Threatened reef corals of the world

10.1371/journal.pone.0034459PLoS ONE73

What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades

<p>Abstract</p> <p>Background</p> <p>The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for <it>Plethodon </it>salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals).</p> <p>Results</p> <p>We find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade), but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that <it>Plethodon </it>have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled).</p> <p>Conclusions</p> <p>Overall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. However, given cases like <it>Plethodon</it>, there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses.</p

Experimental Gastric Carcinogenesis in Cebus apella Nonhuman Primates

The evolution of gastric carcinogenesis remains largely unknown. We established two gastric carcinogenesis models in New-World nonhuman primates. In the first model, ACP03 gastric cancer cell line was inoculated in 18 animals. In the second model, we treated 6 animals with N-methyl-nitrosourea (MNU). Animals with gastric cancer were also treated with Canova immunomodulator. Clinical, hematologic, and biochemical, including C-reactive protein, folic acid, and homocysteine, analyses were performed in this study. MYC expression and copy number was also evaluated. We observed that all animals inoculated with ACP03 developed gastric cancer on the 9th day though on the 14th day presented total tumor remission. In the second model, all animals developed pre-neoplastic lesions and five died of drug intoxication before the development of cancer. The last surviving MNU-treated animal developed intestinal-type gastric adenocarcinoma observed by endoscopy on the 940th day. The level of C-reactive protein level and homocysteine concentration increased while the level of folic acid decreased with the presence of tumors in ACP03-inoculated animals and MNU treatment. ACP03 inoculation also led to anemia and leukocytosis. The hematologic and biochemical results corroborate those observed in patients with gastric cancer, supporting that our in vivo models are potentially useful to study this neoplasia. In cell line inoculated animals, we detected MYC immunoreactivity, mRNA overexpression, and amplification, as previously observed in vitro. In MNU-treated animals, mRNA expression and MYC copy number increased during the sequential steps of intestinal-type gastric carcinogenesis and immunoreactivity was only observed in intestinal metaplasia and gastric cancer. Thus, MYC deregulation supports the gastric carcinogenesis process. Canova immunomodulator restored several hematologic measurements and therefore, can be applied during/after chemotherapy to increase the tolerability and duration of anticancer treatments

Physicochemical characteristics of citrus jelly with non cariogenic and functional sweeteners

In this study the effect of sweeteners with low glycemic index and non-cariogenic characteristics (isomaltulose, oligofructose and tagatose) in jelly prepared with citrus juice has been evaluated considering a citrus jelly formulated with sucrose as reference. The soluble solids, moisture content, pH, water activity, antioxidant capacity, optical and mechanical properties of jelly made using different sweeteners was determined during storage. Besides, mesophilic aerobics and moulds and yeasts was also counted to determine their stability over time. Sensory evaluation of the citrus jelly has also been done. The results showed the antioxidant activity decreased during storage in all formulations. Tagatose increased lightness whereas coordinates a*, b* and chrome of all the jellies prepared using new sweeteners were lower than jellies with sucrose. However, citrus jelly with only oligofructose or tagatose or with the mixture of isomaltulose and tagatose were most closely resembled to the control jelly with respect to mechanical properties. Jelly prepared with the combination of isomaltulose and tagatose in equal proportions obtained the best score in the sensorial analysis.The authors would like to thank the Serigo-Andres family for donating the raw materials, and also the GVA projects GV/2013/029, GV/2014/012 as well as the Universitat Politecnica de Valencia (Spain) for the financial support given to this research study (UPV PAID-06-12 SP20120889).Rubio-Arraez, S.; Capella Hernández, JV.; Castelló Gómez, ML.; Ortolá Ortolá, MD. (2016). Physicochemical characteristics of citrus jelly with non cariogenic and functional sweeteners. Journal of Food Science and Technology. 53(10):3642-3650. https://doi.org/10.1007/s13197-016-2319-4S364236505310Álvarez J, Pastoriza S, Alonso-Olalla R, Delgado-Andrade C, Rufián-Henares JA (2014) Nutritional and physicochemical characteristic of commercial Spanish citrus juices. Food Chem 164:396–405AOAC (2000) Official methods of analysis of AOAC international, 17th edn. Gaithersburg, MDCalzada-León R, Ruiz-Reyes ML, Altamirano-Bustamante N, Padrón-Martínez MM (2013) Features of the noncaloric sweeteners and their use in children. Acta Pediatr Méx 34(3):141–153Chacón-Villalobos A (2006) Current perspectives agribusiness oligofructosaccharides (FOS). Agron Mesoam 17(2):265–286De Oliva-Neto P, Menão PTP (2009) Isomaltulose production from sucrose by protaminobacter rubrum immobilized in calcium alginate. Bioresour Technol 100:252–4256de Queiroz Pane D, Dias CB, Meinhart AD, Ballus CA, Godoy HT (2015) Evaluation of the sweetener content in diet/light/zero foods and drinks by HPLC-DAD. J Food Sci Tech 52(11):6900–6913Edwards WP (2002) The science of goodies. Acribia S.A, SpainFood and Drug Administration (FDA) (2005) GRAS Notification Isomaltulose (PALATINOSE). http://www.fda.gov/ucm/groups/fdagov-public/@fdagovfoodsgen/documents/document/ucm268989.pdf . Accessed 12 July 2015Food and Drug Administration (FDA) (2010) GRAS Notification Tagatose. GRN No.352. http://www.fda.gov/ucm/groups/fdagov-public/@fdagov-foods-gen/documents/document/ucm269560.pdf . Accessed 12 July 2015Food and Drug Administration (FDA) (2011) GRAS Notification Oligofructose. GRN No.392. http://www.fda.gov/ucm/groups/fdagov-public/@fdagov-foodsgen/documents/document/ucm277112.pdf . Accessed 12 July 2015GME (2015) Gelatine manufactured Europe gelatine properties. http://www.gelatine.org/en/about-gelatine/properties.html . Accessed 12 July 2015ISO (2003) Sensory analysis. Guidelines for the use of quantitative response scales [ref. no.ISO 4121:2003]. International Organization for Standardization, GenevaISO (2008) Sensory analysis Vocabulary [ref. no.ISO 5492:2008]. International Organization for Standardization, GenevaLedur MJ, Tessaro I, Zapata CP (2013) Physicochemical characterization of Saccharides Powder obtained from Yacon Roots (Smallanthus sonchifolius) by membrane technology. Braz Arch Biol Technol 56(6):1024–1033Levin GV (2002) Tagatose, the new GRAS sweetener and health product. J Med Food 5(1):23–36Lina BAR, Jonker G, Kozianowski G (2002) Isomaltulose (Palatinose review of biological and toxicologycal studies). Food Chem Toxicol 40(10):1375–1381O’Donnell K, Kearsley M (2012) Sweeteners and sugar alternatives in food technology, 2nd edn. Wiley, ChichesterOh DK (2007) Tagatose: properties, applications, and biotechnological processes. Appl Microb Biotechnol 76(1):1–8Pacual MR, Calderón-Pascual V (2000) Food Microbiology. Analytical methodology for foods and drinks, 2nd edn. Diaz de Santos, MadridPeinado I, Rosa E, Heredia A, Andrés A (2012) Rheological characteristics of healthy sugar substituted spreadable strawberry product. J Food Eng 113(3):365–373Peinado I, Rosa E, Heredia A, Escriche I, Andrés A (2013) Optical, mechanical and sensorial properties of strawberry spreadable products formulated with isomaltulose. Food Bioprocess Tech 6(9):2353–2364Periche A, Heredia A, Escriche I, Andrés A, Castelló ML (2014) Optical, mechanical and sensory properties of based-isomaltulose gummy confections. Food Biosci 7:37–44Periche A, Heredia A, Escriche I, Andrés A, Castelló ML (2015a) Potential use of isomaltulose to produce healthier marshmallows. LWT-Food Sci Technol 62(1):605–612Periche Á, Castelló ML, Heredia A, Escriche I (2015b) Stevia rebaudiana, Oligofructose and isomaltulose as sugar replacers in Marshmallows: stability and antioxidant properties. J Food Process Preserv. doi: 10.1111/jfpp.12653Petersen-Skytte U (2006) Tagatose. In: Mitchell H (ed) Sweeteners and sugar alternatives in food technology. Blackwell Publishing, Oxford, pp 262–292Pimentel TC, Madrona GS, Prudencio SH (2015) Probiotic clarified apple juice with oligofructose or sucralose as sugar substitutes: sensory profile and acceptability. LWT–Food. Sci Technol 62(1):838–846Rababah TM, Al-Mahasneh MA, Kilani I, Yang W, Alhamad MN, Ereifeja E, Al-U’datta M (2011) Effect of jam processing and storage on total phenolics, antioxidant activity, and anthocyanins of different fruits. J Sci Food Agric 91:1096–1102Rubio-Arraez S, Sahuquillo S, Capella JV, Ortolá MD, Castelló ML (2015) Influence of healthy sweeteners (Tagatose and Oligofructose) on the physicochemical characteristics of orange marmalade. J Texture Stud 46(4):272–280Shahidi F, Liyana-Pathirana CM, Wall DS (2006) Antioxidant activity of white and black sesame seeds and their hull fractions. 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Antimicrobial activity and rutin identification of honey produced by the stingless bee Melipona compressipes manaosensis and commercial honey

Background: Honey has been identified as a potential alternative to the widespread use of antibiotics, which are of significant concern considering the emergence of resistant bacteria. In this context, this study aimed to evaluate the antimicrobial activity of honey samples produced by a stingless bee species and by Apis sp. against pathogenic bacteria, as well as to identify the presence of phenolic compounds.Methods: Honey samples from the stingless bee M. compressipes manaosensis were collected twice, during the dry and rainy seasons. Three commercial honey samples from Apis sp. were also included in this study. Two different assays were performed to evaluate the antibacterial potential of the honey samples: agar-well diffusion and broth macrodilution. Liquid-liquid extraction was used to assess phenolic compounds from honey. HPLC analysis was performed in order to identify rutin and apigenin on honey samples. Chromatograms were recorded at 340 and 290 nm.Results: Two honey samples were identified as having the highest antimicrobial activity using the agar diffusion method. Honey produced by Melipona compressipes manaosensis inhibited the growth of Staphylococcus aureus, Escherichia coli (0157: H7), Proteus vulgaris, Shigella sonnei and Klebsiella sp. A sample of honey produced by Apis sp. also inhibited the growth of Salmonella paratyphi. The macrodilution technique presented greater sensitivity for the antibacterial testing, since all honey samples showed activity. Flavonoid rutin was identified in the honey sample produced by the stingless bee.Conclusions: Honey samples tested in this work showed antibacterial activity against Gram-positive and Gram-negative bacteria. The results reported herein highlight the potential of using honey to control bacterial growth. © 2013 Pimentel et al.; licensee BioMed Central Ltd