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Relevant bibliographies by topics / Biochemical engineering

Academic literature on the topic 'Biochemical engineering'

Author: Grafiati

Published: 4 June 2021

Last updated: 31 July 2024

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Journal articles on the topic "Biochemical engineering"

1

Miot, Sylvie, and Jean-Louis Boulay. "Biochemical engineering." Current Opinion in Biotechnology 13, no. 2 (April 2002): 83. http://dx.doi.org/10.1016/s0958-1669(02)00290-2.

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Lee, Kelvin H., and Vassily Hatzimanikatis. "Biochemical engineering." Current Opinion in Biotechnology 13, no. 2 (April 2002): 85–86. http://dx.doi.org/10.1016/s0958-1669(02)00306-3.

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Zabriskie, DaneW. "Biochemical engineering." Current Opinion in Biotechnology 7, no. 2 (April 1996): 187–89. http://dx.doi.org/10.1016/s0958-1669(96)80011-5.

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May, Sheldon W., and Robert D. Schwartz. "Biochemical engineering." Current Opinion in Biotechnology 8, no. 2 (April 1997): 145–47. http://dx.doi.org/10.1016/s0958-1669(97)80092-4.

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Mittal, G. S. "Biochemical Engineering." Canadian Institute of Food Science and Technology Journal 22, no. 4 (October 1989): 338. http://dx.doi.org/10.1016/s0315-5463(89)70422-3.

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Carrondo, Manuel JT, and John G. Aunins. "Biochemical engineering." Current Opinion in Biotechnology 15, no. 5 (October 2004): 441–43. http://dx.doi.org/10.1016/j.copbio.2004.08.014.

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Yarmush, Martin, and Henrik Pedersen. "Biochemical engineering." Current Opinion in Biotechnology 6, no. 2 (January 1995): 189–91. http://dx.doi.org/10.1016/0958-1669(95)80030-1.

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Larsson, G., S. B. Jørgensen, M. N. Pons, B. Sonnleitner, A. Tijsterman, and N. Titchener-Hooker. "Biochemical engineering science." Journal of Biotechnology 59, no. 1-2 (December 1997): 3–9. http://dx.doi.org/10.1016/s0168-1656(97)00158-2.

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Lyddiatt, Andrew. "Advanced biochemical engineering." Chemical Engineering Science 43, no. 2 (1988): 403–4. http://dx.doi.org/10.1016/0009-2509(88)85060-7.

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Winkler, M. A. "Advance biochemical engineering." Chemical Engineering Journal 38, no. 1 (May 1988): B14—B15. http://dx.doi.org/10.1016/0300-9467(88)80063-7.

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Dissertations / Theses on the topic "Biochemical engineering"

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Conejeros, Raul. "Optimisation of biochemical engineering systems." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621770.

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Wong, Kelvin Wai Wah. "Fundamentals and application of metabolic engineering /." View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?CENG%202006%20WONG.

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Hutchinson, Ucrecia Faith. "Biochemical processes for Balsamic-styled vinegar engineering." Thesis, Cape Peninsula University of Technology, 2019. http://hdl.handle.net/20.500.11838/3048.

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Thesis (PhD (Chemical Engineering))--Cape Peninsula University of Technology, 2019
The South African wine industry is constantly facing several challenges which affect the quality of wine, the local/global demand and consequently the revenue generated. These challenges include the ongoing drought, bush fires, climate change and several liquor amendment bills aimed at reducing alcohol consumption and alcohol outlets in South Africa. It is therefore critical for the wine industry to expand and find alternative ways in which sub-standard or surplus wine grapes can be used to prevent income losses and increase employment opportunities. Traditional Balsamic Vinegar (TBV) is a geographically and legislative protected product produced only in a small region in Italy. However, the methodology can be used to produce similar vinegars in other regions. Balsamic-styled vinegar (BSV), as defined in this thesis, is a vinegar produced by partially following the methods of TBV while applying process augmentation techniques. Balsamic-styled vinegar is proposed to be a suitable product of sub-standard quality or surplus wine grapes in South Africa. However, the production of BSV necessitates the use of cooked (high sugar) grape must which is a less favourable environment to the microorganisms used during fermentation. Factors that negatively affect the survival of the microorganisms include low water activity due to the cooking, high osmotic pressure and high acidity. To counteract these effects, methods to improve the survival of the non-Saccharomyces yeasts and acetic acid bacteria used are essential. The primary aim of this study was to investigate several BSV process augmentation techniques such as, aeration, agitation, cell immobilization, immobilized cell reusability and oxygen mass transfer kinetics in order to improve the performance of the microbial consortium used during BSV production. The work for this study was divided into four (4) phases. For all the phases a microbial consortium consisting of non-Saccharomyces yeasts (n=5) and acetic acid bacteria (n=5) was used. Inoculation of the yeast and bacteria occurred simultaneously. The 1st phase of the study entailed evaluating the effect of cells immobilized by gel entrapment in Ca-alginate beads alongside with free-floating cells (FFC) during the production of BSV. Two Ca-alginate bead sizes were tested i.e. small (4.5 mm) and large (8.5 mm) beads to evaluate the effects of surface area or bead size on the overall acetification rates. Ca-alginate beads and FFC fermentations were also evaluated under static and agitated (135 rpm) conditions. The 2nd phase of the study involved studying the cell adsorption technique for cell immobilization which was carried-out using corncobs (CC) and oak wood chips (OWC), while comparing to FFC fermentations. At this phase of the study, other vinegar bioreactor parameters such as agitation and aeration were studied in contrast to static fermentations. One agitation setting (135 rpm) and two aeration settings were tested i.e. high (0.3 vvm min−1) and low (0.15 vvm min−1) aeration conditions. Furthermore, to assess the variations in cell adsorption capabilities among individual yeast and AAB cells, the quantification of cells adsorbed on CC and OWC prior- and post-fermentation was conducted using the dry cell weight method. The 3rd phase of the study entailed evaluating the reusability abilities of all the matrices (small Ca-alginate beads, CC and OWC) for successive fermentations. The immobilized cells were evaluated for reusability on two cycles of fermentation under static conditions. Furthermore, the matrices used for cell immobilization were further analysed for structure integrity by scanning electron microscopy (SEM) before and after the 1st cycle of fermentations. The 3rd phase of the study also involved the sensorial (aroma and taste) evaluations of the BSV’s obtained from the 1st cycle of fermentation in order to understand the sensorial effects of the Ca-alginate beads, CC and OWC on the final BSV. The 4th phase of the study investigated oxygen mass transfer kinetics during non-aerated and aerated BSV fermentation. The dynamic method was used to generate several dissolved oxygen profiles at different stages of the fermentation. Consequently, the data obtained from the dynamic method was used to compute several oxygen mass transfer parameters, these include oxygen uptake rate ( 𝑟𝑟𝑂𝑂2 ), the stoichiometric coefficient of oxygen consumption vs acid yield (𝑌𝑌𝑂𝑂/𝐴𝐴), the oxygen transfer rate (𝑁𝑁𝑂𝑂2 ), and the volumetric mass transfer coefficients (𝐾𝐾𝐿𝐿𝑎𝑎). During all the phases of the study samples were extracted on weekly intervals to evaluate pH, sugar, salinity, alcohol and total acidity using several analytical instruments. The 4th phase of the study involved additional analytical tools, i.e. an oxygen µsensor to evaluate dissolved oxygen and the ‘Speedy breedy’ to measure the respiratory activity of the microbial consortium used during fermentation. The data obtained from the 1st phase of the study demonstrated that smaller Ca-alginate beads resulted in higher (4.0 g L-1 day−1) acetification rates compared to larger (3.0 g L-1 day−1) beads, while freely suspended cells resulted in the lowest (0.6 g L-1 day−1) acetification rates. The results showed that the surface area of the beads had a substantial impact on the acetification rates when gel entrapped cells were used for BSV fermentation. The 2nd phase results showed high acetification rates (2.7 g L-1 day−1) for cells immobilized on CC in contrast to cells immobilized on OWC and FFC, which resulted in similar and lower acetification rates. Agitated fermentations were unsuccessful for all the treatments (CC, OWC and FFC) studied. Agitation was therefore assumed to have promoted cell shear stress causing insufficient acetification during fermentations. Low aerated fermentations resulted in better acetification rates between 1.45–1.56 g L-1 day−1 for CC, OWC and FFC. At a higher aeration setting, only free-floating cells were able to complete fermentations with an acetification rate of 1.2 g L-1 day−1. Furthermore, the adsorption competence data showed successful adsorption on CC and OWC for both yeasts and AAB with variations in adsorption efficiencies, whereby OWC displayed a lower cell adsorption capability compared to CC. On the other hand, OWC were less efficient adsorbents due to their smooth surface, while the rough surface and porosity of CC led to improved adsorption and, therefore, enhanced acetification rates. The 3rd phase results showed a substantial decline in acetification rates on the 2nd cycle of fermentations when cells immobilized on CC and OWC were reused. While cells entrapped in Ca-alginate beads were able to complete the 2nd cycle of fermentations at reduced acetification rates compared to the 1st cycle of fermentations. The sensory results showed positive ratings for BSV’s produced using cells immobilized in Ca-alginate beads and CC. However, BSV’s produced using OWC treatments were neither ‘liked nor disliked’ by the judges. The SEM imaging results further showed a substantial loss of structural integrity for Ca-alginate beads after the 1st cycle fermentations, with minor changes in structural integrity of CC being observed after the 1st cycle fermentations. OWC displayed the same morphological structure before and after the 1st cycle fermentations which was attributed to their robustness. Although Ca-alginate beads showed a loss in structural integrity, it was still assumed that Ca-alginate beads provided better protection against the harsh environmental conditions in contrast to CC and OWC adsorbents due to the acetification rates obtained on both cycles. The 4th phase data obtained from the computations showed that non-aerated fermentations had a higher 𝑌𝑌𝑂𝑂/𝐴𝐴, 𝑟𝑟𝑂𝑂2 , 𝑁𝑁𝑂𝑂2 and a higher 𝐾𝐾𝐿𝐿𝑎𝑎 . It was clear that aerated fermentations had a lower aeration capacity due to an inappropriate aeration system design and an inappropriate fermentor. Consequently, aeration led to several detrimental biochemical changes in the fermentation medium thus affecting 𝐾𝐾𝐿𝐿𝑎𝑎 and several oxygen mass transfer parameters which serve as a driving force. Overall, it was concluded that the best method for BSV production is the use of cells entrapped in small alginate beads or cells adsorbed on CC under static and non-aerated fermentations. This conclusion was based on several factors such as cell affinity/cell protection, acetification rates, fermentation period and sensorial contributions. However, cells entrapped in Ca-alginate beads had the highest acetification rates. The oxygen mass transfer computations demonstrated a high 𝐾𝐾𝐿𝐿𝑎𝑎 when Ca-alginate beads were used under static-non-aerated conditions compared to fermentations treated with CC. Therefore, a fermentor with a high aeration capacity needs to be designed to best suit the two BSV production systems (Ca-alginate beads and CC). It is also crucial to develop methods which can increase the robustness of Ca-alginate beads in order to improve cell retention and reduce the loss of structural integrity for subsequent cycles of fermentation. Studies to define parameters used for upscaling the BSV production process for large scale productions are also crucial.

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Guise, Andrew David. "A biochemical engineering study of lysozyme refolding." Thesis, University of Bath, 1996. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337816.

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Campbell, Sean Thomas. "Protein Engineering for Biochemical Interrogation and System Design." Diss., The University of Arizona, 2015. http://hdl.handle.net/10150/560940.

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Proteins are intimately involved in almost every cellular phenomenon, from life to death. Understanding the interactions of proteins with each other and other macromolecules and the ability to rationally redesign them to improve their activities or control their function are of considerable current interest. Split-protein methodologies provide an avenue for achieving many of these goals. Since the original discovery of conditionally activated split-ubiquitin, the field has grown exponentially to include the activities of over a dozen different proteins. The flexibility of the systems has resulted in their use across a wide spectrum, both literally and figuratively, to primarily screen, visualize and quantitate macromolecular interactions in a variety of biological systems. In another arena, there is significant interest the apoptosis-regulating proteins: the Bcl-2 family. These proteins are found in many cell types and control, through expression levels as well as other mechanisms, the apoptotic state of a protein as governed by intrinsic death signals generated from such sources as DNA damage and viral infection. The apoptotic function of these proteins are mainly governed by a single type of interaction: the helix:receptor binding of the BH3-Only helices to the anti-apoptotic receptor proteins. While this often promiscuous helix:receptor interaction has received much scrutiny, the nature of the anti-apoptotic binding pocket, especially with regard to the specific residues that govern the interaction, has been lacking. With the high sensitivity and rapid analysis platform afforded by the cell-free split-luciferase analysis methodology, we devised and carried out the first systematic and large scale alanine mutagenesis of all five major anti-apoptotic members of the Bcl-2 family, validated these results both with biophysical methods as well as correlation with previous studies. Our results help explain how different receptors can bind a wide range of helices and also uncovered details regarding binding that are not possible with structural or computational analysis alone. In a second area of research, we have utilized the interaction of BH3 helices and their receptors for designing small molecule controlled protein kinases and phosphatases. In this protein design area, BH3-Only helices were inserted using a knowledge based approach into particular loops within both a protein kinase and a protein phosphatase. The BH3-Only helix interaction with added receptors, such as Bcl-xL provided an allosteric switch for turning-off the activity of the helix-inserted enzymes. The activity of the enzymes could then be turned-on by the addition of a cell-permeable small molecule that is known to bind the receptor. This plug-and-play design was demonstrated to be successful for two very different enzyme classes and likely provides a general and tunable biological element for controlling the activity of one or more proteins and enzymes in a biochemical networks.

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Mandel, Johannes Julius. "Graph-Based Modelling and Reverse-Engineering of Biochemical Networks." Thesis, Ulster University, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.487658.

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The term biological system encompasses all living systems within which components interact with one another on different levels of organisation. It is the goal of systems biology to explain how biological function emerges from the structure and dynamics of biological systems. The position of systems biology is that the functioning of biological systems is explicable in terms of the dynamic interaction of the components of that system. Reproducing these dynamics using computational models is therefore a promising way to inferring the causal relationships underlying biological function.This standpoint places systems thinking firmly on the centre stage of biological reasoning. However modelling complex systemic interactions is notoriously difficult for humans. It therefore becomes important to develop computer tools which support the modelling of biological systems. Such tools must harness the power of mathematics, engineering and computer science to support the creation of integrated and executable working models of biologigal systems.

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Rocha, Andrea M. "Computational Discovery of Phenotype Related Biochemical Processes for Engineering." Scholar Commons, 2011. http://scholarcommons.usf.edu/etd/3315.

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Application of bioengineering technologies for enhanced biological hydrogen production is a promising approach that may play a vital role in sustainable energy. Due to the ability of several naturally occurring microorganisms to generate hydrogen through varying metabolic processes, biological hydrogen has become an attractive alternative energy and fuel source. One area of particular interest is the production of biological hydrogen in organically-rich engineered systems, such as those associated with waste treatment. Despite the potential for high energy yields, hydrogen yields generated by bacteria in waste systems are often limited due to a focus on microbial utilization of organic material towards cellular growth rather than production of biogas. To address this concern and to improve upon current technological applications, metabolic engineering approaches may be applied to known hydrogen producing organisms. However, to successfully modify metabolic pathways, full understanding of metabolic networks involved in expression of microbial traits in hydrogen producing organisms is necessary. Because microbial communities associated with hydrogen production are capable of exhibiting a number of phenotypes, attempts to apply metabolic engineering concepts have been restricted due to limited information regarding complex metabolic processes and regulatory networks involved in expression of microbial traits associated with biohydrogen production. To bridge this gap, this dissertation focuses on identification of phenotype-related biochemical processes within sets of phenotype-expressing organisms. Specifically, through co-development and application of evolutionary genome-scale phenotype-centric comparative network analysis tools, metabolic and cellular components related to three phenotypes (i.e., dark fermentative, hydrogen production and acid tolerance) were identified. The computational tools employed for the systematic elucidation of key phenotype-related genes and subsystems consisted of two complementary methods. The first method, the Network Instance-Based Biased Subgraph Search (NIBBS) algorithm, identified phenotype-related metabolic genes and subsystems through comparative analysis of multiple genome-scale metabolic networks. The second method was the multiple alignments of metabolic pathways for identification of conserved metabolic sub-systems in small sets of phenotype-expressing microorganisms. For both methodologies, key metabolic genes and sub-systems that are likely to be related to hydrogen production and acid-tolerance were identified and hypotheses regarding their role in phenotype expression were generated. In addition, analysis of hydrogen producing enzymes generated by NIBBS revealed the potential interplay, or cross-talk, between metabolic pathways. To identify phenotype-related subnetworks, three complementary approaches were applied to individual, and sets of phenotype-expressing microorganisms. In the first method, the Dense ENriched Subgraph Enumeration (DENSE) algorithm, partial "prior knowledge" about the proteins involved in phenotype-related processes are utilized to identify dense, enriched sets of known phenotype-related proteins in Clostridium acetobutylicum. The second approach utilized a bi-clustering algorithm to identify phenotype-related functional association modules associated with metabolic controls of phenotype-related pathways. Last, through comparison of hundreds of genome-scale networks of functionally associated proteins, the á, â-motifs approach, was applied to identify phenotype-related subsystems. Application of methodologies for identification of subnetworks resulted in detection of regulatory proteins, transporters, and signaling proteins predicted to be related to phenotype-expression. Through analysis of protein interactions, clues to the functional roles and associations of previously uncharacterized proteins were identified (DENSE) and hypotheses regarding potentially important acid-tolerant mechanisms were generated (á, â-motifs). Similar to the NIBBS algorithm, analysis of functional modules predicted by the bi-clustering algorithm suggest cross-talk is occurring between pathways associated with hydrogen production. The ability of these phenotype-centric comparative network analysis tools to identify both known and potentially new biochemical process is important for providing further understanding and insights into metabolic networks and system controls involved in the expression of microbial traits. In particular, identification of phenotype-related metabolic components through a systems approach provides the underlying foundation for the development of improved bioengineering technologies and experimental design for enhanced biological hydrogen production.

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Akintoye, Ayodele. "Continuous chromatographic biochemical reaction-separation." Thesis, Aston University, 1989. http://publications.aston.ac.uk/9739/.

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Combined bioreaction separation studies have been carried out for the first time on a moving port semi-continuous counter-current chromatographic reactor-separator (SCCR-S1) consisting of twelve 5.4cm id x 75cm long columns packed with calcium charged cross-linked polystyrene resin (KORELA V07C). The inversion of sucrose to glucose and fructose in the presence of the enzyme invertase and the biochemIcal synthesis of dextran and fructose from sucrose in the presence of the enzyme dextransucrase were investigated. A dilute stream of the appropriate enzyme in deionised water was used as the eluent stream. The effect of switch time, feed concentration, enzyme activity, eluent rate and enzyme to feed concentration ratio on the combined bioreaction-separation were investigated. For the invertase reaction, at 20.77% w/v sucrose feed concentrations complete conversions were achieved. The enzyme usage was 34% of the theoretical enzyme amount needed to convert an equivalent amount of sucrose over the same time period when using a conventional fermenter. The fructose rich (FRP) and glucose rich (GRP) product purities obtained were over 90%. By operating at 35% w/v sucrose feed concentration and employing the product splitting and recycling techniques, the total concentration and purity of the GRP increased from 32% w/v to 4.6% and from 92.3% to 95% respectively. The FRP concentration also increased from 1.82% w/v to 2.88% w/v. A mathematical model was developed for the combined reaction-separation and used to simulate the continuous inversion of sucrose and product separation using the SCCR-S1. In the biosynthesis of dextran studies, 52% conversion of a 2% w/v sucrose concentration feed was achieved. An average dextran molecular weight of 4 millIon was obtained in the dextran rich (DRP) product stream. The enzyme dextransucrase was purifed successfully using centrifugation and ultrafiltration techniques.

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McEuen, Scott Jacob. "Thermal analysis of biochemical systems." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/81702.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2013.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 109-112).
Scientists, both academic and industrial, develop two main types of drugs: 1) small molecule drugs, which are usually chemically synthesized and are taken orally and 2) large molecule, biotherapeutic, or protein-based drugs, which are often synthesized via ribosome transcription in bacteria cells and are injected. Historically, the majority of drug development, revenue, and products has come from small molecule drugs. However, recently biotherapeutic drugs have become more common due to their increased potency and specificity (the ability to chemically bond to the targeted protein of interest). Researchers now estimate that as much as 50% of current drug development activities (pre-market approval) are focused on these protein-based drugs. There are several well-documented steps necessary in the development of a new large molecule drug. One critical element during the end of the biotherapeutic drug discovery phase and the beginning of the manufacturing phase is known as preformulation or formulation development. During this stage scientists systematically test the effects of adding various excipients (non-protein additives added to enhance the protein stability, solubility, activity of the drug, etc.) to the potential large molecule drug. Differential scanning calorimetry (DSC) is a common technique used to perform these formulation studies. In a classic DSC experiment, a protein is heated from 20-80°C and the heat absorbed while the protein unfolds is measured. Many researchers prefer the use of a DSC instrument because of its label-free nature, meaning that no fluorescent or radio-labeled tag is necessary to perform the measurement. The heat absorbed during the unfolding event(s) is directly measured. However, current commercial DSC instruments suffer from high protein consumption (especially when compared to other labeled techniques), low sensitivity, and slow throughput. The aim of this thesis is to address two of the three areas mentioned above: high protein consumption and slow throughput. Since many formulation development studies are performed at therapeutic or high protein concentrations, one can reduce the experimental cell volume and thereby reduce the amount of protein material consumed. However, since there is less sample, less heat is produced. While in the literature there are several heat transfer models that describe how a DSC instrument literature there are several heat transfer models that describe how a DSC instrument functions, there are surprisingly few heat transfer models that detail how ambient temperature disturbances impact the thermal measurement. To better describe this behavior, a simplified state-space thermal model was created to predict the disturbance rejection of a custom DSC instrument. This model was verified experimentally using linear stochastic system identification techniques. To reduce sample throughput, the prototype calorimeter cell was made from disposable materials. Because the majority of protein systems are thermodynamically irreversible, at elevated temperatures the protein solution often aggregates and needs to be cleaned before a subsequent experiment can be run. This cleaning process constitutes a significant portion of the overall time to run an experiment. This thesis documents a fully functional DSC instrument that, while not completely disposable, has been designed, built, and tested with disposable microfluidic materials. Future work would then solve the technical hurdles of repeatably loading disposable microfluidic cells into the DSC instrument.
by Scott Jacob McEuen.
Ph.D.

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Goel, Gautam. "Biochemical Systems Toolbox." Thesis, Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/14509.

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The field of biochemical systems modeling and analysis is faced with an unprecedented flood of data from experimental methodologies of molecular biology. While these techniques continue to leapfrog ahead in the speed, volume and finesse with which they generate data, the methods of data analysis and interpretation, however, are still playing the catch-up game. The notions of systems analysis have found a new foothold, under the banner of Systems Biology, with the promise of uncovering the rationale for the designs of biological systems from their parts lists, as they are generated by experimentation and sorted and managed by bioinformatics tools. With an aim to complement hypothesis-driven and reductionistic biological research, and not replace it, a systems biologist relies on the tools of mathematical and computational modeling to be able to contribute meaningfully to any ongoing bio-molecular systems research. These systems analysis tools, however, should not only have their roots steeped well in the theoretical foundations of biochemistry, mathematics and numerical computation, but they should be married to a framework that facilitates the required systems way of thought for all its users computational scientists, experimentalists and molecular biologists alike. Hopefully, such framework-based tools would go beyond just providing fancy GUIs, numerical packages for integrating ODEs and/or optimization libraries. The intent of this thesis is to present a framework and toolbox for biochemical systems modeling, with an application in metabolic pathway analysis and/or metabolic engineering. The research presented here builds upon the tenets of a very well established and generic approach to biological systems modeling and analysis, called Biochemical Systems Theory (BST), which is almost forty years old. The nuances of modeling and practical hurdles to analysis are presented in the context of a real-time case study of analyzing the glucolytic pathway in the bacterium Lactococcus lactis. Alongside, the thesis presents the features of a MATLAB-based software application that has been built upon the framework of BST and is aptly named as Biochemical Systems Toolbox (BSTBox). The thesis presents novel contributions, made by the author during the course of his research, to state-of-the-art techniques in parameter estimation, and robustness and sensitivity analysis topics that, as this thesis will show, remain to be the most restrictive bottlenecks in the world of biological systems modeling and analysis.

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Books on the topic "Biochemical engineering"

1

Katoh, Shigeo, Jun-ichi Horiuchi, and Fumitake Yoshida, eds. Biochemical Engineering. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2015. http://dx.doi.org/10.1002/9783527684984.

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1957-, Clark Douglas S., ed. Biochemical engineering. New York: M. Dekker, 1996.

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Dumont, Fabian E. Biochemical engineering. Hauppauge, NY: Nova Science Publishers, 2009.

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F, Ollis David, ed. Biochemical engineering fundamentals. 2nd ed. New York: McGraw-Hill, 1986.

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1935-, Lim Henry C., Venkatasubramanian K, Engineering Foundation (U.S.), and International Conference on Biochemical Engineering (4th : 1984 : Galway, Ireland), eds. Biochemical engineering IV. New York, N.Y: New York Academy of Sciences, 1986.

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Matthias, Reuss, and International Symposium on Biochemical Engineering--Stuttgart (2nd : 1990), eds. Biochemical engineering, Stuttgart. Stuttgart: Fischer, 1991.

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1928-, Bungay Henry R., and Belfort Georges, eds. Advanced biochemical engineering. New York: Wiley, 1987.

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1947-, Shuler Michael L., Weigand William A, Engineering Foundation (U.S.), and Biochemical Engineering Conference (5th : 1987 : New England College), eds. Biochemical engineering V. New York, N.Y: New York Academy of Sciences, 1987.

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1947-, Shuler Michael L., Weigand William A, New York Academy of Sciences., Engineering Foundation, and Biochemical Engineering Conference, (5th : 1987 : New England College), eds. Biochemical engineering 5. New York: New York Academy of Sciences, 1987.

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Henrik, Pedersen, Mutharasan Rajakannu, DiBiasio David, and Biochemical Engineering Conference (7th : 1991 : Santa Barbara, Calif.), eds. Biochemical engineering VII. New York, N.Y: New York Academy of Sciences, 1992.

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Book chapters on the topic "Biochemical engineering"

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Dutta, Rajiv. "Genetic Engineering." In Fundamentals of Biochemical Engineering, 176–96. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-77901-8_7.

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Nielsen, Jens, John Villadsen, and Gunnar Lidén. "Biochemical Reaction Networks." In Bioreaction Engineering Principles, 119–88. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4615-0767-3_5.

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Villadsen, John, Jens Nielsen, and Gunnar Lidén. "Biochemical Reaction Networks." In Bioreaction Engineering Principles, 151–214. Boston, MA: Springer US, 2011. http://dx.doi.org/10.1007/978-1-4419-9688-6_5.

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Boghossian, Nicolas, Oliver Kohlbacher, and Hans-Peter Lenhof. "BALL: Biochemical Algorithms Library." In Algorithm Engineering, 330–44. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/3-540-48318-7_26.

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Humphrey, Arthur E. "Biochemical Engineering — Past, Present, and Future." In Biochemical Engineering for 2001, 3–7. Tokyo: Springer Japan, 1992. http://dx.doi.org/10.1007/978-4-431-68180-9_1.

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Rogers, Peter L. "Strategic Planning and New Directions in Biochemical Engineering." In Biochemical Engineering for 2001, 8–13. Tokyo: Springer Japan, 1992. http://dx.doi.org/10.1007/978-4-431-68180-9_2.

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Xiao, Shou-Jun, Gregory Kenausis, and Marcus Textor. "Biochemical Modification of Titanium Surfaces." In Engineering Materials, 417–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56486-4_13.

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Kazuyuki, Shimizu. "An Overview and Future Perspective for Bioprocess Systems Engineering." In Biochemical Engineering for 2001, 765–67. Tokyo: Springer Japan, 1992. http://dx.doi.org/10.1007/978-4-431-68180-9_204.

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Ryu, Dewey D. Y., and J. Y. Kim. "Engineering and Genetic Approaches to Optimization of Recombinant Fermentation Process." In Biochemical Engineering for 2001, 133–37. Tokyo: Springer Japan, 1992. http://dx.doi.org/10.1007/978-4-431-68180-9_34.

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Nielsen, Jens, John Villadsen, and Gunnar Lidén. "Biochemical Reactions — A First Look." In Bioreaction Engineering Principles, 47–93. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4615-0767-3_3.

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Conference papers on the topic "Biochemical engineering"

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Ghosh, Soma, Saraswathi Vishveshwara, and Nagasuma Chandra. "Inferring biochemical routes from biochemical networks." In 2013 Biomedical Sciences and Engineering Conference (BSEC). IEEE, 2013. http://dx.doi.org/10.1109/bsec.2013.6618500.

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Williams, A. P. "A practice initiated learning strategy for biochemical engineering." In Third Conference on Engineering Education - Access, Retention and Standards. IEE, 2003. http://dx.doi.org/10.1049/ic:20030225.

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"Biochemical Signals and Material Characteristics." In 2018 7th International Conference on Medical Engineering and Biotechnology. Clausius Scientific Press, 2018. http://dx.doi.org/10.23977/medeb.2018.07014.

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Byun, Eunjeong, Juhong Nam, Hyunji Shim, Esther Kim, Albert Kim, and Seunghyun Song. "Ultrasonic Hydrogel Biochemical Sensor System." In 2020 42nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) in conjunction with the 43rd Annual Conference of the Canadian Medical and Biological Engineering Society. IEEE, 2020. http://dx.doi.org/10.1109/embc44109.2020.9176216.

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Hori, Yutaka, and Richard M. Murray. "Engineering principles of synthetic biochemical oscillators with negative cyclic feedback." In 2015 54th IEEE Conference on Decision and Control (CDC). IEEE, 2015. http://dx.doi.org/10.1109/cdc.2015.7402292.

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Lin, Ying, Vladimir Ilchenko, Jay Nadeau, and Lute Maleki. "Biochemical detection with optical whispering-gallery resonaters." In Lasers and Applications in Science and Engineering, edited by Alexis V. Kudryashov, Alan H. Paxton, and Vladimir S. Ilchenko. SPIE, 2007. http://dx.doi.org/10.1117/12.716591.

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Park, Sung-Yong, Sheraz Kalim, Caitlin Callahan, Michael A. Teitell, and Eric P. Y. Chiou. "Light-driven microfluidic platforms for droplet-based biochemical analysis." In SPIE NanoScience + Engineering, edited by Kishan Dholakia and Gabriel C. Spalding. SPIE, 2009. http://dx.doi.org/10.1117/12.828134.

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Voloshynska, Katerina, Tetjana Ilashchuka, Olexander Prydij, and Maria Gruia. "Dynamics of blood plasma by spectropolarimetry and biochemical techniques." In SPIE NanoScience + Engineering, edited by Hooman Mohseni, Massoud H. Agahi, and Manijeh Razeghi. SPIE, 2014. http://dx.doi.org/10.1117/12.2061731.

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Chiang, Hui-Ju Katherine, Jie-Hong R. Jiang, and Francois Fages. "Reconfigurable neuromorphic computation in biochemical systems." In 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, 2015. http://dx.doi.org/10.1109/embc.2015.7318517.

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Fan, W. J., M. X. Lin, M. Y. Zhao, Q. H. Xie, and B. Wang. "High-speed automatic biochemical immune assembly line." In 2022 5th World Conference on Mechanical Engineering and Intelligent Manufacturing (WCMEIM). IEEE, 2022. http://dx.doi.org/10.1109/wcmeim56910.2022.10021551.

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Reports on the topic "Biochemical engineering"

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Zhong, Xiaojing. Aggregation Effects in Generalized Linear Models: A Biochemical Engineering Application. Ames (Iowa): Iowa State University, January 2019. http://dx.doi.org/10.31274/cc-20240624-126.

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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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Stern, David, and Gadi Schuster. Manipulating Chloroplast Gene Expression: A Genetic and Mechanistic Analysis of Processes that Control RNA Stability. United States Department of Agriculture, June 2004. http://dx.doi.org/10.32747/2004.7586541.bard.

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New potential for engineering chloroplasts to express novel traits has stimulated research into relevant techniques and genetic processes, including plastid transformation and gene regulation. This BARD-funded research dealt with the mechanisms that influence chloroplast RNA accumulation, and thus gene expression. Previous work on cpRNA catabolism has elucidated a pathway initiated by endonucleolytic cleavage, followed by polyadenylation and exonucleolytic degradation. A major player in this process is the nucleus-encoded exoribo-nuclease/polymerase polynucleotide phosphorylase (PNPase). Biochemical characterization of PNPase has revealed a modular structure that controls its RNA synthesis and degradation activities, which in turn are responsive to the phosphate (P) concentration. During the funding period, new insights emerged into the molecular mechanism of RNA metabolism in the chloroplast and cyanobacteria, suggesting strategies for improving agriculturally-important plants or plants with novel introduced traits.

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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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Barkan, Alice, and Zach Adam. The Role of Proteases in Regulating Gene Expression and Assembly Processes in the Chloroplast. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7695852.bard.

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Chloroplasts house many biochemical processes that are essential for plant viability. Foremost, among these is photosynthesis, which requires the protein-rich thylakoid membrane system. The activation of chloroplast genes encoding thylakoid membrane proteins and the targeting and assembly of these proteins together with their nuclear-encoded partners are essential for the elaboration of the thylakoid membrane. Several nuclear-encoded proteins that regulate chloroplast gene expression and that mediate the targeting of proteins to the thylakoid membrane have been identified in recent years, and many more remain to be discovered. The abundance of such proteins is critical and is likely to be determined to a significant extent by their stability, which in turn, is influenced by chloroplast protease activities. The primary goal of this project was to link specific proteases to specific substrates, and in particular, to specific regulatory and assembly proteins. We proposed a two-pronged approach, involving genetic analysis of the consequences of the mutational loss of chloroplast proteases, and biochemical analysis of the degradation pathways of specific proteins that have been shown to control chloroplast gene expression. Our initial bioinformatic analysis of chloroplast proteases allowed us to identify the set of pro teases that is targeted to the chloroplast. We used that information to recover three Arabidopsis mutants with T - DNA insertions in specific chloroplast protease genes. We carried out the first analysis of the stability of a regulator of chloroplast gene expression (CRS2), and found that the protein is much less stable than are typical components of the photosynthetic apparatus. Genetic reagents and analytical methods were developed that have set the stage for a rapid advancement of our understanding of chloroplast proteolysis. The results obtained may be useful for manipulating the expression of transgenes in the chloroplast and for engineering plants whose photosynthetic activity is optimized under harsh environmental conditions.

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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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Lewinsohn, Efraim, Eran Pichersky, and Shimon Gepstein. Biotechnology of Tomato Volatiles for Flavor Improvement. United States Department of Agriculture, April 2001. http://dx.doi.org/10.32747/2001.7575277.bard.

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The main objectives of the research project were: 1. The manipulation, by genetic engineering techniques, of the terpenoid pathway in tomato fruit. Specifically, to test the hypothesis whether overexpression of linalool synthase in tomato fruits will result in the diversion of intermediates of the carotene biosynthetic pathway to linalool, demonstrating that linalool synthase is a key regulatory enzyme, and possibly improving tomato flavor. 2. The elucidation of the biochemical pathway leading to eugenol and methyl eugenol, and the manipulation of this pathway to determine key enzymes and to improve flavor in tomato. Background, conclusions and implications The different proportions of volatile components present in foods often determine their flavor properties. Two of the ten most important flavor compounds in tomatoes, linalool and eugenol, are emitted by the flowers of Clarkia breweri, (Onagraceae), a plant native to California, and are also present in sweet basil (Ocimum basilicum, Lamiaceae). We have studied the key enzymes and genes involved in the production of these flavorants. Linalool synthase, the key enzyme in linalool biosynthesis and its corresponding gene were isolated and characterized from Clarkia breweri. The gene was coupled to a fruit-specific tomato promotor (E8) and was used to transform tomatoes. The transgenic tomatoes produced S-linalool and 1-hydroxylinalool, compounds absent from the fruits of controls. The transgenesis did not adversely affect the overall appearance of the plants nor the levels of other terpenoids present such as carotenoids and vitamin E. Our work has proven that the terpenoid pathway in tomatoes can be modified by the introduction and expression of foreign genes coding for the enzymes controlling the production of monoterpenoid flavor compounds. We have also isolated novel enzymes and genes that are involved in the formation of eugenol and methyl eugenol from Clarkia breweri and basil. An EST library of basil glandular trichomes (the site of eugenol and methyl eugenol biosynthesis) was prepared. More than 1,200 genes have been preliminary characterized and a few of them have been confirmed by functional expression, to be involved in eugenol and methyl eugenol biosynthesis. These genes have augmented the still small repertoire of genes that are available to modify the aroma of agricultural produce by genetic engineering.

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Zhao, Bingyu, Saul Burdman, Ronald Walcott, Tal Pupko, and Gregory Welbaum. Identifying pathogenic determinants of Acidovorax citrulli toward the control of bacterial fruit blotch of cucurbits. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598168.bard.

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The specific objectives of this BARD proposal were: Use a comparative genomics approach to identify T3Es in group I, II and III strains of A. citrulli. Determine the bacterial genes contributing to host preference. Develop mutant strains that can be used for biological control of BFB. Background to the topic: Bacterial fruit blotch (BFB) of cucurbits, caused by Acidovoraxcitrulli, is a devastating disease that affects watermelon (Citrulluslanatus) and melon (Cucumismelo) production worldwide, including both Israel and USA. Three major groups of A. citrullistrains have been classified based on their virulence on host plants, genetics and biochemical properties. The host selection could be one of the major factors that shape A. citrullivirulence. The differences in the repertoire of type III‐ secreted effectors (T3Es) among the three A. citrulligroups could play a major role in determining host preferential association. Currently, there are only 11 A. citrulliT3Es predicted by the annotation of the genome of the group II strain, AAC00‐1. We expect that new A. citrulliT3Es can be identified by a combination of bioinformatics and experimental approaches, which may help us to further define the relationship of T3Es and host preference of A. citrulli. Implications, both scientific and agricultural: Enriching the information on virulence and avirulence functions of T3Es will contribute to the understanding of basic aspects of A. citrulli‐cucurbit interactions. In the long term, it will contribute to the development of durable BFB resistance in commercial varieties. In the short term, identifying bacterial genes that contribute to virulence and host preference will allow the engineering of A. citrullimutants that can trigger SAR in a given host. If applied as seed treatments, these should significantly improve the effectiveness and efficacy of BFB management in melon and atermelon production.

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Schuster, Gadi, and David Stern. Integration of phosphorus and chloroplast mRNA metabolism through regulated ribonucleases. United States Department of Agriculture, August 2008. http://dx.doi.org/10.32747/2008.7695859.bard.

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New potential for engineering chloroplasts to express novel traits has stimulated research into relevant techniques and genetic processes, including plastid transformation and gene regulation. This proposal continued our long time BARD-funded collaboration research into mechanisms that influence chloroplast RNA accumulation, and thus gene expression. Previous work on cpRNA catabolism has elucidated a pathway initiated by endonucleolytic cleavage, followed by polyadenylation and exonucleolytic degradation. A major player in this process is the nucleus-encoded exoribonuclease/polymerasepolynucleotidephoshorylase (PNPase). Biochemical characterization of PNPase has revealed a modular structure that controls its RNA synthesis and degradation activities, which in turn are responsive to the phosphate (P) concentration. However, the in vivo roles and regulation of these opposing activities are poorly understood. The objectives of this project were to define how PNPase is controlled by P and nucleotides, using in vitro assays; To make use of both null and site-directed mutations in the PNPgene to study why PNPase appears to be required for photosynthesis; and to analyze plants defective in P sensing for effects on chloroplast gene expression, to address one aspect of how adaptation is integrated throughout the organism. Our new data show that P deprivation reduces cpRNA decay rates in vivo in a PNPasedependent manner, suggesting that PNPase is part of an organismal P limitation response chain that includes the chloroplast. As an essential component of macromolecules, P availability often limits plant growth, and particularly impacts photosynthesis. Although plants have evolved sophisticated scavenging mechanisms these have yet to be exploited, hence P is the most important fertilizer input for crop plants. cpRNA metabolism was found to be regulated by P concentrations through a global sensing pathway in which PNPase is a central player. In addition several additional discoveries were revealed during the course of this research program. The human mitochondria PNPase was explored and a possible role in maintaining mitochondria homeostasis was outlined. As polyadenylation was found to be a common mechanism that is present in almost all organisms, the few examples of organisms that metabolize RNA with no polyadenylation were analyzed and described. Our experiment shaded new insights into how nutrient stress signals affect yield by influencing photosynthesis and other chloroplast processes, suggesting strategies for improving agriculturally-important plants or plants with novel introduced traits. Our studies illuminated the poorly understood linkage of chloroplast gene expression to environmental influences other than light quality and quantity. Finely, our finding significantly advanced the knowledge about polyadenylation of RNA, the evolution of this process and its function in different organisms including bacteria, archaea, chloroplasts, mitochondria and the eukaryotic cell. These new insights into chloroplast gene regulation will ultimately support plant improvement for agriculture

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Sessa, Guido, and Gregory Martin. MAP kinase cascades activated by SlMAPKKKε and their involvement in tomato resistance to bacterial pathogens. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7699834.bard.

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The research problem: Pseudomonas syringae pv. tomato (Pst) and Xanthomonas campestrispv. vesicatoria (Xcv) are the causal agents of tomato bacterial speck and spot diseases, respectively. These pathogens colonize the aerial parts of the plant and cause economically important losses to tomato yield worldwide. Control of speck and spot diseases by cultural practices or chemicals is not effective and genetic sources of resistance are very limited. In previous research supported by BARD, by gene expression profiling we identified signaling components involved in resistance to Xcvstrains. Follow up experiments revealed that a tomato gene encoding a MAP kinase kinase kinase (MAPKKKe) is required for resistance to Xcvand Pststrains. Goals: Central goal of this research was to investigate the molecular mechanisms by which MAPKKKεand associated MAP kinase cascades regulate host resistance. Specific objectives were to: 1. Determine whether MAPKKKεplays a broad role in defense signaling in plants; 2. Identify components of MAP kinase cascades acting downstream of MAPKKKε; 3. Determine the role of phosphorylation-related events in the function of MAPKKKε; 4. Isolate proteins directly activated by MAPKKKε-associatedMAPK modules. Our main achievements during this research program are in the following major areas: 1. Characterization of MAPKKKεas a positive regulator of cell death and dissection of downstream MAP kinase cascades (Melech-Bonfil et al., 2010; Melech-Bonfil and Sessa, 2011). The MAPKKKεgene was found to be required for tomato resistance to Xcvand Pstbacterial strains and for hypersensitive response cell death triggered by different R gene/effector gene pairs. In addition, overexpression analysis demonstrated that MAPKKKεis a positive regulator of cell death, whose activity depends on an intact kinase catalytic domain. Epistatic experiments delineated a signaling cascade downstream of MAPKKKεand identified SIPKK as a negative regulator of MAPKKKε-mediated cell death. Finally, genes encoding MAP kinase components downstream of MAPKKKεwere shown to contribute to tomato resistance to Xcv. 2. Identification of tomato proteins that interact with MAPKKKεand play a role in plant immunity (Oh et al., 2011). We identified proteins that interact with MAPKKKε. Among them, the 14-3-3 protein TFT7 was required for cell death mediated by several R proteins. In addition, TFT7 interacted with the MAPKK SlMKK2 and formed homodimersin vivo. Thus, TFT7 is proposed to recruit SlMKK2 and MAPKKK client proteins for efficient signal transfer. 3. Development of a chemical genetic approach to identify substrates of MAPKKKε-activated MAP kinase cascades (Salomon et al., 2009, 2011). This approach is based on engineering the kinase of interest to accept unnatural ATP analogs. For its implementation to identify substrates of MAPKKKε-activated MAP kinase modules, we sensitized the tomato MAP kinase SlMPK3 to ATP analogs and verified its ability to use them as phosphodonors. By using the sensitized SlMPK3 and radiolabeled N6(benzyl)ATP it should be possible to tag direct substrates of this kinase. 4. Development of methods to study immunity triggered by pathogen-associated molecular patterns (PAMPs) in tomato and N. benthamiana plants (Kim et al., 2009; Nguyen et al. 2010). We developed protocols for measuring various PTI-associatedphenotypes, including bacterial populations after pretreatment of leaves with PAMPs, induction of reporter genes, callose deposition at the cell wall, activation of MAP kinases, and a luciferase-based reporter system for use in protoplasts. Scientific and agricultural significance: Our research activities discovered and characterized a signal transduction pathway mediating plant immunity to bacterial pathogens. Increased understanding of molecular mechanisms of immunity will allow them to be manipulated by both molecular breeding and genetic engineering to produce plants with enhanced natural defense against disease. In addition, we successfully developed new biochemical and molecular methods that can be implemented in the study of plant immunity and other aspects of plant biology.

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