Nyanza Gulf is a large, shallow and long river-influenced embayment located in northeastern Lake Victoria. The gulf opens to the main lake through the narrow and deep Rusinga Channel, the exchange zone between the two ecosystems with different physical chemical and biogeochemical conditions. The main goals of this study are to characterize physicochemical and nutrient gradients along the gulf-main-lake transect, characterize and quantify the water and nutrient fluxes between the gulf and the main lake, and assess the response of phytoplankton community and photosynthesis to the spatially varying physical and nutrient conditions along the study transect. Between March 2005 and March 2006, measurements of physicochemical profiles as well as nutrient and the phytoplankton community analysis were conductued monthly along the study transect. Additionally, analysis of different surficial sediment phosphorus fractions was done in order to asses the potential role of bottom sediment in contributing to phosphorus enrichment in the lake water column. A box mass balance model was used to calculate the exchange of water and nutrient fluxes between different zones along the study transect and to estimate ecosystem metabolism in the gulf and the channel. Spatial variability in physicochemical and biogeochemical conditions was observed along the study transect, especially between the shallow and river-influenced inner-gulf, the deep and physically active Rusinga Channel, and the main lake, mainly in response to river inputs and varying morphometry along the study transect. The gulf had significantly higher electrical conductivity (EC), turbidity, total nitrogen (TN), and dissolved reactive silica (DRSi) but the levels declined monotonically along the channel in response to mixing with the main lake water. The channel and the main lake had, respectively, significantly higher dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) compared to the gulf. Spatial variability in morphometry and exposure to varying wind forcing lead to differential mixing and differential heating and cooling along the transect, resulting in density driven fronts and horizontal exchange of water and nutrients between the gulf and the main lake. Upwelling and downwelling maintained mixing conditions in the channel which consequently influenced nutrient recycling, the light environment and hence affecting phytoplankton community composition and productivity. The net residual water flow from the gulf to the main lake was 36 m3/s but the mixing flux was approximately 20 times higher and both fluxes accounted for a gulf exchange time of 1981 days. The advective and mixing fluxes between the gulf and the main lake resulted in net export of dissolved inorganic phosphorus (DIP; 400 kg P/d) from the main lake into the gulf and net export of DRSi (10 t Si/d) from the gulf into the main lake. In the deep, narrow and physically active Rusinga Channel there was net production of dissolved nutrients whereas in the gulf there was net consumption of dissolved nutrients, which helped to maintain high net ecosystem production (NEP; 566 mg C/m2/d) in the gulf in contrast the channel which showed net heterotrophy. The high NEP in the gulf and the associated high nutrient demand coupled with possibly low SRP to DIN supply ratio lead to P limitation of algal growth in the gulf as indicated by all indicators of nutrient status. This has important implications for management since increased P input into the gulf will translate into increased algal blooms in the gulf and therefore compromise water quality. Spatial variability in physical conditions and nutrient status along the study transect influenced phytoplankton community composition and photosynthesis. The shallow and turbid gulf was dominated by cyanobacteria but diatoms dominated in the channel in response to reduced turbidity and increased physical mixing and nutrient availability (DRSi, SRP). In the main lake seasonal stratification and deep mixing depth favoured both cyanobacteria and diatoms. The phytoplankton community in channel had a higher photosynthetic capacity (Fv/Fm, PBm) compared to both the gulf and the main lake.

<p>The chlorophyll a/b binding (CAB) genes play a very central role in all photosynthetic systems and are for Avena sativa (oat) totally unexplored. This dissertation investigates a large number of EST sequences and this investigation characterises the CAB genes in oat, with help from the evolutionary background of oat and the comparison to a reference organism and similar species.</p>

No description available.

ABSTRACT Benthic foraminifers that host algal symbionts are similar to corals in that they rely on their algal endosymbionts for their energy needs, calcify prolifically, and are sensitive to changes in environmental conditions. They are abundant in the benthos of coastal coral-reef areas and are found throughout the tropical and subtropical regions. Pulse Amplitude Modulated (PAM) chlorophyll fluorometry and chlorophyll a extraction techniques were used to quantify and compare the photosynthetic responses of the benthic foraminiferal, Archaias angulatus and their isolated endosymbionts, Chlamydomonas hedleyi, to short-term changes in temperature. Maximum quantum efficiency (Fv/Fm) and rapid light curves (RLCs), from which relative electron transport rates (rETR) of photosystem II (PSII) were derived, were investigated over a thermal range from 4.4° to 33.9 °C in three experiments that were 7 to 31 days in duration. Typical mean yields (Fv/Fm for healthy holobionts (symbionts in hospite) were 0.6 - 0.7, and for isolated symbionts 0.5 - 0.6. Chronic photoinhibition, indicated by significant decreases in Fv/Fm, occurred at temperatures above 31.0°C; there was minimal reduction in efficiency in cooler treatments. The trends between holobiont and symbionts were very similar in all of the photophysiological parameters measured [yield, photoefficiency (<α>), ETRmax and minimum saturating irradiance (Ek)] and supported the temperature range findings in terms of the tolerance of the specimens in the low temperatures up to 31.0 °C. For all photochemical measurements assessed, the holobiont values tended to be somewhat higher than those for the symbionts, with the exception of Ek, possibly indicating a tight coupling in the host-symbiont response during photosynthesis. Chlorophyll a (<μ>g/foram) was negatively correlated with temperature (r = -0.37, p < 0.001) in Experiments 1 and 2. However, in all 3 experiments, chlorophyll a was variable, suggesting a high degree of individual variability in A. angulatus and the ability to acclimate. Some differences observed among treatments may be related to differences in seasons when the specimens were collected and in length of time in culture prior to experiments. Holobiont median rETR light curve trends and photophysiological derived parameters recorded median Ek ranges of ~100-150 <μ>mol photons m-2 s-1, observed ETRmax light intensities of ~200 <μ>mol photons m-2 s-1 and photoinhibition, induced by increasing irradiance intensities, which occurred > 500 <μ>mol photons m-2 s-1. These light curve trends and derived parameters generally supported previous photosynthesis O2 and CO2 gas production studies of A. angulatus. The differences in responses associated with acclimation should be considered in design of future experimental studies. This was the first known physiological study of the viable temperature range and photobiology of A. angulatus using chlorophyll fluorometry methods. Though commonly found in Caribbean and Atlantic waters ranging from 14.0 - 31.0 °C, these results indicate a wider thermal-tolerance range for A. angulatus than was previously known. Keywords: Foraminifera, Chlamydomonas sp., PAM fluorometry, photosynthesis, algal symbiosis

Recent experiments show evidence for long-lived electronic coherence in several photosynthetic complexes, for example in the Fenna-Matthews-Olson complex of green sulfur bacteria. The experiments raise questions about the microscopic reasons for this quantum coherence and its role to the functioning of these highly evolved biological systems. The present thesis addresses both questions. We find that an interplay of electronic coherence and the fluctuating phonon environment is responsible for the high exciton transport efficiency in these complexes and generalize this idea to the concept of environment-assisted quantum transport (ENAQT). In addition, we quantify the contribution of coherent dynamics to the efficiency and thus to the biological functioning. We determine the effect of temporal (non-Markovian) and spatial correlations and develop an ab initio propagation method based on atomistic detail which predicts the long-lived coherence. The research in photosynthetic energy transfer can inspire new designs for the control of excitons in engineered systems. We develop a method for computing the Forster coupling between semiconductor nanoparticle quantum dots. The focus is on the size and shape dependence and the presence of a spatially varying dielectric environment and metallic gates. A separation of the wavefunction into slowly and fast varying part provides the basis for an efficient computation on a real-space grid. Finally, the simulation of structured models of photosynthetic energy transfer is a challenging task using conventional computing resources. To this end, we propose a special-purpose superconducting device based on flux quantum bits and quantum LC resonators and show that parameters can be engineered such that this simulation becomes possible. / Chemistry and Chemical Biology

According to previous research, students show difficulties in understanding photosynthesis and respiration, and basic ecological concepts like energy flow in ecosystems. There are successful teaching units accomplished in this area and many of them can be described as inquiry-based teaching. One definition of inquiry-based teaching is that it involves everything from finding problems, investigating them, debating with peers and trying to explain and give solutions. Accordingly students need to be confronted with challenging questions and empirical data to reason about and teachers need to implement student-generated inquiry discussion since students often stay silent and do not express their thoughts during science lessons. This thesis will focus on young peoples’ understanding of the functioning of plants, students’ participation during biology lessons, and how biology teaching is accomplished in primary and secondary school. Two school classroom projects focusing on teaching about plants and ecology are described. Four teachers and their 4th, 5th and 6th grade classes plus two science teachers and their three 8th grade classes collaborated. Photosynthesis and respiration were made concrete by using tasks where plants, plant cells, germs, seeds and the gas exchange were used. The aim was to listen to students’ reasoning in both teaching and interview situations. Learning outcome, as described by students’ reasoning in the classrooms and in individual interviews but also by their test results, is especially focused. Student-student and student-teacher interactions have been analysed with an ethnographic approach in the classroom context. The plant tasks encouraged the students’ in primary school to develop scientific reasoning and the interviews confirmed that the students had learned about photosynthesis. The ecology teaching in secondary school showed a substantial understanding confirmed both by students’ oral and written reasoning. Analyses of test results and understanding as presented in interviews did not always correspond. The interviews showed the importance of letting students try to explain concepts and to correct themselves. Primary students’ reasoning and understanding about photosynthesis were in the interviews almost the same as the secondary students’. The secondary students’ questioning during the lectures showed wonderments and interest for ecology from a broader view than in the content presented by the teachers and the textbooks, but the large classes and disruptive students stole too much time from the teachers’ management in the classroom. Students’ knowledge was underestimated and their interest in ecology faded away. / Tidigare forskning visar att elever har svårigheter att förstå processer som fotosyntes, cellandning och ekologiska samband, såsom energiflöden i ekosystem. Lyckosamma undervisningsprojekt inom det här området kan ofta beskrivas som ”inquiry-based”. Ett sätt att definiera ”inquiry-based” är att det innefattar allt ifrån att hitta problem, undersöka dem, debattera med andra elever och till att försöka förklara och ge lösningar. Utifrån detta visas att elever behöver bli konfronterade med utmanande frågor och empiriska data att resonera utifrån. Lärarna behöver också arbeta med att föra in studentdiskussioner eftersom det visat sig att många elever ofta är tysta och inte uttrycker sina tankar och spekulationer under NO-lektionerna. Den här avhandlingen fokuserar på elevernas förståelse av växternas funktion, elevernas deltagande under biologilektionerna och på hur biologiundervisning genomförs i mellan- och högstadiet. Två skolprojekt med fokus på växter och ekologi beskrivs. Fyra klasslärare och deras klasser i årskurs 4, 5 och 6, plus två NO-lärare och deras tre klasser i årskurs 8 samarbetade. Fotosyntes och cellandning konkretiserades med hjälp av växter, växtceller, groddar, frön och några gas-utbytesreaktioner. Syftet var att lyssna på vad eleverna resonerade om, både i undervisningssituationer och vid intervju. Elevernas förståelse utifrån deras resonerande men också utifrån deras testresultat fokuserades. Elev-elev- och elev-lärarinteraktioner analyserades med hjälp av en etnografisk ansats i klassrums-kontexten. Uppgifterna med konkret växtmaterial uppmuntrade mellanstadieeleverna att utveckla ett naturvetenskapligt resonerande och intervjuerna bekräftade att eleverna hade lärt sig om fotosyntes. Ekologiundervisningen på högstadiet resulterade i en påtaglig förståelse, som bekräftades utifrån elevernas muntliga och skriftliga resonerande. Analysen av förståelse visad i provresultat och vid intervju överensstämde inte alltid. Intervjuerna visade betydelsen av att låta eleverna både få förklara begrepp och att rätta sig själva i sina förklaringar. I intervjusituationen visade det sig att mellanstadieelevernas resonerande och förståelse av fotosyntes gott kunde mäta sig med högstadieelevernas. Elevernas sätt att ställa frågor under lektionsgenomgångarna visade på funderingar och ett intresse för ekologi, som hade en större bredd än det innehåll som lärare och lärobok presenterade, men stora klasser och störande elever stal alldeles för mycket av lärarens tid för att det skulle vara möjligt att genomföra bra undervisning i klassrummet. Elevernas kunskaper underskattades och deras intresse tonade bort.

Οι πράσινοι καρποί φέρουν ενεργούς χλωροπλάστες, οι οποίοι επιτελούν φωτοσύνθεση και αναπτύσσονται σε ένα ιδιαίτερο μικροπεριβάλλον, που διαφέρει σημαντικά από αυτό των φύλλων. Συγκεκριμένα, χαρακτηρίζεται από υποξία, πολύ υψηλές συγκεντρώσεις CO2 και χαμηλές εντάσεις φωτός, ιδιαίτερα στα εσώτερα σημεία του καρπού. Οι συνθήκες αυτές διαμορφώνονται από τα ανατομικά χαρακτηριστικά των καρπών και από τον υψηλό μεταβολικό ρυθμό που επιδεικνύουν. Τα ιδιαίτερα χαρακτηριστικά του εσωτερικού του καρπού επηρεάζουν αντίστοιχα τα επίπεδα των συνολικών χλωροφυλλών (Chla+b) και τις σχετικές αναλογίες των φωτοσυνθετικών χρωστικών του (Chla/b, Car/Chla+b). Στην παρούσα εργασία, το ενδιαφέρον μας εστιάζεται στη μελέτη των φωτοσυνθετικών χρωστικών των καρπών και στη σύγκριση του προτύπου που διαμορφώνεται μεταξύ φύλλων, περικαρπίων και σπερμάτων, σε όσο το δυνατόν περισσότερα φυτικά είδη. Για τον σκοπό αυτό επιλέξαμε να αξιοποιήσουμε τους αντίστοιχους δείκτες της in vivo ανακλαστικότητας (NDI, δείκτης Chla/b και PRI) ως μια γρήγορη, ευαίσθητη και μη καταστρεπτική μέθοδο εκτίμησης των φωτοσυνθετικών χρωστικών. Παράλληλα, θέλοντας να ελέγξουμε την αξιοπιστία των ανωτέρω δεικτών ανακλαστικότητας και στους καρπούς, προσδιορίσαμε τα επίπεδα των φωτοσυνθετικών χρωστικών και των σχετικών αναλογιών τους και με την παραδοσιακή μέθοδο της εκχύλισης-φασματοφωτομέτρησης. Τα αποτελέσματά μας έδειξαν ότι σε όλες τις περιπτώσεις, τα περικάρπια περιέχουν σαφώς λιγότερες συνολικές χλωροφύλλες και ακολουθούν τα σπέρματα με ακόμα λιγότερες. Η σχετική αναλογία Chla/b είναι χαμηλότερη στα περικάρπια και τα σπέρματα έναντι των φύλλων, γεγονός που μπορεί εν μέρει να ερμηνευθεί ως σκιόφιλη προσαρμογή (περίπτωση σπερμάτων). Ωστόσο, οι εξωτερικές (πλήρως φωτιζόμενες) και οι εσωτερικές (σκιαζόμενες) πλευρές των περικαρπίων εμφανίζουν ίδια επίπεδα του λόγου Chla/b στα περισσότερα είδη που μελετήθηκαν. Αυτό μας υποδεικνύει ότι, ενδεχομένως, άλλοι παράγοντες πέραν του φωτός επηρεάζουν τη σχετική αναλογία των δύο χλωροφυλλών. Επιπρόσθετα, παρατηρήθηκε μη αναμενόμενη, αυξημένη σχετική αναλογία των συνολικών καροτενοειδών σε σχέση με τις συνολικές χλωροφύλλες (Car/Chla+b) των περικαρπίων και των σπερμάτων έναντι των αντίστοιχων φύλλων, εύρημα που χρήζει επίσης περαιτέρω μελέτης. / Green fruits contain active chloroplasts, which are driving the reactions of photosynthesis and function in a particular microenvironment, completely different from that of leaves. This microenvironment is characterized by hypoxia, extremely high internal CO2 concentrations and low light intensity, especially in the inner part of the fruit. The above conditions are shaped by fruit anatomical features and their high metabolic rhythm. The special characteristics of the fruit’s internal affect the total chlorophyll concentration (Chla+b), the ratio of Chla to Chlb (Chla/b) and the carotenoid to chlorophylls ratio (Car/Chla+b). In this study, the photosynthetic pigment profile of green fruits (pericarps and seeds) of 15 different species was investigated, with the corresponding leaves serving as controls. To this aim, the appropriate in vivo spectral reflectance indices (NDI, Chla/b index and PRI) were used, as a rapid, sensitive and non-destructive method for photosynthetic pigment estimation. In order to assess the reliability of the above indices in fruits, we estimated in parallel the photosynthetic pigment levels and their ratios with traditional extracting methods. Our results indicated that compared to leaves, pericarps are characterized by lower levels of total chlorophylls followed by seeds with even lower. The Chla/b ratio is lower in pericarps and seeds. As a consequence the lower Chla/b ratio could only partly be attributed to a shade adaptation. However, the exposed and shaded sides of pericarps displayed similar values for Chla/b ratio in the most of the species tested. Moreover, pericarps and seeds showed unexpectedly, higher carotenoid/chlorophyll ratios.

The increasing food demand as well as the need to predict the impact of warming climate on vegetation makes it critical to find the best tools to assess crop production and carbon dioxide (CO₂) exchange between the land and atmosphere. Photosynthesis is a good indicator of crop production and CO₂ exchange. Chlorophyll fluorescence (ChF) is directly related to photosynthesis. ChF can be measured at leaf-scale using active techniques and at field-scales using passive techniques. The measurement principles of both techniques are different. In this study, three overarching questions about ChF were addressed: Q1) How water, nutrient and ambient light conditions determine the relationships between photosynthesis and ChF? Which is the optimum irradiance level for detecting water and nutrient deficit conditions with ChF?; Q2) which are the limits within which active and passive techniques are comparable?; and Q3) What is the seasonal relationship between photosynthesis and ChF when nitrogen is the limiting factor? To address these questions, two main experiments were conducted: Exp1) Concurrent photosynthesis and ChF light-response curves were measured in camelina and wheat plants growing under (i) intermediate-light and (ii) high-light conditions respectively. Plant stress was induced by (i) withdrawing water, and (ii) applying different nitrogen levels; and Exp2) coincident active and passive ChF measurements were made in a wheat field under different nitrogen treatments. The results indicated ChF has a direct relationship with photosynthesis when water or nitrogen drives the relationship. This study demonstrates that the light level at which plants were grown was optimum for detecting water and nutrient deficit with ChF. Also, the results showed that for leaf-average-values, active measurements can be used to better understand the daily and seasonal behavior of passive ChF. Further, the seasonal relation between photosynthesis and ChF with nitrogen stress was not a simple linear function. Our study showed that at times in the season when nitrogen was sufficient and photosynthesis was highest, ChF decreased because these two processes compete for available energy. These results demonstrated that ChF is a reliable indicator of crop stress and has great potential for better understand the CO₂ exchange between the land and atmosphere.

During photosynthesis, two multi-protein complexes, photosystems (PS) I and II work in tandem to convert the light-energy absorbed by the light-harvesting antennae into chemical energy, which is subsequently used to assimilate atmospheric carbon dioxide into organic carbon compounds. This is the main nutritional basis for life on Earth. The photosynthetic antenna of higher plants comprises at least ten different pigment-binding proteins (LHC), which play important roles in photosynthesis. Chlorophyll and carotenoid molecules associated with the LHC proteins are organised into an array, which can be modulated, thereby optimising light-harvesting processes and protection against oxidative damage under conditions of excessive light absorption. All ten LHC proteins have been conserved through eons of evolution, suggesting that there are strong evolutionary pressures to retain all ten proteins, and hence that each protein has a unique function. The light-harvesting antenna of higher plant PSI consists of at least four proteins, Lhca1-4, collectively called LHCI. By constructing transgenic Arabidopsis thaliana plants in which each Lhca gene has been individually repressed or knocked-out, a collection of plants with different Lhca protein contents was obtained. The objective was to use these plants to study the structure, function and regulation of the Lhca proteins in vivo. The major findings of this work are as follows. Removing single Lhca proteins influenced the stability of the other Lhca proteins, showing that there is a high degree of inter-dependency between the polypeptides in LHCI, and hence that a full set of Lhca proteins is important for maintaining the structural integrity of LHCI. This has provided insight into the organisation of LHCI by revealing clues about the relative positions of each Lhca protein in the antenna complex. The physiological consequences of removing individual Lhca proteins were dependent on the degree of antenna depletion. Plants with relatively small antenna changes could compensate, to some extent, for the loss of LHCI, while larger depletions had profound effects on whole plant resulting in growth reductions. The fitness of each Lhca plant was assessed by measuring their seed production in the harsh conditions in the field. We found that all Lhca-deficient plants produced fewer seeds under some conditions, with seed-production compared to wild type varying between 10-80% depending on the extent of LHCI reduction. Therefore, we conclude that each Lhca protein is important for plant fitness, and hence for the survival of the species. PSI is characterised by a pool of pigments absorbing light in the red end of the solar visible spectrum, thought to be especially important for plants in dense vegetation systems where the incident light is enriched in wavelengths higher than 690 nm. A majority of these pigments are situated on LHCI and, based on in-vitro studies, were thought to be mainly associated with Lhca4. Using our plants, we have established that red pigments are indeed present on all Lhca proteins and that these pigments become even more red upon association with PSI.

During photosynthesis sunlight is absorbed by photosynthetic pigments and converted into organic compounds, such as carbohydrates. Photosynthesis needs to be highly regulated, since both too much and too little light are harmful to plant. If too little light is absorbed, a plant cannot store enough energy, which will have effects on growth and fitness of the plant. With too much light absorbed, a dangerous side reaction of photosynthesis, the production of reactive oxygen species can happen. These reactive oxygen species can damage the proteins in the chloroplast and the lipids of the chloroplast. To avoid the production of reactive oxygen species, plants have evolved many mechanisms, which act on different time-scales and different levels of organization. As a first measure, when the absorbed light is exceeding the capacity for its utilization, is to switch the light-harvesting antenna from efficient light harvesting to energy dissipation. This process is called feedback de-excitation (FDE). The protein PsbS is essential for this process as well as a functioning xanthophylls cycle with the enzyme violaxanthin de-epoxidase (VDE). I have investigated the effects of plants with changes in their ability to dissipate excess excitation energy in the model plants species Arabidopsis thaliana. Three genotypes with either increased or decreased capacity for FDE were used during my experiments. The first genotype over-expresses the PsbS gene, having approximately two-fold increased amounts of PsbS and FDE. The second is a PsbS deletion mutant with no PsbS protein and no FDE. The third genotype cannot perform the conversion of violaxanthin to zeaxanthin, because the enzyme VDE is missing. This mutant has some FDE left. Arabidopsis thaliana is an annual plant, which flowers only once in its lifetime. Therefore, when counting the seeds produced an estimation of fitness can be made from the amount of seeds produced. This was done during my experiments and shown that FDE is a trait and that plants with increased FDE have a higher fitness and vice versa. This was also the case for a collection of plants lacking a single protein from the light harvesting antenna. All of these genotypes had a fitness reduction, proving that their function is not redundant. In an attempt to explain why the fitness is reduced in plants with altered FDE, photosynthetic measurements, as well as a determination of the transcriptome and the metabolome was performed. Plants lacking FDE had higher levels of photoinhibition, leading both to lower rates of photosynthesis and to higher repair cost. This could in part explain the reduction in fitness. These plants also had major changes in their transcriptome and their metabolome. Primary metabolism was most effected, for example carbohydrate and amino acid metabolism. But there were also changes in secondary metabolism such as an up regulation of the biosynthesis of anthocyanins.