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Academic literature on the topic 'Biochemical Pathways'

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Published: 4 June 2021

Last updated: 6 September 2023

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Journal articles on the topic "Biochemical Pathways"

Breuer, Eun-Kyoung Yim, Mandi M. Murph, and Rolf J. Craven. "Biochemical Pathways in Cancer." Biochemistry Research International 2012 (2012): 1–2. http://dx.doi.org/10.1155/2012/268504.

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Sanford, Chris, Matthew L. K. Yip, Carl White, and John Parkinson. "Cell++—simulating biochemical pathways." Bioinformatics 22, no. 23 (October 11, 2006): 2918–25. http://dx.doi.org/10.1093/bioinformatics/btl497.

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Schunk, Axel. "Datenbank der „Biochemical Pathways”︁." Nachrichten aus der Chemie 52, no. 11 (November 2004): 1155–57. http://dx.doi.org/10.1002/nadc.20040521113.

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Burrows, R. B., G. R. Warnes, and R. C. Hanumara. "Statistical modelling of biochemical pathways." IET Systems Biology 1, no. 6 (November 1, 2007): 353–60. http://dx.doi.org/10.1049/iet-syb:20060074.

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Pardini, Giovanni, Paolo Milazzo, and Andrea Maggiolo-Schettini. "Component identification in biochemical pathways." Theoretical Computer Science 587 (July 2015): 104–24. http://dx.doi.org/10.1016/j.tcs.2015.03.013.

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Smith, C. L., A. D. Bolton, H. M. Abdolmalkey, and R. Shafa. "Biochemical pathways linked to schizophrenia." European Psychiatry 23 (April 2008): S177. http://dx.doi.org/10.1016/j.eurpsy.2008.01.992.

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BRAUSE, R. "ADAPTIVE MODELING OF BIOCHEMICAL PATHWAYS." International Journal on Artificial Intelligence Tools 13, no. 04 (December 2004): 851–62. http://dx.doi.org/10.1142/s0218213004001855.

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In bioinformatics, biochemical pathways can be modeled by many differential equations. It is still an open problem how to fit the huge amount of parameters of the equations to the available data. Here, the approach of systematically learning the parameters is necessary. In this paper, for the small, important example of inflammation modeling a network is constructed and different learning algorithms are proposed. It turned out that due to the nonlinear dynamics evolutionary approaches are necessary to fit the parameters for sparse, given data.

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Holme, P., M. Huss, and H. Jeong. "Subnetwork hierarchies of biochemical pathways." Bioinformatics 19, no. 4 (March 1, 2003): 532–38. http://dx.doi.org/10.1093/bioinformatics/btg033.

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Tominaga, Kazuto, Yoshikazu Suzuki, Keiji Kobayashi, Tooru Watanabe, Kazumasa Koizumi, and Koji Kishi. "Modeling Biochemical Pathways Using an Artificial Chemistry." Artificial Life 15, no. 1 (January 2009): 115–29. http://dx.doi.org/10.1162/artl.2009.15.1.15108.

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Artificial chemistries are candidates for methodologies that model and design biochemical systems. If artificial chemistries can deal with such systems in beneficial ways, they may facilitate activities in the new area of biomolecular engineering. In order to explore such possibilities, we illustrate four models of biochemical pathways described in our artificial chemistry based on string pattern matching and recombination. The modeled pathways are the replication of DNA, transcription from DNA to mRNA, translation from mRNA to protein, and the oxidation of fatty acids. The descriptions show that the present approach has good modularity and scalability that will be useful for modeling a huge network of pathways. Moreover, we give a procedure to perform reasoning in the artificial chemistry, which checks whether a specified collection of molecules can be generated in a given model, and we demonstrate that it works on a model that describes a natural biochemical pathway.

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Liu, Qinghua, and Zain Paroo. "Biochemical Principles of Small RNA Pathways." Annual Review of Biochemistry 79, no. 1 (June 7, 2010): 295–319. http://dx.doi.org/10.1146/annurev.biochem.052208.151733.

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Dissertations / Theses on the topic "Biochemical Pathways"

Goddard, Maria Nadia. "Manipulating biochemical pathways in rice." Thesis, University of Nottingham, 2004. http://eprints.nottingham.ac.uk/28567/.

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The brown planthopper, Nilaparvata lugens, is a pest of rice in tropical regions. Its direct feeding results in loss in yield and plant death ("hopper bum"). Several compounds that stimulate insect attraction have been detected in rice plants colonised by N. lugens, including 1,2-dimethoxybenzene or veratrole. Electro-physiological studies and highresolution gas chromatography have identified veratrole as an attractant of N. lugens. Veratrole is a product of salicylic acid, a derivative of the phenyl propanoid pathway. Salicylic acid is decarboxylated to catechol, a step which is encoded by salicylate hydroxylase. Catechol is subsequently methylated to veratrole, which is released as a volatile compound from rice leaves. Mature scutellum-derived rice calli from (Oryza sativa) cv.Taipei 309 were transformed, using microprojectile bombardment, with pROB5 containing the hpt gene conferring resistance to the antibiotic hygromycin and pSLJ7307 carrying the nahG gene derived from Pseudomonas putida and coding for the enzyme salicylate hydroxylase. Following selection on hygromycin-containing medium, 17 independent transgenic rice plants were regenerated from >3600 bombarded calli, with a transformation frequency of 0.47%. Transgenic plants were confirmed by RT-PCR. Plant lines were classified as high expressors (10 lines) and low expressors (7 lines) depending on salicylate hydroxylase production. All transgenic lines exhibited higher enzyme activity than wild-type plants. Transgenic plants produced had altered metabolism for antioxidant enzymes such as catalase, ascorbate peroxidase and superoxide dismutase and reactive oxygen species such as hydrogen peroxide. Plants unable to accumulate salicylic acid exhibited delayed transcription of pathogenesis related genes and may therefore be compromised in their ability to respond to pathogen attack and mechanical wounding. Enhanced veratrole production was corroborated using gas chromatography of volatiles released from transgenic undamaged and mechanically damaged plants. Bioassays indicated that N. lugens were more attracted to high expressing plants than to wild-type plants, making more visits to areas containing transgenic rice leaves than areas containing non-transformed leaves and spending longer in these areas. Manipulating the production of veratrole by enhancing salicylate hydroxylase activity has therefore modified attraction of the N. lugens for high expressing nahG positive rice plants.

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Daae, Elisabeth Bull. "Mathematical modelling of biochemical pathways." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327023.

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Soda, Takahiro. "Converging biochemical pathways in psychiatric disorders." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/73775.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 2012.
Cataloged from PDF version of thesis.
Includes bibliographical references.
According to the World Health Organization, neuropsychiatric diseases account for approximately one third of years lost to disability. Yet, despite this huge disease burden, there is a lack of new treatments under development: approved treatments all essentially target the same target(s), if the target itself is known. There is now considerable evidence for a common set of heritable risk for psychiatric disorders including schizophrenia, bipolar disorder, as well as autism. Many of these risk alleles affect genes implicated in neuronal development with known roles at an early stage; these genes would have an effect on the individual before the onset of overt symptoms or diagnosis. Furthermore, many of the genes identified are known to participate in established pathways that are relevant for neuronal development and function. It is important then to address the causality between these signaling pathways that are important for neurodevelopment, and the risk of developing neuropsychiatric disorder. The work presented in this thesis represents two projects that aim to work toward this goal. The first project pertains to the mechanisms of transcriptional repression by DISC1 on ATF4-mediated gene transcription. The second project presents some initial steps towards uncovering the role of BCL9 in neuronal development.
by Takahiro Soda.
Ph.D.

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Mavrovouniotis, Michael L. (Michael Loizos). "Computer-aided design of biochemical pathways." Thesis, Massachusetts Institute of Technology, 1988. http://hdl.handle.net/1721.1/14449.

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Webhofer, Christian. "Antidepressant activated biochemical pathways and biomarker candidates." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-159303.

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Most of the commonly used antidepressants block monoamine reuptake transporters to enhance serotonergic or noradrenergic neurotransmission. Effects besides or downstream of increased monoaminergic neurotransmission are poorly understood and yet presumably important for the drugs’ mode of action. In my PhD thesis I employed proteomics and metabolomics technologies combined with in silico analyses and identified cellular pathways affected by antidepressant drug treatment. DBA/2 mice were treated with paroxetine as a representative Selective Serotonin Reuptake Inhibitor (SSRI). Hippocampal protein levels were compared between chronic paroxetine- and vehicle-treated animals using in vivo 15N metabolic labeling combined with mass spectrometry. I also studied chronic changes in the hippocampus using unbiased metabolite profiling and the time course of metabolic changes with the help of a targeted polar metabolomics profiling platform. I identified profound alterations related to hippocampal energy metabolism. Glycolytic metabolite levels acutely increased while Krebs cycle metabolite levels decreased upon chronic treatment. Changes in energy metabolism were influenced by altered glycogen metabolism rather than by altered glycolytic or Krebs cycle enzyme levels. Increased energy levels were reflected by an increased ATP/ADP ratio and by increased ratios of high-to-low energy purines and pyrimidines. Paralleling the shift towards aerobic glycolysis upon paroxetine treatment I identified decreased levels of Krebs cycle and oxidative phosphorylation enzyme levels upon the antidepressant-like 15N isotope effect in high-anxiety behavior mice. In the course of my analyses I also identified GABA, galactose-6-phosphate and leucine as biomarker candidates for the assessment of chronic paroxetine treatment effects in the periphery and myo-inositol as biomarker candidate for an early assessment of chronic treatment effects. The identified antidepressant drug treatment affected molecular pathways and novel SSRI modes of action warrant consideration in antidepressant drug development efforts.

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Tomlinson, Esther Jane. "Studies on the evolution of biochemical pathways." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240380.

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Pooler, Amy Melissa. "Regulation of biochemical pathways involved in neurodegeneration." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/31177.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 2005.
Includes bibliographical references.
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline and memory loss. Although much is known about how AD affects the brain, the cause of this disease remains elusive. Current AD treatments target symptoms of the disease but do not prevent or slow the underlying neurodegeneration. Therefore, research into the biochemical mechanisms of AD is necessary in order to develop a better understanding of how to treat it. Misprocessing of the amyloid precursor protein (APP) in the brains of AD patients leads to accumulation of the amyloidogenic peptide AD. A soluble APP fragment (APPS) is formed when APP is cleaved within the AP region, thereby preventing AP formation. Activation of 5-HT2A or 5-HT2c receptors has been shown to increase APPS secretion in vitro; therefore, we determined whether activation of these receptors might have a similar effect in vivo. We found that a 5-HT2A/2c agonist affected brain APP metabolism in guinea pigs by increasing CSF levels of APPS and, following chronic treatment, by decreasing levels of AP. Our data indicate that activation of brain 5-HT2c receptors may be useful for treating AD by reducing AP production. Traumatic brain injury is a risk factor for AD, although the reason is unknown. To explore this relationship, we examined the effect of the inflammatory mediator PGE2 on production of APP in cultured microglia. We found that PGE2 treatment stimulated APP overexpression and that this effect was likely mediated by the prostaglandin EP2 receptor and the cAMP signaling cascade. Therefore, EP2 receptor antagonists may constitute an additional target for prevention of AD following brain injury.
(cont.) The neuropathology associated with AD includes neuritic dystrophy and degeneration. Therefore, restoration of neuritic growth and repair of phospolipid membranes may be important for treating AD. We found that treatment of NGF- differentiated PC 12 cells with the phospholipid precursor uridine enhanced neurite outgrowth by both enhancing phosphatide biosynthesis and by stimulating a G-protein receptor-coupled signaling pathway. Subsequently, we found that the HMG-CoA reductase inhibitor pravastatin enhanced neurite outgrowth in rat hippocampal neurons, not by affecting cholesterol synthesis, but by inhibition of isoprenoid formation. Stimulation of neurite growth by either uridine or statins may reduce AD risk by averting neuritic dystrophy and degeneration. However, further studies must be conducted to determine whether they are able to affect neuritic processes in vivo.
by Amy Melissa Pooler.
Ph.D.

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Caldecott, Keith. "Role of the xrs double strand break repair pathway in response to DNA damage induced by topoisomerase II-inhibiting antitumour drugs." Thesis, University College London (University of London), 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.279158.

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Schubert, Kathryn M. "Biochemical characterization of signaling pathways regulating cell survival." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ61171.pdf.

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Wegner, Katja. "Visualisation of biochemical pathways and their simulation results." Berlin Logos-Verl, 2006. http://deposit.d-nb.de/cgi-bin/dokserv?id=2865577&prov=M&dok_var=1&dok_ext=htm.

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Books on the topic "Biochemical Pathways"

Michal, Gerhard, and Dietmar Schomburg, eds. Biochemical Pathways. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118657072.

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Gerhard, Michal, ed. Biochemical pathways: An atlas of biochemistry and molecular biology. New York: Wiley, 1999.

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Biochemical pathways: An atlas of biochemistry and molecular biology. 2nd ed. Hoboken, N.J: John Wiley & Sons, 2012.

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E, Bornberg-Bauer, ed. Workshop on Computation of Biochemical Pathways and Genetic Networks: Villa Bosch, Heidelberg, August 12-13, 1999 : proceedings. Berlin: Logos, 1999.

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Workshop on Computation of Biochemical Pathways and Genetic Networks (3rd 2003 Heidelberg, Germany). 3rd Workshop on Computation of Biochemical Pathways and Genetic Networks : EML Research, Villa Bosch, Heidelberg, October 6-7, 2003. Edited by Gauges R. Berlin: Logos, 2003.

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M, Lad Pramod, Kaptein John S, and Lin Ching-Kow E, eds. Signal transduction in leukocytes: G protein-related and other pathways. Boca Raton: CRC Press, 1996.

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Germany) Workshop on Computation of Biochemical Pathways and Genetic Networks (2nd 2001 Heidelberg. 2nd Workshop on Computation of Biochemical Pathways and Genetic Networks: European Media Laboratory, Villa Bosch, Heidelberg, June 21-22, 2001 ; [Proceedings]. Edited by Gauges R. (Ralph), Van Gend C. (Carel), and Kummer U. (Ursula). Berlin: Logos, 2001.

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Germany) Workshop on Computation of Biochemical Pathways and Genetic Networks (6th 2010 Heidelberg. 6th Workshop on Computation of Biochemical Pathways and Genetic Networks: A BIOMS event : BIOQUANT, University of Heidelberg, September 16-17, 2010. Edited by Hübner K. (Katrin), Johann T. (Tim), Kummer U. (Ursula), Levering J. (Jennifer), and BIOMS. Berlin: Logos Verlag Berlin, 2010.

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Workshop on Computation of Biochemical Pathways and Genetic Networks (4th 2005 Heidelberg, Germany). 4th Workshop on Computation of Biochemical Pathways and Genetic Networks: A BioSim event : EML research, Villa Bosch, Heidelberg, September 12-13, 2005. Edited by Kummer U. (Ursula) and EML Research (Firm). Berlin: Logos, 2005.

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Andrea, Denke, and Elstner Erich, eds. Different pathways through life: Biochemical aspects of plant biology and medicine : in honor to [sic] Prof. Erich F. Elstner on the occasion of his 60th birthday. Muenchen: Lincom Europa, 1999.

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Book chapters on the topic "Biochemical Pathways"

Michal, Gerhard, and Dietmar Schomburg. "Introduction and General Aspects." In Biochemical Pathways, 1–13. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch1.

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Schomburg, Dietmar. "Biochemical Networks, Bioinformatics and Systems Biology." In Biochemical Pathways, 366–73. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch10.

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Michal, Gerhard, and Dietmar Schomburg. "The Cell and Its Contents." In Biochemical Pathways, 14–36. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch2.

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Wünschiers, Röbbe, Martina Jahn, Dieter Jahn, Ida Schomburg, Susanne Peifer, Elmar Heinzle, Helmut Burtscher, et al. "Metabolism." In Biochemical Pathways, 37–209. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch3.

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Jahn, Martina, Dieter Jahn, Röbbe Wünschiers, Stefan Ries, and Petra Dersch. "Protein Biosynthesis, Modifications and Degradation." In Biochemical Pathways, 210–60. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch4.

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Klumpp, Klaus. "Viruses." In Biochemical Pathways, 261–71. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch5.

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Just, Wilhelm, Horst Klima, and Gerhard Michal. "Transport." In Biochemical Pathways, 272–85. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch6.

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Niederfellner, Gerhard. "Signal Transduction and Cellular Communication." In Biochemical Pathways, 286–324. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch7.

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Rieber, Ernst Peter, and Anton Haselbeck. "Immune System." In Biochemical Pathways, 325–56. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch8.

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Müller, Peter. "Blood Coagulation and Fibrinolysis." In Biochemical Pathways, 357–65. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118657072.ch9.

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Conference papers on the topic "Biochemical Pathways"

Papadopoulos, G., and M. Brown. "Feature Sensitivity on Biochemical Signaling Pathways." In 2007 4th Symposium on Computational Intelligence in Bioinformatics and Computational Biology. IEEE, 2007. http://dx.doi.org/10.1109/cibcb.2007.4221247.

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Hillston, Jane. "Quantitative analysis of biochemical signalling pathways." In 2nd International ICST Conference on Performance Evaluation Methodologies and Tools. ICST, 2007. http://dx.doi.org/10.4108/smctools.2007.1995.

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Ghosh, Krishnendu. "Multiscale System Modeling of Biochemical Pathways." In 8th International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS). ACM, 2015. http://dx.doi.org/10.4108/icst.bict.2014.258008.

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Wu, Zujian, Wei Pang, and George M. Coghill. "Stepwise modelling of biochemical pathways based on qualitative model learning." In 2013 13th UK Workshop on Computational Intelligence (UKCI). IEEE, 2013. http://dx.doi.org/10.1109/ukci.2013.6651284.

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Bove, Pasquale, Alessio Micheli, Paolo Milazzo, and Marco Podda. "Prediction of Dynamical Properties of Biochemical Pathways with Graph Neural Networks." In 11th International Conference on Bioinformatics Models, Methods and Algorithms. SCITEPRESS - Science and Technology Publications, 2020. http://dx.doi.org/10.5220/0008964700320043.

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Wu, Zujian, and Huiqin Du. "A study of parallel and evolutionary framework for modelling biochemical signalling pathways." In 2016 2nd IEEE International Conference on Computer and Communications (ICCC). IEEE, 2016. http://dx.doi.org/10.1109/compcomm.2016.7924810.

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Liu, Chunmei, Hui Li, Alison Leonce, Legand Burge, John Trimble, Peter Keiller, and Abdul-Aziz Yakubu. "A Heuristic Algorithm for Finding the Longest Pathways in a Biochemical Network." In 2010 International Conference on Machine Learning and Applications (ICMLA). IEEE, 2010. http://dx.doi.org/10.1109/icmla.2010.81.

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Paviolo, Chiara, John W. Haycock, Paul R. Stoddart, and Sally L. McArthur. "Effects of laser-exposed gold nanorods on biochemical pathways of neuronal cells." In SPIE Micro+Nano Materials, Devices, and Applications, edited by James Friend and H. Hoe Tan. SPIE, 2013. http://dx.doi.org/10.1117/12.2033575.

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Lapid, Hadas, Assaf Marron, Smadar Szekely, and David Harel. "Using Reactive-System Modeling Techniques to Create Executable Models of Biochemical Pathways." In 7th International Conference on Model-Driven Engineering and Software Development. SCITEPRESS - Science and Technology Publications, 2019. http://dx.doi.org/10.5220/0007572504540464.

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Reports on the topic "Biochemical Pathways"

Dudareva, Natalia, Alexander Vainstein, Eran Pichersky, and David Weiss. Integrating biochemical and genomic approaches to elucidate C6-C2 volatile production: improvement of floral scent and fruit aroma. United States Department of Agriculture, September 2007. http://dx.doi.org/10.32747/2007.7696514.bard.

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The specific objectives of approved proposal include to: 1. Elucidate the C6-C2 biochemical pathways leading to the biosynthesis of phenylacetaldehyde, phenylethyl alcohol and phenylethyl acetate in floral tissues of ornamentally important plants, pefunia and roses. 2. Isolate and characterrze genes responsible for the production of these C6-C2 compounds and those involved in the regulation of the pathway using genomic and transcriptomic tools. 3. Determine whether altering the expression of key genes of this pathway can result in changing the aroma characteristics of flowers. Aldehydes are intermediates in a variety of biochemical pathways including those involved in the metabolism of carbohydrates, vitamins, steroids, amino acids, benzylisoquinoline alkaloids, hormones, and lipids. In plants they are also synthesized in response to environmental stresses such as salinity, cold, and heat shock or as flavors and aromas in fruits and flowers. Phenylacetaldehyde along with 2-phenylethanol and its acetate ester, are important scent compounds in numerous flowers, including petunias and roses. However, little is known about the biosynthesis of these volatile compounds in plants. We have shown that the formation PHA and 2-phenylethanol from Phe does not occur via trans-cinnamic acid and instead competes with the key enzyme of phenypropanoid metabolism Pheammonia-lyase (PAL) for Phe utilization. Using functional genomic approach and comparative gene expression profiling, we have isolated and characterized a novel enzyme from petunia and rose flowers that catalyzes the formation of the Ca-Czcompound phenylacetaldehyde (PHA) from L-phenylalanine (Phe) by the removal of both the carboxyl and amino groups. This enzyme, designated as phenylacetaldehyde synthases (PAAS), is a bifunctional enzyme that catalyzes the unprecedented efficient coupling of phenylalanine decarboxylation to oxidation, generating phenylacetaldehyde, CO2, ammonia, and hydrogen peroxide in stoichiometric amounts. Down-regulation of PAAS expression via RNA interference-based (RNAi) technology in petunia resulted in no PHA emission when compared with controls. These plants also produced no 2-phenylethanol, supporting our conclusion that PHA is a precursor of 2-phenylethanol. To understand the regulation of scent formation in plants we have also generated transgenic petunia and tobacco plants expressing the rose alcohol acetyltransferase (RhAAT) gene under the control of a CaMV-35S promoter. Although the preferred substrate of RhAAT in vitro is geraniol, in transgenic petunia flowers, it used phenylethyl alcohol and benzyl alcohol to produce the corresponding acetate esters, not generated by control flowers. These results strongly point to the dependence of volatile production on substrate availability. Analysis of the diurnal regulation of scent production in rose flowers revealed that although the daily emission of most scent compounds is synchronized, various independently evolved mechanisms control the production, accumulation and release of different volatiles. This research resulted in a fundamental discovery of biochemical pathway, enzymes and genes involved in biosynthesis of C6-C2s compounds, and provided the knowledge for future engineering plants for improved scent quality.

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Davis, Ryan E., Nicholas J. Grundl, Ling Tao, Mary J. Biddy, Eric C. Tan, Gregg T. Beckham, David Humbird, David N. Thompson, and Mohammad S. Roni. Process Design and Economics for the Conversion of Lignocellulosic Biomass to Hydrocarbon Fuels and Coproducts: 2018 Biochemical Design Case Update; Biochemical Deconstruction and Conversion of Biomass to Fuels and Products via Integrated Biorefinery Pathways. Office of Scientific and Technical Information (OSTI), November 2018. http://dx.doi.org/10.2172/1483234.

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Chamovitz, A. Daniel, and Georg Jander. Genetic and biochemical analysis of glucosinolate breakdown: The effects of indole-3-carbinol on plant physiology and development. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597917.bard.

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Genetic and biochemical analysis of glucosinolate breakdown: The effects of indole-3-carbinol on plant physiology and development Glucosinolates are a class of defense-related secondary metabolites found in all crucifers, including important oilseed and vegetable crops in the Brassica genus and the well-studied model plant Arabidopsis thaliana. Upon tissue damage, such as that provided by insect feeding, glucosinolates are subjected to catalysis and spontaneous degradation to form a variety of breakdown products. These breakdown products typically have a deterrent effect on generalist herbivores. Glucosinolate breakdown products also contribute to the anti-carcinogenic effects of eating cabbage, broccoli and related cruciferous vegetables. Indole-3-carbinol, a breakdown product of indol-3-ylmethylglucosinolate, forms conjugates with several other plant metabolites. Although some indole-3-carbinol conjugates have known functions in defense against herbivores and pathogens, most play as yet unidentified roles in plant metabolism, and possibly also plant development. At the outset, our proposal had three main hypotheses: (1) There is a specific detoxification pathway for indole-3-carbinol; (2) Metabolites derived from indole-3-carbinol are phloem-mobile and serve as signaling molecules; and (3) Indole-3-carbinol affects plant cell cycle and cell-differentiation pathways. The experiments were designed to enable us to elucidate how indole-3-carbinol and related metabolites affect plants and their interactions with herbivorous insects. We discovered that indole-3- carbinol rapidly and reversibly inhibits root elongation in a dose-dependent manner, and that this inhibition is accompanied by a loss of auxin activity in the root meristem. A direct interaction between indole-3-carbinol and the auxin perception machinery was suggested, as application of indole-3-carbinol rescued auxin-induced root phenotypes. In vitro and yeast-based protein interaction studies showed that indole-3-carbinol perturbs the auxin-dependent interaction of TIR1 with Aux/IAA proteins, supporting the notion that indole-3-carbinol acts as an auxin antagonist. Furthermore, transcript profiling experiments revealed the influence of indole-3-carbinol on auxin signaling in root tips, and indole-3-carbinol also affected auxin transporters. Brief treatment with indole-3-carbinol led to a reduction in the amount of PIN1 and to mislocalization of PIN2. The results indicate that chemicals induced by herbivory, such as indole-3-carbinol, function not only to repel herbivores, but also as signaling molecules that directly compete with auxin to fine tune plant growth and development, which implies transport of indole-3- carbinol that we are as yet unsuccessful in detecting. Our results indicate that plant defensive metabolites also have secondary functions in regulating aspects of plant metabolism, thereby providing diversity in defense-related plant signaling pathways. Such diversity of of signaling by defensive metabolites would be beneficial for the plant, as herbivores and pathogens would be less likely to mount effective countermeasures. We propose that growth arrest can be mediated directly by the herbivory-induced chemicals, in our case, indole-3-carbinol. Thus, glucosinolate breakdown to I3C following herbivory would have two outcomes: (1) Indole-3-carbinaol would inhibit the herbivore, while (2) at the same time inducing growth arrest within the plant. Thus, our results indicate that I3C is a defensive phytohormone that modulates auxin signaling, leading to growth arrest.

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Naim, Michael, Andrew Spielman, Shlomo Nir, and Ann Noble. Bitter Taste Transduction: Cellular Pathways, Inhibition and Implications for Human Acceptance of Agricultural Food Products. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7695839.bard.

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Historically, the aversive response of humans and other mammals to bitter-taste substances has been useful for survival, since many toxic constituents taste bitter. Today, the range of foods available is more diverse. Many bitter foods are not only safe for consumption but contain bitter constituents that provide nutritional benefits. Despite this, these foods are often eliminated from our current diets because of their unacceptable bitterness. Extensive technology has been developed to remove or mask bitterness in foods, but a lack of understanding of the mechanisms of bitterness perception at the taste receptor level has prevented the development of inhibitors or efficient methods for reducing bitterness. In our original application we proposed to: (a) investigate the time course and effect of selected bitter tastants relevant to agricultural products on the formation of intracellular signal molecules (cAMP, IP3, Ca2+) in intact taste cells, in model cells and in membranes derived therefrom; (b) study the effect of specific bitter taste inhibitors on messenger formation and identify G-proteins that may be involved in tastant-induced bitter sensation; (c) investigate interactions and self-aggregation of bitter tastants within membranes; (d) study human sensory responses over time to these bitter-taste stimuli and inhibitors in order to validate the biochemical data. Quench-flow module (QFM) and fast pipetting system (FPS) allowed us to monitor fast release of the aforementioned signal molecules (cGMP, as a putative initial signal was substituted for Ca2+ ions) - using taste membranes and intact taste cells in a time range below 500 ms (real time of taste sensation) - in response to bitter-taste stimulation. Limonin (citrus) and catechin (wine) were found to reduce cellular cAMP and increase IP3 contents. Naringin (citrus) stimulated an IP3 increase whereas the cheese-derived bitter peptide cyclo(leu-Trp) reduced IP3 but significantly increased cAMP levels. Thus, specific transduction pathways were identified, the results support the notion of multiple transduction pathways for bitter taste and cross-talk between a few of those transduction pathways. Furthermore, amphipathic tastants permeate rapidly (within seconds) into liposomes and taste cells suggesting their availability for direct activation of signal transduction components by means of receptor-independent mechanisms within the time course of taste sensation. The activation of pigment movement and transduction pathways in frog melanophores by these tastants supports such mechanisms. Some bitter tastants, due to their amphipathic properties, permeated (or interacted with) into a bitter tastant inhibitor (specific phospholipid mixture) which apparently forms micelles. Thus, a mechanism via which this bitter taste inhibitor acts is proposed. Human sensory evaluation experiments humans performed according to their 6-n-propyl thiouracil (PROP) status (non-tasters, tasters, super-tasters), indicated differential perception of bitterness threshold and intensity of these bitter compounds by different individuals independent of PROP status. This suggests that natural products containing bitter compounds (e.g., naringin and limonin in citrus), are perceived very differently, and are in line with multiple transduction pathways suggested in the biochemical experiments. This project provides the first comprehensive effort to explore the molecular basis of bitter taste at the taste-cell level induced by economically important and agriculturally relevant food products. The findings, proposing a mechanism for bitter-taste inhibition by a bitter taste inhibitor (made up of food components) pave the way for the development of new, and perhaps more potent bitter-taste inhibitors which may eventually become economically relevant.

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Ely, Roger L., and Frank W. R. Chaplen. Metabolic Engineering of Light and Dark Biochemical Pathways in Wild-Type and Mutant Strains of Synechocystis PCC 6803 for Maximal, 24-Hour Production of Hydrogen Gas. Office of Scientific and Technical Information (OSTI), March 2014. http://dx.doi.org/10.2172/1122862.

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Paran, Ilan, and Molly Jahn. Genetics and comparative molecular mapping of biochemical and morphological fruit characters in Capsicum. United States Department of Agriculture, March 2005. http://dx.doi.org/10.32747/2005.7586545.bard.

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Original objectives: The overall goal of our work was to gain information regarding the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper and to develop tools based on this information to assist in crop improvement. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoid (pungency) content (3) Determine possible association between capsaicinoid and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoid in pepper fruit and identify candidate genes for C.locus. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was poorly understood prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous SSR markers. This map has been integrated with a number of other independent maps resulting in the publication of a single resource map consisting of more than 2000 markers. Unlike previous maps based primarily on tomato-originated RFLP markers, the new maps are based on PCR markers that originate in Capsicum providing a comprehensive and versatile resource for marker-assisted selection in pepper. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, a character unique to pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master regulatoar for capsaicinoid accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTL that control capsaicinoid content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTL that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTL controlling fruit shape, fs3.1 and fs10.1, that differentiate elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advances in our understanding of important processes of pepper fruit development including the isolation and characterization of several well known genes. These results also provided the basis for the development of molecular tools that can be implemented for pepper improvement. A total of eleven refereed publications have resulted from this work, and several more are in preparation.

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Dunn, J., M. Johnson, Z. Wang, M. Wang, K. Cafferty, J. Jacobson, E. Searcy, et al. Supply Chain Sustainability Analysis of Three Biofuel Pathways. Biochemical Conversion of Corn Stover to Ethanol Indirect Gasification of Southern Pine to Ethanol Pyrolysis of Hybrid Poplar to Hydrocarbon Fuels. Office of Scientific and Technical Information (OSTI), July 2014. http://dx.doi.org/10.2172/1149252.

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Fridman, Eyal, and Eran Pichersky. Tomato Natural Insecticides: Elucidation of the Complex Pathway of Methylketone Biosynthesis. United States Department of Agriculture, December 2009. http://dx.doi.org/10.32747/2009.7696543.bard.

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Plant species synthesize a multitude of specialized compounds 10 help ward off pests. and these in turn may well serve as an alternative to synthetic pesticides to reduce environmental damage and health risks to humans. The general goal of this research was to perform a genetic and biochemical dissection of the natural-insecticides methylketone pathway that is specific to the glandular trichomes of the wild species of tomato, Solanumhabrochaites f. glabratum (accession PI126449). Previous study conducted by us have demonstrated that these compounds are synthesized de novo as a derivate pathway of the fatty acid biosynthesis, and that a key enzyme. designated MethylketoneSynthase 1 (MKS 1). catalyzes conversion of the intermediate B-ketoacyl- ACPs to the corresponding Cn-1 methylketones. The approach taken in this proposed project was to use an interspecific F2 population. derived from the cross between the cultivated lV182 and the wild species PIl26449. for three objectives: (i) Analyze the association between allelic status of candidate genes from the fatty acid biosynthesis pathway with the methylketone content in the leaves (ii) Perform bulk segregant analysis of genetic markers along the tomato genome for identifying genomic regions that harbor QTLs for 2TD content (iii) Apply differential gene expression analysis using the isolated glands of bulk segregant for identifying new genes that are involved in the pathway. The genetic mapping in the interspecific F2 population included app. 60 genetic markers, including the candidate genes from the FAS pathway and SSR markers spread evenly across the genome. This initial; screening identified 5 loci associated with MK content including the candidate genes MKS1, ACC and MaCoA:ACP trans. Interesting observation in this genetic analysis was the connection between shape and content of the glands, i.e. the globularity of the four cells, typical to the wild species. was associated with increased MK in the segregating population. In the next step of the research transcriptomic analysis of trichomes from high- and 10w-MK plants was conducted. This analysis identified a new gene, Methy1ketone synthase 2 (MKS2), whose protein product share sequence similarity to the thioesterase super family of hot-dog enzymes. Genetic analysis in the segregating population confirmed its association with MK content, as well as its overexpression in E. coli that led to formation of MK in the media. There are several conclusions drawn from this research project: (i) the genetic control of MK accumulation in the trichomes is composed of biochemical components in the FAS pathway and its vicinity (MKS 1 and MKS2). as well as genetic factors that mediate the morphology of these specialized cells. (ii) the biochemical pathway is now realized different from what was hypothesized before with MKS2 working upstream to I\1KS 1 and serves as the interface between primary (fatty acids) and secondary (MK) metabolism. We are currently testing the possible physical interactions between these two proteins in vitro after the genetic analysis showed clear epistatic interactions. (iii) the regulation of the pathway that lead to specialized metabolism in the wild species is largely mediated by transcription and one of the achievements of this project is that we were able to isolate and verify the specificity of the MKS1 promoter to the trichomes which allows manipulation of the pathways in these cells (currently in progress). The scientific implications of this research project is the advancement in our knowledge of hitherto unknown biochemical pathway in plants and new leads for studying a new family in plants (hot dog thioesterase). The agricultural and biotechnological implication are : (i) generation of new genetic markers that could assist in importing this pathway to cultivated tomato hence enhancing its natural resistance to insecticides, (ii) the discovery of MKS2 adds a new gene for genetic engineering of plants for making new fatty acid derived compounds. This could be assisted with the use of the isolated and verified MKS1 promoter. The results of this research were summarized to a manuscript that was published in Plant Physiology (cover paper). to a chapter in a proceeding book. and one patent was submitted in the US.

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Jensen, Roy A. Biochemical-Pathway Diversity in Archabacteria. Fort Belvoir, VA: Defense Technical Information Center, June 1988. http://dx.doi.org/10.21236/ada209596.

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Jensen, Roy A. Biochemical-Pathway Diversity in Archaebacteria. Fort Belvoir, VA: Defense Technical Information Center, August 1990. http://dx.doi.org/10.21236/ada226200.

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