Building Morphological Chains for Agglutinative Languages

In this paper, we build morphological chains for agglutinative languages by using a log-linear model for the morphological segmentation task. The model is based on the unsupervised morphological segmentation system called MorphoChains. We extend MorphoChains log linear model by expanding the candidate space recursively to cover more split points for agglutinative languages such as Turkish, whereas in the original model candidates are generated by considering only binary segmentation of each word. The results show that we improve the state-of-art Turkish scores by 12% having a F-measure of 72% and we improve the English scores by 3% having a F-measure of 74%. Eventually, the system outperforms both MorphoChains and other well-known unsupervised morphological segmentation systems. The results indicate that candidate generation plays an important role in such an unsupervised log-linear model that is learned using contrastive estimation with negative samples.Comment: 10 pages, accepted and presented at the CICLing 2017 (18th International Conference on Intelligent Text Processing and Computational Linguistics

Structure and membrane organization of photosystem II in green plants

Photosystem II (PSII) is the pigment protein complex embedded in the thylakoid membrane of higher plants, algae, and cyanobacteria that uses solar energy to drive the photosynthetic water-splitting reaction. This chapter reviews the primary, secondary, tertiary, and quaternary structures of PSII as well as the function of its constituent subunits. The understanding of in vivo organization of PSII is based in part on freeze-etched and freeze-fracture images of thylakoid membranes. These images show a resolution of about 40-50 Angstrom and so provide information mainly on the localization heterogeneity, dimensions, and shapes of membrane-embedded PSII complexes. Higher resolution of about 15-40 Angstrom has been obtained from single particle images of isolated PSII complexes of defined and differing subunit composition and from electron crystallography of 2-D crystals. Observations are discussed in terms of the oligomeric state and subunit organization of PSII and its antenna components.</p

Localization of the 23-kDa subunit of the oxygen-evolving complex of photosystem II by electron microscopy

A dimeric photosystem II light-harvesting II super complex (PSII-LHCII SC), isolated by sucrose density gradient centrifugation, was previously structurally characterized. This PSII-LHCII SC bound the 33-kDa subunit of the oxygen-evolving complex (OEC), but lacked the 23-kDa and 17-kDa subunits of the OEC. Here the isolation procedure was modified by adding 1 M glycine betaine (1-carboxy-N,N,N-trimethylmethanaminium hydroxide inner salt) to the sucrose gradient mixture. This procedure yielded PSII-LHCII SC that contained both the 33-kDa and the 23-kDa subunits and had twice the oxygen-evolving capacity of the super complexes lacking the 23-kDa polypeptide. Addition of CaCl2 to PSII-LHCII SC with the 23-kDa subunit attached did not increase the oxygen-evolution rate. This suggests that the 23-kDa subunit is bound in a functional manner and is present in significant amounts. Over 5000 particle projections extracted from electron microscope images of negatively stained PSII-LHCII SC, isolated in the presence and absence of glycine betaine, were analyzed using single-particle image-averaging techniques. Both the 23-kDa and 33-kDa subunits could be visualized in top-view and side-view projections. In the side view the 23-kDa subunit is seen to protrude 0.5-1 nm further than the 33-kDa subunit, giving the PSII particle a maximal height of 9.5 nm. Measured from the centres of the masses, the two 33-kDa subunits associated with the dimeric PSII-LHCII SC are separated by 6.3 nm. The corresponding distance between the two 23-kDa subunits is 8.8 nm.

Plants lacking the main light-harvesting complex retain photosystem II macro-organization

Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure—the major trimeric complexes (LHCII) that bind 70% of PSII chlorophyll and three minor monomeric complexes—which together form PSII supercomplexes. The antenna complexes are essential for collecting sunlight and regulating photosynthesis, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function

Organization of the AAA(+) adaptor protein PspA is an oligomeric ring

The 25.3 kDa "adaptor" protein, PspA (dphage shock protein A), is found in the cytoplasm and in association with the inner membrane of certain bacteria. PspA plays critical roles in negatively regulating the phage shock response and maintaining membrane integrity, especially during the export of proteins such as virulence factors. Homologues of PspA function exist for thylakoid biogenesis. Here we report the first three-dimensional reconstruction of a PspA assembly from Escherichia coli, visualized by electron microscopy and single particle analysis to a resolution of 30 Angstrom. The assembly forms a 9-fold rotationally symmetric ring with an outer diameter of 200 Angstrom, an inner diameter of 95 Angstrom, and a height of similar to85 Angstrom. The molecular mass of the complex was calculated to be 1023 kDa by size exclusion chromatography, suggesting that each of the nine domains is likely to be composed of four PspA subunits. The functional implications of this PspA structure are discussed in terms of its interaction with the protein export machinery of the bacterial cell and its AAA(+) protein partner, PspF

Time-course global expression profiles of Chlamydomonas reinhardtii during photo-biological H₂ production.

We used a microarray study in order to compare the time course expression profiles of two Chlamydomonas reinhardtii strains, namely the high H₂ producing mutant stm6glc4 and its parental WT strain during H₂ production induced by sulfur starvation. Major cellular reorganizations in photosynthetic apparatus, sulfur and carbon metabolism upon H₂ production were confirmed as common to both strains. More importantly, our results pointed out factors which lead to the higher H₂ production in the mutant including a higher starch accumulation in the aerobic phase and a lower competition between the H₂ase pathway and alternative electron sinks within the H₂ production phase. Key candidate genes of interest with differential expression pattern include LHCSR3, essential for efficient energy quenching (qE). The reduced LHCSR3 protein expression in mutant stm6glc4 could be closely related to the high-light sensitive phenotype. H₂ measurements carried out with the LHCSR3 knock-out mutant npq4 however clearly demonstrated that a complete loss of this protein has almost no impact on H₂ yields under moderate light conditions. The nuclear gene disrupted in the high H₂ producing mutant stm6glc4 encodes for the mitochondrial transcription termination factor (mTERF) MOC1, whose expression strongly increases during -S-induced H₂ production in WT strains. Studies under phototrophic high-light conditions demonstrated that the presence of functional MOC1 is a prerequisite for proper LHCSR3 expression. Furthermore knock-down of MOC1 in a WT strain was shown to improve the total H₂ yield significantly suggesting that this strategy could be applied to further enhance H₂ production in other strains already displaying a high H₂ production capacity. By combining our array data with previously published metabolomics data we can now explain some of the phenotypic characteristics which lead to an elevated H₂ production in stm6glc4

One-step isolation and biochemical characterization of a highlyactive plant PSII monomeric core

We describe a one-step detergent solubilization protocol for isolating a highly active form of Photosystem II (PSII) from Pisum sativum L. Detailed characterization of the preparation showed that the complex was a monomer having no light harvesting proteins attached. This core reaction centre complex had, however, a range of low molecular mass intrinsic proteins as well as the chlorophyll binding proteins CP43 and CP47 and the reaction centre proteins D1 and D2. Of particular note was the presence of a stoichiometric level of PsbW, a low molecular weight protein not present in PSII of cyanobacteria. Despite the high oxygen evolution rate, the core complex did not retain the PsbQ extrinsic protein although there was close to a full complement of PsbO and PsbR and partial level of PsbP. However, reconstitution of PsbP and PsbPQ was possible. The presence of PsbP in absence of LHCII and other chlorophyll a/b binding proteins confirms that LHCII proteins are not a strict requirement for the assembly of this extrinsic polypeptide to the PSII core in contrast with the conclusion of Caffarri et al. (2009)

Phylogenetic and molecular analysis of hydrogen-producing green algae

A select set of microalgae are reported to be able to catalyse photobiological H2 production from water. Based on the model organism Chlamydomonas reinhardtii, a method was developed for the screening of naturally occurring H2-producing microalgae. By purging algal cultures with N2 in the dark and subsequent illumination, it is possible to rapidly induce photobiological H2 evolution. Using NMR spectroscopy for metabolic profiling in C. reinhardtii, acetate, formate, and ethanol were found to be key compounds contributing to metabolic variance during the assay. This procedure can be used to test algal species existing as axenic or mixed cultures for their ability to produce H2. Using this system, five algal isolates capable of H2 production were identified in various aquatic systems. A phylogenetic tree was constructed using ribosomal sequence data of green unicellular algae to determine if there were taxonomic patterns of H2 production. H2-producing algal species were seen to be dispersed amongst most clades, indicating an H2-producing capacity preceded evolution of the phylum Chlorophyta

Improved photobiological H-2 production in engineered green algal cells

Oxygenic photosynthetic organisms use solar energy to split water (H2O) into protons (H+), electrons (e(-)), and oxygen. A select group of photosynthetic microorganisms, including the green alga Chlamydomonas reinhardtii, has evolved the additional ability to redirect the derived H+ and e(-) to drive hydrogen (H-2) production via the chloroplast hydrogenases HydA1 and A2 (H(2)ase). This process occurs under anaerobic conditions and provides a biological basis for solar-driven H-2 production. However, its relatively poor yield is a major limitation for the economic viability of this process. To improve H-2 production in Chlamydomonas, we have developed a new approach to increase H+ and e(-) supply to the hydrogenases. In a first step, mutants blocked in the state 1 transition were selected. These mutants are inhibited in cyclic e(-) transfer around photosystem I, eliminating possible competition for e(-) with H(2)ase. Selected strains were further screened for increased H-2 production rates, leading to the isolation of Stm6. This strain has a modified respiratory metabolism, providing it with two additional important properties as follows: large starch reserves ( i.e. enhanced substrate availability), and a low dissolved O-2 concentration (40% of the wild type (WT)), resulting in reduced inhibition of H2ase activation. The H-2 production rates of Stm6 were 5 - 13 times that of the control WT strain over a range of conditions ( light intensity, culture time, +/- uncoupler). Typically, similar to 540 ml of H-2 liter(-1) culture ( up to 98% pure) were produced over a 10-14-day period at a maximal rate of 4 ml h(-1) ( efficiency = similar to 5 times the WT). Stm6 therefore represents an important step toward the development of future solar-powered H-2 production systems