Optical fibre-based detection of DNA hybridization

A dual-peak LPFG (long-period fibre grating), inscribed in an optical fibre, has been employed to sense DNA hybridization in real time, over a 1 h period. One strand of the DNA was immobilized on the fibre, while the other was free in solution. After hybridization, the fibre was stripped and repeated detection of hybridization was achieved, so demonstrating reusability of the device. Neither strand of DNA was fluorescently or otherwise labelled. The present paper will provide an overview of our early-stage experimental data and methodology, examine the potential of fibre gratings for use as biosensors to monitor both nucleic acid and other biomolecular interactions and then give a summary of the theory and fabrication of fibre gratings from a biological standpoint. Finally, the potential of improving signal strength and possible future directions of fibre grating biosensors will be addressed.

Comparative genomic hybridization analysis of craniopharyngiomas

Object. Craniopharyngioma is the most common childhood brain tumor and is thought to arise from embryonic remnants of the Rathke pouch. Some craniopharyngiomas are monoclonal in origin and hence presumably harbor somatic genetic alterations, although the precise molecular mechanisms involved in craniopharyngioma development are unknown. The goal of this study was to identify genetic alterations in craniopharyngiomas. Methods. To gain insight into the molecular mechanisms involved in development of these tumors, the authors analyzed nine adamantinomatous craniopharyngiomas by using comparative genomic hybridization. Six tumors (67%) displayed at least one genomic alteration, and three had six or more alterations. Only two tumors displayed a decrease in DNA copy number, and in all others an increase in DNA copy number was noted. Conclusions. The authors conclude that a subset of craniopharyngiomas consists of monoclonal tumors arising from activation of oncogenes located at specific chromosomal loci.

'Why don't you try it again?' A comparison of parent led, home based interventions aimed at increasing children's consumption of a disliked vegetable

Previous research suggests that the use of modelling and non-food rewards may be effective at increasing tasting, and consequential liking and acceptance, of a previously disliked food. Although successful school-based interventions have been developed, there is a lack of research into home-based interventions using these methods. This study aimed to develop and investigate the efficacy of a parent led home-based intervention for increasing children's acceptance of a disliked vegetable. A total of 115 children aged 2-4 years were allocated to one of four intervention groups or to a no-treatment control. The four intervention conditions were: repeated exposure; modelling and repeated exposure; rewards and repeated exposure; or modelling, rewards and repeated exposure. Children in all of the intervention conditions were exposed by a parent to daily offerings of a disliked vegetable for 14 days. Liking and consumption of the vegetable were measured pre and post-intervention. Significant increases in post-intervention consumption were seen in the modelling, rewards and repeated exposure condition and the rewards and repeated exposure condition, compared to the control group. Significant post-intervention differences in liking were also found between the experimental groups. Liking was highest (>60%) in the modelling, rewards and repeated exposure group and the rewards and repeated exposure group, intermediate (>26%) in the modelling and repeated exposure and repeated exposure groups, and lowest in the control group (10%). Parent led interventions based around modelling and offering incentives may present cost efficient ways to increase children's vegetable consumption.

Impact of Vegetable Preparation Method and Taste-Test on Vegetable Preference for First Grade Children in the United States

How children rate vegetables may be influenced by the preparation method. The primary objective of this study was for first grade students to be involved in a cooking demonstration and to taste and rate vegetables raw and cooked. First grade children of two classes (N= 52: 18 boys and 34 girls (approximately half Hispanic) that had assented and had signed parental consent participated in the study. The degree of liking a particular vegetable was recorded by the students using a hedonic scale of five commonly eaten vegetables tasted first raw (pre-demonstration) and then cooked (post-demonstration). A food habit questionnaire was filled out by parents to evaluate their mealtime practices and beliefs about their child’s eating habits. Paired sample t-tests revealed significant differences in preferences for vegetables in their raw and cooked states. Several mealtime characteristics were significantly associated with children’s vegetable preferences. Parents who reported being satisfied with how often the family eats evening meals together were more likely to report that their child eats adequate vegetables for their health (p=0.026). Parents who stated that they were satisfied with their child’s eating habits were more likely to report that their child was trying new foods (p<.001). Cooking demonstrations by nutrition professionals may be an important strategy that can be used by parents and teachers to promote vegetable intake. It is important that nutrition professionals provide guidance to encourage consumption of vegetables for parents so that they can model the behavior of healthy food consumption to their children.

Social determinants of fruit and vegetable intake and validation of Pro-Children Eating Habits Questionnaire for 3rd and 5th grade children

BACKGROUND: The Pro Children Eating Habits Questionnaire has been evaluated as a valid and reliable tool in Europe to measure determinants of fruit and vegetable intake for children; however, it has not been validation for United States populations. The purpose of this study was to (1) assess the reliability and discrimination validity of fruit and vegetable correlates for the Pro Children Eating Habits Questionnaire; (2) investigate the predictive validity of determinants of fruit and vegetable consumption for multi-ethnic elementary school children; and, (3) to assess the association of social determinants with fruit and vegetable consumption. METHODS: One hundred and thirty elementary school students from the 3rd and 5th grades completed this cross-sectional study. RESULTS: Fruit and vegetable determinants, had satisfactory internal consistencies. No differences were found between the test and the retest for the individual questions with the exception of the question for mean perceived vegetable intake. The discriminatory validity indicated the questionnaire could show differences across grade and gender levels for barriers of fruit and vegetables but not for other factors. Grade together with gender explained barriers to eating fruit and vegetables. Greater availability of fruit in the home and school was associated with higher frequency of consumption. CONCLUSIONS: The results of this study indicate the Pro-Children Eating Habits Questionnaire may be a reliable and valid tool for assessing fruit and vegetable consumption of children in the United States.

Análise microbiológica da cavidade interna de implantes dentais osseointegrados utilizando o checkerboard DNA-DNA hybridization

Introduction: Infiltration of organic fluids and microorganisms at the abutment/implant interface may result in bacterial infection of peri-implant tissues. Internal colonization of periodontal pathogens may be caused by bacteria trapped during installation or penetration of abutment/implant leakage. The aim of this study was to detect periodontal pathogens in the internal area of dental implants before loading. Materials and Methods: Seventy-eight implants in 32 partially edentulous subjects were selected for this evaluation. A bacterial biofilm sample of the internal surface of each implant was taken and analyzed for the presence of 40 microorganisms by checkerboard DNA-DNA hybridization, prior to installation of healing or any other prosthetic abutment. Discussion: Bacteria were detected in 20 patients (62.5%), distributed in 41 implants (52.6%). Forty-seven percent of implants showed no bacterial detection. Spontaneous early implant exposure to oral cavity during the healing period was not significant (P >0.05) to increase bacterial prevalence, but implants placed at mandible had higher bacterial prevalence than maxillary ones. Conclusion: The internal surface of dental implants can serve as a reservoir of periodontal pathogens for future implant/abutment interface.

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Peer reviewed

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

Peer reviewed

Perceived barriers towards healthy eating and their association with fruit and vegetable consumption

Acknowledgements The authors would like to thank the anonymous reviewer, staff at the Health Economics Research Unit and the Rowett Institute of Nutrition and Health for helpful comments on the manuscript. Funding This work was supported by the Scottish Government Rural and Environment Science and Analytical Services (RESAS) division.

Production of Polyhydroxyalkanoates by Pseudomonas mendocina using vegetable oils and their characterisation

Synthesis of Polyhydroxyalkanoates (PHAs) by Pseudomonas mendocina, using different vegetable oils such as, coconut oil, groundnut oil, corn oil and olive oil, as the sole carbon source was investigated for the first time. The PHA yield obtained was compared with that obtained during the production of PHAs using sodium octanoate as the sole carbon source. The fermentation profiles at shaken flask and bioreactor levels revealed that vegetable oils supported the growth of Pseudomonas mendocina and PHA accumulation in this organism. Moreover, when vegetable oil (coconut oil) was used as the sole carbon source, fermentation profiles showed better growth and polymer production as compared to conditions when sodium octanoate was used as the carbon source. In addition, comparison of PHA accumulation at shaken flask and fermenter level confirmed the higher PHA yield at shaken flask level production. The highest cell mass found using sodium octanoate was 1.8 g/L, whereas cell mass as high as 5.1 g/L was observed when coconut oil was used as the feedstock at flask level production. Moreover, the maximum PHA yield of 60.5% dry cell weight (dcw) was achieved at shaken flask level using coconut oil as compared to the PHA yield of 35.1% dcw obtained using sodium octanoate as the sole carbon source. Characterisations of the chemical, physical, mechanical, surface and biocompatibility properties of the polymers produced have been carried out by performing different analyses as described in the second chapter of this study. Chemical analysis using GC and FTIR investigations showed medium chain length (MCL) PHA production in all conditions. GC-MS analysis revealed a unique terpolymer production, containing 3-hydroxyoctanoic acid, 3-hydroxydecanoic acid and 3-hydroxydodecanoic acid when coconut oil, groundnut oil, olive oil, and corn oil were used as the carbon source. Whereas production of the homopolymer containing 3-hydroxyoctanoic acid was observed when sodium octanoate was used as the carbon source. MCL-PHAs produced in this study using sodium octanoate, coconut oil, and olive oil exhibited melting transitions, indicating that each of the PHA was crystalline or semi-crystalline polymer. In contrast, the thermal properties of PHAs produced from groundnut and corn oils showed no melting transition, indicating that they were completely amorphous or semi-crystalline, which was also confirmed by the X-Ray Diffraction (XRD) results obtained in this study. Mechanical analysis of the polymers produced showed higher stiffness of the polymer produced from coconut oil than the polymer from sodium octanoate. Surface characterisation of the polymers using Scanning Electron Microscopy (SEM) revealed a rough surface topography and surface contact angle measurement revealed their hydrophobic nature. Moreover, to investigate the potential applicability of the produced polymers as the scaffold materials for dental pulp regeneration, multipotent human Mesenchymal stem cells (hMSCs) were cultured onto the polymer films. Results indicated that these polymers are not cytotoxic towards the hMSCs and could support their attachment and proliferation. Highest cell growth was observed on the polymer samples produced from corn oil, followed by the polymer produced using coconut oil. In conclusion, this work established, for the first time, that vegetable oils are a good economical source of carbon for production of MCL-PHA copolymers effectively by Pseudomonas mendocina. Moreover, biocompatibility studies suggest that the produced polymers may have potential for dental tissue engineering application.

Morphological and Phylogenetic Characterization of New Gephyrocapsa Isolates Suggests Introgressive Hybridization in the Emiliania/Gephyrocapsa Complex (Haptophyta)

The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the Noëlaerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1 bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.

Morphological and Phylogenetic Characterization of New Gephyrocapsa Isolates Suggests Introgressive Hybridization in the Emiliania/Gephyrocapsa Complex (Haptophyta)

The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the Noëlaerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1 bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.