Staff View
Computational and biophysical tools to investigate the coupling of the light and dark reactions of photosynthetic organisms at the photosystem and cellular levels

Descriptive

TitleInfo
Title
Computational and biophysical tools to investigate the coupling of the light and dark reactions of photosynthetic organisms at the photosystem and cellular levels
Name (type = personal)
NamePart (type = family)
Zournas
NamePart (type = given)
Apostolos
DisplayForm
Apostolos Zournas
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Dismukes
NamePart (type = given)
Gerard
DisplayForm
Gerard C Dismukes
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = personal)
NamePart (type = family)
Androulakis
NamePart (type = given)
Ioannis
DisplayForm
Ioannis Androulakis
Affiliation
Advisory Committee
Role
RoleTerm (authority = local)
member
Name (type = personal)
NamePart (type = family)
Zhang
NamePart (type = given)
Haoran
DisplayForm
Haoran Zhang
Affiliation
Advisory Committee
Role
RoleTerm (authority = local)
member
Name (type = personal)
NamePart (type = family)
Lun
NamePart (type = given)
Desmond
DisplayForm
Desmond Lun
Affiliation
Advisory Committee
Role
RoleTerm (authority = local)
member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
School of Graduate Studies
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (encoding = w3cdtf); (qualifier = exact); (keyDate = yes)
2023
DateOther (encoding = w3cdtf); (type = degree); (qualifier = exact)
2023-01
CopyrightDate (encoding = w3cdtf); (qualifier = exact)
2023
Language
LanguageTerm (authority = ISO 639-3:2007); (type = text)
English
Abstract (type = abstract)
Photosynthetic molecular machinery is the primary source of energy in the biosphere of the earth. Plants, algae, and cyanobacteria have evolved over billions of years to harness the light energy of the sun and convert it to chemical energy to produce biomass and perform all the required cellular processes. Light energy is used to extract electrons from water as well as generate a proton gradient along the thylakoid membrane, the energy in which is ultimately used to fix carbon (mainly in the form of CO2 and HCO3+) through the Calvin Benson Bassham (CBB) cycle. Human civilization is dependent on this biomass to generate food, feed, as well as a variety of value-added chemicals such as biofuels. In order to meet the needs of the continuously growing global population, there is a need to better understand the biological processes that enable carbon fixation. In the photosynthetic research community, these processes have primarily been monitored through O2 evolution and Chlorophyll Fluorescence yield, both arising from the light-dependent water-splitting protein, Photosystem II (PSII). The water oxidation cycle is a four-step process, releasing O2 once every cycle. This process has been traditionally modeled using Kok-type Hidden Markov Chain models (HMMs) that include 3 parameters: misses, double hits, and backward transitions. However, these models do not offer any insight into the underlying mechanisms for any of these processes. The first objective of this thesis was to extract that mechanistic knowledge from these models. To do so, I built an ordinary differential equation (ODE)-based model of PSII, namely RODE1, and developed a framework to discretize the solutions of the ODEs to connect them to the parameters calculated in the Kok-type HMM models. This work showed that the efficiency of charge separation in the donor side of PSII, where electrons are extracted from water utilizing photons is tightly controlled by the acceptor side of PSII, where electrons are transferred to Plastoquinone (PQ), a loosely bound 2 e- carrier which shuttles the electrons downstream to the Photosynthetic Electron Transport Chain (PETC). Even though our approach could accurately predict forward electron transfer within PSII, it lacked the prediction of backward transitions, a process where electrons are moved from the acceptor side to the donor side. Exploring the mechanistic process of backward transitions was the second objective of this thesis. This was achieved by expanding the model to include the appropriate reactions and applying it to O2 evolution data acquired from C. ohadii, a desert crust alga, which has been previously shown to have uncharacteristically high backward transitions. This study showed that the process of backward transitions is again regulated by the donor and the acceptor side. We showed that the PSII microstates that allow for backward transitions were the ones where the loosely bound PQ at the donor side (QB) would carry a single electron in the form of a semiquinone, rather than being fully oxidized (0 e-) or fully reduced (2 e-). The proposed mechanism for backward transitions is a potential pathway for Cyclic Electron Flow around PSII (PSII-CEF) which is a mechanism that can be used for photoprotection (dissipative PSII-CEF) or to increase the proton gradient across the thylakoid membrane (generative PSII-CEF). The last objective of this thesis was to develop a method to study the PETC from water to CO2, which are the primary source, and the terminal acceptor of electrons respectively. The developed method utilizes Fast Repetition Rate fluorometry (FRRf) to monitor changes in charge separation efficiency in multiple time scales, from ╬╝s to minutes. We showed how the kinetic features observed in our method respond to altering photosynthetic electron transport through multiple treatments and identified the redox events that each kinetic feature corresponds to. Among other redox events, we identified how Cyclic Electron Flow around PSI (PSI-CEF) appears in our measurements and how the PETC is connected to dark metabolism.
Subject (authority = RUETD)
Topic
Biophysics
Subject (authority = RUETD)
Topic
Biochemistry
Subject (authority = local)
Topic
Chl - fluorescence
Subject (authority = local)
Topic
Kinetic model
Subject (authority = local)
Topic
Oxygen evolution
Subject (authority = local)
Topic
PSII
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
http://dissertations.umi.com/gsnb.rutgers:12283
PhysicalDescription
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
148 pages : illustrations
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
RelatedItem (type = host)
TitleInfo
Title
School of Graduate Studies Electronic Theses and Dissertations
Identifier (type = local)
rucore10001600001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/t3-6thj-0869
Back to the top

Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Zournas
GivenName
Apostolos
Role
Copyright holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2023-02-23T12:13:01
AssociatedEntity
Name
Apostolos Zournas
Role
Copyright holder
Affiliation
Rutgers University. School of Graduate Studies
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
Back to the top

Technical

RULTechMD (ID = TECHNICAL1)
ContentModel
ETD
OperatingSystem (VERSION = 5.1)
windows xp
CreatingApplication
Version
1.7
ApplicationName
Microsoft® Word for Microsoft 365
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2023-01-03T18:00:19
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2023-01-03T18:00:19
Back to the top
Version 8.5.3
Rutgers University Libraries - Copyright ©2023