Mechanics of the IL2RA Gene Activation Revealed by Modeling and Atomic Force Microscopy

Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs) TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC) formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static

Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase

We have used a stepwise increase in ligand complexity approach to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) to its total affinity for human 8-oxoguanine DNA glycosylase (OGG1) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA. Non-specific OGG1 interactions with 10–13 nt pairs within its DNA-binding cleft provides approximately 5 orders of magnitude of its affinity for DNA (ΔG° approximately −6.7 kcal/mol). The relative contribution of the oxoG unit of DNA (ΔG° approximately −3.3 kcal/mol) together with other specific interactions (ΔG° approximately −0.7 kcal/mol) provide approximately 3 orders of magnitude of the affinity. Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the kcat term instead; the rate increases by 6–7 orders of magnitude for cognate DNA as compared with non-cognate one. The kcat values for substrates of different sequences correlate with the DNA twist, while the KM values correlate with ΔG° of the DNA fragments surrounding the lesion (position from −6 to +6). The functions for predicting the KM and kcat values for different sequences containing oxoG were found

Complete Sequencing and Pan-Genomic Analysis of Lactobacillus delbrueckii subsp. bulgaricus Reveal Its Genetic Basis for Industrial Yogurt Production

Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) is an important species of Lactic Acid Bacteria (LAB) used for cheese and yogurt fermentation. The genome of Lb. bulgaricus 2038, an industrial strain mainly used for yogurt production, was completely sequenced and compared against the other two ATCC collection strains of the same subspecies. Specific physiological properties of strain 2038, such as lysine biosynthesis, formate production, aspartate-related carbon-skeleton intermediate metabolism, unique EPS synthesis and efficient DNA restriction/modification systems, are all different from those of the collection strains that might benefit the industrial production of yogurt. Other common features shared by Lb. bulgaricus strains, such as efficient protocooperation with Streptococcus thermophilus and lactate production as well as well-equipped stress tolerance mechanisms may account for it being selected originally for yogurt fermentation industry. Multiple lines of evidence suggested that Lb. bulgaricus 2038 was genetically closer to the common ancestor of the subspecies than the other two sequenced collection strains, probably due to a strict industrial maintenance process for strain 2038 that might have halted its genome decay and sustained a gene network suitable for large scale yogurt production

Norms of Presentational Force

This is the author's accepted manuscript, made available with permission of the American Forensic Association.Can style or presentational devices reasonably compel us to believe, agree, act? I submit that they can, and that the normative pragmatic project explains how. After describing a normative pragmatic approach to presentational force, I analyze and evaluate presentational force in Susan B. Anthony's "Is it a Crime for a U. S. Citizen to Vote" as it apparently proceeds from logic, emotion, and style. I conclude with reflections on the compatibility of the normative pragmatic approach with the recently-developed pragma-dialectical treatment of presentational devices

The expanded tomato fruit volatile landscape

[EN] The present review aims to synthesize our present knowledge about the mechanisms implied in the biosynthesis of volatile compounds in the ripe tomato fruit, which have a key role in tomato flavour. The difficulties in identifiying not only genes or genomic regions but also individual target compounds for plant breeding are addressed. Ample variability in the levels of almost any volatile compound exists, not only in the populations derived from interspecific crosses but also in heirloom varieties and even in commercial hybrids. Quantitative trait loci (QTLs) for all tomato aroma volatiles have been identified in collections derived from both intraspecific and interspecific crosses with different wild tomato species and they (i) fail to co-localize with structural genes in the volatile biosynthetic pathways and (ii) reveal very little coincidence in the genomic regions characterized, indicating that there is ample opportunity to reinforce the levels of the volatiles of interest. Some of the identified genes may be useful as markers or as biotechnological tools to enhance tomato aroma. Current knowledge about the major volatile biosynthetic pathways in the fruit is summarized. Finally, and based on recent reports, it is stressed that conjugation to other metabolites such as sugars seems to play a key role in the modulation of volatile release, at least in some metabolic pathways.We wish to thank the Metabolomics facility at the IBMCP for technical assistance. AG was supported by grants from MinECO and FECYT. This work was facilitated by the European-funded COST action FA1106 QualityFruit.Rambla Nebot, JL.; Tikunov, Y.; Monforte Gilabert, AJ.; Bovy, A.; Granell Richart, A. (2014). The expanded tomato fruit volatile landscape. Journal of Experimental Botany. 65(16):4613-4623. doi:10.1093/jxb/eru128S461346236516Abegaz, E. G., Tandon, K. S., Scott, J. W., Baldwin, E. A., & Shewfelt, R. L. (2004). Partitioning taste from aromatic flavor notes of fresh tomato (Lycopersicon esculentum, Mill) to develop predictive models as a function of volatile and nonvolatile components. Postharvest Biology and Technology, 34(3), 227-235. doi:10.1016/j.postharvbio.2004.05.023Alba, J. M., Montserrat, M., & Fernández-Muñoz, R. (2008). Resistance to the two-spotted spider mite (Tetranychus urticae) by acylsucroses of wild tomato (Solanum pimpinellifolium) trichomes studied in a recombinant inbred line population. Experimental and Applied Acarology, 47(1), 35-47. doi:10.1007/s10493-008-9192-4Baldwin, E. A., Goodner, K., & Plotto, A. (2008). Interaction of Volatiles, Sugars, and Acids on Perception of Tomato Aroma and Flavor Descriptors. Journal of Food Science, 73(6), S294-S307. doi:10.1111/j.1750-3841.2008.00825.xBaldwin, E. A., Goodner, K., Plotto, A., Pritchett, K., & Einstein, M. (2004). Effect of Volatiles and their Concentration on Perception of Tomato Descriptors. Journal of Food Science, 69(8), S310-S318. doi:10.1111/j.1750-3841.2004.tb18023.xBaldwin, E. A., Scott, J. W., Shewmaker, C. K., & Schuch, W. (2000). Flavor Trivia and Tomato Aroma: Biochemistry and Possible Mechanisms for Control of Important Aroma Components. HortScience, 35(6), 1013-1022. doi:10.21273/hortsci.35.6.1013Bender, G., Hummel, T., Negoias, S., & Small, D. M. (2009). Separate signals for orthonasal vs. retronasal perception of food but not nonfood odors. Behavioral Neuroscience, 123(3), 481-489. doi:10.1037/a0015065Bezman, Y., Mayer, F., Takeoka, G. R., Buttery, R. G., Ben-Oliel, G., Rabinowitch, H. D., & Naim, M. (2003). Differential Effects of Tomato (Lycopersicon esculentumMill) Matrix on the Volatility of Important Aroma Compounds†. Journal of Agricultural and Food Chemistry, 51(3), 722-726. doi:10.1021/jf020892hButtery, R. G., Seifert, R. M., Guadagni, D. G., & Ling, L. C. (1971). Characterization of additional volatile components of tomato. Journal of Agricultural and Food Chemistry, 19(3), 524-529. doi:10.1021/jf60175a011Buttery, R. G., Takeoka, G., Teranishi, R., & Ling, L. C. (1990). Tomato aroma components: identification of glycoside hydrolysis volatiles. Journal of Agricultural and Food Chemistry, 38(11), 2050-2053. doi:10.1021/jf00101a010Buttery, R. G., Teranishi, R., Flath, R. A., & Ling, L. C. (1989). Fresh Tomato Volatiles. ACS Symposium Series, 213-222. doi:10.1021/bk-1989-0388.ch017Buttery, R. G., Teranishi, R., Ling, L. C., Flath, R. A., & Stern, D. J. (1988). Quantitative studies on origins of fresh tomato aroma volatiles. Journal of Agricultural and Food Chemistry, 36(6), 1247-1250. doi:10.1021/jf00084a030Carrari, F., Baxter, C., Usadel, B., Urbanczyk-Wochniak, E., Zanor, M.-I., Nunes-Nesi, A., … Fernie, A. R. (2006). Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network Behavior. Plant Physiology, 142(4), 1380-1396. doi:10.1104/pp.106.088534Causse, M., Friguet, C., Coiret, C., Lépicier, M., Navez, B., Lee, M., … Grandillo, S. (2010). Consumer Preferences for Fresh Tomato at the European Scale: A Common Segmentation on Taste and Firmness. Journal of Food Science, 75(9), S531-S541. doi:10.1111/j.1750-3841.2010.01841.xCausse, M. (2002). QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits. Journal of Experimental Botany, 53(377), 2089-2098. doi:10.1093/jxb/erf058Chen, G., Hackett, R., Walker, D., Taylor, A., Lin, Z., & Grierson, D. (2004). Identification of a Specific Isoform of Tomato Lipoxygenase (TomloxC) Involved in the Generation of Fatty Acid-Derived Flavor Compounds. Plant Physiology, 136(1), 2641-2651. doi:10.1104/pp.104.041608Du, X., Finn, C. E., & Qian, M. C. (2010). Bound Volatile Precursors in Genotypes in the Pedigree of ‘Marion’ Blackberry (RubusSp.). Journal of Agricultural and Food Chemistry, 58(6), 3694-3699. doi:10.1021/jf9034089Floss, D. S., & Walter, M. H. (2009). Role of carotenoid cleavage dioxygenase 1 (CCD1) in apocarotenoid biogenesis revisited. Plant Signaling & Behavior, 4(3), 172-175. doi:10.4161/psb.4.3.7840Gardner, H. W., Grove, M. J., & Salch, Y. P. (1996). Enzymic Pathway to Ethyl Vinyl Ketone and 2-Pentenal in Soybean Preparations. Journal of Agricultural and Food Chemistry, 44(3), 882-886. doi:10.1021/jf950509rGoff, S. A. (2006). Plant Volatile Compounds: Sensory Cues for Health and Nutritional Value? Science, 311(5762), 815-819. doi:10.1126/science.1112614González-Mas, M. C., Rambla, J. L., Alamar, M. C., Gutiérrez, A., & Granell, A. (2011). Comparative Analysis of the Volatile Fraction of Fruit Juice from Different Citrus Species. PLoS ONE, 6(7), e22016. doi:10.1371/journal.pone.0022016Goulet, C., Mageroy, M. H., Lam, N. B., Floystad, A., Tieman, D. M., & Klee, H. J. (2012). Role of an esterase in flavor volatile variation within the tomato clade. Proceedings of the National Academy of Sciences, 109(46), 19009-19014. doi:10.1073/pnas.1216515109Granell, A., & Rambla, J. L. (2013). Biosynthesis of Volatile Compounds. The Molecular Biology and Biochemistry of Fruit Ripening, 135-161. doi:10.1002/9781118593714.ch6Guadagni, D. G., Buttery, R. G., & Okano, S. (1963). Odour thresholds of some organic compounds associated with food flavours. Journal of the Science of Food and Agriculture, 14(10), 761-765. doi:10.1002/jsfa.2740141014Hemmerlin, A., Hoeffler, J.-F., Meyer, O., Tritsch, D., Kagan, I. A., Grosdemange-Billiard, C., … Bach, T. J. (2003). Cross-talk between the Cytosolic Mevalonate and the Plastidial Methylerythritol Phosphate Pathways in Tobacco Bright Yellow-2 Cells. Journal of Biological Chemistry, 278(29), 26666-26676. doi:10.1074/jbc.m302526200Howe, G. A., Lee, G. I., Itoh, A., Li, L., & DeRocher, A. E. (2000). Cytochrome P450-Dependent Metabolism of Oxylipins in Tomato. Cloning and Expression of Allene Oxide Synthase and Fatty Acid Hydroperoxide Lyase. Plant Physiology, 123(2), 711-724. doi:10.1104/pp.123.2.711Ilg, A., Beyer, P., & Al-Babili, S. (2008). Characterization of the rice carotenoid cleavage dioxygenase 1 reveals a novel route for geranial biosynthesis. FEBS Journal, 276(3), 736-747. doi:10.1111/j.1742-4658.2008.06820.xKlee, H. J. (2010). Improving the flavor of fresh fruits: genomics, biochemistry, and biotechnology. New Phytologist, 187(1), 44-56. doi:10.1111/j.1469-8137.2010.03281.xKlee, H. J., & Giovannoni, J. J. (2011). Genetics and Control of Tomato Fruit Ripening and Quality Attributes. Annual Review of Genetics, 45(1), 41-59. doi:10.1146/annurev-genet-110410-132507Klee, H. J., & Tieman, D. M. (2013). Genetic challenges of flavor improvement in tomato. Trends in Genetics, 29(4), 257-262. doi:10.1016/j.tig.2012.12.003Koeduka, T., Fridman, E., Gang, D. R., Vassao, D. G., Jackson, B. L., Kish, C. M., … Pichersky, E. (2006). Eugenol and isoeugenol, characteristic aromatic constituents of spices, are biosynthesized via reduction of a coniferyl alcohol ester. Proceedings of the National Academy of Sciences, 103(26), 10128-10133. doi:10.1073/pnas.0603732103Kovács, K., Fray, R. G., Tikunov, Y., Graham, N., Bradley, G., Seymour, G. B., … Grierson, D. (2009). Effect of tomato pleiotropic ripening mutations on flavour volatile biosynthesis. Phytochemistry, 70(8), 1003-1008. doi:10.1016/j.phytochem.2009.05.014Kochevenko, A., Araújo, W. L., Maloney, G. S., Tieman, D. M., Do, P. T., Taylor, M. G., … Fernie, A. R. (2012). Catabolism of Branched Chain Amino Acids Supports Respiration but Not Volatile Synthesis in Tomato Fruits. Molecular Plant, 5(2), 366-375. doi:10.1093/mp/ssr108KURODA, H., OSHIMA, T., KANEDA, H., & TAKASHIO, M. (2005). Identification and Functional Analyses of Two cDNAs That Encode Fatty Acid 9-/13-Hydroperoxide Lyase (CYP74C) in Rice. Bioscience, Biotechnology, and Biochemistry, 69(8), 1545-1554. doi:10.1271/bbb.69.1545Lê, S., & Ledauphin, S. (2006). You like tomato, I like tomato: Segmentation of consumers with missing values. Food Quality and Preference, 17(3-4), 228-233. doi:10.1016/j.foodqual.2005.08.001Lengard, V., & Kermit, M. (2006). 3-Way and 3-block PLS regressions in consumer preference analysis. Food Quality and Preference, 17(3-4), 234-242. doi:10.1016/j.foodqual.2005.05.005Lewinsohn, E., Sitrit, Y., Bar, E., Azulay, Y., Meir, A., Zamir, D., & Tadmor, Y. (2005). Carotenoid Pigmentation Affects the Volatile Composition of Tomato and Watermelon Fruits, As Revealed by Comparative Genetic Analyses. Journal of Agricultural and Food Chemistry, 53(8), 3142-3148. doi:10.1021/jf047927tLiavonchanka, A., & Feussner, I. (2006). Lipoxygenases: Occurrence, functions and catalysis. Journal of Plant Physiology, 163(3), 348-357. doi:10.1016/j.jplph.2005.11.006Mageroy, M. H., Tieman, D. M., Floystad, A., Taylor, M. G., & Klee, H. J. (2011). A Solanum lycopersicum catechol-O-methyltransferase involved in synthesis of the flavor molecule guaiacol. The Plant Journal, 69(6), 1043-1051. doi:10.1111/j.1365-313x.2011.04854.xMaloney, G. S., Kochevenko, A., Tieman, D. M., Tohge, T., Krieger, U., Zamir, D., … Klee, H. J. (2010). Characterization of the Branched-Chain Amino Acid Aminotransferase Enzyme Family in Tomato. Plant Physiology, 153(3), 925-936. doi:10.1104/pp.110.154922Marilley, L. (2004). Flavours of cheese products: metabolic pathways, analytical tools and identification of producing strains. International Journal of Food Microbiology, 90(2), 139-159. doi:10.1016/s0168-1605(03)00304-0Marlatt, C., Ho, C. T., & Chien, M. (1992). Studies of aroma constituents bound as glycosides in tomato. Journal of Agricultural and Food Chemistry, 40(2), 249-252. doi:10.1021/jf00014a016Mathieu, S., Cin, V. D., Fei, Z., Li, H., Bliss, P., Taylor, M. G., … Tieman, D. M. (2008). Flavour compounds in tomato fruits: identification of loci and potential pathways affecting volatile composition. Journal of Experimental Botany, 60(1), 325-337. doi:10.1093/jxb/ern294Matsui, K. (2006). Green leaf volatiles: hydroperoxide lyase pathway of oxylipin metabolism. Current Opinion in Plant Biology, 9(3), 274-280. doi:10.1016/j.pbi.2006.03.002Matsui, K., Kurishita, S., Hisamitsu, A., & Kajiwara, T. (2000). A lipid-hydrolysing activity involved in hexenal formation. Biochemical Society Transactions, 28(6), 857-860. doi:10.1042/bst0280857Matsui, K., Ujita, C., Fujimoto, S., Wilkinson, J., Hiatt, B., Knauf, V., … Feussner, I. (2000). Fatty acid 9- and 13-hydroperoxide lyases from cucumber1. FEBS Letters, 481(2), 183-188. doi:10.1016/s0014-5793(00)01997-9Mita, G., Quarta, A., Fasano, P., De Paolis, A., Di Sansebastiano, G. P., Perrotta, C., … Santino, A. (2005). Molecular cloning and characterization of an almond 9-hydroperoxide lyase, a new CYP74 targeted to lipid bodies*. Journal of Experimental Botany, 56(419), 2321-2333. doi:10.1093/jxb/eri225Moummou, H., Tonfack, L. B., Chervin, C., Benichou, M., Youmbi, E., Ginies, C., … van der Rest, B. (2012). Functional characterization of SlscADH1, a fruit-ripening-associated short-chain alcohol dehydrogenase of tomato. Journal of Plant Physiology, 169(15), 1435-1444. doi:10.1016/j.jplph.2012.06.007Nagegowda, D. A. (2010). Plant volatile terpenoid metabolism: Biosynthetic genes, transcriptional regulation and subcellular compartmentation. FEBS Letters, 584(14), 2965-2973. doi:10.1016/j.febslet.2010.05.045Negoias, S., Visschers, R., Boelrijk, A., & Hummel, T. (2008). New ways to understand aroma perception. Food Chemistry, 108(4), 1247-1254. doi:10.1016/j.foodchem.2007.08.030Noordermeer, M. A., Veldink, G. A., & Vliegenthart, J. F. . (1999). Alfalfa contains substantial 9-hydroperoxide lyase activity and a 3Z :2E -enal isomerase. FEBS Letters, 443(2), 201-204. doi:10.1016/s0014-5793(98)01706-2Ortiz-Serrano, P., & Gil, J. V. (2007). Quantitation of Free and Glycosidically Bound Volatiles in and Effect of Glycosidase Addition on Three Tomato Varieties (Solanum lycopersicumL.). Journal of Agricultural and Food Chemistry, 55(22), 9170-9176. doi:10.1021/jf0715673Ortiz-Serrano, P., & Gil, J. V. (2010). Quantitative Comparison of Free and Bound Volatiles of Two Commercial Tomato Cultivars (Solanum lycopersicumL.) during Ripening. Journal of Agricultural and Food Chemistry, 58(2), 1106-1114. doi:10.1021/jf903366rOrzaez, D., Medina, A., Torre, S., Fernández-Moreno, J. P., Rambla, J. L., Fernández-del-Carmen, A., … Granell, A. (2009). A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation. Plant Physiology, 150(3), 1122-1134. doi:10.1104/pp.109.139006Piombino, P., Sinesio, F., Moneta, E., Cammareri, M., Genovese, A., Lisanti, M. T., … Grandillo, S. (2013). Investigating physicochemical, volatile and sensory parameters playing a positive or a negative role on tomato liking. Food Research International, 50(1), 409-419. doi:10.1016/j.foodres.2012.10.033Rick, C. M., Uhlig, J. W., & Jones, A. D. (1994). High alpha-tomatine content in ripe fruit of Andean Lycopersicon esculentum var. cerasiforme: developmental and genetic aspects. Proceedings of the National Academy of Sciences, 91(26), 12877-12881. doi:10.1073/pnas.91.26.12877Sánchez, G., Besada, C., Badenes, M. L., Monforte, A. J., & Granell, A. (2012). A Non-Targeted Approach Unravels the Volatile Network in Peach Fruit. PLoS ONE, 7(6), e38992. doi:10.1371/journal.pone.0038992Simkin, A. J., Schwartz, S. H., Auldridge, M., Taylor, M. G., & Klee, H. J. (2004). The tomato carotenoid cleavage dioxygenase 1 genes contribute to the formation of the flavor volatiles β-ionone, pseudoionone, and geranylacetone. The Plant Journal, 40(6), 882-892. doi:10.1111/j.1365-313x.2004.02263.xSinesio, F., Cammareri, M., Moneta, E., Navez, B., Peparaio, M., Causse, M., & Grandillo, S. (2010). Sensory Quality of Fresh French and Dutch Market Tomatoes: A Preference Mapping Study with Italian Consumers. Journal of Food Science, 75(1), S55-S67. doi:10.1111/j.1750-3841.2009.01424.xSpeirs, J., Lee, E., Holt, K., Yong-Duk, K., Steele Scott, N., Loveys, B., & Schuch, W. (1998). Genetic Manipulation of Alcohol Dehydrogenase Levels in Ripening Tomato Fruit Affects the Balance of Some Flavor Aldehydes and Alcohols. Plant Physiology, 117(3), 1047-1058. doi:10.1104/pp.117.3.1047Tadmor, Y., Fridman, E., Gur, A., Larkov, O., Lastochkin, E., Ravid, U., … Lewinsohn, E. (2002). Identification ofmalodorous, a Wild Species Allele Affecting Tomato Aroma That Was Selected against during Domestication. Journal of Agricultural and Food Chemistry, 50(7), 2005-2009. doi:10.1021/jf011237xTandon, K. S., Baldwin, E. A., Scott, J. W., & Shewfelt, R. L. (2003). Linking Sensory Descriptors to Volatile and Nonvolatile Components of Fresh Tomato Flavor. Journal of Food Science, 68(7), 2366-2371. doi:10.1111/j.1365-2621.2003.tb05774.xTieman, D., Bliss, P., McIntyre, L. M., Blandon-Ubeda, A., Bies, D., Odabasi, A. Z., … Klee, H. J. (2012). The Chemical Interactions Underlying Tomato Flavor Preferences. Current Biology, 22(11), 1035-1039. doi:10.1016/j.cub.2012.04.016Tieman, D. M., Loucas, H. M., Kim, J. Y., Clark, D. G., & Klee, H. J. (2007). Tomato phenylacetaldehyde reductases catalyze the last step in the synthesis of the aroma volatile 2-phenylethanol. Phytochemistry, 68(21), 2660-2669. doi:10.1016/j.phytochem.2007.06.005Tieman, D., Taylor, M., Schauer, N., Fernie, A. R., Hanson, A. D., & Klee, H. J. (2006). Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde. Proceedings of the National Academy of Sciences, 103(21), 8287-8292. doi:10.1073/pnas.0602469103Tieman, D. M., Zeigler, M., Schmelz, E. A., Taylor, M. G., Bliss, P., Kirst, M., & Klee, H. J. (2006). Identification of loci affecting flavour volatile emissions in tomato fruits. Journal of Experimental Botany, 57(4), 887-896. doi:10.1093/jxb/erj074Tieman, D., Zeigler, M., Schmelz, E., Taylor, M. G., Rushing, S., Jones, J. B., & Klee, H. J. (2010). Functional analysis of a tomato salicylic acid methyl transferase and its role in synthesis of the flavor volatile methyl salicylate. The Plant Journal, 62(1), 113-123. doi:10.1111/j.1365-313x.2010.04128.xTikunov, Y. M., de Vos, R. C. H., González Paramás, A. M., Hall, R. D., & Bovy, A. G. (2009). A Role for Differential Glycoconjugation in the Emission of Phenylpropanoid Volatiles from Tomato Fruit Discovered Using a Metabolic Data Fusion Approach. Plant Physiology, 152(1), 55-70. doi:10.1104/pp.109.146670Tikunov, Y., Lommen, A., de Vos, C. H. R., Verhoeven, H. A., Bino, R. J., Hall, R. D., & Bovy, A. G. (2005). A Novel Approach for Nontargeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles. Plant Physiology, 139(3), 1125-1137. doi:10.1104/pp.105.068130Tikunov, Y. M., Molthoff, J., de Vos, R. C. H., Beekwilder, J., van Houwelingen, A., van der Hooft, J. J. J., … Bovy, A. G. (2013). NON-SMOKY GLYCOSYLTRANSFERASE1 Prevents the Release of Smoky Aroma from Tomato Fruit. The Plant Cell, 25(8), 3067-3078. doi:10.1105/tpc.113.114231Tzin, V., Rogachev, I., Meir, S., Moyal Ben Zvi, M., Masci, T., Vainstein, A., … Galili, G. (2013). Tomato fruits expressing a bacterial feedback-insensitive 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase of the shikimate pathway possess enhanced levels of multiple specialized metabolites and upgraded aroma. Journal of Experimental Botany, 64(14), 4441-4452. doi:10.1093/jxb/ert250Ursem, R., Tikunov, Y., Bovy, A., van Berloo, R., & van Eeuwijk, F. (2008). A correlation network approach to metabolic data analysis for tomato fruits. Euphytica, 161(1-2), 181-193. doi:10.1007/s10681-008-9672-yVancanneyt, G., Sanz, C., Farmaki, T., Paneque, M., Ortego, F., Castanera, P., & Sanchez-Serrano, J. J. (2001). Hydroperoxide lyase depletion in transgenic potato plants leads to an increase in aphid performance. Proceedings of the National Academy of Sciences, 98(14), 8139-8144. doi:10.1073/pnas.141079498Vogel, J. T., Tan, B.-C., McCarty, D. R., & Klee, H. J. (2008). The Carotenoid Cleavage Dioxygenase 1 Enzyme Has Broad Substrate Specificity, Cleaving Multiple Carotenoids at Two Different Bond Positions. Journal of Biological Chemistry, 283(17), 11364-11373. doi:10.1074/jbc.m710106200Vogel, J. T., Tieman, D. M., Sims, C. A., Odabasi, A. Z., Clark, D. G., & Klee, H. J. (2010). Carotenoid content impacts flavor acceptability in tomato (Solanum lycopersicum). Journal of the Science of Food and Agriculture, 90(13), 2233-2240. doi:10.1002/jsfa.4076Walter, M. H., Floss, D. S., & Strack, D. (2010). Apocarotenoids: hormones, mycorrhizal metabolites and aroma volatiles. Planta, 232(1), 1-17. doi:10.1007/s00425-010-1156-3Zanor, M. I., Rambla, J.-L., Chaïb, J., Steppa, A., Medina, A., Granell, A., … Causse, M. (2009). Metabolic characterization of loci affecting sensory attributes in tomato allows an assessment of the influence of the levels of primary metabolites and volatile organic contents. Journal of Experimental Botany, 60(7), 2139-2154. doi:10.1093/jxb/erp086Zhang, B., Chen, K., Bowen, J., Allan, A., Espley, R., Karunairetnam, S., & Ferguson, I. (2006). Differential expression within the LOX gene family in ripening kiwifruit. Journal of Experimental Botany, 57(14), 3825-3836. doi:10.1093/jxb/erl151Zorrilla-Fontanesi, Y., Rambla, J.-L., Cabeza, A., Medina, J. J., Sánchez-Sevilla, J. F., Valpuesta, V., … Amaya, I. (2012). Genetic Analysis of Strawberry Fruit Aroma and Identification of O-Methyltransferase FaOMT as the Locus Controlling Natural Variation in Mesifurane Content. Plant Physiology, 159(2), 851-870. doi:10.1104/pp.111.18831

Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere.

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO2 in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO2 may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO2 on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO2 concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO2 on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO2 on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions