Photosystem I Incorporation into Metal Organic Frameworks for Advanced Bio-hybrid Photoactive Materials

Metal-organic frameworks (MOFs) are a new type of hybrid material with unique properties that allow for diverse functionality and have shown promise for use in gas storage and separation, catalysis, chemical sensors, supercapacitors, drug delivery, and proton conduction in membranes for fuel cells. Metal ion nodes are connected by organic struts to create infinite crystalline porous networks with tunable geometries and chemical functionalities that have led to more than 20,000 different MOF structures reported in the past decade. These lattices have uniform pore sizes that can range from 0.4 to 10 nm and have set new records for free volume and internal surface area. MOFs offer unique advantages as a porous material over purely inorganic crystallines, such as zeolites, and purely organic aerogels or polymers. The atomic positions of the lattice can be known at the sub-angstrom level, determined almost exclusively by the coordination geometry of the metal node and the topology of the organic linker. Additionally, the chemical composition of the structure can be altered one functional group at a time via pre- or post-synthetic modification of the linkers. This leads to the ability to finely control both the geometry and chemistry of the MOFs; as form begets function, all mechanical, chemical, optical, and electrical properties can be rationally tuned. The vast majority of research on MOFs has centered around their microporosity. The ability to create very small, uniform pores potentially allows for more efficient means of gas and liquid separation. Because this is a new material, the idea of optimizing the already exceptional properties of MOFs is appealing. Due the immense number of possible combinations of metal nodes and organic linkers, there is indication that they hold true promise for utilization in electronic and optoelectronic devices. We have proposed and executed a new method for embedding, protecting, and activating the Photosystem I protein complex inside the ZIF-8 framework

The chlorosome: a prototype for efficient light harvesting in photosynthesis

Three phyla of bacteria include phototrophs that contain unique antenna systems, chlorosomes, as the principal light-harvesting apparatus. Chlorosomes are the largest known supramolecular antenna systems and contain hundreds of thousands of BChl c/d/e molecules enclosed by a single membrane leaflet and a baseplate. The BChl pigments are organized via self-assembly and do not require proteins to provide a scaffold for efficient light harvesting. Their excitation energy flows via a small protein, CsmA embedded in the baseplate to the photosynthetic reaction centres. Chlorosomes allow for photosynthesis at very low light intensities by ultra-rapid transfer of excitations to reaction centres and enable organisms with chlorosomes to live at extraordinarily low light intensities under which no other phototrophic organisms can grow. This article reviews several aspects of chlorosomes: the supramolecular and molecular organizations and the light-harvesting and spectroscopic properties. In addition, it provides some novel information about the organization of the baseplate

The physiological importance of photosynthetic ferredoxin NADP+ oxidoreductase (FNR) isoforms in wheat

Ferredoxin NADP+ oxidoreductase (FNR) enzymes catalyse electron transfer between ferredoxin and NADPH. In plants, a photosynthetic FNR (pFNR) transfers electrons from reduced ferredoxin to NADPH for the final step of linear electron flow, providing reductant for carbon fixation. pFNR is also thought to play important roles in two different mechanisms of cyclic electron flow around photosystem I; and photosynthetic reductant is itself partitioned between competing linear, cyclic, and alternative electron flow pathways. Four pFNR protein isoforms in wheat that display distinct reaction kinetics with leaf-type ferredoxin have previously been identified. It has been suggested that these isoforms may be crucial to the regulation of reductant partition between carbon fixation and other metabolic pathways. Here the 12 cm primary wheat leaf has been used to show that the alternative N-terminal pFNRI and pFNRII protein isoforms have statistically significant differences in response to the physiological parameters of chloroplast maturity, nitrogen regime, and oxidative stress. More specifically, the results obtained suggest that the alternative N-terminal forms of pFNRI have distinct roles in the partitioning of photosynthetic reductant. The role of alternative N-terminal processing of pFNRI is also discussed in terms of its importance for thylakoid targeting. The results suggest that the four pFNR protein isoforms are each present in the chloroplast in phosphorylated and non-phosphorylated states. pFNR isoforms vary in putative phosphorylation responses to physiological parameters, but the physiological significance requires further investigation

Realtime Analysis of Large-Scale Data [Finale Version]

Upcoming facilities in photon science offer entirely new research opportunities for scientists. Although the amount of data taken by the detector devices will increase drastically, only a fraction of the data can be used in subsequent analyses. Inherent limitations in the experimental setup result in a huge amount of empty or meaningless images being taken. The aim of this thesis is to develop algorithms for selecting suitable data and thereby make such experiments feasible in the first place

Realtime Analysis of Large-Scale Data

In photon science more and more data are taken. It is not possible anymore to store and process all data offline. In this book, we explore strategies for handling this large amount of data. A neural network as well as techniques from image processing are used to efficiently categorize and select useful data. We also indicate why many sophisticated algorithms cannot be used in this context. In addition, a prototype for data selection is presented, discussed, and benchmarked

Computing Network of Diseases and Pharmacological Entities through the Integration of Distributed Literature Mining and Ontology Mapping

The proliferation of -omics (such as, Genomics, Proteomics) and -ology (such as, System Biology, Cell Biology, Pharmacology) have spawned new frontiers of research in drug discovery and personalized medicine. A vast amount (21 million) of published research results are archived in the PubMed and are continually growing in size. To improve the accessibility and utility of such a large number of literatures, it is critical to develop a suit of semantic sensitive technology that is capable of discovering knowledge and can also infer possible new relationships based on statistical co-occurrences of meaningful terms or concepts. In this context, this thesis presents a unified framework to mine a large number of literatures through the integration of latent semantic analysis (LSA) and ontology mapping. In particular, a parameter optimized, robust, scalable, and distributed LSA (DiLSA) technique was designed and implemented on a carefully selected 7.4 million PubMed records related to pharmacology. The DiLSA model was integrated with MeSH to make the model effective and efficient for a specific domain. An optimized multi-gram dictionary was customized by mapping the MeSH to build the DiLSA model. A fully integrated web-based application, called PharmNet, was developed to bridge the gap between biological knowledge and clinical practices. Preliminary analysis using the PharmNet shows an improved performance over global LSA model. A limited expert evaluation was performed to validate the retrieved results and network with biological literatures. A thorough performance evaluation and validation of results is in progress

Light-acclimation and regulation of photosynthesis in autotrophic Chlamydomonas reinhardtii

Photosynthetic light reactions take place in the thylakoid membranes, where lightdriven electron transfer occurs from water to carbon dioxide through two photosystems (PSII and PSI), between of which is an electron-transferring agent called plastoquinone (PQ). PQ is present in the thylakoids as a pool (PQ-pool) that consists of its reduced and oxidized forms. The ratio of the two forms of PQ has long been known to control the movement of the Light-harvesting complex II trimers between PSII and PSI, a phenomenon termed as state transitions. Most of our understanding on algal photosynthesis originates from plant studies. However, as our knowledge of the algal system has increased, it is now clear that deeper understanding, e.g. about regulation of algal light reactions, is required. This thesis set out to examine how the green alga Chlamydomonas reinhardtii withstands strong light that damages the photosynthetic machinery. The results demonstrate how mutant strain cells resistant against photoinhibition of PSII perform better under high light and how they divert the resources saved from less active PSII repair to biomass production. The photoinhibition-tolerance of the mutant is hypothesized to be partly due to changes in the redox potentials inside PSII. However, it is also shown that even a wild-type population of Chlamydomonas can survive under extreme light intensities via modifications to the photosynthetic machinery. This variation-dependent acclimation enables the cells to cope with the increased photon flux. The demonstrated acclimation contains numerous changes in the properties of PSII, such as significantly reduced rate of singlet oxygen production. However, the acclimated cells exhibit signs of severe photoinhibition. Lastly, this work highlights the dynamics of the PQ-pool and its relation to state transitions in Chlamydomonas. The PQ-pool of Chlamydomonas is shown to be of similar size as in cyanobacteria and plants. It is highly reduced under almost all light conditions applied, possibly due to fairly similar wavelength dependence profiles of algal PSII and PSI. The non-photochemical reduction and oxidation of PQ are very active in the used alga. It is also shown that state transitions do not correlate with the PQ-pool redox state in Chlamydomonas as in plants, and that light states respond more to the intensity, rather than the quality of light in autotrophic Chlamydomonas. KEYWORDS: Light-acclimation, Chlamydomonas, high light, photoinhibition, photosynthesis, photosystem II, plastoquinone pool, state transitionsYhteyttämisen valoreaktiot tapahtuvat tylakoidikalvoilla, joihin ankkuroituneet valoreaktiokeskukset (PSII ja PSI) käyttävät kerättyä valoenergiaa elektronien siirtämiseen. PSII:n ja PSI:n välissä elektroneja siirtää plastokinoni (PQ), jonka pelkistyneet ja hapettuneet muodot muodostavat fotokemiallisesti aktiivisen plastokinonivarannon (PQ-pooli). PQ-poolin hapetus-pelkistys-asteen on jo kauan tiedetty säätelevän valoa keräävien antenniproteiinien liikettä PSII:n ja PSI:n välillä. Tätä ilmiötä kutsutaan tilasiirtymiksi. Tietomme viherlevien yhteyttämisestä pohjautuu paljolti kasvitutkimuksiin. On kuitenkin selvää, että esimerkiksi levien valoreaktioiden säätely eroaa kasveista, mikä painottaa levillä tehtävän tutkimuksen tärkeyttä niiden yhteyttämisreaktioiden ymmärtämiseksi. Tämä työ tutki viherlevä Chlamydomonas reinhardtiin kykyä sietää valoolosuhteita, joiden tiedetään vahingoittavan yhteyttämiskoneistoa. Tuloksissa esitetään, kuinka PSII:n fotoinhibitiolle vastustuskykyinen mutanttikanta kykenee uudelleenohjaamaan resursseja biomassan tuotantoon, jotka villityypissä kuluvat PSII:n korjausreaktioihin. Mutantin fotoinhibition sietokyvyn arvellaan osittain johtuvan PSII:n sisäisten redox-potentiaalien muutoksista. Myös villityypin Chlamydomonas kykenee kasvamaan hyvin korkeassa valon intensiteetissä. Tämä ominaisuus riippuu solupopulaation sisäisen vaihtelun määrästä, joka lisää akklimaatiokykyisten solujen lukumäärää kasvatuksessa. Akklimaation seurauksena useat yhteyttämiskoneiston ominaisuudet muuttuvat, joista huomionarvoisin on singlettihapen muodostumisen merkittävä hidastuminen. Muutoksista riippumatta, akklimoituneet solut ovat silti alttiita fotoinhibitiolle. Työ tarkasteli myös Chlamydomonaksen PQ-poolin hapetus-pelkitys-tilaa ja sen vaikutusta tilasiirtymiin. Tuloksena todettiin Chlamydomonaksen PQ-poolin olevan samaa kokoluokkaa kuin syanobakteereilla ja kasveilla. Lisäksi se pysyi korkeasti pelkistyneenä lähes kaikissa valo-olosuhteissa, minkä oletettiin johtuvan levien PSII:n ja PSI:n hyvin samankaltaisesta kapasiteetista kerätä valoa. Ei-fotokemialliset reaktiot vaikuttivat myös voimakkaasti levien PQ-pooliin. Toisin kuin kasveilla, Chlamydomonaksen tilasiirtymien todettiin reagoivan pääasiallisesti valon intensiteetin, ei laadun, vaihteluun. ASIASANAT: Chlamydomonas, fotoinhibitio, plastokinonivaranto, sopeutuminen, tilasiirtymät, valoreaktiokeskus II, voimakas valo, yhteyttämine

A study of the growth and hydrogen production of Cyanothece sp. ATCC 51142

Hydrogen (H2) has long been promoted as an ideal fuel, as it permits a completely clean combustion and has great potential to provide clean power needed for transport and electricity generation. The unicellular, nitrogen-fixing cyanobacterium Cyanothece sp. ATCC 51142 is a promising strain with a remarkable capability of producing large quantities of H2. Under anaerobic condition, the cyanobacterium carries out the biological fixation of atmospheric nitrogen (N2) into ammonia (NH3), concurrently producing H2 as by-product. The aim of this thesis was to improve our understanding of the growth and H2 production of Cyanothece sp. ATCC 51142 in order to develop a continuous and practical cyanobacterial H2 production process. In order to achieve effective H2 production, it is prerequisite to grow dense and healthy Cyanothece 51142 cultures. Favourable cyanobacterial growth conditions included a continuous illumination at 207 - 320 μmol m-2 s-1, temperature of 35 °C and nitrogen-replete (addition of nitrate salts) condition. The critical temperature, which induces photoinhibition upon the cyanobacterium, was found at 40 °C. In the case of H2 production, favourable conditions included a continuous illumination at low light intensities of 46 – 92 μmol m-2 s-1, temperature of 30 °C, nitrogen-fixing (sole presence of atmospheric N2) and photoheterotrophic (sole presence of organic glycerol substrate) growth condition. In order to effectively handle incompatible requirements between the cyanobacterial growth and its sequential H2 production, a novel two-stage chemostat photobioreactor (PBR) system was designed and developed, with an aim to improve H2 production yield as well as extend its production duration. The system has been operated non-stop for consecutive 31 days without any losses in its performance and subsequently demonstrated a remarkable improvement in H2 production, with more than 6.4 times higher yield than that of a single-stage batch system. With the continuous mode of operation, a continuous collection of produced biomass from the PBR is also permitted (more than 7.3 times improvement in biomass yield than that of a single-stage batch system). At an industrial scale, this biomass could undergo further downstream processing to generate a multistreamline of high valued by-products such as e.g. vitamins, pharmaceuticals and human nutrition, which can subsequently contribute to a significant improvement in an economic viability of biohydrogen process.Open Acces

Spacelab Science Results Study

Beginning with OSTA-1 in November 1981 and ending with Neurolab in March 1998, a total of 36 Shuttle missions carried various Spacelab components such as the Spacelab module, pallet, instrument pointing system, or mission peculiar experiment support structure. The experiments carried out during these flights included astrophysics, solar physics, plasma physics, atmospheric science, Earth observations, and a wide range of microgravity experiments in life sciences, biotechnology, materials science, and fluid physics which includes combustion and critical point phenomena. In all, some 764 experiments were conducted by investigators from the U.S., Europe, and Japan. The purpose of this Spacelab Science Results Study is to document the contributions made in each of the major research areas by giving a brief synopsis of the more significant experiments and an extensive list of the publications that were produced. We have also endeavored to show how these results impacted the existing body of knowledge, where they have spawned new fields, and if appropriate, where the knowledge they produced has been applied