Relevant bibliographies by topics / Systems physiology

Academic literature on the topic 'Systems physiology'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Systems physiology"

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Kuepfer, Lars. "Towards whole‐body systems physiology." Molecular Systems Biology 6, no. 1 (January 2010): 409. http://dx.doi.org/10.1038/msb.2010.70.

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ZARET, B. "Topics in integrated systems physiology." Journal of Nuclear Cardiology 7, no. 5 (September 2000): 405. http://dx.doi.org/10.1067/mnc.2000.109798.

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Petersen, O. H., and C. Bear. "Physiology: Two glucagon transducing systems." Nature 323, no. 6083 (September 1986): 18. http://dx.doi.org/10.1038/323018a0.

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Land, Michael F. "Comparative Physiology of Sensory Systems." Trends in Neurosciences 8 (January 1985): 372—IN8. http://dx.doi.org/10.1016/0166-2236(85)90133-x.

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Šrobár, Fedor. "Fröhlich Systems in Cellular Physiology." Prague Medical Report 113, no. 2 (2012): 95–104. http://dx.doi.org/10.14712/23362936.2015.25.

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Electromagnetic fields are usually absent in the picture of processes taking place in living cells which is dominated by biochemistry, molecular genetics and microscopic morphology. Yet experimental and theoretical studies suggest that this omission is not justified. At the end of 1960’s H. Fröhlich elaborated a semi-phenomenological model of polar oscillating units that are metabolically driven, exchange energy with the cell’s internal heat reservoir, and store part of the energy in excited vibrational modes in such way, that mode with the lowest frequency becomes highly excited, while the higher-order modes remain near thermal equilibrium. This affords energy-hungry chemical reactions to take place while the rest of the cell is not exposed to heat stress. At present, part of the cytoskeleton – microtubules – are deemed to fulfil the role of oscillating units. The paper provides an introduction to the Fröhlich ideas for readers with background in medicine and biology in that it avoids mathematical formulas and relies on figures to convey information about the basic properties of the model. The essential features of the Fröhlich model – most notably the energy condensation – are demonstrated on ensemble encompassing three coupled vibration modes that can be exactly described using original diagrammatic method.
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Sherman, Arthur. "Dynamical systems theory in physiology." Journal of General Physiology 138, no. 1 (June 27, 2011): 13–19. http://dx.doi.org/10.1085/jgp.201110668.

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Randall Thomas, S. "Kidney modeling and systems physiology." Wiley Interdisciplinary Reviews: Systems Biology and Medicine 1, no. 2 (September 2009): 172–90. http://dx.doi.org/10.1002/wsbm.14.

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Paul, Martin, Ali Poyan Mehr, and Reinhold Kreutz. "Physiology of Local Renin-Angiotensin Systems." Physiological Reviews 86, no. 3 (July 2006): 747–803. http://dx.doi.org/10.1152/physrev.00036.2005.

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Since the first identification of renin by Tigerstedt and Bergmann in 1898, the renin-angiotensin system (RAS) has been extensively studied. The current view of the system is characterized by an increased complexity, as evidenced by the discovery of new functional components and pathways of the RAS. In recent years, the pathophysiological implications of the system have been the main focus of attention, and inhibitors of the RAS such as angiotensin-converting enzyme (ACE) inhibitors and angiotensin (ANG) II receptor blockers have become important clinical tools in the treatment of cardiovascular and renal diseases such as hypertension, heart failure, and diabetic nephropathy. Nevertheless, the tissue RAS also plays an important role in mediating diverse physiological functions. These focus not only on the classical actions of ANG on the cardiovascular system, namely, the maintenance of cardiovascular homeostasis, but also on other functions. Recently, the research efforts studying these noncardiovascular effects of the RAS have intensified, and a large body of data are now available to support the existence of numerous organ-based RAS exerting diverse physiological effects. ANG II has direct effects at the cellular level and can influence, for example, cell growth and differentiation, but also may play a role as a mediator of apoptosis. These universal paracrine and autocrine actions may be important in many organ systems and can mediate important physiological stimuli. Transgenic overexpression and knock-out strategies of RAS genes in animals have also shown a central functional role of the RAS in prenatal development. Taken together, these findings may become increasingly important in the study of organ physiology but also for a fresh look at the implications of these findings for organ pathophysiology.
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Weyers, Marc H. "Vertebrate circadian systems. Structure and physiology." Behavioural Processes 11, no. 3 (August 1985): 333–34. http://dx.doi.org/10.1016/0376-6357(85)90032-4.

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Joyner, Michael J., and Bengt Saltin. "Exercise physiology and human performance: systems biology before systems biology!" Journal of Physiology 586, no. 1 (January 1, 2008): 9. http://dx.doi.org/10.1113/jphysiol.2007.148411.

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Dissertations / Theses on the topic "Systems physiology"

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Santin, Joseph M. "Context-dependence of physiological systems: environment-physiology interactions in the respiratory control system." Wright State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=wright149336916471128.

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Christensen, Heather R. "Molecular and Integrated Systems Physiology of Prolactin." University of Cincinnati / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1314040076.

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Butler, Jamie Andrew. "Data-based mechanistic modelling of systems in plant physiology." Thesis, Lancaster University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369469.

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Healey, Jennifer Anne. "Wearable and automotive systems for affect recognition from physiology." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/9067.

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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.
Includes bibliographical references (p. 152-158).
Novel systems and algorithms have been designed and built to recognize affective patterns in physiological signals. Experiments were conducted for evaluation of the new systems and algorithms in three types of settings: a highly constrained laboratory setting, a largely unconstrained ambulatory environment, and a less unconstrained automotive environment. The laboratory experiment was designed to test for the presence of unique physiological patterns in each of eight different emotions given a relatively motionless seated subject, intentionally feeling and expressing these states. This experiment generated a large dataset of physiological signals containing many day-to-day variations, and the proposed features contributed to a success rate of 81% for discriminating all eight emotions and rates of up to 100% for subsets of emotion based on similar emotion qualities. New wearable computer systems and sensors were developed and tested on subjects who walked, jogged, talked, and otherwise went about daily activities. Although in the unconstrained ambulatory setting, physical motion often overwhelmed affective signals, the systems developed in this thesis are currently useful as activity monitors, providing an image diary correlated with physiological signals. Automotive systems were used to detect physiological stress during the natural but physically driving task. This generated a large database of physiological signals covering over 36 hours of driving. Algorithms for detecting driver stress achieved a recognition rates of 96% using stress ratings based on task conditions for validation and 89% accuracy using questionnaires analysis for validation. Further results in which metrics of stress from video tape annotations of the drive were correlated with physiological features showed highly significant correlations (up to r = .77 for over 4000 samples). Together, these three experiments show a range of success in recognizing affect from physiology, showing high recognition rates in somewhat constrained conditions and highlighting the need for more automatic context sensing in unconmore automatic context sensing in unconstrained conditions. The recognition rates obtained thus far lend support to the hypothesis that many emotional differences can be automatically discriminated in patterns of physiological changes.
by Jennifer A. Healey.
Ph.D.
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Rees, J. A. "Studies on adhesive gland systems in monogeneans." Thesis, University of East Anglia, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372362.

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Long, Lu. "The Anglo-tensin and endothelin systems in hypoxia-induced pulmonary hypertension." Thesis, Imperial College London, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312091.

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Du, Beau Amy. "Neurotransmitter phenotypes of descending systems in the rat lumbar spinal cord." Thesis, University of Glasgow, 2013. http://theses.gla.ac.uk/4721/.

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Sensorimotor processes within the spinal cord are profoundly influenced by descending systems from the brain yet the neurotransmitter phenotypes of these systems remains enigmatic. Using tract tracing methods, this study identifies the neurochemical content of axons descending from the sensorimotor cortex and sites within the anatomically diverse reticular formation. There are several classes of neurons in spinal lumbar segments targeted by these descending systems which contribute to recruiting adaptively appropriate motor patterns. This study investigates the neuronal targets of descending systems and the neurochemical content of their inputs. Immunofluorescent tissue containing labelled neuronal processes were examined and reconstructed interneurons were defined according to their neuronal geometry and morphology across laminar boundaries.
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Knight, Anthony. "A systems pharmacology approach to the adenosine A1 receptor." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/75201/.

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The majority of drugs are prescribed on the premise that their desired and undesired effects are well characterised. However, the mechanisms underlying these effects can be elusive and are of interest to the pharmaceutical industry in terms of rational drug design. G protein-coupled receptors are a significant class of drug target that are capable of influencing multiple signalling processes, and downstream effects, simultaneously through a variety of effectors, such as G proteins or –β-arrestins. The effector activated by a given receptor is often a function of the ligand. This is termed functional selectivity and can contribute to adverse drug effects. Understanding functional selectivity in a mammalian setting is hindered by cross-talk between many competing signalling components. The Sc. cerevisiae pheromone response can be modified to isolate individual mammalian receptor- G protein interactions. Therefore, this simple organism represents an excellent tool to study functional selectivity. Further, the simplicity of this organism allows this pathway to be mathematically modelled. By applying mathematical models to mammalian GPCR signalling in yeast it is possible to extract experimentally inaccessible quantitative parameters underlying functional selectivity. This interdisciplinary approach to pharmacological mechanisms is an example of systems pharmacology. Here a systems pharmacology approach is applied to adenosine receptor signalling in yeast with a view to understanding the contribution of the ligand, receptor and G protein to functional selectivity. The first stage of this process was expression and characterisation of adenosine A1R, A2AR, A2BR and A3R subtypes in yeast. Here, the A1R and A2R subtypes were shown to be functional in yeast, but the A3R response was limited. The A1R signals through G proteins representing the inhibitory G αi family in yeast, while the A2AR and A2BR signal through both inhibitory and stimulatory G protein equivalents. Here ligand bias is quantified but further extended to describe adenosine receptor selectivity. Further, the yeast system was used to inform novel fluorescent compound development. Fluorescent ligand-binding rates would ultimately inform modelling studies. A minimal mathematical framework was developed to described A1R signalling in yeast. Ordinary differential equation models recreate dynamic cellular processes. Here an ODE model was applied to experimental time course data to predict rate constants throughout the yeast G protein cycle in the presence of the mammalian A1R. This model predicts that G protein subtype influences the ligand-receptor-G protein interactions of the A1R in yeast. Further modification of the system and fluorescent technologies may help validate these predictions.
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Ashrafian, Hutan. "Global bio-systems modulation and the translational metabolic physiology of bariatric surgery." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/25304.

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The global pandemic of obesity continues to escalate worldwide and results in severe multisystem metabolic dysfunction in the expanding population of its sufferers. It is associated with the concurrent pathologies of type 2 diabetes, cardiovascular disease, cancer and sleep apnea, which have also increased in prevalence over the past decade. Obesity can be mapped in social networks and is recognised as a fundamental element of the metabolic syndrome contributing to the global burden of diabesity and oncobesity. Its impact on global health has resulted in a massive burden on healthcare services and is among the most prominent contributors to mounting healthcare costs. Despite its pathological impact, the non-surgical management of obesity through behavioural, lifestyle and pharmacotherapies has not offered dependable benefits in severely obese patients. Bariatric surgery has demonstrated consistent weight loss in morbidly obese subjects and is increasingly performed worldwide to treat morbid obesity. Furthermore, these operations may produce beneficial metabolic effects especially with respect to improvement in type 2 diabetes and the metabolic syndrome. Understanding surgical weight loss mechanisms and metabolic modulation is required to enhance patient benefits and operative outcomes. A surgical model of Roux-en-Y gastric bypass (RYGB) was developed as an experimental platform to investigate the metabolic effects of bariatric surgery. The model was studied through a systems biology approach to characterize systemic and gastro-intestinal surgical metabolic modulation. Analysis of postoperative faecal samples from this rodent model revealed a powerful shift in gut microbial ecology and also highlighted the role of RYGB surgery in regulating the cross-talk between the gut microbiome and its mammalian host. Similar metabolic changes were also identified in human subjects undergoing bariatric surgery. Analysis of plasma and cardiac tissue revealed shifts in metabolic activity, reflected by enhanced cardiac energy metabolism. Overall, the results of this work identify some of the potential mechanisms behind bariatric surgical weight loss and systemic metabolic enhancement. This study not only supports the term metabolic surgery but also identifies the global multi-systemic benefits of bariatric surgical procedures. As such, the findings presented in this thesis may in future contribute to the enhancement of current bariatric procedures and the development of the next-generation of innovative metabolic therapies.
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Bierbower, Sonya M. "ENVIRONMENTAL EFFECTS ON BEHAVIOR AND PHYSIOLOGY IN CRAYFISH." UKnowledge, 2010. http://uknowledge.uky.edu/gradschool_diss/778.

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Despite dramatic morphological differences between animals from different taxa, several important features in organization and sensory system processing are similar across animals. Because of this similarity, a number of different organisms including mammals, insects, and decapod crustaceans serve as valuable model systems for understanding general principles of environmental effects. This research examines intrinsic and extrinsic factors by behaviorally and physiologically means to identify the impact of environmental conditions on two distinct crayfish species- Procambarus clarkii (surface) and Orconectes australis packardi (cave). The research identified behavioral and physiological responses in these two morphological and genetically distinct species. The studies also examined multiple levels of complexity including social behavior, an autonomic response, chemosensory capabilities and neuronal communication, identified comparative similarities/differences, addressed learning and environmental influences on learning and examined behavioral and cellular responses to high levels of carbon dioxide. I found environmental factors directly influence crayfish behavior of social interactions. Interactions were more aggressive, more intense and more likely to end with a physical confrontation when they took place 'in water' than 'out of water'. The modified social interaction resulted in a altered fighting strategy. A study on motor task learning was undertaken which showed similar learning trends among these crayfish species despite their reliance on different sensory modalities. I also demonstrated learning was dependent on perceived stress by the organism. Previously trained crayfish inhibited from completing a task showed significant increase in an autonomic stress response. Studies on the behavioral and physiological responses to CO2 revealed that high [CO2] is a repellent in a concentration dependent manner. The autonomic responses in heart rate and an escape tailflip reflex shows complete cessation with high [CO2]. A mechanistic effect of CO2 is by blocking glutamate receptors at the neuromuscular junction and through inhibition of the motor nerve within the CNS.
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Books on the topic "Systems physiology"

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S, Liebovitch Larry, and West Bruce J, eds. Fractal physiology. New York: Published for the American Physiological Society by Oxford University Press, 1994.

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Walker, Denise. Body systems. North Mankato, MN: Smart Apple Media, 2007.

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Sensory systems: Anatomy and physiology. Amsterdam: Academic Press, 2003.

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Nguyen, David H. Systems Biology of Tumor Physiology. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-25601-6.

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G, Levitzky Michael, ed. Medical physiology: A systems approach. New York: McGraw-Hill, 2011.

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Physiological systems in insects. Amsterdam: Elsevier, 2007.

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Sherwood, Lauralee. Human physiology: From cells to systems. 3rd ed. Belmont, CA: Wadsworth Pub. Co., 1997.

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Sherwood, Lauralee. Human physiology: From cells to systems. St. Paul: West Pub. Co., 1989.

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Human physiology: From cells to systems. 5th ed. Australia: Thomson/Brooks/Cole, 2004.

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Sherwood, Lauralee. Human physiology: From cells to systems. 7th ed. Australia: Brooks/Cole, Cengage Learning, 2010.

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Book chapters on the topic "Systems physiology"

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Schmidt, R. F., and M. Wiesendanger. "Motor Systems." In Human Physiology, 82–123. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-73831-9_5.

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Goswami, Nandu, Jerry Joseph Batzel, and Giovanna Valenti. "Human Systems Physiology." In Generation and Applications of Extra-Terrestrial Environments on Earth, 255–66. New York: River Publishers, 2022. http://dx.doi.org/10.1201/9781003338277-31.

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Chen, Shangbin, and Alexey Zaikin. "Systems and Modelling." In Quantitative Physiology, 11–21. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-33-4033-6_2.

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Bassingthwaighte, James B., Larry S. Liebovitch, and Bruce J. West. "Chaos? in Physiological Systems." In Fractal Physiology, 300–327. New York, NY: Springer New York, 1994. http://dx.doi.org/10.1007/978-1-4614-7572-9_13.

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Hallett, Mark. "Physiology of Volition." In Understanding Complex Systems, 127–43. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-03205-9_7.

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Norbury, Chris J. "Cell Cycle, Physiology." In Encyclopedia of Systems Biology, 353–54. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_7.

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Ivanov, Plamen Ch, and Ronny P. Bartsch. "Network Physiology: Mapping Interactions Between Networks of Physiologic Networks." In Understanding Complex Systems, 203–22. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-03518-5_10.

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Hollandsworth, James G. "Physiological Systems." In Physiology and Behavior Therapy, 17–40. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-7023-9_2.

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Nation, James L. "Sensory Systems." In Insect Physiology and Biochemistry, 283–300. 4th ed. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003279822-13.

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Trowers, Eugene, and Marc Tischler. "Clinical Gastrointestinal Physiology: A Systems Approach." In Gastrointestinal Physiology, 1–8. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-07164-0_1.

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Conference papers on the topic "Systems physiology"

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Pietarila, Kristie, Sudhagar Subramaniam, and Satish Nair. "Gender-Based Differences in Thermal Physiology." In International Conference On Environmental Systems. 400 Commonwealth Drive, Warrendale, PA, United States: SAE International, 2003. http://dx.doi.org/10.4271/2003-01-2505.

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Cioletti, Louis A., Duane L. Pierson, and S. K. Mishra. "Microbial Growth and Physiology in Space: A Review." In International Conference On Environmental Systems. 400 Commonwealth Drive, Warrendale, PA, United States: SAE International, 1991. http://dx.doi.org/10.4271/911512.

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Zhao Jin, Yu Quan, Zhao Xiaohua, and Li Ning. "Effects of drinking upon driving performance and physiology indicators." In 2012 7th International Conference on System of Systems Engineering (SoSE). IEEE, 2012. http://dx.doi.org/10.1109/sysose.2012.6333659.

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Halim, A. Hanif, and I. Ismail. "Online PID controller tuning using tree physiology optimization." In 2016 6th International Conference on Intelligent and Advanced Systems (ICIAS). IEEE, 2016. http://dx.doi.org/10.1109/icias.2016.7824036.

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Popescu, Gheorghe. "EFFECT OF PRUNING SYSTEMS ON LEAF PHYSIOLOGY AND GRAPEVINE PERFORMANCE." In 18th International Multidisciplinary Scientific GeoConference SGEM2018. Stef92 Technology, 2018. http://dx.doi.org/10.5593/sgem2018/6.2/s25.021.

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Skweres, Joyce A., Virginia J. Bassinger, and S. K. Mishra, and Duane L. Pierson. "Effects of Refrigerating Preinoculated Vitek Cards on Microbial Physiology and Antibiotic Susceptibility." In International Conference On Environmental Systems. 400 Commonwealth Drive, Warrendale, PA, United States: SAE International, 1992. http://dx.doi.org/10.4271/921214.

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Sawka, Michael N., and Kent B. Pandolf. "Upper Body Exercise: Physiology and Training Application for Human Presence in Space." In International Conference On Environmental Systems. 400 Commonwealth Drive, Warrendale, PA, United States: SAE International, 1991. http://dx.doi.org/10.4271/911461.

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Hosseini, Mohammad, Richard R. Berlin, and Lui Sha. "A physiology-aware communication architecture for distributed emergency medical CPS." In ICCPS '17: ACM/IEEE 8th International Conference on Cyber-Physical Systems. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3055004.3064841.

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"Physiology-based Affect Recognition During Driving in Virtual Environment for Autism Intervention." In 2nd International Conference on Physiological Computing Systems. SCITEPRESS - Science and and Technology Publications, 2015. http://dx.doi.org/10.5220/0005331301370145.

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Hosseini, Mohammad, Yu Jiang, Ali Yekkehkhany, Richard R. Berlin, and Lui Sha. "A Mobile Geo-Communication Dataset for Physiology-Aware DASH in Rural Ambulance Transport." In MMSys'17: Multimedia Systems Conference 2017. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3083187.3083211.

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Reports on the topic "Systems physiology"

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Worden, Alexandra Z., Stephen Callister, Joshua Stuart, and Richard Smith. Final Report: Connecting genomic capabilities to physiology and response: Systems biology of the widespread alga Micromonas. Office of Scientific and Technical Information (OSTI), September 2014. http://dx.doi.org/10.2172/1158817.

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Bloch, Guy, Gene E. Robinson, and Mark Band. Functional genomics of reproduction and division of labor in a key non-Apis pollinator. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7699867.bard.

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i. List the original objectives, as defined in the approved proposal, and any revisions made at the beginning or during the course of project. Our objectives were: 1) develop state-of-the-art functional genomics tools for B. terrestris. These resources will be then used to: 2) characterize genes and molecular pathways that are associated with reproduction, 3) characterize genes and molecular pathways associated with specialization in foraging or nursing activities, and 4) determine the extent to which juvenile hormone (JH) is involved in the regulation of reproduction and division of labor. 5) Use RNA interference to down regulate genes associated with reproductive physiology, division of labor, or both. A decrease in the cost of RNA sequencing enabled us to further use the BARD support to extend our research to three additional related projects: A) The regulation of body size which is crucial for understanding both reproduction (castedetermination) and (size based) division of labor in bumblebees. B) Analyze RNA editing in our RNA sequencing data which improves the molecular understanding of the systems we study. C) The influence of JH on the fat body in addition to the brain on which we focused in our proposal. The fat body is a key tissue regulating insect reproduction and health. ii. Background to the topic. Bees are by far the most important pollinators in agricultural and natural ecosystems. The recent collapse of honey bee populations, together with declines in wild bee (including bumble bee) populations, puts their vital pollination services under severe threat. A promising strategy for circumventing this risk is the domestication and mass-rearing of non-Apis bees. This approach has been successfully implemented for several bumble bees including Bombusterrestris in Israel, and B. impatiens in the US, which are mass-reared in captivity. In spite of their critical economic and environmental value, little is known about the physiology and molecular biology of bumble bees. In this collaborative project we developed functional genomics tools for the bumble bee B. terrestris and use these tools for a first thorough study on the physiology and molecular biology of reproduction, dominance, and division of labor in a bumble bee. iii. Major conclusions, solutions. The valuable molecular data of this project together with the functional tools and molecular information generated in this BARD funded project significantly advanced the understanding of bumblebee biology which is essential for maintaining their vital pollination services for US and Israel agriculture.
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Ron, Eliora, and Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7695860.bard.

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The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.
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Savaldi-Goldstein, Sigal, and Siobhan M. Brady. Mechanisms underlying root system architecture adaptation to low phosphate environment. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600024.bard.

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In order to advance our understanding towards potential biotechnology improvement of plant performance, we studied root responses to limited P in two different plants, Arabidopsis and tomato. Arabidopsis is among the most studied model plants that allows rapid application of molecular and developmental experiments while tomato is an important crop, with application in agriculture. Using Arabidopsis we found that steroid hormones modulate the extent of root elongation in response to limited P, by controlling the accumulation of iron in the root. We also found that the availability of P and iron control the activity of the steroid hormone in the root. Finally, we revealed the genes involved in this nutrient-hormone interaction. Hence, the ferroxidase LPR1 that promotes iron accumulation in response to low P is repressed by the transcription factor BES1/BZR1. Low P inhibits the steroid hormone pathway by enhancing the accumulation of BKI1. High levels of BKI1 inhibit the activity of the steroid hormone receptor at the cell surface and iron accumulation increases inside the root, resulting in a slow growth. Together, the extent of root elongation depends on interactions between an internal cue (steroid hormone) and cues derived from the availability of P and iron in the environment. Using tomato, we found that the response of two cultivated tomato varieties (M82 and New Yorker) to limited P is distinct from that of the wild species, Solanumpennellii. This is implicated at both the levels of root development and whole plant physiology. Specifically, while the root system architecture of cultivated tomato is modulated by limited P availability, that of the wild type species remained unaffected. The wild species appears to be always behaving as if it is always in phosphate deprived conditions, despite sufficient levels of phosphate. Hyper-accumulation of metals appears to mediate this response. Together, this knowledge will be used to isolate new genes controlling plant adaptation to limited P environment.
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Granot, David, and Noel Michelle Holbrook. Role of Fructokinases in the Development and Function of the Vascular System. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7592125.bard.

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Plant vascular tissues are superhighways whose development and function have profound implications for productivity, yield and stress response. Preliminary studies by the PI indicated that sugar metabolism mediated by fructokinases (FRKs) has a pronounced effect on the transport properties of the xylem. The goal of this research was to determine how the main fructokinase gene, FRK2, and the only plastidic fructokinase, FRK3, influence vascular development and physiology, emphasizing processes that occur at both the cellular and organismic level. We found that both genes are expressed in vascular tissues, but FRK3 is expressed primarily in vascular tissues of mature petioles. Vascular anatomy of plants with antisense suppression of FRK2 uncovered that FRK2 is necessary for xylem and phloem development, most likely due to its role in vascular cell-wall synthesis, and affects vascular development all over the plant. As a result, suppression of FRK2 reduced hydraulic conductivity of roots, stem and leaves and restricted sugar phloem transport. Vascular anatomy of plants with RNAi suppression of FRK3 uncovered that FRK3 is required for vascular development in mature petiole but its role is partially complemented by FRK2. Suppression of FRK3 combined with partial suppression of FRK2 had effects completely different from that of FRK2 suppression, resulting in wilting of mature leaves rather than young leaves of FRK2 suppressed plants, and decreased export of photoassimilates. This primary effect of FRK2 suppression on mature petioles had a secondary effect, reducing the hydraulic conductivity in roots and stem. The very fact that a plastidic fructokinase plays a role in vascular development is quite surprising and we are still seeking to uncover its metabolic mode-of-action. Yet, it is clear that these two fructokinases have different roles in the coordination between photosynthetic capacity and vascular development. We have started analyzing the role of the last third FRK, FRK1, and discovered that it is also expressed exclusively in vascular tissues. It appears therefore, that all FRKs studied here are involved in vascular development. An interesting unexpected outcome of this study was the connection of FRK2 with hormonal regulation of vascular development, most likely auxin. This observation together with the yet to be solved questions on the exact roles of FRK3 are the subjects of our current efforts.
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Harman, Gary E., and Ilan Chet. Enhancement of plant disease resistance and productivity through use of root symbiotic fungi. United States Department of Agriculture, July 2008. http://dx.doi.org/10.32747/2008.7695588.bard.

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The objectives of the project were to (a) compare effects ofT22 and T-203 on growth promotion and induced resistance of maize inbred line Mol7; (b) follow induced resistance of pathogenesis-related proteins through changes in gene expression with a root and foliar pathogen in the presence or absence of T22 or T-203 and (c) to follow changes in the proteome of Mol? over time in roots and leaves in the presence or absence of T22 or T-203. The research built changes in our concepts regarding the effects of Trichoderma on plants; we hypothesized that there would be major changes in the physiology of plants and these would be reflected in changes in the plant proteome as a consequence of root infection by Trichoderma spp. Further, Trichoderma spp. differ in their effects on plants and these changes are largely a consequence of the production of different elicitors of elicitor mixtures that are produced in the zone of communication that is established by root infection by Trichoderma spp. In this work, we demonstrated that both T22 and T-203 increase growth and induce resistance to pathogens in maize. In Israel, it was shown that a hydrophobin is critical for root colonization by Trichoderma strains, and that peptaibols and an expansin-like protein from Ttrichoderma probably act as elicitors of induced resistance in plants. Further, this fungus induces the jasmonate/ethylene pathway of disease resistance and a specific cucumber MAPK is required for transduction of the resistance signal. This is the first such gene known to be induced by fungal systems. In the USA, extensive proteomic analyses of maize demonstrated a number of proteins are differentially regulated by T. harzianum strain T22. The pattern of up-regulation strongly supports the contention that this fungus induces increases in plant disease resistance, respiratory rates and photosynthesis. These are all very consistent with the observations of effects of the fungus on plants in the greenhouse and field. In addition, the chitinolytic complex of maize was examined. The numbers of maize genes encoding these enzymes was increased about 3-fold and their locations on maize chromosomes determined by sequence identification in specific BAC libraries on the web. One of the chitinolytic enzymes was determined to be a heterodimer between a specific exochitinase and different endochitinases dependent upon tissue differences (shoot or root) and the presence or absence of T. harzianum. These heterodimers, which were discovered in this work, are very strongly antifungal, especially the one from shoots in the presence of the biocontrol fungus. Finally, RNA was isolated from plants at Cornell and sent to Israel for transcriptome assessment using Affymetrix chips (the chips became available for maize at the end of the project). The data was sent back to Cornell for bioinformatic analyses and found, in large sense, to be consistent with the proteomic data. The final assessment of this data is just now possible since the full annotation of the sequences in the maize Affy chips is just now available. This work is already being used to discover more effective strains of Trichoderma. It also is expected to elucidate how we may be able to manipulate and breed plants for greater disease resistance, enhanced growth and yield and similar goals. This will be possible since the changes in gene and protein expression that lead to better plant performance can be elucidated by following changes induced by Trichoderma strains. The work was in, some parts, collaborative but in others, most specifically transcriptome analyses, fully synergistic.
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Chang, Min Cheol, Yoo Jin Choo, and Sohyun Kim. Effect of Prehabilitation for Patients with Frailty Undergoing Colorectal Cancer Surgery: A Systematic Review and Meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, November 2022. http://dx.doi.org/10.37766/inplasy2022.11.0105.

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Review question / Objective: We performed a meta-analysis to assess the impact of prehabilitation before colorectal surgery on functional outcome and postoperative complications in patients with frailty. Condition being studied: Colorectal cancer is a common disease in the elderly, and over 65 years of age accounts for more than 50% of all patients with colorectal cancer. The patients with colorectal cancer surgery showed 8.7% major morbidity and mortality and 31.6% minor complications. The high complication rate of patients with colorectal surgery is related to the fact that there are many elderly patients. Frailty is common in elderly patients, and the frailty is associated with adverse perioperative outcomes. The frail patients with colorectal surgery showed worse postoperative morbidity, mortality and prolonged length of hospital stay. Although the frailty results from irresistible aging-associated decline in reserve and function across multiple physiologic systems, several attempts have been conducted to improve frailty in patients with colorectal cancer surgery and consequently improve the postoperative outcomes. Prehabilitation was one of these attempts for improving physical activity and postoperative outcomes on patients with frailty undergoing colorectal cancer surgery. So far, several studies conducted clinical trials for determining whether prehabilitation has positive effect on improving postoperative outcomes in patients with frailty undergoing colorectal surgery. However, the results of these previous studies are controversial.
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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.

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Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report
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LaBonte, Don, Etan Pressman, Nurit Firon, and Arthur Villordon. Molecular and Anatomical Characterization of Sweetpotato Storage Root Formation. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7592648.bard.

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Original objectives: Anatomical study of storage root initiation and formation. Induction of storage root formation. Isolation and characterization of genes involved in storage root formation. During the normal course of storage root development. Following stress-induced storage root formation. Background:Sweetpotato is a high value vegetable crop in Israel and the U.S. and acreage is expanding in both countries and the research herein represents an important backstop to improving quality, consistency, and yield. This research has two broad objectives, both relating to sweetpotato storage root formation. The first objective is to understand storage root inductive conditions and describe the anatomical and physiological stages of storage root development. Sweetpotato is propagated through vine cuttings. These vine cuttings form adventitious roots, from pre-formed primordiae, at each node underground and it is these small adventitious roots which serve as initials for storage and fibrous (non-storage) “feeder” roots. What perplexes producers is the tremendous variability in storage roots produced from plant to plant. The marketable root number may vary from none to five per plant. What has intrigued us is the dearth of research on sweetpotato during the early growth period which we hypothesize has a tremendous impact on ultimate consistency and yield. The second objective is to identify genes that change the root physiology towards either a fleshy storage root or a fibrous “feeder” root. Understanding which genes affect the ultimate outcome is central to our research. Major conclusions: For objective one, we have determined that the majority of adventitious roots that are initiated within 5-7 days after transplanting possess the anatomical features associated with storage root initiation and account for 86 % of storage root count at 65 days after transplanting. These data underscore the importance of optimizing the growing environment during the critical storage root initiation period. Water deprivation during this phenological stage led to substantial reduction in storage root number and yield as determined through growth chamber, greenhouse, and field experiments. Morphological characterization of adventitious roots showed adjustments in root system architecture, expressed as lateral root count and density, in response to water deprivation. For objective two, we generated a transcriptome of storage and lignified (non-storage) adventitious roots. This transcriptome database consists of 55,296 contigs and contains data as regards to differential expression between initiating and lignified adventitious roots. The molecular data provide evidence that a key regulatory mechanism in storage root initiation involves the switch between lignin biosynthesis and cell division and starch accumulation. We extended this research to identify genes upregulated in adventitious roots under drought stress. A subset of these genes was expressed in salt stressed plants.
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Eyal, Yoram, Gloria Moore, and Efraim Lewinsohn. Study and Manipulation of the Flavanoid Biosynthetic Pathway in Citrus for Flavor Engineering and Seedless Fruit. United States Department of Agriculture, October 2003. http://dx.doi.org/10.32747/2003.7570547.bard.

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The proposal was aimed to identify and functionally characterize key genes/enzymes in the citrus flavanone neohesperidoside biosynthetic pathway and to use them as tools for metabolic engineering to decrease bitterness levels in grapefruit. The proposed section on fruit seediness was dropped as suggested by the reviewers of the proposal. Citrus flavor and aroma is composed of complex combinations of soluble and volatile compounds. The former includes mainly sugars, acids and flavanones, a subgroup of flavonoids that includes bitter compounds responsible for the bitter flavor of grapefruit and pummelo. Bitter species contain mostly bitter flavanone neohesperidosides, while non-bitter species contain mostly tasteless flavanone rutinosides. Both flavanone versions are diglycosides consisting of a rhamnose-glucose oligosaccharide a-linked at position 7 to the flavanone skeleton. However, in the bitter neohesperidosides the rhamnose is attached at position 2 of the glucose moiety, while in the tasteless rutinosides the rhamnose is attached at position 6 of the glucose moiety. Thus, the position of the rhamnose moiety, determined by the specificity of the last enzymes in the pathway- rhamnosyltransferase (1,2 or 1,6 specificity), is the determinant of the bitter flavor. Flavanones, like all flavonoids are synthesized via one of the branches of the phenylpropanoid pathway; the first committed step is catalyzed by the enzyme Chalcone synthase (CHS) followed by Chalcone isomerase (CHI). During the course of the work a key gene/enzyme in the biosynthesis of the bitter flavanones, a 1,2 rhamnosyltransferase (1,2RT), was functionally characterized using a transgenic cell-culture biotransformation system, confirming that this gene is a prime candidate for metabolic engineering of the pathway. This is the first direct functional evidence for the activity of a plant recombinant rhamnosyltransferase, the first confirmed rhamnosyltransferase gene with 1,2 specificity and the second confirmed rhamnosyltransferase gene altogether in plants. Additional genes of the flavanone pathway that were isolated during this work and are potential tools for metabolic engineering include (I) A putative 1,6 rhamnosyltransferase (1,6RT) from oranges, that is presumed to catalyze the biosynthesis of the tasteless flavanones. This gene is a prime candidate for use in future metabolic engineering for decreased bitterness and is currently being functionally characterized using the biotransformation system developed for characterizing rhamnosyltransferases. (2) A putative 7-0-glucosyltransferase presumed to catalyze the first glycosylation step of the flavanone aglycones. Silencing of gene expression in grapefruit was attempted using three genes: (1) The "upstream" flavonoid biosynthesis genes CHS and CHI, by antisense and co-suppression; and (2) The "downstream" 1,2R T, by an RNAi approach. CHS and CHI silencing resulted in some plants with a dramatically decreased level of the bitter flavanone neohesperidoside naringin in leaves. We have yet to study the long-term effect of silencing these genes on tree physiology, and on the actual bitterness of fruit. The effect of 1,2RT silencing on naringin content in grapefruit has yet to be examined, but a slow growth phenotype for these plants was noted. We speculate that silencing of the final glycosylation step of the flavanones delays their evacuation to the vacuole, resulting in accumulation of flavanones in the cytoplasm, causing inhibitory effects on plant growth. This speculation is yet to be established at the product level. Future metabolic engineering experiments are planned with 1,6RT following functional characterization.
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