Modeling Photosynthesis And Related Metabolic Processes
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Modeling Photosynthesis And Related Metabolic Processes
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Author :
language : en
Publisher:
Release Date : 2014
Modeling Photosynthesis And Related Metabolic Processes written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
Mathematical modeling of biological systems is a powerful tool to systematically investigate the functions of biological processes and their relationship with the environment. To obtain accurate and biologically interpretable predictions, a modeling framework has to be devised whose assumptions best approximate the examined scenario and which copes with the trade-off of complexity of the underlying mathematical description: with attention to detail or high coverage. Correspondingly, the system can be examined in detail on a smaller scale or in a simplified manner on a larger scale. In this thesis, the role of photosynthesis and its related biochemical processes in the context of plant metabolism was dissected by employing modeling approaches ranging from kinetic to stoichiometric models. The Calvin-Benson cycle, as primary pathway of carbon fixation in C3 plants, is the initial step for producing starch and sucrose, necessary for plant growth. Based on an integrative analysis for model ranking applied on the largest compendium of (kinetic) models for the Calvin-Benson cycle, those suitable for development of metabolic engineering strategies were identified. Driven by the question why starch rather than sucrose is the predominant transitory carbon storage in higher plants, the metabolic costs for their synthesis were examined. The incorporation of the maintenance costs for the involved enzymes provided a model-based support for the preference of starch as transitory carbon storage, by only exploiting the stoichiometry of synthesis pathways. Many photosynthetic organisms have to cope with processes which compete with carbon fixation, such as photorespiration whose impact on plant metabolism is still controversial. A systematic model-oriented review provided a detailed assessment for the role of this pathway in inhibiting the rate of carbon fixation, bridging carbon and nitrogen metabolism, shaping the C1 metabolism, and influencing redox signal transduction ...
Integrated Modeling Of Phototrophic Metabolism Leveraging Multi Omics Datasets
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Author : Debolina Sarkar
language : en
Publisher:
Release Date : 2022
Integrated Modeling Of Phototrophic Metabolism Leveraging Multi Omics Datasets written by Debolina Sarkar and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022 with categories.
Rapid progress in high-throughput experimental technologies has enabled generation of large-scale systems biology datasets. These span all biological hierarchies from genomics describing the genetic make-up, transcriptomics and proteomics at the gene and enzyme expression level, metabolomics that helps quantify the amount and nature of resultant biomolecules, to finally phenomics that describes the overall traits of an individual. This veritable data deluge necessitates algorithmic and computational advances that can leverage multi-omics integration, in order to facilitate the analysis of complex systems and extract meaningful insights. Flux balance analysis (FBA) using genome-scale metabolic (GSM) models provide an advantageous platform for doing so as these models are (relatively) parameter-free, can be constructed using the annotated genome alone and simulated in linear time offering scale-up benefits. GSMs model a network view of metabolism, wherein metabolites are cast as nodes in a graph linked via edges representing all possible biochemical conversions occurring within an organism. In Chapter 1, we present an overview of constraints-based analysis of metabolic networks, including the reconstruction of GSM models, their use within an optimization-based scheme such as FBA, and the various applications of such models. Next, we describe the extension of metabolic modeling frameworks, originally designed for microbial systems, to the study of plants. This is accompanied by its own set of challenges, such as accurately capturing the division of roles between the various tissue and organ systems and dealing with systematic biases that are typically associated with poorly annotated non-model systems. Finally, we explore how the incorporation of new data types, modeling schemes, and computational tools have impacted FBA by helping increase its predictive power and scope. FBA has proven to be quite adept at describing aggregated metabolite flows, i.e., providing a snapshot of metabolism as averaged over the entire growth cycle. However, it is also time invariant, and thus does not accommodate temporally varying cell processes such as sequestering different biomass components at various time points in a growth cycle However, we know from experiments that many organisms including cyanobacteria have a lifestyle that is heavily tailored around light availability and thus show metabolic oscillations. In Chapter 2, we present a framework called CycleSyn that augments FBA by accounting for such temporal trends. CycleSyn discretizes a growth cycle into individual time periods (called Time Point Models or TPMs), each described by its own GSM model. The flow of metabolites across TPMs is allowed while inventorying metabolite levels and only allowing for the utilization of currently or previously produced compounds. Additional time-dependent constraints can also be imposed to capture the cyclic nature of cellular processes. CycleSyn was used to develop a diurnal FBA model of Synechocystis sp. PCC 6803 metabolism. Predicted flux and metabolite pools were in line with published studies, paving the way for constructing time-resolved GSM models. Additionally, the metabolic reorganization that would be required to enable Synechocystis PCC 6803 to fix nitrogen by temporally separating it from photosynthesis was also explored. Similar to modeling multiple metabolic models at once in CycleSyn, in Chapter 3 we extend this to modeling multiple organisms together as in a community, so as to discern the underlying interactions. This community comprised a genetically streamlined unicellular cyanobacterium called Candidatus Atelocyanobacterium thalassa (or UCYN-A) living in a symbiosis with a phototrophic microalga. We used metabolic modeling to glean insights into UCYN-A's unique physiology and metabolic processes governing the symbiotic association. To this end, we developed an optimization-based framework that infers all possible trophic scenarios consistent with the observed data. Possible mechanisms employed by UCYN-A to accommodate diazotrophy with daytime carbon fixation by the host (i.e., two mutually incompatible processes) were also elucidated. We found that the metabolic functions of the two constituents, and UCYN-A's streamlined genome is optimized to support maximal nitrogen fixation flux, alluding that this symbiosis is as close to being a functional 'nitroplast' as any observed till date. We envision that the developed framework using UCYN-A and its algal host will be used as a roadmap and motivate the study of similarly unique microbial systems in the future. Understanding how genomic mutations impact the overall phenotype of an organism has been a focus of efforts aimed at improving growth yield, determining genetic markers governing a trait, and understanding adaptive processes. This has been performed conventionally using genome-wide association studies, which seek to identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. In Chapter 4, we propose a complementary tool called SNPeffect that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect was used to explain differential growth rate and metabolite accumulation in Arabidopsis and poplar as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicated that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally-characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino-acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition. Thus far, we have developed computational frameworks that examine how the metabolism of an organism dictates its total phenotype and interactions with other organisms in a community. In Chapter 5, we take the next step by examining ways in which an organism can impact its host, specifically how the infant gut microbiome is shaped. Fecal samples from newborn infants showed that gut bacteria is detectable by 16 h after birth. However, analysis of the microbiome, proteome, and metabolome data did not suggest a single genomic signature for neonatal gut colonization. Using flux balance modeling, we found E. coli to be the most common early colonizer. The appearance of bacteria was associated with decreased levels of free amino acids and an increase in products of bacterial fermentation, primarily acetate and succinate. Among all the microbial species found, these observations were only consistent with E. coli growing under anaerobic conditions using amino acid fermentation to support maximal ATP yield. These results provide a deep characterization of the first microbes in the human gut and show how the biochemical environment is altered by their appearance. Finally, in Chapter 6, we conclude with our efforts to develop computational frameworks enabling the integration of heterogeneous datasets within constraints-based optimization. We discuss current challenges associated with such modeling frameworks and their uses, and finally present future perspectives for augmenting these models with the incorporation of diverse data types, multi-scale modeling, cross-cutting applications.
Molecular Biology Of The Cell
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Author : Bruce Alberts
language : en
Publisher:
Release Date : 2002
Molecular Biology Of The Cell written by Bruce Alberts and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2002 with Cytology categories.
Biochemical Models Of Leaf Photosynthesis
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Author : Susanna Von Caemmerer
language : en
Publisher: CSIRO PUBLISHING
Release Date : 2000
Biochemical Models Of Leaf Photosynthesis written by Susanna Von Caemmerer and has been published by CSIRO PUBLISHING this book supported file pdf, txt, epub, kindle and other format this book has been release on 2000 with Science categories.
Increasing concerns of global climatic change have stimulated research in all aspects of carbon exchange. This has restored interest in leaf-photosynthetic models to predict and assess changes in photosynthetic CO2 assimilation in different environments. This is a comprehensive presentation of the most widely used models of steady-state photosynthesis by an author who is a world authority. Treatments of C3, C4 and intermediate pathways of photosynthesis in relation to environment have been updated to include work on antisense transgenic plants. It will be a standard reference for the formal analysis of photosynthetic metabolism in vivo by advanced students and researchers.
Biological Control Of Rice Diseases
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Author : Samuel S. Gnanamanickam
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-07-14
Biological Control Of Rice Diseases written by Samuel S. Gnanamanickam and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-07-14 with Science categories.
There is suf?cient need to document all the available data on biological control of rice diseases in a small volume. Part of this need rests on the global importance of rice to human life. In the ?rst chapter, I have tried to show that rice is indeed life for most people in Asia and shortages in production and availability can lead to a food crisis. While rice is cultivated in most continents, biological disease management attains special relevance to rice farmers of Africa, Asia, and also perhaps, Latin America. These farmers are resource-poor and might not be able to afford the cost of expensive chemical treatments to control devastating rice pathogens such as Magnaporthe oryzae (blast), Xanthomonas oryzae pv. oryzae (bacterial leaf blight), Rhizoctonia solani (sheath blight) and the virus, rice tungro disease. In an earlier volume that I developed under the title, Biological Control of Crop Diseases (Dekker/CRC Publishers, 2002), I included transgenic crops generated for the management of plant pathogens as biological control under the umbrella of a broad de?nition. Dr Jim Cook who wrote the Foreword for the volume lauded the inclusion of transgenic crops and induced systemic resistance (ISR) as a positive trend toward acceptance of host plant resistance as part of biocontrol. I continue to subscribe to this view.
Crop Photosynthesis
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Author : N.R. Baker
language : en
Publisher: Elsevier
Release Date : 2013-10-22
Crop Photosynthesis written by N.R. Baker and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-10-22 with Science categories.
Since photosynthetic performance is a fundamental determinant of yield in the vast majority of crops, an understanding of the factors limiting photosynthetic productivity has a crucial role to play in crop improvement programmes. Photosynthesis, unlike the majority of physiological processes in plants, has been the subject of extensive studies at the molecular level for many years. This reductionist approach has resulted in the development of an impressive and detailed understanding of the mechanisms of light capture, energy transduction and carbohydrate biosynthesis, processes that are clearly central to the success of the plant and the productivity of crops. This volume examines in the widest context the factors determining the photosynthetic performance of crops. The emphasis throughout the book is on the setting for photosynthesis rather than the fundamental process itself. The book will prove useful to a wide range of plant scientists, and will encourage a more rapid integration of disciplines in the quest to understand and improve the productivity of crops by the procedures of classical breeding and genetic manipulation.
Regulation Of Photosynthesis
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Author : Eva-Mari Aro
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-04-11
Regulation Of Photosynthesis written by Eva-Mari Aro and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-04-11 with Science categories.
This book covers the expression of photosynthesis related genes including regulation both at transcriptional and translational levels. It reviews biogenesis, turnover, and senescence of thylakoid pigment protein complexes and highlights some crucial regulatory steps in carbon metabolism.
Climate Change And Terrestrial Ecosystem Modeling
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Author : Gordon Bonan
language : en
Publisher: Cambridge University Press
Release Date : 2019-02-21
Climate Change And Terrestrial Ecosystem Modeling written by Gordon Bonan and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-02-21 with Mathematics categories.
Provides an essential introduction to modeling terrestrial ecosystems in Earth system models for graduate students and researchers.
Discoveries In Photosynthesis
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Author : Govindjee
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-07-15
Discoveries In Photosynthesis written by Govindjee and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-07-15 with Science categories.
"Life Is Bottled Sunshine" [Wynwood Reade, Martyrdom of Man, 1924]. This inspired phrase is a four-word summary of the significance of photosynthesis for life on earth. The study of photosynthesis has attracted the attention of a legion of biologists, biochemists, chemists and physicists for over 200 years. Discoveries in Photosynthesis presents a sweeping overview of the history of photosynthesis investigations, and detailed accounts of research progress in all aspects of the most complex bioenergetic process in living organisms. Conceived of as a way of summarizing the history of research advances in photosynthesis as of millennium 2000, the book evolved into a majestic and encyclopedic saga involving all of the basic sciences. The book contains 111 papers, authored by 132 scientists from 19 countries. It includes overviews; timelines; tributes; minireviews on excitation energy transfer, reaction centers, oxygen evolution, light-harvesting and pigment-protein complexes, electron transport and ATP synthesis, techniques and applications, biogenesis and membrane architecture, reductive and assimilatory processes, transport, regulation and adaptation, Genetics, and Evolution; laboratories and national perspectives; and retrospectives that end in a list of photosynthesis symposia, books and conferences. Informal and formal photographs of scientists make it a wonderful book to have. This book is meant not only for the researchers and graduate students, but also for advanced undergraduates in Plant Biology, Microbiology, Cell Biology, Biochemistry, Biophysics and History of Science.
Terrestrial Photosynthesis In A Changing Environment
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Author : Jaume Flexas
language : en
Publisher: Cambridge University Press
Release Date : 2012-07-19
Terrestrial Photosynthesis In A Changing Environment written by Jaume Flexas and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-07-19 with Science categories.
An integrated guide to photosynthesis in an environmentally dynamic context, covering all aspects from basic concepts to methodologies.