopias jubatus). Two sea lions were fed a diet of fish (five species) and squid (one species), and DNA was extracted from the soft component of collected scats. Most of the DNA obtained came from the predator, but prey DNA could be amplified using prey-specific primers. The four prey species fed in consistent daily proportions throughout the trial were detected in more than 90% of the scat DNA extractions. Squid and sockeye salmon, which were fed as a relatively small percentage of the daily diet, were detected as reliably as the more abundant diet items. Prey detection was erratic in scats collected when the daily diet was fed in two meals that differed in prey composition, suggesting that prey DNA is passed in meal specific pulses. Prey items that were removed from the diet following one day of feeding were only detected in scats collected within 48 h of ingestion. Proportions of fish DNA present in eight scat samples (evaluated through the screening of clone libraries) were roughly proportional to the mass of prey items consumed, raising the possibility that DNA quantification methods could provide semi-quantitative diet composition data. This study should be of broad interest to researchers studying diet since it highlights an approach that can accurately identify prey species and is not dependent on prey hard parts surviving digestion. PMID:15836654

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

    PubMed

    Rabkin, S W; Campbell, H

    2015-05-01

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

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

    PubMed

    Zhao, Hua; Shen, Kai

    2014-01-01

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

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

    SciTech Connect

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

    1994-12-31

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

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

    PubMed

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

    2001-07-01

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

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

    PubMed

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

    1987-05-01

    The British physician A.T.W. Simeons described in 1954 a new method for dieting. He combined a reduction diet (500 kcal per day) with daily injections of the pregnancy hormone human chorionic gonadotropin (hCG) (125 IU i.m.). According to Simeons the patient should not lose more weight during a 4-to-6 weeks' diet than without hCG, but the injections should facilitate to maintain the diet and to lose body weight at specific parts of the body (e.g. hip, belly, thigh). After the first publication various studies conducted with male and female patients analysed the efficacy of the "Cura romana". 10 of these studies showed positive and another 10 studies negative results with regard to hCG-related weight reduction. Two of these studies with positive results were double-blind studies (hCG vs. placebo). Most of them were reports on therapeutical experiences and were not controlled studies. According to these reports the body proportions normalized and the feeling of hunger was tolerable. Four out of 10 studies with negative results were controlled studies (hCG vs. control without hCG), whereas 6 were double-blind studies. These studies showed a significant weight reduction during dieting, but no differences between treatment groups in respect of body weight, body proportions and feeling of hunger. One of them is the only German study conducted by Rabe et al. in 1981 in which 82 randomised premenopausal volunteers had been dieting either with hCG or without hCG injections. In recent publications describing mostly well-documented double-blind studies authors largely reject hCG administration in dieting. Supporters of the hCG diet must prove the efficacy of this method in controlled studies according to the German Drug Law. Until then the opinion of the German steroid toxicology panel is still valid, that hCG is ineffective in dieting and should not be used (Bolt 1982 a, 1982 b). PMID:3609673

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

    PubMed Central

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

    2015-01-01

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

  12. Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus).

    PubMed

    Srivathsan, Amrita; Sha, John C M; Vogler, Alfried P; Meier, Rudolf

    2015-03-01

    Faecal samples are of great value as a non-invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation of endangered species. Direct shotgun sequencing of faecal DNA could give information on these simultaneously, but this approach is largely untested. Here, we used two faecal samples to characterize the diet of two red-shanked doucs langurs (Pygathrix nemaeus) that were fed known foliage, fruits, vegetables and cereals. Illumina HiSeq produced ~74 and 67 million paired reads for these samples, of which ~ 10,000 (0.014%) and ~ 44,000 (0.066%), respectively, were of chloroplast origin. Sequences were matched against a database of available chloroplast 'barcodes' for angiosperms. The results were compared with 'metabarcoding' using PCR amplification of the P6 loop of trnL. Metagenomics identified seven and nine of the likely 16 diet plants while six and five were identified by metabarcoding. Metabarcoding produced thousands of reads consistent with the known diet, but the barcodes were too short to identify several plant species to genus. Metagenomics utilized multiple, longer barcodes that combined had greater power of identification. However, rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus, if chloroplast genomes were used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.

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

    PubMed

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

    2016-04-01

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

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

    PubMed

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

    2005-07-01

    Many mass disasters result in loss of lives. Law enforcement and/or public safety and health officials often have the responsibility for identifying the human remains found at the scene, so they can be returned to their families. The recovered human remains range from being relatively intact to highly degraded. DNA-based identity testing is a powerful tool for victim identification in that the data are not restricted to any particular one to one body landmark comparison and DNA profile comparisons can be used to associate separated remains or body parts. Even though DNA typing is straightforward, a disaster is a chaotic environment that can complicate effective identification of the remains. With some planning, or at least identification of the salient features to consider, stress can be reduced for those involved in the identification process. General guidelines are provided for developing an action plan for identification of human remains from a mass disaster by DNA analysis. These include: (1) sample collection, preservation, shipping and storage; (2) tracking and chain of custody issues; (3) laboratory facilities; (4) quality assurance and quality control practices; (5) parsing out work; (6) extraction and typing; (7) interpretation of results; (8) automation; (9) software for tracking and managing data; (10) the use of an advisory panel; (11) education and communication; and (12) privacy issues. In addition, key technologies that may facilitate the identification process are discussed, such as resin based DNA extraction, real-time PCR for quantitation of DNA, use of mini-STRs, SNP detection procedures, and software. Many of the features necessary for DNA typing of human remains from a mass disaster are the same as those for missing persons' cases. Therefore, developing a missing persons DNA identification program would also provide the basis for a mass disaster human remains DNA identification program. PMID:15975517

  15. Adherence to Mediterranean diet and risk of cancer: an updated systematic review and meta-analysis of observational studies.

    PubMed

    Schwingshackl, Lukas; Hoffmann, Georg

    2015-12-01

    The aim of the present systematic review and meta-analysis of observational studies was to gain further insight into the effects of adherence to Mediterranean Diet (MD) on overall cancer mortality, incidence of different types of cancer, and cancer mortality risk in cancer survivors. Literature search was performed using the electronic databases PubMed, and EMBASE until 2 July 2015. We included either cohort (for specific tumors only incidence cases were used) or case-control studies. Study specific risk ratios, hazard ratios, and odds ratios (RR/HR/OR) were pooled using a random effect model. The updated review process showed 23 observational studies that were not included in the previous meta-analysis (total number of studies evaluated: 56 observational studies). An overall population of 1,784,404 subjects was included in the present update. The highest adherence score to an MD was significantly associated with a lower risk of all-cause cancer mortality (RR: 0.87, 95% CI 0.81-0.93, I(2) = 84%), colorectal cancer (RR: 0.83, 95% CI 0.76-0.89, I(2) = 56%), breast cancer (RR: 0.93, 95% CI 0.87-0.99, I(2) =15%), gastric cancer (RR: 0.73, 95% CI 0.55-0.97, I(2) = 66%), prostate cancer (RR: 0.96, 95% CI 0.92-1.00, I(2) = 0%), liver cancer (RR: 0.58, 95% CI 0.46-0.73, I(2) = 0%), head and neck cancer (RR: 0.40, 95% CI 0.24-0.66, I(2) = 90%), pancreatic cancer (RR: 0.48, 95% CI 0.35-0.66), and respiratory cancer (RR: 0.10, 95% CI 0.01-0.70). No significant association could be observed for esophageal/ovarian/endometrial/and bladder cancer, respectively. Among cancer survivors, the association between the adherence to the highest MD category and risk of cancer mortality, and cancer recurrence was not statistically significant. The updated meta-analyses confirm a prominent and consistent inverse association provided by adherence to an MD in relation to cancer mortality and risk of several cancer types.

  16. Diet history: Method and applications.

    PubMed

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

    2015-02-26

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

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

    EPA Science Inventory

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

  18. Deciphering DNA-based asymmetric catalysis through intramolecular Friedel-Crafts alkylations.

    PubMed

    Park, Soyoung; Ikehata, Keiichi; Watabe, Ryo; Hidaka, Yuta; Rajendran, Arivazhagan; Sugiyama, Hiroshi

    2012-10-28

    We describe asymmetric intramolecular Friedel-Crafts alkylations with a DNA-based hybrid catalyst and propose a plausible binding model. This study shows promise for studying relationships between the helical chirality of DNA and enantioselectivity of the chemical reaction. PMID:22986468

  19. [Space diet].

    PubMed

    Luigi, R

    1989-06-01

    Food prepared for astronauts meets various physical and biological requirements determined by living conditions in a space environment. Onboard systems, work programs, launch costs impose weight and volume limitations. For all investigated food items, the manufacturing technique must take into account all flight specific mechanical parameters. From a nutrition and sanitation standpoint, food packs must be designed to comply with certain specific effects of long term flights ans selected food items must be thoroughly safe, which requires very strict laboratory testing. The diet must also be varied, if possible it should match astronauts' personal preferences. Food preparations must be easy to use. Space food items are original applications of existing technologies: they are of very high quality.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2015-12-01

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

  4. A critical analysis of UK public health policies in relation to diet and nutrition in low-income households.

    PubMed

    Attree, Pamela

    2006-04-01

    Diet and nutrition, particularly among low-income groups, is a key public health concern in the UK. Low levels of fruit and vegetable consumption, and obesity, especially among children, have potentially severe consequences for the future health of the nation. From a public health perspective, the UK government's role is to help poorer families make informed choices within healthy frameworks for living. However, the question is - to what extent are such policies in accordance with lay experiences of managing diet and nutrition on a low-income? This paper critically examines contemporary public health policies aimed at improving diet and nutrition, identifying the underlying theories about the influences on healthy eating in poor families, and exploring the extent to which these assumptions are based on experiential accounts. It draws on two qualitative systematic reviews - one prioritizing low-income mothers' accounts of 'managing' in poverty; and the other focusing on children's perspectives. The paper finds some common ground between policies and lay experiences, but also key divergencies. Arguably, the emphasis of public health policy on individual behaviour, coupled with an ethos of empowered consumerism, underplays material limitations on 'healthy eating' for low-income mothers and children. Health policies fail to take into account the full impact of structural influences on food choices, or recognize the social and emotional factors that influence diet and nutrition. In conclusion, it is argued that while health promotion campaigns to improve low-income families' diets do have advantages, these are insufficient to outweigh the negative effects of poverty on nutrition.

  5. Diets that Work

    MedlinePlus

    ... Balance › Diets that Work Fact Sheet Diets that Work February 2014 Download PDFs English Espanol Editors Susan ... there? It can be hard to know what works and what’s healthy. Everyone wants a diet that ...

  6. Diet myths and facts

    MedlinePlus

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    EPA Science Inventory

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

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

    PubMed

    Cao, Liaoran; Lv, Chao; Yang, Wei

    2013-08-13

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-03-01

    In Oman, the presence of highly productive marine environments, coupled with relatively limited land resources, have led to intense exploitation of coastal resources, but the question of the seasonality of occupation of coastal sites remains open. Our aim is to evaluate the contribution of marine resources to the diet of the Neolithic population of Ra's al-Hamra 5 (RH-5) to shed new light on its mobility, using stable isotopes and radiocarbon ((14)C) dating as dietary tracers. Charcoal, shell, human bone and enamel apatite from eight contemporary graves were sampled. Graves are thought to provide the best chance to obtain marine and terrestrial remains that were contemporary with the human remains in order to calculate the marine reservoir effect (MRE) for this period. Inter-individual variation in human bone apatite δ(13)C value is small, suggesting a homogenous diet. Bone apatite (14)C ages are very close to the shell ages while enamel is significantly younger and plots near the charcoal ages. Older enamel ages were obtained when a stronger acetic treatment was used, demonstrating that the young ages are due to diagenetic alteration rather than a diachronic change in diet and that only bone apatite retained in vivo dietary signals. Bone ages indicate a heavy reliance on marine resources and it is therefore unlikely that the individuals analyzed here were leaving the coast seasonally, although mobility along the coast cannot be excluded. PMID:24264052

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

    PubMed

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

    2014-03-01

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

  14. Microwave-induced inactivation of DNA-based hybrid catalyst in asymmetric catalysis.

    PubMed

    Zhao, Hua; Shen, Kai

    2016-03-01

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

  15. Understanding the DASH diet

    MedlinePlus

    ... The diet was first created to help lower high blood pressure . It is also a healthy way to lose weight. ... traditional low-salt diet. The DASH diet emphasizes foods high in ... lower blood pressure. To follow the DASH diet for weight loss, ...

  16. DNA-based Simultaneous Identification of Three Terminalia Species Targeting Adulteration

    PubMed Central

    Sharma, Sonal; Shrivastava, Neeta

    2016-01-01

    Background: Various parts of three Terminalia species, namely, Terminalia arjuna (stem bark), Terminalia bellirica (fruit), and Terminalia chebula (fruit) are widely known for their therapeutic principles and other commercial values. However, stem bark of T. bellirica and T. chebula along with Terminalia tomentosa are reported as adulterants of T. arjuna. Correct botanical identification is very critical for safe and effective herbal drugs. DNA-based identification approaches are advancing the conventional methods and sometime proved more beneficial. Objective: The purpose of the study was to develop polymerase chain reaction (PCR) method using internal transcribed spacer (ITS) region to ascertain the identity of T. arjuna herbal material as well as detection of mixing of other three Terminalia species. Materials and Methods: DNA from stem barks samples were isolated and subjected to ITS region amplification and sequencing. Sequences were compared for polymorphic nucleotides determination to develop species-specific primers. Final primers were selected on the basis of in silico analysis and experimentally validated. PCR assays for botanical identification of Terminalia species were developed. Sensitivity testing and assay validation were also performed. Results: The PCR assays developed for Terminalia species were resulted in definite amplicons of the corresponding species. No cross-reactivity of the primers was detected. Sensitivity was found enough to amplify as low as 2 ng of DNA. Mixing of DNA in various concentrations for validation also proved the sensitivity of assay to detect original botanicals in the mixture. The developed methods proved very specific and sensitive to authenticate Arjuna bark to develop evidence-based herbal medicines. SUMMARY Internal transcribed spacer-based species-specific polymerase chain reaction.(PCR) assays were developed to authenticate Terminalia arjuna stem bark and to identify substitution/adulteration of Terminalia bellirica

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

    Knight, Christine

    2016-08-01

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

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

    PubMed

    Knight, Christine

    2016-08-01

    The Scottish diet is associated in the UK media and popular discourse with unhealthy deep-fried foods. In addition to the stereotype's negative effects on perceptions of Scottish food, culture and people, there is evidence that the stereotype of the Scottish diet has negative effects on food behaviour and public health in Scotland, having been shown to encourage consumption of deep-fried foods and discourage positive dietary change. The most notorious deep-fried food associated with Scotland is the deep-fried Mars bar (DFMB), arguably invented in Stonehaven (near Aberdeen), and first reported in the Scottish and UK press in 1995. This article reports findings from an analysis of newspaper references to the DFMB in the two highest selling newspapers in Scotland, the Scottish Sun and the Daily Record, between 2011 and 2014. A keyword search ("deep fried Mars bar") using the online media database Lexis Library generated 97 unique records, and the resulting dataset was analysed thematically and discursively. Analysis showed that both newspapers clearly associated the DFMB with Scotland. Further, both newspapers portrayed the DFMB and the broader "deep-fried" Scottish diet stereotype ambivalently (mixed positive and negative associations). However, the Daily Record actively criticised the DFMB stereotype much more often than did the Scottish Sun. These findings suggest that the Scottish population encounters different messages in the press about food and nutrition from people elsewhere in the UK, and that these messages vary depending on choice of media in Scotland. Given the known negative effects of the stereotype, differences in Scottish media discourse should be considered a potential factor in persistent health inequalities affecting Scotland. Educational efforts, and opening discussion with journalists and amongst the Scottish public, may be helpful. PMID:27125430

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

    PubMed

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

    2013-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    Cancer.gov

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

  8. Diet, exercise or diet with exercise: comparing the effectiveness of treatment options for weight-loss and changes in fitness for adults (18-65 years old) who are overfat, or obese; systematic review and meta-analysis.

    PubMed

    Clark, James E

    2015-01-01

    There are number of means of methods to alter body composition, and metabolic issues, available for the adult who is overfat. The following is a systematic review and meta-analysis focused on comparing changes from treatment program for adults who are overfat based on analysis of aggregated effect size (ES) of inducing changes. So as to determine the relative effectiveness of such protocols and intervention plans of choice. This tiered meta-analysis of 66-population based studies, and 162-studywise groups, a clear pattern of ES being established across and within treatments. First, hypocaloric balance is necessary for changing body composition, but the effectiveness for establishing imbalance does not equate with the effectiveness for body compositional changes, or any biomarkers associated with metabolic issues. With analysis showing that there is a necessity to include exercise in combination with diet effectively elicit changes in body composition and biomarkers of metabolic issues. More importantly, the combination, resistance training (RT) was more effective than endurance training (ET) or combination of RT and ET, particularly when progressive training volume of 2-to-3 sets for 6-to-10 reps at an intensity of ≥75% 1RM, utilizing whole body and free-weight exercises, at altering body compositional measures (ES of 0.47, 0.30, and 0.40 for loss of BM, FM, and retention of FFM respectively) and reducing total cholesterol (ES = 0.85), triglycerides (ES = 0.86) and low-density lipoproteins (ES = 0.60). Additionally RT was more effective at reducing fasting insulin levels (ES = 3.5) than ET or ET and RT. Even though generally lower ES than RT, the inclusion of ET was more effective when performed at high intensity (e.g. ≥70% VO2max or HRmax for 30-minutes 3-4x's/wk), or in an interval training style than when utilizing the relatively common prescribed method of low-to-moderate (e.g., 50-70% VO2max or HRmax for at least equal time) steady state

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

    PubMed Central

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

    2015-01-01

    Knowledge of infant diet and feeding practices among children of mothers with eating disorders is essential to promote healthy eating in these children. This study compared the dietary patterns of 6-month-old children of mothers with anorexia nervosa, bulimia nervosa, binge eating disorder, and eating disorder not otherwise specified - purging subtype, to the diet of children of mothers with no eating disorders. The study was based on 53,879 mothers in the Norwegian Mother and Child Cohort Study (MoBa). Latent class analysis (LCA) was used to identify discrete latent classes of infant diet based on the mothers’ responses to questions about 16 food items. LCA identified five classes, characterized by primarily homemade vegetarian food (4% of the infants in the sample), homemade traditional food (8%), commercial infant cereals (35%), commercial jarred baby food (39%), and a mix of all food groups (11%). We then estimated the association between the different latent dietary classes and maternal eating disorders using a multinomial logistic regression model. Infants of mothers with bulimia nervosa had a lower probability of being in the homemade traditional food class compared to the commercial jarred baby food class, than the referent without an eating disorder (O.R. 0.59; 95% CI 0.36–0.99). Infants of mothers with binge eating disorder had a lower probability of being in the homemade vegetarian class compared to the commercial jarred baby food class, than the referent (O.R. 0.77; 95% CI 0.60–0.99), but only before controlling for relevant confounders. Anorexia nervosa and eating disorder not otherwise specified-purging subtype were not statistically significant associated with any of the dietary classes. These results suggest that in the general population, maternal eating disorders may to some extent influence the child’s diet as early as 6 months after birth; however, the extent to which these differences influence child health and development remain an

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  12. Analysis of nutrient concentrations in the diet, serum, and urine of giraffe from surveyed North American zoological institutions.

    PubMed

    Sullivan, Kathleen; van Heugten, Eric; Ange-van Heugten, Kimberly; Poore, Matthew H; Dierenfeld, Ellen S; Wolfe, Barbara

    2010-01-01

    The objectives of the present research were to conduct a survey to investigate the health history and feeding practices of giraffe in captivity in North America and to obtain samples of hay, concentrate, browse, urine, and serum to compare across zoos, possible factors relating to the development of urolithiasis. Forty-one out of 98 institutions contacted responded, representing 218 giraffe. All responding zoos fed concentrate and alfalfa hay was the primary forage. Sixty-five percent of zoos fed browse and 43 different species of browse were listed. Six zoos reported a history of urolithiasis, seven reported wasting syndrome, and 10 reported sudden death. The median daily amount (as fed) of concentrate and hay offered were 5.45 kg (range of 2.73-9.55 kg) and 6.82 kg (range of 2.53-12.50 kg), respectively. The concentrate:hay ratio of the offered diet ranged from 0.22 to 3.47 with a median value of 0.79. Forty-three percent of the institutions offered a ratio greater than 1:1. Samples of concentrate and hay (six zoos), serum (five zoos), and urine (seven zoos) were obtained for chemical analyses. Analyzed nutrient content of the consumed diet, measured by weighing feed and orts for three consecutive days, met recommendations for giraffe, but was excessive for crude protein and P. Concentrate:hay and serum P were positively correlated (r=0.72; P<0.05). High dietary P content and a high level of concentrate relative to hay may be contributing factors to urolith formation and warrant further investigation.

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

    PubMed

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

    2011-06-14

    In primates, age, sex, and social status can strongly influence access to food resources. In Pan, these criteria are assumed to influence access to vertebrate meat. However, the significance of meat in terms of its role in the nutrition of Pan is still debated. Here we present a study using stable carbon and nitrogen isotope ratios in hair samples from habituated, wild bonobos (Pan paniscus) to explore these issues. Over a period of 5 mo hair samples were collected from fresh bonobo nests at LuiKotale, Democratic Republic of Congo. Hair samples were assigned to known individuals and were of sufficient length to allow the evaluation of isotopic variation over several months. Samples of plant foods and sympatric fauna were also analyzed. The δ(13)C and δ(15)N results of the bonobo hair were remarkably homogeneous over time and for the group as a whole. There are no differences in diet between the sexes. Within the group of males, however, there was a positive correlation between dominance status and δ(15)N. The isotopic data indicate that the contribution of fauna to bonobo diet is marginal and that plant food is the dietary protein source. In only some cases did elevated δ(15)N hair values correlate with observed faunivory and not correspond to the δ(15)N measured in the dominant plant foods. Given the large variation in hunting and meat eating of Pan across the African continent, the detection of seasonal changes in faunivory by elevated δ(15)N values in sectioned ape hair is a promising approach. PMID:21628564

  14. DNA bases assembled on the Au(110)/electrolyte interface: a combined experimental and theoretical study.

    PubMed

    Salvatore, Princia; Nazmutdinov, Renat R; Ulstrup, Jens; Zhang, Jingdong

    2015-02-19

    Among the low-index single-crystal gold surfaces, the Au(110) surface is the most active toward molecular adsorption and the one with fewest electrochemical adsorption data reported. Cyclic voltammetry (CV), electrochemically controlled scanning tunneling microscopy (EC-STM), and density functional theory (DFT) calculations have been employed in the present study to address the adsorption of the four nucleobases adenine (A), cytosine (C), guanine (G), and thymine (T), on the Au(110)-electrode surface. Au(110) undergoes reconstruction to the (1 × 3) surface in electrochemical environment, accompanied by a pair of strong voltammetry peaks in the double-layer region in acid solutions. Adsorption of the DNA bases gives featureless voltammograms with lower double-layer capacitance, suggesting that all the bases are chemisorbed on the Au(110) surface. Further investigation of the surface structures of the adlayers of the four DNA bases by EC-STM disclosed lifting of the Au(110) reconstruction, specific molecular packing in dense monolayers, and pH dependence of the A and G adsorption. DFT computations based on a cluster model for the Au(110) surface were performed to investigate the adsorption energy and geometry of the DNA bases in different adsorbate orientations. The optimized geometry is further used to compute models for STM images which are compared with the recorded STM images. This has provided insight into the physical nature of the adsorption. The specific orientations of A, C, G, and T on Au(110) and the nature of the physical adsorbate/surface interaction based on the combination of the experimental and theoretical studies are proposed, and differences from nucleobase adsorption on Au(111)- and Au(100)-electrode surfaces are discussed.

  15. DNA bases assembled on the Au(110)/electrolyte interface: a combined experimental and theoretical study.

    PubMed

    Salvatore, Princia; Nazmutdinov, Renat R; Ulstrup, Jens; Zhang, Jingdong

    2015-02-19

    Among the low-index single-crystal gold surfaces, the Au(110) surface is the most active toward molecular adsorption and the one with fewest electrochemical adsorption data reported. Cyclic voltammetry (CV), electrochemically controlled scanning tunneling microscopy (EC-STM), and density functional theory (DFT) calculations have been employed in the present study to address the adsorption of the four nucleobases adenine (A), cytosine (C), guanine (G), and thymine (T), on the Au(110)-electrode surface. Au(110) undergoes reconstruction to the (1 × 3) surface in electrochemical environment, accompanied by a pair of strong voltammetry peaks in the double-layer region in acid solutions. Adsorption of the DNA bases gives featureless voltammograms with lower double-layer capacitance, suggesting that all the bases are chemisorbed on the Au(110) surface. Further investigation of the surface structures of the adlayers of the four DNA bases by EC-STM disclosed lifting of the Au(110) reconstruction, specific molecular packing in dense monolayers, and pH dependence of the A and G adsorption. DFT computations based on a cluster model for the Au(110) surface were performed to investigate the adsorption energy and geometry of the DNA bases in different adsorbate orientations. The optimized geometry is further used to compute models for STM images which are compared with the recorded STM images. This has provided insight into the physical nature of the adsorption. The specific orientations of A, C, G, and T on Au(110) and the nature of the physical adsorbate/surface interaction based on the combination of the experimental and theoretical studies are proposed, and differences from nucleobase adsorption on Au(111)- and Au(100)-electrode surfaces are discussed. PMID:25611676

  16. Proteomic Analysis in Type 2 Diabetes Patients before and after a Very Low Calorie Diet Reveals Potential Disease State and Intervention Specific Biomarkers

    PubMed Central

    Dharuri, Harish K.; Jeyakar, Skhandhan; Snel, Marieke; Juhasz, Peter; Lynch, Moira; Hines, Wade; Li, Xiaohong; Jazet, Ingrid M.; Adourian, Aram; Hilbers, Peter A. J.; Smit, Johannes W. A.; Van Dijk, Ko Willems

    2014-01-01

    Very low calorie diets (VLCD) with and without exercise programs lead to major metabolic improvements in obese type 2 diabetes patients. The mechanisms underlying these improvements have so far not been elucidated fully. To further investigate the mechanisms of a VLCD with or without exercise and to uncover possible biomarkers associated with these interventions, blood samples were collected from 27 obese type 2 diabetes patients before and after a 16-week VLCD (Modifast ∼450 kcal/day). Thirteen of these patients followed an exercise program in addition to the VCLD. Plasma was obtained from 27 lean and 27 obese controls as well. Proteomic analysis was performed using mass spectrometry (MS) and targeted multiple reaction monitoring (MRM) and a large scale isobaric tags for relative and absolute quantitation (iTRAQ) approach. After the 16-week VLCD, there was a significant decrease in body weight and HbA1c in all patients, without differences between the two intervention groups. Targeted MRM analysis revealed differences in several proteins, which could be divided in diabetes-associated (fibrinogen, transthyretin), obesity-associated (complement C3), and diet-associated markers (apolipoproteins, especially apolipoprotein A-IV). To further investigate the effects of exercise, large scale iTRAQ analysis was performed. However, no proteins were found showing an exercise effect. Thus, in this study, specific proteins were found to be differentially expressed in type 2 diabetes patients versus controls and before and after a VLCD. These proteins are potential disease state and intervention specific biomarkers. Trial Registration Controlled-Trials.com ISRCTN76920690 PMID:25415563

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

    PubMed

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

    2010-09-01

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

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

    PubMed Central

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

    2016-01-01

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

  19. Caffeine in the diet

    MedlinePlus

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

  20. Diet and Exercise Tips

    MedlinePlus

    ... Health News & Publications Annual Meeting Calendar Diet and Exercise Tips Diet and Exercise Tips News media interested in covering the latest ... Health Statistics concludes that 35 percent of adults exercise regularly (more than 6 of 10 don’t), ...

  1. Ketogenic Diets and Pain

    PubMed Central

    Masino, Susan A.; Ruskin, David N.

    2014-01-01

    Ketogenic diets are well-established as a successful anticonvulsant therapy. Based on overlap between mechanisms postulated to underlie pain and inflammation, and mechanisms postulated to underlie therapeutic effects of ketogenic diets, recent studies have explored the ability for ketogenic diets to reduce pain. Here we review clinical and basic research thus far exploring the impact of a ketogenic diet on thermal pain, inflammation, and neuropathic pain. PMID:23680946

  2. Diets for Constipation

    PubMed Central

    2014-01-01

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

  3. Diet, Nutrition, and Cancer Epigenetics.

    PubMed

    Sapienza, Carmen; Issa, Jean-Pierre

    2016-07-17

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

    Zanton, G I

    2016-06-01

    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 (CP) levels in lactating dairy cow diets. The final database of studies meeting the selection criteria contained 55 publications with 23 classified as using a continuous (80 diets) and 34 classified as using a change-over (173 diets) experimental design (2 publications reported results from trials using both designs). Mixed model, weighted analysis of covariance was conducted on production measures in response to CP including the continuous covariates year of publication and average days in milk (DIM) and the discrete classification covariate of experimental design. The model was evaluated for curvilinearity in the response to CP, variance heterogeneity, and coincidence in the response between experimental designs, with P<0.05 indicating significant effects and P<0.15 indicating trends. On average, cows in experiments using continuous designs had a lower initial DIM, were on treatment longer, and produced a greater yield of milk and milk protein than cows in experiments using change-over designs. Production responses to increasing CP were increased dry matter intake (DMI), milk and component yield, and feed efficiency (milk Mcal/kg of DMI), and decreased milk N:intake N. Response in milk yield and feed efficiency to increased CP interacted with experimental design where continuous experiments had greater milk yield and feed efficiency response at higher levels of CP. Interaction between CP and design effects on yield of milk protein and fat or milk N:intake N did not approach significance. The database is limited by the lower number of continuous studies and the differences in average DIM between designs; nevertheless, it is concluded that DMI, milk protein yield, milk fat yield, and milk N:intake N responses to CP did not depend on experimental design. Response of milk yield and feed efficiency to

  7. Diet for rapid weight loss

    MedlinePlus

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

  8. A stereological analysis of NPY, POMC, Orexin, GFAP astrocyte, and Iba1 microglia cell number and volume in diet-induced obese male mice.

    PubMed

    Lemus, Moyra B; Bayliss, Jacqueline A; Lockie, Sarah H; Santos, Vanessa V; Reichenbach, Alex; Stark, Romana; Andrews, Zane B

    2015-05-01

    The hypothalamic arcuate nucleus (ARC) contains 2 key neural populations, neuropeptide Y (NPY) and proopiomelanocortin (POMC), and, together with orexin neurons in the lateral hypothalamus, plays an integral role in energy homeostasis. However, no studies have examined total neuronal number and volume after high-fat diet (HFD) exposure using sophisticated stereology. We used design-based stereology to estimate NPY and POMC neuronal number and volume, as well as glial fibrillary acidic protein (astrocyte marker) and ionized calcium-binding adapter molecule 1 (microglia marker) cell number in the ARC; as well as orexin neurons in the lateral hypothalamus. Stereological analysis indicated approximately 8000 NPY and approximately 9000 POMC neurons in the ARC, and approximately 7500 orexin neurons in the lateral hypothalamus. HFD exposure did not affect total neuronal number in any population. However, HFD significantly increased average NPY cell volume and affected NPY and POMC cell volume distribution. HFD reduced orexin cell volume but had a bimodal effect on volume distribution with increased cells at relatively small volumes and decreased cells with relatively large volumes. ARC glial fibrillary acidic protein cells increased after 2 months on a HFD, although no significant difference after 6 months on chow diet or HFD was observed. No differences in ARC ionized calcium-binding adapter molecule 1 cell number were observed in any group. Thus, HFD affects ARC NPY or POMC neuronal cell volume number not cell number. Our results demonstrate the importance of stereology to perform robust unbiased analysis of cell number and volume. These data should be an empirical baseline reference to which future studies are compared.

  9. Ultrafast dynamics of solvation and charge transfer in a DNA-based biomaterial.

    PubMed

    Choudhury, Susobhan; Batabyal, Subrata; Mondol, Tanumoy; Sao, Dilip; Lemmens, Peter; Pal, Samir Kumar

    2014-05-01

    Charge migration along DNA molecules is a key factor for DNA-based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA-based materials for the intactness of the DNA structure and their dynamic role in the charge-transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA-cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well-known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as-prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature-dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge-transfer dynamics.

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

    USGS Publications Warehouse

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

    2010-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  12. The Friedreich's ataxia protein frataxin modulates DNA base excision repair in prokaryotes and mammals.

    PubMed

    Thierbach, René; Drewes, Gunnar; Fusser, Markus; Voigt, Anja; Kuhlow, Doreen; Blume, Urte; Schulz, Tim J; Reiche, Carina; Glatt, Hansruedi; Epe, Bernd; Steinberg, Pablo; Ristow, Michael

    2010-11-15

    DNA-repair mechanisms enable cells to maintain their genetic information by protecting it from mutations that may cause malignant growth. Recent evidence suggests that specific DNA-repair enzymes contain ISCs (iron-sulfur clusters). The nuclearencoded protein frataxin is essential for the mitochondrial biosynthesis of ISCs. Frataxin deficiency causes a neurodegenerative disorder named Friedreich's ataxia in humans. Various types of cancer occurring at young age are associated with this disease, and hence with frataxin deficiency. Mice carrying a hepatocyte-specific disruption of the frataxin gene develop multiple liver tumours for unresolved reasons. In the present study, we show that frataxin deficiency in murine liver is associated with increased basal levels of oxidative DNA base damage. Accordingly, eukaryotic V79 fibroblasts overexpressing human frataxin show decreased basal levels of these modifications, while prokaryotic Salmonella enterica serotype Typhimurium TA104 strains transformed with human frataxin show decreased mutation rates. The repair rates of oxidative DNA base modifications in V79 cells overexpressing frataxin were significantly higher than in control cells. Lastly, cleavage activity related to the ISC-independent repair enzyme 8-oxoguanine glycosylase was found to be unaltered by frataxin overexpression. These findings indicate that frataxin modulates DNA-repair mechanisms probably due to its impact on ISC-dependent repair proteins, linking mitochondrial dysfunction to DNA repair and tumour initiation.

  13. Multifunctional DNA-based biomemory device consisting of ssDNA/Cu heterolayers.

    PubMed

    Lee, Taek; El-Said, Waleed Ahmed; Min, Junhong; Choi, Jeong-Woo

    2011-01-15

    In the present study, we developed a novel DNA-based biomemory device that was comprised of ssDNA/Cu heterolayers on Au electrodes. As a conducting material, a thiol-modified single strand DNA (26 bp) was designed and immobilized on the Au electrode without the need for any linker material. Cu(2+) ions, which acted as the active site, were then chemically absorbed on the external structure of ssDNA through electrostatic interactions. The presence of the fabricated ssDNA/Cu heterolayer was confirmed by surface plasmon resonance (SPR) spectroscopy and Raman spectroscopy. Cyclic voltammetry experiments were carried out to investigate the redox properties of ssDNA/Cu hybrids to obtain the oxidation and reduction potential. Based on measured oxidation and reduction potential, a ROM-type, 3-state type, and WORM type DNA memory functions were demonstrated by chronoamperometry (CA) and open circuit potential amperometry (OCPA). This proposed device acts and operates the memory function very well. In the near future, DNA based biomemory device in this study could provide the alternative to the inorganic electronic device when molecular scaled immobilization control and signal measurement are achieved. PMID:21051218

  14. The application of a DNA-based identification technique to over-the-counter herbal medicines.

    PubMed

    Kazi, Tazimuddin; Hussain, Nazreen; Bremner, Paul; Slater, Adrian; Howard, Caroline

    2013-06-01

    Reliable methods to identify medicinal plant material are becoming more important in an increasingly regulated market place. DNA-based methods have been recognised as a valuable tool in this area with benefits such as being unaffected by the age of the plant material, growth conditions and harvesting techniques. It is possible that the methods of production used for medicinal plant products will degrade or remove DNA. So how applicable are these techniques to processed medicinal plant products? A simple PCR-based identification technique has been developed for St. John's Wort, Hypericum perforatum L. Thirteen St. John's Wort products were purchased including capsules, tablets and tinctures. DNA was extracted from each product, and the species specific PCR test conducted. DNA was successfully extracted from all thirteen products, using a fast and efficient modified method for extracting DNA from tinctures. Only four products yielded the full length ITS region (850 bp) due to the quality of the DNA. All of the products tested positive for H. perforatum DNA. DNA-based identification methods can complement existing methods of authentication. This paper shows that these methods are applicable to a wide range of processed products, provided that they are designed to account for the possibility of DNA degradation. PMID:23500384

  15. [Sustainable diet: history lessons].

    PubMed

    Fatati, Giuseppe

    2015-11-01

    Global dietary patterns changed dramatically in the past 50 years, presenting both a boom and a threat to the health and well-being of populations everywhere. We need sustainable diets, with low-input, local and seasonal agro-ecological food productions as well as short distance production-consumption nets for fair trade. The development of a global food system able to guarantee everyone a balanced food intake requires health professionals an awareness and a commitment to increasingly complex education. Dietary changes such as the adherence of to the Mediterranean Dietary Pattern can reduce the environmental footprint and thus the use of natural resources. Increased focus on improving the utilization of freshwater fishes and the correct use of the waters of rivers and lakes should also be encouraged. Cultural heritage, food quality and culinary skills are other key aspects determining sustainable dietary patterns and food security. The Mediterranean street food (Mediterraneità), for intrinsic characteristics, can represent valid model to address the main issues concerning the sustainable food system. The issues of sustainability offer a great opportunity to nutritional science and scientists to play a more central role in the political analysis of future food systems. We are confident that preserve the past helps us understand the present and build for the future, the Mediterranean lifestyle is much more than the Mediterranean diet and, finally, the rivers and the lakes may be our future. PMID:26668038

  16. [Sustainable diet: history lessons].

    PubMed

    Fatati, Giuseppe

    2015-11-01

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

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

    PubMed Central

    2016-01-01

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

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

    PubMed

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

    2013-10-01

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

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

    PubMed

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

    2013-03-27

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

  20. Fast Parallel Molecular Algorithms for DNA-Based Computation: Solving the Elliptic Curve Discrete Logarithm Problem over GF(2n)

    PubMed Central

    Li, Kenli; Zou, Shuting; Xv, Jin

    2008-01-01

    Elliptic curve cryptographic algorithms convert input data to unrecognizable encryption and the unrecognizable data back again into its original decrypted form. The security of this form of encryption hinges on the enormous difficulty that is required to solve the elliptic curve discrete logarithm problem (ECDLP), especially over GF(2n), n ∈ Z+. This paper describes an effective method to find solutions to the ECDLP by means of a molecular computer. We propose that this research accomplishment would represent a breakthrough for applied biological computation and this paper demonstrates that in principle this is possible. Three DNA-based algorithms: a parallel adder, a parallel multiplier, and a parallel inverse over GF(2n) are described. The biological operation time of all of these algorithms is polynomial with respect to n. Considering this analysis, cryptography using a public key might be less secure. In this respect, a principal contribution of this paper is to provide enhanced evidence of the potential of molecular computing to tackle such ambitious computations. PMID:18431451

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

    PubMed

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

    2013-01-01

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

  2. A DNA-Based Assessment of the Phylogenetic Position of a Morphologically Distinct, Anchialine-Lake-Restricted Seahorse.

    PubMed

    Rose, Emily; Masonjones, Heather D; Jones, Adam G

    2016-11-01

    Isolated populations provide special opportunities to study local adaptation and incipient speciation. In some cases, however, morphological evolution can obscure the taxonomic status of recently founded populations. Here, we use molecular markers to show that an anchialine-lake-restricted population of seahorses, originally identified as Hippocampus reidi, appears on the basis of DNA data to be Hippocampus erectus We collected seahorses from Sweetings Pond, on Eleuthera Island, Bahamas, during the summer of 2014. We measured morphological traits and sequenced 2 genes, cytochrome b and ribosomal protein S7, from 19 seahorses in our sample. On the basis of morphology, Sweetings Pond seahorses could not be assigned definitively to either of the 2 species of seahorse, H. reidi and H. erectus, that occur in marine waters surrounding the Bahamas. However, our DNA-based phylogenetic analysis showed that the Sweetings Pond fish were firmly nested within the H. erectus clade with a Bayesian posterior probability greater than 0.99. Thus, Sweetings Pond seahorses most recently shared a common ancestor with H. erectus populations from the Western Atlantic. Interestingly, the seahorses from Sweetings Pond differ morphologically from other marine populations of H. erectus in having a more even torso to tail length ratio. The substantial habitat differences between Sweetings Pond and the surrounding coastal habitat make Sweetings Pond seahorses particularly interesting from the perspectives of conservation, local adaptation, and incipient speciation.

  3. A DNA-based nanomechanical device used to characterize the distortion of DNA by Apo-SoxR protein.

    PubMed

    Liu, Chunhua; Kim, Eunsuk; Demple, Bruce; Seeman, Nadrian C

    2012-02-01

    DNA-based nanomechanical devices can be used to characterize the action of DNA-distorting proteins. Here, we have constructed a device wherein two DNA triple-crossover (TX) molecules are connected by a shaft, similar to a previous device that measured the binding free energy of integration host factor. In our case, the binding site on the shaft contains the sequence recognized by SoxR protein, the apo form of which is a transcriptional activator. Another active form is oxidized [2Fe-2S] SoxR formed during redox sensing, and previous data suggest that activated Fe-SoxR distorts its binding site by localized DNA untwisting by an amount that corresponds to ~2 bp. A pair of dyes report the fluorescence resonance energy transfer (FRET) signal between the two TX domains, reflecting changes in the shape of the device upon binding of the protein. The TX domains are used to amplify the signal expected from a relatively small distortion of the DNA binding site. From FRET analysis of apo-SoxR binding, the effect of apo-SoxR on the original TX device is similar to the effect of shortening the TX device by 2 bp. We estimate that the binding free energy of apo-SoxR on the DNA target site is 3.2-6.1 kcal/mol. PMID:22257222

  4. Effect of fat additions to diets of dairy cattle on milk production and components: a meta-analysis and meta-regression.

    PubMed

    Rabiee, A R; Breinhild, K; Scott, W; Golder, H M; Block, E; Lean, I J

    2012-06-01

    The objectives of this study were to critically review randomized controlled trials, and quantify, using meta-analysis and meta-regression, the effects of supplementation with fats on milk production and components by dairy cows. We reviewed 59 papers, of which 38 (containing 86 comparisons) met eligibility criteria. Five groups of fats were evaluated: tallows, calcium salts of palm fat (Megalac, Church and Dwight Co. Inc., Princeton, NJ), oilseeds, prilled fat, and other calcium salts. Milk production responses to fats were significant, and the estimated mean difference was 1.05 kg/cow per day, but results were heterogeneous. Milk yield increased with increased difference in dry matter intake (DMI) between treatment and control groups, decreased with predicted metabolizable energy (ME) balance between these groups, and decreased with increased difference in soluble protein percentage of the diet between groups. Decreases in DMI were significant for Megalac, oilseeds, and other Ca salts, and approached significance for tallow. Feeding fat for a longer period increased DMI, as did greater differences in the amount of soluble protein percentage of the diet between control and treatment diets. Tallow, oilseeds, and other Ca salts reduced, whereas Megalac increased, milk fat percentage. Milk fat percentage effects were heterogeneous for fat source. Differences between treatment and control groups in duodenal concentrations of C18:2 and C 18:0 fatty acids and Mg percentage reduced the milk fat percentage standardized mean difference. Milk fat yield responses to fat treatments were very variable. The other Ca salts substantially decrease, and the Megalac and oilseeds increased, fat yield. Fat yield increased with increased DMI difference between groups and was lower with an increased estimated ME balance between treatment and control groups, indicating increased partitioning of fat to body tissue reserves. Feeding fats decreased milk protein percentage, but results were

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

    PubMed

    Senés-Guerrero, Carolina; Schüßler, Arthur

    2016-01-01

    Arbuscular mycorrhizal fungi (AMF) are obligate symbionts of most land plants. They have great ecological and economic importance as they can improve plant nutrition, plant water supply, soil structure, and plant resistance to pathogens. We describe two approaches for the DNA-based characterization and identification of AMF, which both can be used for single fungal spores, soil, or roots samples and resolve closely related AMF species: (a) Sanger sequencing of a 1.5 kb extended rDNA-barcode from clone libraries, e.g., to characterize AMF isolates, and (b) high throughput 454 GS-FLX+ pyrosequencing of a 0.8 kb rDNA fragment, e.g., for in-field monitoring. PMID:26791499

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

    PubMed Central

    2016-01-01

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

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

    PubMed

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

    2005-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  9. DNA-based immunotherapy for HPV-associated head and neck cancer.

    PubMed

    Aggarwal, Charu

    2016-10-01

    Squamous cell carcinoma of the head and neck (SCCHN) accounts for 3% of all cancers. Most patients present with locally advanced disease, where multimodality therapies are used with curative intent. Despite favorable early local treatment results, about one third of the patients will eventually develop metastatic disease. Immunotherapy offers a novel therapeutic strategy beyond cytotoxic chemotherapy, with initial approvals in melanoma and non-small-cell lung cancer. HPV-associated SCCHN is a distinct subset, with unique epidemiology and treatment outcomes. Both subsets of SCCHN (HPV-related or not) are particularly favorable for immunotherapy, as immune evasion and dysregulation have been shown to play a key role in the initiation and progression of disease. This review focuses on the latest developments in immunotherapy in SCCHN, with a particular focus on DNA-based approaches including vaccine and adoptive cellular therapies. PMID:27605067

  10. A DNA-based system for selecting and displaying the combined result of two input variables

    PubMed Central

    Liu, Huajie; Wang, Jianbang; Song, Shiping; Fan, Chunhai; Gothelf, Kurt V.

    2015-01-01

    Oligonucleotide-based technologies for biosensing or bio-regulation produce huge amounts of rich high-dimensional information. There is a consequent need for flexible means to combine diverse pieces of such information to form useful derivative outputs, and to display those immediately. Here we demonstrate this capability in a DNA-based system that takes two input numbers, represented in DNA strands, and returns the result of their multiplication, writing this as a number in a display. Unlike a conventional calculator, this system operates by selecting the result from a library of solutions rather than through logic operations. The multiplicative example demonstrated here illustrates a much more general capability—to generate a unique output for any distinct pair of DNA inputs. The system thereby functions as a lookup table and could be a key component in future, more powerful data-processing systems for diagnostics and sensing. PMID:26646059

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

    PubMed

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

    2015-08-01

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

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

    PubMed

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

    2015-08-01

    Chemical modification and spontaneous loss of nucleotide bases from DNA are estimated to occur at the rate of thousands per human cell per day. DNA base excision repair (BER) is a critical mechanism for repairing such lesions in nuclear and mitochondrial DNA. Defective expression or function of proteins required for BER or proteins that regulate BER have been consistently associated with neurological dysfunction and disease in humans. Recent studies suggest that DNA lesions in the nuclear and mitochondrial compartments and the cellular response to those lesions have a profound effect on cellular energy homeostasis, mitochondrial function and cellular bioenergetics, with especially strong influence on neurological function. Further studies in this area could lead to novel approaches to prevent and treat human neurodegenerative disease. PMID:26002197

  13. DNA-based immunotherapy for HPV-associated head and neck cancer.

    PubMed

    Aggarwal, Charu

    2016-10-01

    Squamous cell carcinoma of the head and neck (SCCHN) accounts for 3% of all cancers. Most patients present with locally advanced disease, where multimodality therapies are used with curative intent. Despite favorable early local treatment results, about one third of the patients will eventually develop metastatic disease. Immunotherapy offers a novel therapeutic strategy beyond cytotoxic chemotherapy, with initial approvals in melanoma and non-small-cell lung cancer. HPV-associated SCCHN is a distinct subset, with unique epidemiology and treatment outcomes. Both subsets of SCCHN (HPV-related or not) are particularly favorable for immunotherapy, as immune evasion and dysregulation have been shown to play a key role in the initiation and progression of disease. This review focuses on the latest developments in immunotherapy in SCCHN, with a particular focus on DNA-based approaches including vaccine and adoptive cellular therapies.

  14. Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification of Ipomoea mauritiana Jacq (Convolvulaceae)

    PubMed Central

    Devaiah, Kambiranda; Balasubramani, Subramani Paranthaman; Venkatasubramanian, Padma

    2011-01-01

    Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation of Chyavanaprash. Tubers of Ipomoea mauritiana Jacq. (Convolvulaceae), Pueraria tuberosa (Roxb. ex Willd.) DC (Fabaceae), Adenia hondala (Gaertn.) de Wilde (Passifloraceae) and pith of Cycas circinalis L. (Cycadaceae) are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA-based markers have been developed to distinguish I. mauritiana from the other Vidari candidates. A putative 600-bp polymorphic sequence, specific to I. mauritiana was identified using randomly amplified polymorphic DNA (RAPD) technique. Furthermore, sequence characterized amplified region (SCAR) primers (IM1F and IM1R) were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323-bp amplicon in authentic I. mauritiana and not in the allied species. PMID:21738554

  15. Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification of Ipomoea mauritiana Jacq (Convolvulaceae).

    PubMed

    Devaiah, Kambiranda; Balasubramani, Subramani Paranthaman; Venkatasubramanian, Padma

    2011-01-01

    Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation of Chyavanaprash. Tubers of Ipomoea mauritiana Jacq. (Convolvulaceae), Pueraria tuberosa (Roxb. ex Willd.) DC (Fabaceae), Adenia hondala (Gaertn.) de Wilde (Passifloraceae) and pith of Cycas circinalis L. (Cycadaceae) are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA-based markers have been developed to distinguish I. mauritiana from the other Vidari candidates. A putative 600-bp polymorphic sequence, specific to I. mauritiana was identified using randomly amplified polymorphic DNA (RAPD) technique. Furthermore, sequence characterized amplified region (SCAR) primers (IM1F and IM1R) were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323-bp amplicon in authentic I. mauritiana and not in the allied species.

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

    PubMed Central

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

    2015-01-01

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

  17. Diet quality and diet costs in German children and adolescents.

    PubMed

    Alexy, U; Schwager, V; Kersting, M

    2014-10-01

    We examined the association between diet costs and diet quality in a sample of children and adolescents using data from the ongoing longitudinal (open cohort) DONALD (Dortmund Nutritional and Anthropometric Longitudinally Designed) study. Children and adolescents aged 4-18 years (255 boys and 239 girls) provided 1100 yearly collected 3-day weighted dietary records. Linear mixed (effects) models were used to analyze the association between diet costs ([euro ;[sol;day, estimated using retail food prices) and the Nutrient Quality Index (NQI) and the Healthy Nutrition Score for Kids and Youth (HuSKY). Analysis were stratified for low-quality records (scoremedian). No significant association was found in the low-quality records, whereas in the high-quality records the association was significantly positive for both scores (HuSKY P=0.016, NQI P<0.0001). In conclusion, a substantial part of our sample could increase their diet quality without a noteworthy increase of expenditure.

  18. Evaluating environmental DNA-based quantification of ranavirus infection in wood frog populations.

    PubMed

    Hall, Emily M; Crespi, Erica J; Goldberg, Caren S; Brunner, Jesse L

    2016-03-01

    A variety of challenges arise when monitoring wildlife populations for disease. Sampling tissues can be invasive to hosts, and obtaining sufficient sample sizes can be expensive and time-consuming, particularly for rare species and when pathogen prevalence is low. Environmental DNA (eDNA)-based detection of pathogens is an alternative approach to surveillance for aquatic communities that circumvents many of these issues. Ranaviruses are emerging pathogens of ectothermic vertebrates linked to die-offs of amphibian populations. Detecting ranavirus infections is critical, but nonlethal methods have the above issues and are prone to false negatives. We report on the feasibility and effectiveness of eDNA-based ranavirus detection in the field. We compared ranavirus titres in eDNA samples collected from pond water to titres in wood frog (Lithobates sylvaticus; n = 5) tadpoles in sites dominated by this one species (n = 20 pond visits). We examined whether ranavirus DNA can be detected in eDNA from pond water when infections are present in the pond and if viral titres detected in eDNA samples correlate with the prevalence or intensity of ranavirus infections in tadpoles. With three 250 mL water samples, we were able to detect the virus in all visits with infected larvae (0.92 diagnostic sensitivity). Also, we found a strong relationship between the viral eDNA titres and titres in larval tissues. eDNA titres increased prior to observed die-offs and declined afterwards, and were two orders of magnitude higher in ponds with a die-off. Our results suggest that eDNA is useful for detecting ranavirus infections in wildlife and aquaculture.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

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

  2. Target-induced formation of gold amalgamation on DNA-based sensing platform for electrochemical monitoring of mercury ion coupling with cycling signal amplification strategy.

    PubMed

    Chen, Jinfeng; Tang, Juan; Zhou, Jun; Zhang, Lan; Chen, Guonan; Tang, Dianping

    2014-01-31

    Heavy metal ion pollution poses severe risks in human health and environmental pollutant, because of the likelihood of bioaccumulation and toxicity. Driven by the requirement to monitor trace-level mercury ion (Hg(2+)), herein we construct a new DNA-based sensor for sensitive electrochemical monitoring of Hg(2+) by coupling target-induced formation of gold amalgamation on DNA-based sensing platform with gold amalgamation-catalyzed cycling signal amplification strategy. The sensor was simply prepared by covalent conjugation of aminated poly-T(25) oligonucleotide onto the glassy carbon electrode by typical carbodiimide coupling. Upon introduction of target analyte, Hg(2+) ion was intercalated into the DNA polyion complex membrane based on T-Hg(2+)-T coordination chemistry. The chelated Hg(2+) ion could induce the formation of gold amalgamation, which could catalyze the p-nitrophenol with the aid of NaBH4 and Ru(NH3)6(3+) for cycling signal amplification. Experimental results indicated that the electronic signal of our system increased with the increasing Hg(2+) level in the sample, and has a detection limit of 0.02nM with a dynamic range of up to 1000nM Hg(2+). The strategy afforded exquisite selectivity for Hg(2+) against other environmentally related metal ions. In addition, the methodology was evaluated for the analysis of Hg(2+) in spiked tap-water samples, and the recovery was 87.9-113.8%. PMID:24439499

  3. Pathological characterization and morphometric analysis of hepatic lesions in SHRSP5/Dmcr, an experimental non-alcoholic steatohepatitis model, induced by high-fat and high-cholesterol diet.

    PubMed

    Horai, Yasushi; Utsumi, Hiroyuki; Ono, Yuko; Kishimoto, Toshimitsu; Ono, Yuuichi; Fukunari, Atsushi

    2016-02-01

    SHRSP5/Dmcr is a newly established substrain of stroke-prone spontaneously hypertensive rat (SHRSP). Recently, high-fat and high-cholesterol (HFC) diet-fed SHRSP5/Dmcr has been reported as a novel rat model of developing hepatic lesions similar to human non-alcoholic steatohepatitis (NASH). The aim of this study was to investigate the detailed pathological conditions induced by HFC diet in SHRSP5/Dmcr rats using molecular biological methods and morphometric analysis. SHRSP5/Dmcr rats at 6 weeks of age were fed on either HFC diet or stroke-prone (SP) diet for 2, 4, 6, 8 and 16 weeks and histopathological changes in the liver, blood chemistry and mRNA expression levels in the liver were investigated. As evidenced by the histopathological examination of the liver of the SHRSP5/Dmcr rats, hepatic steatosis and lobular inflammation were present, with gradual increasing severity from 2 weeks after the introduction of the HFC diet. Partial hepatic fibrosis was detected at 6 weeks and spread over the entire region of the liver with more severe bridging formation by 16 weeks. The degrees of NASH-like hepatic lesions such as steatosis (the size distribution of lipid droplets), inflammation and fibrosis were quantified by morphometric analysis. Eosinophilic inclusion bodies encountered in the hepatocytes had immunoreactivity with Cox-4 and double-membrane walls, identified as mega-mitochondria. Serum ALT and bilirubins, and the mRNA expression levels related to fibrosis were closely correlated with hepatic histopathological changes. The clear feeding time-dependent progression of NASH-like hepatic lesion in HFC diet-fed SHRSP5/Dmcr rats reinforced the conclusion that this strain might be a useful model of NASH and of inflammatory fibrotic liver disease. PMID:27037502

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

    PubMed Central

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

    2016-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. Men, food, and prostate cancer: gender influences on men's diets.

    PubMed

    Mróz, Lawrence W; Chapman, Gwen E; Oliffe, John L; Bottorff, Joan L

    2011-03-01

    Although healthy eating might enhance long-term survival, few men with prostate cancer make diet changes to advance their well-being. Men's typically poor diets and uninterest in self-health may impede nutrition interventions and diet change. Food choice behavior is complex involving many determinants, including gender, which can shape men's health practices, diets, and prostate cancer experiences. Developing men-centered prostate cancer nutrition interventions to engage men (and where appropriate their partners) in promoting healthy diets can afford health benefits. This article presents an overview and synthesis of current knowledge about men's food practices and provides an analysis of diet and diet change behaviors for men with prostate cancer. Masculinity and gender relations theory are discussed in the context of men's food practices, and suggestions for future applications to nutrition and prostate cancer research and diet interventions are made. PMID:20798140

  8. Men, food, and prostate cancer: gender influences on men's diets.

    PubMed

    Mróz, Lawrence W; Chapman, Gwen E; Oliffe, John L; Bottorff, Joan L

    2011-03-01

    Although healthy eating might enhance long-term survival, few men with prostate cancer make diet changes to advance their well-being. Men's typically poor diets and uninterest in self-health may impede nutrition interventions and diet change. Food choice behavior is complex involving many determinants, including gender, which can shape men's health practices, diets, and prostate cancer experiences. Developing men-centered prostate cancer nutrition interventions to engage men (and where appropriate their partners) in promoting healthy diets can afford health benefits. This article presents an overview and synthesis of current knowledge about men's food practices and provides an analysis of diet and diet change behaviors for men with prostate cancer. Masculinity and gender relations theory are discussed in the context of men's food practices, and suggestions for future applications to nutrition and prostate cancer research and diet interventions are made.

  9. Multiple univariate data analysis reveals the inulin effects on the high-fat-diet induced metabolic alterations in rat myocardium and testicles in the preobesity state.

    PubMed

    Duan, Yixuan; An, Yanpeng; Li, Ning; Liu, Bifeng; Wang, Yulan; Tang, Huiru

    2013-07-01

    Obesity is a worldwide epidemic and a well-known risk factor for many diseases affecting billions of people's health and well-being. However, little information is available for metabolic changes associated with the effects of obesity development and interventions on cardiovascular and reproduction systems. Here, we systematically analyzed the effects of high-fat diet (HFD) and inulin intake on the metabolite compositions of myocardium and testicle using NMR spectroscopy. We developed a useful high-throughput method based on multiple univariate data analysis (MUDA) to visualize and efficiently extract information on metabolites significantly affected by an intervention. We found that HFD caused widespread metabolic changes in both rat myocardium and testicles involving fatty acid β-oxidation together with the metabolisms of choline, amino acids, purines and pyrimidines even before HFD caused significant body-weight increases. Inulin intake ameliorated some of the HFD-induced metabolic changes in both myocardium (3-HB, lactate and guanosine) and testicle tissues (3-HB, inosine and betaine). A remarkable elevation of scyllo-inositol was also observable with inulin intake in both tissues. These findings offered essential information for the inulin effects on the HFD-induced metabolic changes and demonstrated this MUDA method as a powerful alternative to traditionally used multivariate data analysis for metabonomics.

  10. Prescription diets for rabbits.

    PubMed

    Proença, Laila Maftoum; Mayer, Jörg

    2014-09-01

    Dietary management can be used with drug therapy for the successful treatment of many diseases. Therapeutic nutrition is well-recognized in dogs and cats and is beginning to increase among other pet species, including rabbits. The nutritional component of some rabbit diseases (eg, urolithiasis) is not completely understood, and the clinician should evaluate the use of prescription diets based on the scientific literature and individual needs. Long-term feeding trials are needed to further evaluate the efficacy of prescription diets in rabbits. Prescription diets are available for selected diseases in rabbits, including diets for immediate-term, short-term, and long-term management. PMID:25155667

  11. General Strategy to Introduce pH-Induced Allostery in DNA-Based Receptors to Achieve Controlled Release of Ligands.

    PubMed

    Porchetta, Alessandro; Idili, Andrea; Vallée-Bélisle, Alexis; Ricci, Francesco

    2015-07-01

    Inspired by naturally occurring pH-regulated receptors, here we propose a rational approach to introduce pH-induced allostery into a wide range of DNA-based receptors. To demonstrate this we re-engineered two model DNA-based probes, a molecular beacon and a cocaine-binding aptamer, by introducing in their sequence a pH-dependent domain. We demonstrate here that we can finely tune the affinity of these model receptors and control the load/release of their specific target molecule by a simple pH change. PMID:26053894

  12. General Strategy to Introduce pH-Induced Allostery in DNA-Based Receptors to Achieve Controlled Release of Ligands.

    PubMed

    Porchetta, Alessandro; Idili, Andrea; Vallée-Bélisle, Alexis; Ricci, Francesco

    2015-07-01

    Inspired by naturally occurring pH-regulated receptors, here we propose a rational approach to introduce pH-induced allostery into a wide range of DNA-based receptors. To demonstrate this we re-engineered two model DNA-based probes, a molecular beacon and a cocaine-binding aptamer, by introducing in their sequence a pH-dependent domain. We demonstrate here that we can finely tune the affinity of these model receptors and control the load/release of their specific target molecule by a simple pH change.

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

    PubMed

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

    2014-01-01

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

  14. Hierarchical cluster analysis as an approach for systematic grouping of diet constituents on basis of fatty acid, energy and cholesterol content: application on consumable lamb products.

    PubMed

    Akbay, A; Elhan, A; Ozcan, C; Demirtaş, S

    2000-08-01

    The role of dietary fat in the etiology of chronic diseases is both a qualitative and a quantitative issue. The dietary fat intake is largely influenced by behavioral and social influences on food choice. Ongoing scientific research has led to dietary recommendations with main concerns being the percentage of saturated, essential fatty acids and cholesterol with respect to total energy intake. However, the compositional complexity of food choice constituting the diet is a critical concept complicating the interpretation of epidemiologic, clinical and laboratory evidence to define the role of dietary fat in the etiology of diseases. This study was conducted on the observation of the need to better systematically classify consumable food based on complex composition and lamb meat is randomly selected as a non-specific subset for application of hierarchical cluster analysis method to obtain the dendogram using average linkage. Data on fat composition of consumable lamb prepared by different methods was obtained from USDA Nutrient Database for Standart Reference. Using agglomerative hierarchical cluster analysis lamb meat was grouped into two main clusters among which one divided into two families of which each was subdivided into two subfamilies based on fatty acids, cholesterol and energy composition. Present work may be considered as a leading study to systematically classify larger food sets. As high fat foods are rich in flavor and overall palatability, the outcome of this study may lead to behaviorally more acceptable but healthier dietary replacements. Besides future use of the results obtained may reveal the effect of complex compositional dietary influences on health and disease and may have superiority to studies questioning individual dietary items. Furthermore, hieararchial cluster analysis may be used to cluster food including other compositional data in food items like amino acids, vitamins, carbohydrates, as well.

  15. Mediterranean diet and longevity.

    PubMed

    Trichopoulou, A; Vasilopoulou, E

    2000-12-01

    Mortality statistics from the WHO database covering the period 1960 to 1990 have provided intriguing evidence that something unusual has been affecting in a beneficial way the health of the Mediterranean population. In recent papers, which evaluated the evidence accumulated over the last three decades, it was concluded that the traditional Mediterranean diet meets several important criteria for a healthy diet. Direct evidence in support of the beneficial properties of the Mediterranean diet has also become available. These data were derived from three studies, which have used a diet score, devised a priori on the basis of eight desirable key features of the traditional common diet in the Mediterranean region. The conclusion of these studies is that a diet that adheres to the principles of the traditional Mediterranean one is associated with longer survival. The Greek version of the Mediterranean diet is dominated by the consumption of olive oil and by high consumption of vegetables and fruits. Antioxidants represent a common element in these foods and an antioxidant action provides a plausible explanation for the apparent benefits. Wild edible greens frequently eaten in rural Greece in the form of salads and pies contain very high quantities of flavonoids-- considerably higher than those found in red wine or black tea. While there is no direct evidence that these antioxidants are central to the benefits of the Mediterranean Diet, indirect evidence from epidemiological data and the increasing understanding of their mechanisms of action suggest that antioxidants may play a major role.

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

    PubMed

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

    2014-06-17

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

  17. [Diet treatment of hyperliproteinemias].

    PubMed

    Louis, J; Antoine, J M; Pointel, J P; Debry, G; Drouin, P

    1983-04-01

    The authors mention the previous conditions to the prescription of a diet for primary hyperlipoproteinemia: definition of the metabolic disease and of its nutritional dependance, precise knowledge of earlier nutritional uses, demonstration of vascular risk factor linked to the hyperlipoproteinemia, i.e. obesity which always requires a hypocaloric diet. A low cholesterol and saturated fatty acid diet reduces by 10% the cholesterolemia, and sometimes exempts from use of medical drugs in moderate hypercholesterolemia. The exceptional hyperchylomicronemia are reduced by drastic reduction of the lipid fraction of the diet, which is compensated by use of MCT. The dietetic treatment of endogenous hypertriglyceridemia depends on their nutritional dependance: an alcohol dependance implies a complete suppression of alcoholic drinks. A glucid dependance implies the suppression of simple carbohydrates and a reduction of the glucidic fraction of the diet. PMID:6346241

  18. Vegetarian diets and children.

    PubMed

    Sanders, T A; Reddy, S

    1994-05-01

    The diets and growth of children reared on vegetarian diets are reviewed. Excessive bulk combined with low energy density can be a problem for children aged < or = 5 y and can lead to imparied growth. Diets that have a high content of phytate and other modifiers of mineral absorption are associated with an increased prevalence of rickets and iron-deficiency anemia. Vitamin B-12 deficiency is a real hazard in unsupplemented or unfortified vegan and vegetarian diets. It is suggested that vegans and vegetarians should use oils with a low ratio of linoleic to linolenic acid in view of the recently recognized role of docosahexaenoic acid in visual functioning. If known pitfalls are avoided, the growth and development of children reared on both vegan and vegetarian diets appears normal.

  19. DIET at the nanoscale

    NASA Astrophysics Data System (ADS)

    Dujardin, G.; Boer-Duchemin, E.; Le Moal, E.; Mayne, A. J.; Riedel, D.

    2016-01-01

    We review the long evolution of DIET (Dynamics at surfaces Induced by Electronic Transitions) that began in the 1960s when Menzel, Gomer and Redhead proposed their famous stimulated desorption model. DIET entered the "nanoscale" in the 1990s when researchers at Bell Labs and IBM realized that the Scanning Tunneling Microscope (STM) could be used as an atomic size source of electrons to electronically excite individual atoms and molecules on surfaces. Resonant and radiant Inelastic Electron Tunneling (IET) using the STM have considerably enlarged the range of applications of DIET. Nowadays, "DIET at the nanoscale" covers a broad range of phenomena at the atomic-scale. This includes molecular dynamics (dissociation, desorption, isomerization, displacement, chemical reactions), vibrational spectroscopy and dynamics, spin spectroscopy and manipulation, luminescence spectroscopy, Raman spectroscopy and plasmonics. Future trends of DIET at the nanoscale offer exciting prospects for new methods to control light and matter at the nanoscale.

  20. DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.

    PubMed

    Monaghan, Michael T; Balke, Michael; Gregory, T Ryan; Vogler, Alfried P

    2005-10-29

    DNA barcoding has been successfully implemented in the identification of previously described species, and in the process has revealed several cryptic species. It has been noted that such methods could also greatly assist in the discovery and delineation of undescribed species in poorly studied groups, although to date the feasibility of such an approach has not been examined explicitly. Here, we investigate the possibility of using short mitochondrial and nuclear DNA sequences to delimit putative species in groups lacking an existing taxonomic framework. We focussed on poorly known tropical water beetles (Coleoptera: Dytiscidae, Hydrophilidae) from Madagascar and dung beetles (Scarabaeidae) in the genus Canthon from the Neotropics. Mitochondrial DNA sequence variation proved to be highly structured, with >95% of the observed variation existing between discrete sets of very closely related genotypes. Sequence variation in nuclear 28S rRNA among the same individuals was lower by at least an order of magnitude, but 16 different genotypes were found in water beetles and 12 genotypes in Canthon, differing from each other by a minimum of two base pairs. The distribution of these 28S rRNA genotypes in individuals exactly matched the distribution of mtDNA clusters, suggesting that mtDNA patterns were not misleading because of introgression. Moreover, in a few cases where sequence information was available in GenBank for morphologically defined species of Canthon, these matched some of the DNA-based clusters. These findings demonstrate that clusters of close relatives can be identified readily in the sequence variation obtained in field collected samples, and that these clusters are likely to correspond to either previously described or unknown species. The results suggest that DNA-assisted taxonomy will not require more than a short fragment of mtDNA to provide a largely accurate picture of species boundaries in these groups. Applied on a large scale, this DNA-based

  1. Traveler’s diarrhea diet

    MedlinePlus

    Diet - traveler's diarrhea; Diarrhea - traveler's - diet; Gastroenteritis - traveler's ... sick because their bodies are used to the bacteria. You can lower your ... diarrhea diet is to make your symptoms better and prevent ...

  2. Diet and Nutrition in Porphyria

    MedlinePlus

    ... Art Sale You are here Home Diet and Nutrition A proper diet is important to all individuals, ... alter food intake. Therefore, attention to diet and nutrition is important in almost any disease. Porphyrias are ...

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

    EPA Science Inventory

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

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

    PubMed

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

    2004-10-20

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

  5. Fad diets in the treatment of diabetes.

    PubMed

    Feinman, Richard D

    2011-04-01

    Use of the term "fad diet" reflects the contentious nature of the debate in the treatment of diabetes and generally targets diets based on carbohydrate restriction, the major challenge to traditional dietary therapy. Although standard low-fat diets more accurately conform to the idea of a practice supported by social pressure rather than scientific data, it is suggested that we might want to give up altogether unscientific terms like "fad" and "healthy." Far from faddish, diets based on carbohydrate restriction have been the historical treatment for diabetes and are still supported by basic biochemistry, and it is argued that they should be considered the "default" diet, the one to try first, in diseases of carbohydrate intolerance or insulin resistance. The barrier to acceptance of low-carbohydrate diets in the past has been concern about saturated fat, which might be substituted for the carbohydrate that is removed. However, recent re-analysis of much old data shows that replacing carbohydrate with saturated fat is, if anything, beneficial. The dialectic of impact of continued hemoglobin A(1c) versus effect of dietary saturated fat in the risk of cardiovascular disease is resolved in direction of glycemic control. Putting biased language behind us and facing the impact of recent results that point to the value of low-carbohydrate diets would offer patients the maximum number of options.

  6. Orthogonal Dual-Triggered Shape-Memory DNA-Based Hydrogels.

    PubMed

    Yu, Xu; Hu, Yuwei; Kahn, Jason S; Cecconello, Alessandro; Willner, Itamar

    2016-10-01

    DNA-based shape-memory hydrogels revealing switchable shape recovery in the presence of two orthogonal triggers are described. In one system, a shaped DNA/acrylamide hydrogel is stabilized by duplex nucleic acids and pH-responsive cytosine-rich, i-motif, bridges. Separation of the i-motif bridges at pH 7.4 transforms the hydrogel into a quasi-liquid, shapeless state, that includes the duplex bridges as permanent shape-memory elements. Subjecting the quasi-liquid state to pH 5.0 or Ag(+) ions recovers the hydrogel shape, due to the stabilization of the hydrogel by i-motif or C-Ag(+) -C bridged i-motif. The cysteamine-induced transformation of the duplex/C-Ag(+) -C bridged i-motif hydrogel into a quasi-liquid shapeless state results in the recovery of the shaped hydrogel in the presence of H(+) or Ag(+) ions as triggers. In a second system, a shaped DNA/acrylamide hydrogel is generated by DNA duplexes and bridging Pb(2+) or Sr(2+) ions-stabilized G-quadruplex subunits. Subjecting the shaped hydrogel to the DOTA or KP ligands eliminates the Pb(2+) or Sr(2+) ions from the respective hydrogels, leading to shapeless, memory-containing, quasi-liquid states that restore the original shapes with Pb(2+) or Sr(2+) ions.

  7. The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module.

    PubMed

    Yim, Aldrin Kay-Yuen; Yu, Allen Chi-Shing; Li, Jing-Woei; Wong, Ada In-Chun; Loo, Jacky F C; Chan, King Ming; Kong, S K; Yip, Kevin Y; Chan, Ting-Fung

    2014-01-01

    The size of digital data is ever increasing and is expected to grow to 40,000 EB by 2020, yet the estimated global information storage capacity in 2011 is <300 EB, indicating that most of the data are transient. DNA, as a very stable nano-molecule, is an ideal massive storage device for long-term data archive. The two most notable illustrations are from Church et al. and Goldman et al., whose approaches are well-optimized for most sequencing platforms - short synthesized DNA fragments without homopolymer. Here, we suggested improvements on error handling methodology that could enable the integration of DNA-based computational process, e.g., algorithms based on self-assembly of DNA. As a proof of concept, a picture of size 438 bytes was encoded to DNA with low-density parity-check error-correction code. We salvaged a significant portion of sequencing reads with mutations generated during DNA synthesis and sequencing and successfully reconstructed the entire picture. A modular-based programing framework - DNAcodec with an eXtensible Markup Language-based data format was also introduced. Our experiments demonstrated the practicability of long DNA message recovery with high error tolerance, which opens the field to biocomputing and synthetic biology. PMID:25414846

  8. Guanine-rich DNA-based peroxidase mimetics for colorimetric assays of alkaline phosphatase.

    PubMed

    Yang, Jinjin; Zheng, Lin; Wang, Yu; Li, Wei; Zhang, Jinli; Gu, Junjie; Fu, Yan

    2016-03-15

    DNA-based peroxidase mimetics are facilely constructed through Cu(II)-coordination with different oligonucleotides involving G20, C20, A20 and T20, respectively, with high peroxidase mimicking activity as well as high stability against proteins. Peroxidase-like activities of DNA-Cu(II) complexes are greatly associated with the sequence composition of DNA templates, which decrease in the following order: G20>C20>A20>T20. G20-Cu(II) complex ([Cu(2+)]/[base]=0.05) possesses the Km value of 0.257 mM toward 3,3',5,5'-tetramethylbenzidine and 102.3mM toward hydrogen peroxide at 25 °C. G20-Cu(II) complexes are employed to develop a colorimetric turn-on assay of alkaline phosphatase with high sensitivity and selectivity, on the basis of pyrophosphate-induced inhibition of their intrinsic peroxidase-like activities. The limit of detection is achieved as 0.84 U/L with the linear response region of 20-200 U/L. Such colorimetric assay system is probably applicable for the quantitative determination of ALP in biological fluids.

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

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

    PubMed

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

    2014-03-25

    Molecular-level security devices have raised ever-increasing interest in recent years to protect data and information from illegal invasion. Prior molecular keypad locks have an output signal dependent upon not only the appropriate combination but also the exact sequence of inputs, but it cannot be reset or reprogrammed. Here, a DNA-based security system with reset and never-reported reprogram function is successfully developed in proof-of-principle, with which one can change the password in case that the system is cracked. The previous password becomes invalid in the reprogrammed security system. Interestingly, more than one password is designed to permit multiple users to access. By harnessing the intrinsic merit of the different passwords, the system can distinguish different user who is endowed with prior authority. The intelligent device is addressed on solid support and facilitates electronic processes, avoiding chemical accumulation in the system by simple removal of the electrode from the input solution and indicating a main avenue for its further development. PMID:24564320

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

    PubMed

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

    2013-01-01

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

  12. Semiquinone formation and DNA base damage by toxic quinones and inhibition by N-acetylcysteine (NAC)

    SciTech Connect

    Lewis, D.C.; Shibamoto, T.

    1986-03-05

    Toxic, mutagenic, carcinogenic, and teratogenic effects have been reported for some quinones as well as compounds metabolized to quinones. Semiquinone radical formation, thymidine degradation, and protection by NAC were studied in a hypoxanthine/xanthine oxidase (HX/XO) system. Quinone, benzo(a)pyrene-3,6-quinone, danthron, doxorubicin, emodin, juglone, menadione, and moniliformin were tested. Diethylstilbestrolquinone, N-acetylquinoneimine, and benzoquinonediimine, hypothesized toxic metabolites of diethylstilbestrol, acetaminophen and p-phenylenediamine, respectively, were synthesized and studied. Semiquinone radical formation was assessed in a HX/XO system monitoring cytochrome C reduction. Large differences in rates of semiquinone radical formation were noted for different quinones, with V/Vo values ranging from 1.2 to 10.6. DNA base degradation, thymine or thymidine glycol formation, and thiobarbituric acid reactive substance (TBARS) production were measured in a similar system containing thymine, thymidine, calf thymus DNA, or deoxyribose. TBARS formation was observed with deoxyribose, but thymidine degradation without TBARS formation was noted with thymidine. NAC (0.5 to 10 mM) caused dose-dependent inhibition of quinone-induced cytochrome C reduction.

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

    NASA Astrophysics Data System (ADS)

    Khomutov, Gennady B.

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

  14. DNA-based high-density memory devices and biomolecular electronics at CSIO

    NASA Astrophysics Data System (ADS)

    Bharadwaj, Lalit M.; Bhondekar, Amol P.; Shukla, A. K.; Bhalla, Vijayender; Bajpai, Ram P.

    2002-11-01

    During the last half century the electronic components and computers have grown more and more powerful with the shrinking dimensions of transistors which is approaching 100nm with about a billion tiny devices working together on a single processor. The laws of quantum mechanics and limitations of materials and fabrication techniques restrict further reduction below 100nm. The most promising area is Biomolecular Electronics concerning design and fabrication of basic electronic components using biomolecules. Various organic polymers are being studied for visualization of individual molecular electronic wires and diode switches but we see enormous potential in use of DNA for such devices due to its inherent characteristics. This is because DNA can act as insulator semiconductor, conductor or superconductor depending upon the base sequence, length and orientation. The DNA can be coated selectively with metals with molecular level precision giving us capability to design molecular electronic components, such as, diode, triode, transistor, etc. This paper discusses the DNA based language developed by our group for coding and decoding any digital information in terms of DNA sequence. Basic arithmetical operations, such as, addition subtraction, multiplication, division and exponential have been defined in terms of DNA sequence and their validity has been demonstrated. Paper will also discuss our programme on study of DNA electrical behaviour in terms of sequence; length and orientation for development of biomolecular electronic components and for understanding DNA damaged chemistry.

  15. DNA based typing, identification and detection systems for food spoilage microorganisms: development and implementation.

    PubMed

    van der Vossen, J M; Hofstra, H

    1996-11-01

    The rapid identification of spoilage microorganisms is of eminent importance to the food industry. It provides the food industry with the opportunity to reduce economical losses by designing adequate intervention measures. The use of identification systems based on biochemical and physiological characteristics resulted often in disappointing identification results and misidentifications. This will inevitably lead to inappropriate strategies to prevent spoilage. This review discusses the potential of the DNA based identification technology including the polymerase chain reaction (PCR) for the identification and specific detection of microorganisms. Fingerprinting methods based on the DNA-probe technology enable a clear insight in the identity of microorganisms on different levels, varying from genus to strain level depending on the systems used. Discrimination between subspecies and strain level is shown to be helpful for investigating routes and sources of contamination. Differentiation at the species level is demonstrated to be essential in order to design a highly specific detection system enabling to signalize a microorganism that belongs to a particular species. Also indicated in this review is the necessity and the technical approach to detect microorganisms that display a particular undesirable trait.

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

    USGS Publications Warehouse

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

    2008-01-01

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

  17. Protein- and DNA-Based Active Immunotherapy Targeting Interleukin-13 Receptor Alpha2

    PubMed Central

    Gibo, Denise M.; MadhanKumar, A.B.; Cladel, Nancy M.; Christensen, Neil D.; Debinski, Waldemar

    2008-01-01

    Abstract High-grade astrocytoma (HGA) is an invariably fatal malignancy with a mean survival of 14 months despite surgery, radiation, and chemotherapy. We have found that a restricted receptor for interleukin-13 (IL-13), IL-13 receptor alpha 2 (IL13Rα2), is abundantly overexpressed in the vast majority of HGAs but is not appreciably expressed in normal tissue, with the exception of the testes. Therefore, IL-13Rα2 is a very attractive target for anti-HGA immunotherapy. In order to test protein and genetic vaccines that target IL13Rα2, we developed a G26-IL13Rα2-expressing syngeneic immunocompetent murine glioma model. Using this glioma model, mice were immunized with recombinant extracellular IL13Rα2 protein (IL13Rα2ex) or a DNA expression vector containing the gene for IL13Rα2 and were subsequently challenged with IL13Rα2(+) G26 tumors. Mice immunized with either recombinant or genetic IL13Rα2, but not mock-immunized controls, demonstrated complete protection against IL13Rα2(+) glioma growth and mortality. Of interest, only the recombinant-protein-based vaccines generated detectable anti-IL13Rα2 antibodies. These studies demonstrate the in vivo efficiency of protein- and DNA-based immunotherapy strategies that target IL13Rα2 that may play a clinical role to eradicate the residual microscopic HGA cells that inevitably cause disease recurrence and mortality. PMID:18976118

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  19. Dipstick test for DNA-based food authentication. Application to coffee authenticity assessment.

    PubMed

    Trantakis, Ioannis A; Spaniolas, Stelios; Kalaitzis, Panagiotis; Ioannou, Penelope C; Tucker, Gregory A; Christopoulos, Theodore K

    2012-01-25

    This paper reports DNA-based food authenticity assays, in which species identification is accomplished by the naked eye without the need of specialized instruments. Strongly colored nanoparticles (gold nanoparticles) are employed as reporters that enable visual detection. Furthermore, detection is performed in a low-cost, disposable, dipstick-type device that incorporates the required reagents in dry form, thereby avoiding multiple pipetting and incubation steps. Due to its simplicity, the method does not require highly qualified personnel. The procedure comprises the following steps: (i) PCR amplification of the DNA segment that flanks the unique SNP (species marker); (ii) a 15 min extension reaction in which DNA polymerase extends an allele-specific primer only if it is perfectly complementary with the target sequence; (iii) detection of the products of the extension reaction within a few minutes by the naked eye employing the dipstick. No purification is required prior to application of the extension products to the dipstick. The method is general and requires only a unique DNA sequence for species discrimination. The only instrument needed is a conventional thermocycler for PCR, which is common equipment in every DNA laboratory. As a model, the method was applied to the discrimination of Coffea robusta and arabica species in coffee authenticity assessment. As low as 5% of Robusta coffee can be detected in the presence of Arabica coffee.

  20. Repair of Oxidative DNA Damage and Cancer: Recent Progress in DNA Base Excision Repair

    PubMed Central

    Scott, Timothy L.; Rangaswamy, Suganya; Wicker, Christina A.

    2014-01-01

    Abstract Significance: Reactive oxygen species (ROS) are generated by exogenous and environmental genotoxins, but also arise from mitochondria as byproducts of respiration in the body. ROS generate DNA damage of which pathological consequence, including cancer is well established. Research efforts are intense to understand the mechanism of DNA base excision repair, the primary mechanism to protect cells from genotoxicity caused by ROS. Recent Advances: In addition to the notion that oxidative DNA damage causes transformation of cells, recent studies have revealed how the mitochondrial deficiencies and ROS generation alter cell growth during the cancer transformation. Critical Issues: The emphasis of this review is to highlight the importance of the cellular response to oxidative DNA damage during carcinogenesis. Oxidative DNA damage, including 7,8-dihydro-8-oxoguanine, play an important role during the cellular transformation. It is also becoming apparent that the unusual activity and subcellular distribution of apurinic/apyrimidinic endonuclease 1, an essential DNA repair factor/redox sensor, affect cancer malignancy by increasing cellular resistance to oxidative stress and by positively influencing cell proliferation. Future Directions: Technological advancement in cancer cell biology and genetics has enabled us to monitor the detailed DNA repair activities in the microenvironment. Precise understanding of the intracellular activities of DNA repair proteins for oxidative DNA damage should provide help in understanding how mitochondria, ROS, DNA damage, and repair influence cancer transformation. Antioxid. Redox Signal. 20, 708–726. PMID:23901781

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

    PubMed

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

    2003-10-01

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

  2. The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module.

    PubMed

    Yim, Aldrin Kay-Yuen; Yu, Allen Chi-Shing; Li, Jing-Woei; Wong, Ada In-Chun; Loo, Jacky F C; Chan, King Ming; Kong, S K; Yip, Kevin Y; Chan, Ting-Fung

    2014-01-01

    The size of digital data is ever increasing and is expected to grow to 40,000 EB by 2020, yet the estimated global information storage capacity in 2011 is <300 EB, indicating that most of the data are transient. DNA, as a very stable nano-molecule, is an ideal massive storage device for long-term data archive. The two most notable illustrations are from Church et al. and Goldman et al., whose approaches are well-optimized for most sequencing platforms - short synthesized DNA fragments without homopolymer. Here, we suggested improvements on error handling methodology that could enable the integration of DNA-based computational process, e.g., algorithms based on self-assembly of DNA. As a proof of concept, a picture of size 438 bytes was encoded to DNA with low-density parity-check error-correction code. We salvaged a significant portion of sequencing reads with mutations generated during DNA synthesis and sequencing and successfully reconstructed the entire picture. A modular-based programing framework - DNAcodec with an eXtensible Markup Language-based data format was also introduced. Our experiments demonstrated the practicability of long DNA message recovery with high error tolerance, which opens the field to biocomputing and synthetic biology.

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

    PubMed

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

    2014-03-25

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

  4. [Principle and application of DNA-based stable isotope probing---a review].

    PubMed

    Jia, Zhongjun

    2011-12-01

    Microbial communities are the engines that drive the global biogeochemical cycle of carbon and nitrogen essential for life on Earth. However, microorganisms have evolved as a result of complex interactions with other organisms and environments. Deciphering the metabolism of microorganisms at the community level in nature will be crucial for a better understanding of the mechanisms that lead to the enormous divergence of microbial ecophysiology. Due to the immense number of uncultivated microbial species and the complexity of microbial communities, delineating community metabolism proves a virtually insurmountable hurdle. By tracing the heavy isotope flow of key elements such as carbon and nitrogen, DNA-based stable isotope probing (DNA-SIP) can provide unequivocal evidence for substrate assimilation by microorganisms in complex environments. The essential prerequisite for a successful DNA-SIP is the identification, with confidence, of isotopically enriched 13C-DNA, of which the amount is generally too low to allow the direct measurement of 13C atom percent of nucleic acid. The methodological considerations for obtaining unambiguous DNA highly enriched in heavy isotope are presented with emphasis on next-generation sequencing technology and metagenomics.

  5. Increased knowledge of Francisella genus diversity highlights the benefits of optimised DNA-based assays

    PubMed Central

    2012-01-01

    Background Recent advances in sequencing technologies offer promising tools for generating large numbers of genomes, larger typing databases and improved mapping of environmental bacterial diversity. However, DNA-based methods for the detection of Francisella were developed with limited knowledge about genetic diversity. This, together with the high sequence identity between several Francisella species, means there is a high risk of false identification and detection of the highly virulent pathogen Francisella tularensis. Moreover, phylogenetic reconstructions using single or limited numbers of marker sequences often result in incorrect tree topologies and inferred evolutionary distances. The recent growth in publicly accessible whole-genome sequences now allows evaluation of published genetic markers to determine optimal combinations of markers that minimise both time and laboratory costs. Results In the present study, we evaluated 38 previously published DNA markers and the corresponding PCR primers against 42 genomes representing the currently known diversity of the genus Francisella. The results highlight that PCR assays for Francisella tularensis are often complicated by low specificity, resulting in a high probability of false positives. A method to select a set of one to seven markers for obtaining optimal phylogenetic resolution or diagnostic accuracy is presented. Conclusions Current multiple-locus sequence-typing systems and detection assays of Francisella, could be improved by redesigning some of the primers and reselecting typing markers. The use of only a few optimally selected sequence-typing markers allows construction of phylogenetic topologies with almost the same accuracy as topologies based on whole-genome sequences. PMID:23009728

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

    PubMed

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

    2013-10-01

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

  7. Back-trajectory modelling and DNA-based species-specific detection methods allow tracking of fungal spore transport in air masses.

    PubMed

    Grinn-Gofroń, Agnieszka; Sadyś, Magdalena; Kaczmarek, Joanna; Bednarz, Aleksandra; Pawłowska, Sylwia; Jedryczka, Malgorzata

    2016-11-15

    Recent advances in molecular detection of living organisms facilitate the introduction of novel methods to studies of the transport of fungal spores over large distances. Monitoring the migration of airborne fungi using microscope based spore identification is limited when different species produce very similar spores. In our study, DNA-based monitoring with the use of species-specific probes allowed us to track the aerial movements of two important fungal pathogens of oilseed rape (Brassica napus L.), i.e., Leptosphaeria maculans and Leptosphaeria biglobosa, which have identical spore shape and size. The fungi were identified using dual-labelled fluorescent probes that were targeted to a β-tubulin gene fragment of either Leptosphaeria species. Spore identification by Real-Time PCR techniques capable of detecting minute amounts of DNA of selected fungal species was combined with back-trajectory analysis, allowing the tracking of past movements of air masses using the Hybrid Single Particle Lagrangian Integrated Trajectory model. Over a study period spanning the previous decade (2006-2015) we investigated two specific events relating to the long distance transport of Leptosphaeria spp. spores to Szczecin in North-West Poland. Based on the above mentioned methods and the results obtained with the additional spore sampler located in nearby Szczecin, and operating at the ground level in an oilseed rape field, we have demonstrated that on both occasions the L. biglobosa spores originated from the Jutland Peninsula. This is the first successful attempt to combine analysis of back-trajectories of air masses with DNA-based identification of economically important pathogens of oilseed rape in Europe. In our studies, the timing of L. biglobosa ascospore dispersal in the air was unlikely to result in the infection of winter oilseed rape grown as a crop plant. However, the fungus could infect other host plants, such as vegetable brassicas, cruciferous weeds, spring rapeseed

  8. Back-trajectory modelling and DNA-based species-specific detection methods allow tracking of fungal spore transport in air masses.

    PubMed

    Grinn-Gofroń, Agnieszka; Sadyś, Magdalena; Kaczmarek, Joanna; Bednarz, Aleksandra; Pawłowska, Sylwia; Jedryczka, Malgorzata

    2016-11-15

    Recent advances in molecular detection of living organisms facilitate the introduction of novel methods to studies of the transport of fungal spores over large distances. Monitoring the migration of airborne fungi using microscope based spore identification is limited when different species produce very similar spores. In our study, DNA-based monitoring with the use of species-specific probes allowed us to track the aerial movements of two important fungal pathogens of oilseed rape (Brassica napus L.), i.e., Leptosphaeria maculans and Leptosphaeria biglobosa, which have identical spore shape and size. The fungi were identified using dual-labelled fluorescent probes that were targeted to a β-tubulin gene fragment of either Leptosphaeria species. Spore identification by Real-Time PCR techniques capable of detecting minute amounts of DNA of selected fungal species was combined with back-trajectory analysis, allowing the tracking of past movements of air masses using the Hybrid Single Particle Lagrangian Integrated Trajectory model. Over a study period spanning the previous decade (2006-2015) we investigated two specific events relating to the long distance transport of Leptosphaeria spp. spores to Szczecin in North-West Poland. Based on the above mentioned methods and the results obtained with the additional spore sampler located in nearby Szczecin, and operating at the ground level in an oilseed rape field, we have demonstrated that on both occasions the L. biglobosa spores originated from the Jutland Peninsula. This is the first successful attempt to combine analysis of back-trajectories of air masses with DNA-based identification of economically important pathogens of oilseed rape in Europe. In our studies, the timing of L. biglobosa ascospore dispersal in the air was unlikely to result in the infection of winter oilseed rape grown as a crop plant. However, the fungus could infect other host plants, such as vegetable brassicas, cruciferous weeds, spring rapeseed

  9. [Breastfeeding and vegan diet].

    PubMed

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

    2005-10-01

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

  10. Can a CNN recognize Catalan diet?

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    EPA Science Inventory

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

  12. Diet for Ataxia

    MedlinePlus

    ... discuss these guidelines with a physical therapist and nutritionist familiar with movement disorders. Ataxia is a complex ... fiber to your diet with your physician or nutritionist, ask them if you might also benefit by ...

  13. Interstitial Cystitis and Diet

    MedlinePlus

    ... IC in Other Languages Associated Conditions Allergies and Sensitivities Celiac Disease Chronic Fatigue Syndrome Chronic Prostatitis Constipation ... Dr. Shorter completed the first validated, systematic food sensitivity questionnaire on IC and diet. Revised Tuesday, April ...

  14. Are Detox Diets Safe?

    MedlinePlus

    ... the "bad" stuff. But the truth is, the human body is designed to purify itself. Detox diets vary. ... fat or fat-free milk or yogurt). The human body is designed to purify itself. You can help ...

  15. Diet - clear liquid

    MedlinePlus

    ... It includes things such as: Clear broth Tea Cranberry juice Jell-O Popsicles This diet is easier ... such as grape juice, filtered apple juice, and cranberry juice Soup broth (bouillon or consommé) Clear sodas, ...

  16. Magnesium in diet

    MedlinePlus

    Diet - magnesium ... Magnesium is needed for more than 300 biochemical reactions in the body. It helps to maintain normal ... There is ongoing research into the role of magnesium in preventing and managing disorders such as high ...

  17. Diet and cancer

    MedlinePlus

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

  18. Protein in diet

    MedlinePlus

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

  19. Diet and Your Liver

    MedlinePlus

    ... scarring of your liver (cirrhosis). For people with liver disease, even a small amount of alcohol can make ... time. Eating an unhealthy diet can lead to liver disease. For example, a person who eats a lot ...

  20. Diet and Health

    PubMed Central

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

    1984-01-01

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

  1. Anti-inflammatory Diets.

    PubMed

    Sears, Barry

    2015-01-01

    Chronic disease is driven by inflammation. This article will provide an overview on how the balance of macronutrients and omega-6 and omega-3 fatty acids in the diet can alter the expression of inflammatory genes. In particular, how the balance of the protein to glycemic load of a meal can alter the generation of insulin and glucagon and the how the balance of omega-6 and omega-3 fatty acids can effect eicosanoid formation. Clinical results on the reduction of inflammation following anti-inflammatory diets are discussed as well as the molecular targets of anti-inflammatory nutrition. To overcome silent inflammation requires an anti-inflammatory diet (with omega-3s and polyphenols, in particular those of Maqui). The most important aspect of such an anti-inflammatory diet is the stabilization of insulin and reduced intake of omega-6 fatty acids. The ultimate treatment lies in reestablishing hormonal and genetic balance to generate satiety instead of constant hunger. Anti-inflammatory nutrition, balanced 40:30:30 with caloric restriction, should be considered as a form of gene silencing technology, in particular the silencing of the genes involved in the generation of silent inflammation. To this anti-inflammatory diet foundation supplemental omega-3 fatty acids at the level of 2-3 g of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) per day should be added. Finally, a diet rich in colorful, nonstarchy vegetables would contribute adequate amounts of polyphenols to help not only to inhibit nuclear factor (NF)-κB (primary molecular target of inflammation) but also activate AMP kinase. Understanding the impact of an anti-inflammatory diet on silent inflammation can elevate the diet from simply a source of calories to being on the cutting edge of gene-silencing technology. PMID:26400429

  2. Appetoff: another diet fad.

    PubMed

    Beckerich, M J

    1989-12-01

    Appetoff diet patches were diet aids introduced to the public in 1987 and removed from the market in 1988 by the FDA for reasons of fraud. The ingredients were supposedly homeopathic concentrations of plant and mineral products. Although 91.6% of persons in this study who used the product for at least 1 week reported weight loss and mild side effects, no active ingredients could be detected by gas chromatography/mass spectrometry.

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

    PubMed

    Kayser, Manfred; Schneider, Peter M

    2009-06-01

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

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

    PubMed

    Kayser, Manfred; Schneider, Peter M

    2009-06-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

  6. Vegan diets and hypothyroidism.

    PubMed

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

    2013-11-20

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

  7. Vegan diets and hypothyroidism.

    PubMed

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

    2013-11-01

    Diets eliminating animal products have rarely been associated with hypothyroidism but may protect against autoimmune disease. Thus, we investigated whether risk of hypothyroidism was associated with vegetarian compared to omnivorous dietary patterns. The Adventist Health Study-2 was conducted among church members in North America who provided data in a self-administered questionnaire. Hypothyroidism was queried at baseline in 2002 and at follow-up to 2008. Diet was examined as a determinant of prevalent (n = 4237 of 65,981 [6.4%]) and incident cases (1184 of 41,212 [2.9%]) in multivariate logistic regression models, controlled for demographics and salt use. In the prevalence study, in addition to demographic characterstics, overweight and obesity increased the odds (OR 1.32, 95% CI: 1.22-1.42 and 1.78, 95% CI: 1.64-1.93, respectively). Vegan versus omnivorous diets tended to be associated with reduced risk (OR 0.89, 95% CI: 0.78-1.01, not statistically significant) while a lacto-ovo diet was associated with increased risk (OR 1.09, 95% CI: 1.01-1.18). In the incidence study, female gender, white ethnicity, higher education and BMI were predictors of hypothyroidism. Following a vegan diet tended to be protective (OR 0.78, 95% CI: 0.59-1.03, not statistically significant). In conclusion, a vegan diet tended to be associated with lower, not higher, risk of hypothyroid disease. PMID:24264226

  8. Specific Carbohydrate Diet: Does It Work?

    MedlinePlus

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    2010-01-01

    Recent epidemiologic studies assessing tree nut (almonds, Brazil nuts, cashews, hazelnuts, macadamia nuts, pecans, pine nuts, pistachios, and walnuts) consumption and the association with nutrient intake and diet quality are lacking. This study determined the association of tree nut consumption and nutrient intake and diet quality using a nationally representative sample of adults. Adults 19+ years (y) (n=13,292) participating in the 1999-2004 National Health and Nutrition Examination Survey were used. Intake was determined from 24-hour diet recalls; tree nut consumers were defined as those consuming > or =(1/4) ounce/day (7.09 g). Means, standard errors, and ANOVA (adjusted for covariates) were determined using appropriate sample weights. Diet quality was measured using the Healthy Eating Index-2005. Among consumers, mean intake of tree nuts/tree nut butters was 1.19 +/- 0.04 oz/d versus 0.01 +/- 0.00 oz/d for non-consumers. In this study, 5.5 +/- 0.3 % of individuals 19-50 y (n=7,049) and 8.4 +/- 0.6 % of individuals 51+ y (n=6,243) consumed tree nuts/tree nut butters. Mean differences (p<0.01) between tree nut consumers and non-consumers of adult shortfall nutrients were: fiber (+5.0 g/d), vitamin E (+3.7 mg AT/d), calcium (+73 mg/d), magnesium (+95 mg/d), and potassium (+260 mg/d). Tree nut consumers had lower sodium intake (-157 mg/d, p<0.01). Diet quality was significantly higher in tree nut consumers (58.0+/-0.4 vs. 48.5+/-0.3, p<0.01). Tree nut consumption was associated with a higher overall diet quality score and improved nutrient intakes. Specific dietary recommendations for nut consumption should be provided for consumers. PMID:20200000

  11. Gains in statistical power from using a dietary biomarker in combination with self-reported intake to strengthen the analysis of a diet-disease association: an example from CAREDS.

    PubMed

    Freedman, Laurence S; Tasevska, Natasa; Kipnis, Victor; Schatzkin, Arthur; Mares, Julie; Tinker, Lesley; Potischman, Nancy

    2010-10-01

    A major problem in detecting diet-disease associations in nutritional cohort studies is measurement error in self-reported intakes, which causes loss of statistical power. The authors propose using biomarkers correlated with dietary intake to strengthen analyses of diet-disease hypotheses and to increase statistical power. They consider combining self-reported intakes and biomarker levels using principal components or a sum of ranks and relating the combined measure to disease in conventional regression analyses. They illustrate their method in a study of the inverse association of dietary lutein plus zeaxanthin with nuclear cataracts, using serum lutein plus zeaxanthin as the biomarker, with data from the Carotenoids in Age-Related Eye Disease Study (United States, 2001-2004). This example demonstrates that the combined measure provides higher statistical significance than the dietary measure or the serum measure alone, and it potentially provides sample savings of 8%-53% over analysis with dietary intake alone and of 6%-48% over analysis with serum level alone, depending on the definition of the outcome variable and the choice of confounders entered into the regression model. The authors conclude that combining appropriate biomarkers with dietary data in a cohort can strengthen the investigation of diet-disease associations by increasing the statistical power to detect them.

  12. Vibrationally resolved photoelectron spectroscopy of electronic excited states of DNA bases: application to the ã state of thymine cation.

    PubMed

    Hochlaf, Majdi; Pan, Yi; Lau, Kai-Chung; Majdi, Youssef; Poisson, Lionel; Garcia, Gustavo A; Nahon, Laurent; Al Mogren, Muneerah Mogren; Schwell, Martin

    2015-02-19

    For fully understanding the light-molecule interaction dynamics at short time scales, recent theoretical and experimental studies proved the importance of accurate characterizations not only of the ground (D0) but also of the electronic excited states (e.g., D1) of molecules. While ground state investigations are currently straightforward, those of electronic excited states are not. Here, we characterized the à electronic state of ionic thymine (T(+)) DNA base using explicitly correlated coupled cluster ab initio methods and state-of-the-art synchrotron-based electron/ion coincidence techniques. The experimental spectrum is composed of rich and long vibrational progressions corresponding to the population of the low frequency modes of T(+)(Ã). This work challenges previous numerous works carried out on DNA bases using common synchrotron and VUV-based photoelectron spectroscopies. We provide hence a powerful theoretical and experimental framework to study the electronic structure of ionized DNA bases that could be generalized to other medium-sized biologically relevant systems.

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

    PubMed

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

    2014-04-01

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

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

    PubMed

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

    2015-08-01

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

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

    PubMed

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

    2016-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whether loci that influence fasting glucose (FG) and fasting insulin (FI) levels, as identified by genome-wide association studies, modify associations of diet with FG or FI is unknown. We utilized data from 15 US and European cohort studies comprising 51,289 persons without diabetes to test whether...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  19. Nutrigenomics in Arma chinensis: transcriptome analysis of Arma chinensis fed on artificial diet and Chinese oak silk moth Antheraea pernyi pupae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The insect predator, Arma chinensis (Fallou), is capable of effectively controlling many pests, such as Colorado potato beetle, cotton bollworm, and mirid bugs. Life history parameters were not as good for A. chinensis when reared on an artificial diet compared to Chinese oak silk moth p...

  20. Diet and physical performance.

    PubMed

    Montain, Scott J; Young, Andrew J

    2003-06-01

    This paper provides a historical summary of military nutrition research into the role of diet for sustaining soldier physical performance. Studies of underfeeding document that physical performance is preserved during several days of underfeeding provided sufficient carbohydrate and minerals are consumed to minimize the diuresis associated with semi-starvation diets and serial intake of carbohydrate is available to support metabolism during prolonged work. The Military Recommended Dietary Allowances, AR 40-25, currently recommends that when restricted rations are required, that the ration contain at least 1,100-1,500 kcal, 50-70 g of protein, and a minimum of 100 g of carbohydrate on a daily basis. This low energy diet, however, is not recommended for subsistence for longer than 10 consecutive days. Dietary carbohydrate intakes of approximately 300-400 g will more closely match the quantity of carbohydrate oxidized to meet daily energy requirements during field operations. Research into the potential advantages of dietary supplements has generally not proved advantageous when compared to eating a well balanced diet. Future investigations of the role of diet for sustaining soldier health and performance should be directed toward a better understanding of the influence of energy intake and macro-nutrient composition for preserving lean body mass, reducing susceptibility to illness and injury and enhancing recovery during and after sustained operations. PMID:12798783

  1. Diet and physical performance.

    PubMed

    Montain, Scott J; Young, Andrew J

    2003-06-01

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

  2. Diet and breast cancer.

    PubMed

    Adlercreutz, H; Mousavi, Y; Höckerstedt, K

    1992-01-01

    It is a general opinion that the Western diet plays a significant role in increasing the risk of breast cancer in the Western World. Recently some likely mechanisms involved in increasing the risk have been disclosed. It has been found that a Western-type diet elevates plasma levels of sex hormones and decreases the sex hormone binding globulin concentration, increasing the availability of these steroids for peripheral tissues. The same diet results in low formation by intestinal bacteria of mammalian lignans and isoflavonoid phyotestrogens from plant precursors. These diphenolic compounds seem to affect hormone metabolism and production and cancer cell growth by many different mechanisms making them strong candidates for a role as cancer protective substances. The sex hormone pattern found in connection with a Western-type diet combined with low lignan and isoflavonoid excretion was found particularly in postmenopausal breast cancer patients and omnivores living in high-risk areas, and to a lesser degree in areas with less risk. However, the pattern observed was not entirely due to diet.

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

    PubMed Central

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

    2013-01-01

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

  4. Maternal diet during early childhood, but not pregnancy, predicts diet quality and fruit and vegetable acceptance in offspring.

    PubMed

    Ashman, Amy M; Collins, Clare E; Hure, Alexis J; Jensen, Megan; Oldmeadow, Christopher

    2016-07-01

    Studies have identified prenatal flavour exposure as a determinant of taste preferences in infants; however, these studies have focused on relatively small samples and limited flavours. As many parents struggle with getting children to accept a variety of nutritious foods, a study of the factors influencing food acceptance is warranted. The objective of this study was to determine whether exposure to a wider variety of fruit and vegetables and overall higher diet quality in utero results in acceptance of a greater variety of these foods and better diet quality for offspring during childhood. This study is a secondary data analysis of pregnant women (n = 52) and their resulting offspring recruited for the Women and Their Children's Health study in NSW, Australia. Dietary intake of mothers and children was measured using food frequency questionnaires. Diet quality and vegetable and fruit variety were calculated using the Australian Recommended Food Score and the Australian Child and Adolescent Recommended Food Score. Associations between maternal and child diet quality and variety were assessed using Pearson's correlations and the total effect of in utero maternal pregnancy diet on childhood diet was decomposed into direct and indirect effect using mediation analysis. Maternal pregnancy and post-natal diet were both correlated with child diet for overall diet quality and fruit and vegetable variety (P < 0.001). Mediation analyses showed that the indirect effect of maternal pregnancy diet on child diet was mediated through maternal post-natal diet, particularly for fruit (P = 0.045) and vegetables (P = 0.055). Nutrition intervention should therefore be aimed at improving diet quality and variety in mothers with young children, in order to subsequently improve eating habits of offspring.

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

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

  6. Vegetarian diets and children.

    PubMed

    Sanders, T A

    1995-08-01

    Although the general health and development of vegan and vegetarian children seem to be normal, there may be subtle differences compared with omnivores. They are at increased risk of iron deficiency, and impaired psychomotor development associated with iron deficiency has been reported in macrobiotic infants. Fortunately, this impairment is not permanent, and follow-up studies have reported higher-than-average intelligence quotients among older macrobiotic children. Several other hazards of vegetarian diets have been identified, including vitamin B12 deficiency, rickets, and a bulky diet that can restrict energy intake in the first few years of life; however, these pitfalls can be avoided easily, and children can be successfully reared on vegetarian diets.

  7. Diet and Dermatology

    PubMed Central

    Desai, Samir P.

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    1990-11-01

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

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

    ERIC Educational Resources Information Center

    Dorociak, Jeffery D.; Vincent, Murray L.

    1985-01-01

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

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

    PubMed

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

    2013-02-01

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

  12. Diet modulation is an effective complementary agent in preventing and treating breast cancer lung metastasis.

    PubMed

    Zhao, Xiangmin; Rezonzew, Gabriel; Wang, Dezhi; Siegal, Gene P; Hardy, Robert W

    2014-08-01

    A significant percentage of breast cancer victims will suffer from metastases indicating that new approaches to preventing breast cancer metastasis are thus needed. Dietary stearate (ST) and chemotherapy have been shown to reduce breast cancer metastasis. We tested the complementary use of dietary ST with a taxol-based chemotherapy which work through separate mechanisms to reduce breast cancer metastasis. We therefore carried out a prevention study in which diets were initiated prior to human MDA-MB-435 cancer cells being injected into the host and a treatment study in which diets were combined with paclitaxel (PTX). Using an orthotopic athymic nude mouse model and three diets [corn oil (CO) control diet, low fat (LF) or ST] the prevention study demonstrated that the ST diet decreased the incidence of lung metastasis by 50 % compared to both the LF and CO diets. The ST diet also reduced the number and size of metastatic lung nodules compared to the LF diet. Results of the treatment study indicated that both the CO and ST diets decreased the number of mice with lung metastasis compared to the LF diet. Both CO and ST also decreased the number of lung metastases per mouse compared to the LF diet however only the ST diet cohort was significant. Histomorphometric analysis of the lung tumor tissue indicated that the ST diet plus PTX decreased angiogenesis compared to the LF diet plus PTX. In conclusion these results support combining diet with chemotherapy in both treatment and prevention settings.

  13. [Acne and diet].

    PubMed

    Melnik, B C

    2013-04-01

    In industrialized countries acne presents as an epidemic disease of civilization affecting sebaceous follicles of adolescents and young adults, associated with increased body mass index and insulin resistance. "Western style" diet, characterized by high glycaemic load and increased consumption of insulinotropic milk proteins, plays an important role in acne pathogenesis. On the cellular level, nutrient-derived metabolic signals are sensed by the metabolic transcription factor FoxO1 and integrated by the regulatory kinase mTORC1. mTORC1, the central hub of protein- and lipid biosynthesis, cell growth and proliferation, is activated by insulin, IGF-1 and branched-chain essential amino acids, especially leucine. The understanding of Western diet-mediated nutrient signalling with over-activated mTORC1 offers a reasonable approach for dietary intervention in acne by lowering glycaemic load and consumption of milk and milk products. A suitable diet attenuating increased mTORC1 activity is a Palaeolithic-like diet with reduced intake of sugar, hyperglycaemic grains, milk and milk products but enriched consumption of vegetables and fish.

  14. Diet and breast cancer.

    PubMed

    Blackburn, George L; Copeland, Trisha; Khaodhiar, Lalita; Buckley, Rita B

    2003-03-01

    Obesity, overweight, and a sedentary lifestyle-all common conditions in breast cancer patients-are likely to be associated with poor survival and poor quality of life in women with breast cancer. Diet-related factors are thought to account for about 30% of cancers in developed countries. Most studies of diet and healthcare have focused on the role of single nutrients, foods, or food groups in disease prevention or promotion. Recent cancer guidelines on nutrition and physical activity emphasize diets that promote maintenance of a healthy body weight and a prudent dietary pattern that is low in red and processed meats and high in a variety of vegetables, fruits, and whole grains. Except for dietary fat, few nutritional factors in adult life have been associated with breast cancer. Extensive data from animal model research, international correlations linking fat intake and breast cancer rates, and case-control studies support the hypothesis that a high-fat diet is conducive to the development of breast cancer in postmenopausal women. Conflicting findings from cohort studies, however, have created uncertainty over the role of dietary fat in breast cancer growth and recurrence. Results from large-scale nutritional intervention trials are expected to resolve such issues. As new and improved data on dietary factors and patterns accumulate, dietary guidelines for cancer risk reduction will become more focused.

  15. Diet and healthy ageing.

    PubMed

    McKevith, Brigid

    2005-12-01

    In the future there will be more people aged 65 years and over ('older adults'). Although the exact mechanisms underlying normal ageing are not fully understood, ageing is generally associated with an increase in chronic diseases, such as cardiovascular disease, diabetes, cancer and osteoporosis. It is becoming clear that it is possible to prevent, slow or reverse the onset of many these by modifying lifestyle factors such as diet. Studies of older adults in a range of countries have highlighted a number of areas in which dietary quality could be improved. It is important to identify dietary patterns in addition to specific dietary components that offer protection against chronic disease. The challenge in the area of diet and healthy ageing is twofold: first, there is a need to improve the diet of older adults; and second, as most chronic diseases begin earlier in life, there is a need to encourage other age groups to adapt their diet so they can enter old age in better health.

  16. Study protocol: differential effects of diet and physical activity based interventions in pregnancy on maternal and fetal outcomes—individual patient data (IPD) meta-analysis and health economic evaluation

    PubMed Central

    2014-01-01

    Background Pregnant women who gain excess weight are at risk of complications during pregnancy and in the long term. Interventions based on diet and physical activity minimise gestational weight gain with varied effect on clinical outcomes. The effect of interventions on varied groups of women based on body mass index, age, ethnicity, socioeconomic status, parity, and underlying medical conditions is not clear. Our individual patient data (IPD) meta-analysis of randomised trials will assess the differential effect of diet- and physical activity-based interventions on maternal weight gain and pregnancy outcomes in clinically relevant subgroups of women. Methods/design Randomised trials on diet and physical activity in pregnancy will be identified by searching the following databases: MEDLINE, EMBASE, BIOSIS, LILACS, Pascal, Science Citation Index, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, Database of Abstracts of Reviews of Effects, and Health Technology Assessment Database. Primary researchers of the identified trials are invited to join the International Weight Management in Pregnancy Collaborative Network and share their individual patient data. We will reanalyse each study separately and confirm the findings with the original authors. Then, for each intervention type and outcome, we will perform as appropriate either a one-step or a two-step IPD meta-analysis to obtain summary estimates of effects and 95% confidence intervals, for all women combined and for each subgroup of interest. The primary outcomes are gestational weight gain and composite adverse maternal and fetal outcomes. The difference in effects between subgroups will be estimated and between-study heterogeneity suitably quantified and explored. The potential for publication bias and availability bias in the IPD obtained will be investigated. We will conduct a model-based economic evaluation to assess the cost effectiveness of the interventions to manage

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

    PubMed

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

    2014-02-15

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

  18. Diet and Inflammatory Bowel Disease.

    PubMed

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

    2015-08-01

    Patients with inflammatory bowel disease (IBD) are increasingly becoming interested in nonpharmacologic approaches to managing their disease. One of the most frequently asked questions of IBD patients is what they should eat. The role of diet has become very important in the prevention and treatment of IBD. Although there is a general lack of rigorous scientific evidence that demonstrates which diet is best for certain patients, several diets-such as the low-fermentable oligosaccharide, disaccharide, monosaccharide, and polyol diet; the specific carbohydrate diet; the anti-inflammatory diet; and the Paleolithic diet-have become popular. This article discusses the diets commonly recommended to IBD patients and reviews the supporting data. PMID:27118948

  19. Is Dieting OK for Kids?

    MedlinePlus

    ... Dictionary of Medical Words En Español What Other Kids Are Reading Back-to-School Butterflies? Read This ... White House Lunch Recipes Is Dieting OK for Kids? KidsHealth > For Kids > Is Dieting OK for Kids? ...

  20. Is the Chilean diet a Mediterranean-type diet?

    PubMed

    Rozowski, Jaime; Castillo, Oscar

    2004-01-01

    Food intake in Chile has changed markedly in the last decades, showing an increase in fat consumption and presently a small fruit and vegetables intake. A parallel is made between the Chilean and Mediterranean diet (mainly the one from Spain, Italy, and Greece), both currently and from 50 years ago. The main differences and similarities are based on food availability. Although Chilean diet seems to be approaching the traditional Mediterranean diet of the 60's, there is concern about changes that are moving away from Chilean traditional diet and towards a western one. A new food pyramid for Chile is proposed based on the traditional Mediterranean-type diet.

  1. Design of different strategies of multivalent DNA-based vaccination against rabies and canine distemper in mice and dogs

    PubMed Central

    2012-01-01

    Background During the vaccination campaigns, puppies younger than 3 months old are not targeted and remain unvaccinated for at least the first year of their lives. Almost half of the reported rabid dogs are 6 months or younger. Hence, we should recommend the vaccination against rabies of young puppies. Unfortunately, owing to the exposure of puppies to infections with either canine parvovirus (CPV) or distemper virus (CDV) after the intervention of the vaccinators, owners are reluctant to vaccinate puppies against rabies. Therefore, it is necessary to include the CPV and CDV valences in the vaccine against rabies. Multivalent DNA-based vaccination in dogs, including rabies and distemper valences, could help in raising vaccine coverage. Methods We have designed monovalent and multivalent DNA-based vaccine candidates for in vitro and in vivo assays. These plasmids encode to the rabies virus glycoprotein and/or the canine distemper virus hemagglutinin. The first strategy of multivalent DNA-based vaccination is by mixing plasmids encoding to a single antigen each. The second is by simply fusing the genes of the antigens together. The third is by adding the foot and mouth disease virus (FMDV) 2A oligopeptide gene into the antigen genes. The last strategy is by the design and use of a bicistronic plasmid with an “Internal Ribosome Entry Site” (IRES) domain. Results The monovalent construct against canine distemper was efficiently validated by inducing higher humoral immune responses compared to cell-culture-derived vaccine both in mice and dogs. All multivalent plasmids efficiently expressed both valences after in vitro transfection of BHK-21 cells. In BALB/c mice, the bicistronic IRES-dependant construct was the most efficient inducer of virus-neutralizing antibodies against both valences. It was able to induce better humoral immune responses compared to the administration of either cell-culture-derived vaccines or monovalent plasmids. The FMDV 2A was also efficient

  2. Ground- and excited-state properties of DNA