bluuebunny/crossref_metadata_2025 huggingface dataset:
CLAIRE: combining sets, search and rules to
better express algorithms
Authors: CASEAU YVES , JOSSET FRANÇOIS-XAVIER , LABURTHE FRANÇOIS
Published: November 2002

This paper presents a programming language which includes paradigms that are usually
associated with declarative languages, such as sets, rules and search, into an imperative
(functional) language. Although these paradigms are separately well known and are available
under various programming environments, the originality of the CLAIRE language comes
from the tight integration, which yields interesting run-time performances, and from the
richness of this combination, which yields new ways in which to express complex algorithmic
patterns with few elegant lines. To achieve the opposite goals of a high abstraction level
(conciseness and readability) and run-time performance (CLAIRE is used as a C++ preprocessor), we have developed two kinds of compiler: first, a pattern pre-processor handles
iterations over both concrete and abstract sets (data types and program fragments), in a
completely user-extensible manner; secondly, an inference compiler transforms a set of logical
rules into a set of functions (demons that are used through procedural attachment).
Using methods of declarative logic
programming for intelligent information agents
Authors: EITER THOMAS , FINK MICHAEL , SABBATINI GIULIANA , TOMPITS HANS
Published: November 2002

At present, the search for specific information on the World Wide Web is faced with
several problems, which arise on the one hand from the vast number of information sources
available, and on the other hand, from their intrinsic heterogeneity, since standards are
missing. A promising approach for solving the complex problems emerging in this context
is the use of multi-agent systems of information agents, which cooperatively solve advanced
information-retrieval problems. This requires advanced capabilities to address complex tasks,
such as search and assessment of information sources, query planning, information merging
and fusion, dealing with incomplete information, and handling of inconsistency. In this
paper, our interest lies in the role which some methods from the field of declarative logic
programming can play in the realization of reasoning capabilities for information agents. In
particular, we are interested to see how they can be used, extended, and further developed
for the specific needs of this application domain. We review some existing systems and
current projects, which typically address information-integration problems. We then focus
on declarative knowledge-representation methods, and review and evaluate approaches and
methods from logic programming and nonmonotonic reasoning for information agents. We
discuss advantages and drawbacks, and point out the possible extensions and open issues.
COUP-TF (chicken ovalbumin upstream promoter transcription factor)-interacting protein 1 (CTIP1) is a sequence-specific DNA binding protein
Authors: AVRAM Dorina , FIELDS Andrew , SENAWONG Thanaset , TOPARK-NGARM Acharawan , LEID Mark
Published: November 2002

Chicken ovalbumin upstream promoter transcription factor (COUP-TF)-interacting proteins 1 and 2 [CTIP1/Evi9/B cell leukaemia (Bcl) l1a and CTIP2/Bcl11b respectively] are highly related C2H2 zinc finger proteins that are abundantly expressed in brain and the immune system, and are associated with immune system malignancies. A selection procedure was employed to isolate high-affinity DNA binding sites for CTIP1. The core binding site on DNA identified in these studies, 5′-GGCCGG-3′ (upper strand), is highly related to the canonical GC box and was bound by a CTIP1 oligomeric complex(es) in vitro. Furthermore, both CTIP1 and CTIP2 repressed transcription of a reporter gene harbouring a multimerized CTIP binding site, and this repression was neither reversed by trichostatin A (an inhibitor of known class I and II histone deacetylases) nor stimulated by co-transfection of a COUP-TF family member. These results demonstrate that CTIP1 is a sequence-specific DNA binding protein and a bona fide transcriptional repressor that is capable of functioning independently of COUP-TF family members. These findings may be relevant to the physiological and/or pathological action(s) of CTIPs in cells that do not express COUP-TF family members, such as cells of the haematopoietic and immune systems.
Cloning and molecular expression analysis of large and small lecithin:retinol acyltransferase mRNAs in the liver and other tissues of adult rats
Authors: ZOLFAGHARI Reza , WANG Yuanping , CHEN Qiuyan , SANCHER Anne , ROSS A. Catharine
Published: November 2002

Retinyl ester, the most abundant form of vitamin A (retinol), is synthesized by the enzyme lecithin:retinol acyltransferase (LRAT). Previously, we cloned a 2.5kb LRAT cDNA from rodent liver which codes for functional LRAT activity. However, Northern blots of tissues probed with the 2.5kb cDNA revealed the presence of a larger transcript of 5kb as well as several smaller transcripts. To elucidate the nature of the large LRAT transcript, a high-molecular-mass adrenal gland cDNA library was screened. Two similar clones of 3962 and 3187nt were identified which appeared to be part of the 3′-untranslated region (UTR) of a 5358nt LRAT mRNA. The 5.3kb cDNA was then amplified from liver by reverse transcriptase PCR (RT-PCR) and demonstrated to encode functional LRAT activity. The 3′-UTR of the 5.3kb cDNA contains several AAUAAA polyadenylation signals. Analysis of the 3′ ends of LRAT mRNA transcripts from liver, intestine and testis showed the usage of both canonical and non-canonical polyadenylation signals. To further analyse the LRAT mRNAs expressed in vivo, Northern blot analysis was performed using four probes spanning sections from the 5′ end to the distal 3′ end of the 5.3kb LRAT cDNA. The results show that the major 5.3kb transcript uses the canonical signal AAUAAA located at nt 5308, and the major short transcript of 1.5kb uses the non-canonical signal AUUAAA located at nt 1330. The 5.3kb LRAT transcript was predominant in the liver of retinoic acid-repleted vitamin A-deficient rats, coincident with increased quantitative expression of LRAT mRNA and enzyme activity. The differential usage of these polyadenylation signals can explain the presence of multiple LRAT mRNA transcripts which are expressed in different tissue-specific patterns.
Water Transport in Impaired Leaf Vein Systems
Authors: Hüve K. , Remus R. , Lüttschwager D. , Merbach W.
Published: November 2002

Abstract: The subject of our investigation was the water regime of broad bean leaves (Vicia faba L.), especially after having mechanically severed parts of the leaf blade and the leaf venation. Under moderate conditions, 18 ‐ 22 °C temperature and 50 ‐ 70 % relative humidity, the leaves remained viable even after extensive damage. Only if more than 90 % of the xylem cross sectional area of a leaf was severed, the leaf wilted. Lesser damage to the xylem cross‐sectional area only resulted in a reduced rate of transpiration and assimilation, compared to intact leaves. The cuts in larger veins were bypassed into small or even very small veins, as shown by xylem transport of dyes. In intact leaves, small veins have a negligible task in long‐distance transport. Here, however, transport velocity in small veins was severalfold increased compared to the measurement of transport velocity in veins of the same size in intact leaves. Thereby, water transport to leaf areas distal from the cut was ensured.
Single Nucleotide Polymorphisms in the Coding Region of the Developmental Gene Gcyc in Natural Populations of the Relict Ramonda myconi (Gesneriaceae)
Authors: Picó F. X. , Möller M. , Ouborg N. J. , Cronk Q. C. B.
Published: November 2002

Abstract: Gcyc is a developmental gene, present in the Gesneriaceae family, that has both highly conserved and highly variable regions. Ramonda myconi (Gesneriaceae) is a paleoendemic plant restricted to mountainous areas of NE Spain. In this study we examine the population variation in the coding region of Gcyc in R. myconi. The fast‐evolving nature of the coding regions of the Gcyc gene plus the ancient history of R. myconi together provide an appropriate background to obtain the first insights into population‐level variation in developmental genes of flowering plants. One locus of Gcyc was specifically amplified and sequenced. Four single nucleotide polymorphisms (SNPs) were detected in the 420 sequenced bases of the gene in two R. myconi populations. The Pyrenean population had only one SNP while all four SNPs were present in the southern population. Three out of four SNPs were non‐synonymous. Such novel results indicate that the detection of SNPs in R. myconi over its entire distribution area could be used as an aid to reconstructing the population history of the species, as well as to investigate the relationship between developmental genes and morphological traits.
Solute Heterogeneity and Osmotic Adjustment in Different Leaf Structures of Semi‐Leafless Pea (Pisum sativum L.) Subjected to Water Stress
Authors: González E. M. , Arrese‐Igor C. , Aparicio‐Tejo P. M. , Royuela M. , Koyro H.‐W.
Published: November 2002

Abstract: Semi‐leafless varieties of pea have considerable agronomic importance and it has been suggested that they may have a superior response to water deficits than conventional varieties. However, these varieties are poorly characterized from a physiological point of view and there is lack of a physiological basis for their supposed better performance under conditions of water deficit. Here, we describe the solute distribution in the different leaf structures of a semi‐leafless pea variety (Pisum sativum L.) under non‐limiting water conditions and under water stress. A conventional variety was subjected to the same conditions for comparative purposes. A detailed study was carried out both at the tissue level and at the single cell level. In control conditions, epidermal vacuoles of tendrils showed a different ion distribution of those of the laminar leaf structures. However, under water deficit, only stipules of the semi‐leafless variety showed a significantly higher capability to increase osmolarity. This occurred by accumulating potassium, magnesium and chloride to a higher extent than other leaf structures. The inability of performing an adequate osmotic adjustment in tendrils may be the cause of the lack of a better response to water deficit.
A Putative Role for the Vacuolar Calcium/Manganese Proton Antiporter AtCAX2 in Heavy Metal Detoxification
Authors: Schaaf G. , Catoni E. , Fitz M. , Schwacke R. , Schneider A. , von Wirén N. , Frommer W. B.
Published: November 2002

Abstract: Regulation of uptake and compartmentation of metal ions is important for the maintenance of metal ion homeostasis. To identify mechanisms involved in the protection of plants from Mn toxicity, wild‐type yeast was transformed with an Arabidopsis cDNA library and transformants were screened on toxic Mn concentrations. Wild‐type yeast could not grow in the presence of 30 mM MnSO4, while two transformants carrying variants of the same gene were able to grow. Database searches revealed that the isolated cDNAs correspond to AtCAX2, previously described as a vacuolar calcium‐proton antiporter. Since no other genes could be identified, AtCAX2 might represent a major function permitting Mn detoxification in this suppressor screen. Furthermore, yeast transformed with the two AtCAX2 cDNAs showed increased sensitivity towards hydrogen peroxide, pointing to a limited availability of cytoplasmic Mn in the presence of AtCAX2 activity. The open reading frames of the cDNA encoded polypeptides that have a 42 and a 92 amino acids shorter N‐terminal region relative to the predicted full‐length coding region of AtCAX2. In contrast to both truncated cDNAs, the full‐length clone was unable to confer Mn resistance to yeast, indicating that, similar to AtCAX1, AtCAX2 also carries an autoinhibitory N‐terminal domain regulating the activity of AtCAX2.
Pollination Biology of Distylous Rubiaceae in the Atlantic Rain Forest, SE Brazil
Authors: de Castro C. C. , de Oliveira P. E.
Published: November 2002

Abstract: Data on pollination biology constitute important clues for the comprehension of pollen flow and genetic differentiation in plant populations. Pollinator type, availability and behaviour may modify morphological and mating patterns in populations of typically distylous species. This study investigates the pollination biology of four distylous species of Rubiaceae in the Atlantic rain forest, SE Brazil. Data on flowering phenology, floral lifespan, stigmatic receptivity, pollen availability, nectar volume and concentration, and pollinator activity were collected. The species studied flower sequentially throughout the wet season, and produce terminal inflorescences which bear small, tubular, diurnal, nectariferous flowers. Despite these similarities, some of the species studied are pollinated by different groups of pollinators, probably due to their distribution, availability of flowers and corolla length. On the other hand, pollinator specificity does not seem to be so important for distylous species. Long mouthparts, like those of most of the recorded pollinators, may reach lower sexual organs and, together with the self‐ and intramorph‐incompatibilities observed, be sufficient to perform legitimate pollination and maintain levels of intermorph mating.
Photosynthesis and Photoprotection in Overwintering Plants
Authors: Adams III W. W. , Demmig‐Adams B. , Rosenstiel T. N. , Brightwell A. K. , Ebbert V.
Published: November 2002

Abstract: Seasonal differences in the capacity of photosynthetic electron transport, leaf pigment composition, xanthophyll cycle characteristics and chlorophyll fluorescence emission were investigated in two biennial mesophytes (Malva neglecta and Verbascum thapsus) that grow in full sunlight, and in leaves/needles of sun and shade populations of several broad‐leafed evergreens and conifers (Vinca minor, Euonymus kiautschovicus, Mahonia repens, Pseudotsuga menziesii [Douglas fir], and Pinus ponderosa). Both mesophytic species maintained or upregulated photosynthetic capacity in the winter and exhibited no upregulation of photoprotection. In contrast, photosynthetic capacity was downregulated in sun leaves/needles of V. minor, Douglas fir, and Ponderosa pine, and even in shade needles of Douglas fir. Interestingly, photosynthetic capacity was upregulated during the winter in shade leaves/needles of V. minor, Ponderosa pine and Euonymus kiautschovicus. Nocturnal retention of zeaxanthin and antheraxanthin, and their sustained engagement in a state primed for energy dissipation, were observed largely in the leaves/needles of sun‐exposed evergreen species during winter. Factors that may contribute to these differing responses to winter stress, including chloroplast redox state, the relative levels of source and sink activity at the whole plant level, and apoplastic versus symplastic phloem loading, are discussed.
Speciation and Species Separation in Hordeum L. (Poaceae) Resolved by Discontinuous Molecular Markers1
Authors: El‐Rabey H. A. , Badr A. , Schäfer‐Pregl R. , Martin W. , Salamini F.
Published: November 2002

Abstract: Amplified fragment length polymorphisms (AFLPs) were used to evaluate the capacity of discontinuous markers to reveal genetic structure within Hordeum, a challenging higher plant genus from the standpoint of natural systematics. Phylogenies of 63 accessions encompassing nine species from four Hordeum sections were inferred from polymorphisms scored at 600 loci. Phylogenies based on sequences from the nuclear internal transcribed spacer (ITS) region were constructed for comparison, but revealed severe sampling errors inherent to single genes. Although superior by virtue of providing genome‐wide estimates of genetic similarity, the adoption of AFLPs in infrageneric studies requires caution. Comigrating AFLP bands studied here could be divided on the basis of band intensity variation into two types that are □ 100 % identical and < 40 % identical in DNA sequence, respectively, in infrageneric comparisons. Thus, the careful selection of AFLP bands to be analyzed bears heavily upon their phylogenetic utility. Within the H. murinum complex, which encompasses three morphologically distinct subspecies, AFLP data from 37 accessions reveal unexpected genetic differentiation between H. murinum, glaucumpopulations to the east and west of Alexandria (Egypt), suggesting the presence of allopatric speciation in the wake of human settlement.
Interaction between Cytokinesis‐Related Callose and Cortical Microtubules in Dividing Cells of the Liverwort Riella helicophylla
Authors: Scherp P. , Grotha R. , Kutschera U.
Published: November 2002

Abstract: In juvenile walls of dividing cells of the liverwort Riella helicophylla the nitroso‐derivative of photolysed Nifedipine (a calcium antagonist) stimulates the deposition of callose. This enhanced biosynthesis of β‐1,3‐glucan can only be observed in the cell plate, the juvenile cell walls and the walls of adjacent cells. An immunocytological analysis of this effect revealed that no cortical microtubules occurred at the sites of callose deposition. The cells of the control displayed a normal distribution of cortical microtubules at the plasma membrane as long as no callose was deposited along the corresponding walls. In a second set of experiments, inhibitors of microtubule polymerization and depolymerization (amiprophosmethyl and taxol, respectively) were used. At low concentrations, these substances also caused a significant stimulation of callose deposition in the plane of cell division. Based on these findings, we propose a regulatory model of callose and cellulose biosynthesis that depends on the binding of the cellulose/callose synthase complex to cortical microtubules that may be mediated by unknown binding protein(s).
Herbivore‐Mediated Competition between Defended and Undefended Plant Species: A Model to Investigate Consequences of Climate Change
Authors: Dormann C. F.
Published: November 2002

Abstract: Optimal levels of anti‐herbivore defence are determined not only by grazing pressure on the target plant, but also by the efficiency of the defence and by competitive interactions with neighbours. In the high Arctic on Svalbard, grazing by reindeer is a process that can be modelled without plant‐to‐herbivore feedback, as reindeer population sizes are not correlated with plant growth. However, growing conditions are extreme: a short season and low temperatures inhibit optimal growth. Therefore, it is possible to model anti‐herbivore defence in competition in this system, assess how its optimum depends on grazing intensity and defence efficiency, and, finally, how global climate change will effect plant‐plant interactions. This model, based on a Lotka‐Volterra type competition and temperature‐dependent growth, indicates that competition is of considerable importance even in extreme environments. Herbivory mediates displacement of the defended plant by releasing it from competition. This process is more pronounced under high grazing pressure than under low pressure. In other words, competition potentially magnifies the effect of herbivory. Elevated temperatures and a longer growing season have no qualitative impact on these processes, as the dominant defended plant profits most.
Analysis of Differential Expression of Barley ESTs during Cold Acclimatization Using Microarray Technology
Authors: Faccioli P. , Lagonigro M. S. , de Cecco L. , Stanca A. M. , Alberici R. , Terzi V.
Published: November 2002

Abstract: Genomics adds a new dimension to genetic analysis, shifting the focus from the study of a single gene to the whole genome. We have successfully applied the genomics approach based on microarray to the study of genes involved in barley responses to cold stress. About 900 EST clones from barley were obtained from a cDNA library of cold acclimatized leaves of cv. Nure and arrayed, and gene expression analysis done on cold acclimatized vs. control plants. The system allowed for reliable detection of differences in mRNA expression levels, and was confirmed by the finding that numerous previously reported cold‐related genes were differentially expressed in treated and untreated plants when evaluated in our arrays. The expression profiles of a sample of genes analysed by the array were confirmed by quantitative RT‐PCR.

Previously, identification of novel plant genes was achieved considering a few genes at a time; now many genes can be found as up‐ or down‐regulated based on a one step procedure. Many of the genes we found to be up‐ or down‐regulated do not have an assigned function. This includes 15 of the 78 up‐regulated and 8 of the 45 down‐regulated clones. Our results add new genes to the group of cold‐regulated genes and provide the opportunity to better understand the complex mechanism of stress tolerance.
Leaf Gas Exchange Characteristics in Relation to Leaf Canopy Position of Myrica faya in its Native Environment (Tenerife, Canary Islands)
Authors: González‐Rodríguez A. M. , Morales D. , Jiménez M. S.
Published: November 2002

Abstract: Diurnal courses of gas exchange were measured throughout one year in fully expanded current‐year leaves in the uppermost canopy (sun leaves, 18 m above ground) and in the lower canopy (shade leaves, 12 m above ground) of Myrica faya Ait., a dominant component of the Canarian laurel forest in Tenerife, Canary Islands, Spain.

M. faya showed large differences between sun and shade leaves in gas exchange characteristics (about 50 % of maximum carbon assimilation rate (Amax) reduction in shade leaves, but this reduction can be higher on specific days) that were modulated by strong light attenuation and high leaf area index (LAI) of the stand. This species presented low Amax, about 10 μmol m‐2 s‐1, high maximum transpiration (E, 8 mmol m‐2 s‐1) and stomatal conductance (gs, 750 mmol m‐2 s‐1) and very low instantaneous water use efficiency (WUE, mean maximum 1.1 mmol mol‐1) and A/gs (mean maximum 23.5 μmol mol‐1). M. faya responded to high air vapour pressure deficit (VPD), decreasing its gs but maintaining relatively high values of A and E during the studied period. Stomatal response to VPD showed a higher sensitivity than its congeners, M. cerifera, and Laurus azorica, tree species co‐occurring in the Canarian laurel forest. In general, all these gas exchange characteristics lead us to consider this species more similar to subtropical plants of humid regions than to species of the Mediterranean region.
Day Length and Temperature Strongly Influence Sexual Reproduction and Expression of a Novel MADS‐Box Gene in the MossPhyscomitrella patens
Authors: Hohe A. , Rensing S. A. , Mildner M. , Lang D. , Reski R.
Published: November 2002

Abstract:The effect of temperature and light conditions on sexual reproduction (sporophyte formation) ofin vitrocultures of the mossPhyscomitrella patenswas analysed. All parameters tested, i.e., temperature, light intensity and day length had a strong impact on the number of sporophytes formed. The highest number of sporophytes, 559 g fresh weight, developed at 15 °C, 8 h light/day with an intensity of 20 μmol/m2/s. In contrast, at 25 °C, as well as with a day length of 16 h per day, the number of sporophytes was drastically reduced. Vegetative growth, determined as fresh weight per petri dish, was impeded under conditions favouring sporophyte formation, probably due to nutrient transfer to the sporophytes. Microscopic documentation of the developing sporophytes revealed that, although archegonia were arranged in bundles at the gametophore apices, usually only one archegonium per gametophore apex developed into a mature sporophyte. From an EST database six novel MADS‐box genes were identified which, in phylogenetic analyses, did not cluster with the known groups of higher plant MADS‐box genes. One of these genes was represented only as a singleton in a cDNA library specifically derived from gametophore apices and developing sporophytes, and, therefore, designated PpMADS‐S. RNA amounts of PpMADS‐S were two to three times higher under conditions that stimulate sporophyte development (15 °C, 8 h light per day) when compared to conditions favouring vegetative growth (25 °C, 16 h light per day), indicating a possible function in sexual reproduction of this moss. Thus, an efficient experimental system was established to study sex organ formation, fertilization and embryo development inPhyscomitrella.
Signalling in Rhizobacteria‐Induced Systemic Resistance in Arabidopsis thaliana
Authors: Pieterse C. M. J. , van Wees S. C. M. , Ton J. , van Pelt J. A. , van Loon L. C.
Published: November 2002

Abstract: To protect themselves from disease, plants have evolved sophisticated defence mechanisms in which the signal molecules salicylic acid, jasmonic acid and ethylene often play crucial roles. Elucidation of signalling pathways controlling disease resistance is a major objective in research on plant‐pathogen interactions. The capacity of a plant to develop a broad spectrum, systemic acquired resistance (SAR) after primary infection with a necrotizing pathogen is well‐known and its signal transduction pathway extensively studied. Plants of which the roots have been colonized by specific strains of non‐pathogenic fluorescent Pseudomonas spp. develop a phenotypically similar form of protection that is called rhizobacteria‐mediated induced systemic resistance (ISR). In contrast to pathogen‐induced SAR, which is regulated by salicylic acid, rhizobacteria‐mediated ISR is controlled by a signalling pathway in which jasmonic acid and ethylene play key roles. In the past eight years, the model plant species Arabidopsis thaliana was explored to study the molecular basis of rhizobacteria‐mediated ISR. Here we review current knowledge of the signal transduction steps involved in the ISR pathway that leads from recognition of the rhizobacteria in the roots to systemic expression of broad‐spectrum disease resistance in aboveground foliar tissues.
The Phototropic Pulvinus of Bean Phaseolus vulgaris L. ‐ Functional Features
Authors: Koller D. , Zamski E.
Published: November 2002

Abstract: The laminar pulvinus of bean (Phaseolus vulgaris L.) is a highly specialized organ for reorienting the lamina, and exhibits positive phototropic curvature. Structural and ultrastructural features of the pulvinus were studied to determine their possible role in its phototropic response. The vascular tissue forms a flexible, relatively inextensible central core enclosed by a starch sheath and surrounded by a multi‐layered motor tissue. Phototropic curvature is a result of opposite anisotropic changes in volume of the cells in the exposed and opposite sectors of the motor tissue. Radial inflexibility of the epidermis and axial plasticity constrain these changes to the pulvinar axis. Anisotropic changes in volume of motor cells reduce the osmotic work involved. Motor cells exhibit features that are associated with high synthetic activity: thick cytoplasm with numerous ribosomes, polysomes, RER and SER, well‐developed mitochondria and a large nucleus. Numerous, well‐developed chloroplasts, with little starch, are increasingly abundant toward the periphery. The intercellular system is limited and partially filled with matrix. Stomata are absent and the motor tissue lacks vascularization. These features support the suggestion that the primary role of the chloroplasts in the photonastic response is photophosphorylation and photosynthetic electron transport (Koller et al., 1995[339]).
Plume–Ridge Interaction: a Geochemical Perspective from the Reykjanes Ridge
Authors: MURTON BRAMLEY J. , TAYLOR REX N. , THIRLWALL MATTHEW F.
Published: November 2002

Plume–ridge interaction in the Reykjanes Ridge and Iceland region is graphically demonstrated by several V-shaped ridges surrounding the spreading axis, indicating mantle flow away from Iceland. It also has significant geochemical effects. Regionally, incompatible element concentrations increase northwards coinciding with decreasing depth and increasing crustal thickness, depth of melting and proximity to Iceland. Major and trace element data show that isolated magma bodies feed individual volcanic systems along the ridge. Fractionation within these systems increases towards 60–61°N, where it coincides with the intersection of a V-shaped ridge, thicker crust and more abundant seamounts. Trace element, Nd and Sr isotopic data reveal dynamic melting and mixing within a southward-thinning, heterogeneous mantle wedge beneath the Reykjanes Ridge. Melting is variable and locally enhanced at 58°N, 59°N, 60°N and 61°N. A total of six mantle components are identified. Some are specific to Iceland whereas others are found only beneath the ridge axis. The geographical distribution of these components reflects their origin within the deep upper and lower mantle and subsequent translation by plume outflow along the entire length of the ridge.
Organization of transmembrane helices in photosystem II: comparison of plants and cyanobacteria
Authors: Barber J. , Nield J.
Published: November 2002

Electron microscopy and X–ray crystallography are revealing the structure of photosystem II. Electron crystallography has yielded a 3D structure at sufficient resolution to identify subunit positioning and transmembrane organization of the reaction–centre core complex of spinach. Single–particle analyses are providing 3D structures of photosystem II–light–harvesting complex II supercomplexes that can be used to incorporate high–resolution structural data emerging from electron and X–ray crystallography. The positions of the chlorins and metal centres within photosystem II are now available. It can be concluded that photosystem II is a dimeric complex with the transmembrane helices of CP47/D2 proteins related to those of the CP43/D1 proteins by a twofold axis within each monomer. Further, both electron microscopy and X–ray analyses show that P
680
is not a 'special pair‘ and that cytochrome
b
559 is located on the D2 side of the reaction centres some distance from P
680
. However, although comparison of the electron microscopy and X–ray models for spinach and
Synechococcus elongatus
show considerable similarities, there seem to be differences in the number and positioning of some small subunits.
Structure of the manganese complex in photosystem II: insights from X–ray spectroscopy
Authors: Yachandra Vittal K.
Published: November 2002

We have used Mn K–edge absorption and Kβ emission spectroscopy to determine the oxidation states of the Mn complex in the various S states. We have started exploring the new technique of resonant inelastic X–ray scattering spectroscopy; this technique can be characterized as a Raman process that uses K–edge energies (1s to 4p,
ca
. 6550 eV) to obtain L–edge–like spectra (2p to 3d,
ca
. 650 eV). The relevance of these data to the oxidation states and structure of the Mn complex is presented. We have obtained extended X–ray absorption fine structure data from the S
0
and S
3
states and observed heterogeneity in the Mn–Mn distances leading us to conclude that there may be three rather than two di–
μ
–oxo–bridged units present per tetranuclear Mn cluster. In addition, we have obtained data using Ca and Sr X–ray spectroscopy that provide evidence for a heteronuclear Mn1Ca cluster. The possibility of three di–
μ
–oxo–bridged Mn–Mn moieties and the proximity of Ca is incorporated into developing structural models for the Mn cluster. The involvement of bridging and terminal O ligands of Mn in the mechanism of oxygen evolution is discussed in the context of our X–ray spectroscopy results.
Photosystem II and photosynthetic oxidation of water: an overview
Authors: Goussias Charilaos , Boussac Alain , Rutherford A. William
Published: November 2002

Conceptually, photosystem II, the oxygen–evolving enzyme, can be divided into two parts: the photochemical part and the catalytic part. The photochemical part contains the ultra–fast and ultra–efficient light–induced charge separation and stabilization steps that occur when light is absorbed by chlorophyll. The catalytic part, where water is oxidized, involves a cluster of Mn ions close to a redox–active tyrosine residue. Our current understanding of the catalytic mechanism is mainly based on spectroscopic studies. Here, we present an overview of the current state of knowledge of photosystem II, attempting to delineate the open questions and the directions of current research.
Electron, proton and hydrogen–atom transfers in photosynthetic water oxidation
Authors: Tommos Cecilia
Published: November 2002

When photosynthetic organisms developed so that they could use water as an electron source to reduce carbon dioxide, the stage was set for efficient proliferation. Algae and plants spread globally and provided the foundation for our atmosphere and for O
2
–based chemistry in biological systems. Light–driven water oxidation is catalysed by photosystem II, the active site of which contains a redox–active tyrosine denoted Y
Z
, a tetramanganese cluster, calcium and chloride. In 1995, Gerald Babcock and co–workers presented the hypothesis that photosynthetic water oxidation occurs as a metallo–radical catalysed process. In this model, the oxidized tyrosine radical is generated by coupled proton/electron transfer and re–reduced by abstracting hydrogen atoms from substrate water or hydroxide–ligated to the manganese cluster. The proposed function of Y
Z
requires proton transfer from the tyrosine site upon oxidation. The oxidation mechanism of Y
Z
in an inhibited and O
2
–evolving photosystem II is discussed. Domino–deprotonation from Y
Z
to the bulk solution is shown to be consistent with a variety of data obtained on metal–depleted samples. Experimental data that suggest that the oxidation of Y
Z
in O
2
–evolving samples is coupled to proton transfer in a hydrogen–bonding network are described. Finally, a dielectric–dependent model for the proton release that is associated with the catalytic cycle of photosystem II is discussed.
Water oxidation chemistry of photosystem II
Authors: Vrettos John S. , Brudvig Gary W.
Published: November 2002

The O
2
–evolving complex of photosystem II catalyses the light–driven four–electron oxidation of water to dioxygen in photosynthesis. In this article, the steps leading to photosynthetic O
2
evolution are discussed. Emphasis is given to the proton–coupled electron–transfer steps involved in oxidation of the manganese cluster by oxidized tyrosine Z (Y
Z
), the function of Ca
2+
and the mechanism by which water is activated for formation of an O–O bond. Based on a consideration of the biophysical studies of photosystem II and inorganic manganese model chemistry, a mechanism for photosynthetic O
2
evolution is presented in which the O–O bond–forming step occurs via nucleophilic attack on an electron–deficient Mn
V
=O species by a calcium–bound water molecule. The proposed mechanism includes specific roles for the tetranuclear manganese cluster, calcium, chloride, Y
Z
and His190 of the D1 polypeptide. Recent studies of the ion selectivity of the calcium site in the O
2
–evolving complex and of a functional inorganic manganese model system that test key aspects of this mechanism are also discussed.
Electrostatics and proton transfer in photosynthetic water oxidation
Authors: Junge Wolfgang , Haumann Michael , Ahlbrink Ralf , Mulkidjanian Armen , Clausen Jürgen
Published: November 2002

Photosystem II (PSII) oxidizes two water molecules to yield dioxygen plus four protons. Dioxygen is released during the last out of four sequential oxidation steps of the catalytic centre (S0⇒ S1, S1⇒ S2, S2⇒ S3, S3⇒ S4→ S0). The release of the chemically produced protons is blurred by transient, highly variable and electrostatically triggered proton transfer at the periphery (Bohr effect). The extent of the latter transiently amounts to more than one H+/e–under certain conditions and this is understood in terms of electrostatics. By kinetic analyses of electron–proton transfer and electrochromism, we discriminated between Bohr–effect and chemically produced protons and arrived at a distribution of the latter over the oxidation steps of 1 : 0 : 1 : 2. During the oxidation of tyr–161 on subunit D1 (YZ), its phenolic proton is not normally released into the bulk. Instead, it is shared with and confined in a hydrogen–bonded cluster. This notion is difficult to reconcile with proposed mechanisms where YZacts as a hydrogen acceptor for bound water. Only in manganese (Mn) depleted PSII is the proton released into the bulk and this changes the rate of electron transfer between YZand the primary donor of PSII P+680from electron to proton controlled. D1–His190, the proposed centre of the hydrogen–bonded cluster around YZ, is probably further remote from YZthan previously thought, because substitution of D1–Glu189, its direct neighbour, by Gln, Arg or Lys is without effect on the electron transfer from YZto P+680(in nanoseconds) and from the Mn cluster to YoxZ.
Structural and functional dynamics of plant photosystem II
Authors: Anderson Jan M. , Chow W. S.
Published: November 2002

Given the unique problem of the extremely high potential of the oxidant P
+
680
that is required to oxidize water to oxygen, the photoinactivation of photosystem II in vivo is inevitable, despite many photoprotective strategies. There is, however, a robustness of photosystem II, which depends partly on the highly dynamic compositional and structural heterogeneity of the cycle between functional and non–functional photosystem II complexes in response to light level. This coordinated regulation involves photon usage (energy utilization in photochemistry) and excess energy dissipation as heat, photoprotection by many molecular strategies, photoinactivation followed by photon damage and ultimately the D1 protein dynamics involved in the photosystem II repair cycle. Compelling, though indirect evidence suggests that the radical pair P
+
680
Pheo
–
in functional PSII should be protected from oxygen. By analogy to the tentative oxygen channel of cytochrome
c
oxidase, oxygen may be liberated from the two water molecules bound to the catalytic site of the Mn cluster, via a specific pathway to the membrane surface. The function of the proposed oxygen pathway is to prevent O
2
from having direct access to P
+
680
Pheo
–
and prevent the generation of singlet oxygen via the triplet–P
680
state in functional photosytem IIs. Only when the, as yet unidentified, potential trigger with a fateful first oxidative step destroys oxygen evolution, will the ensuing cascade of structural perturbations of photosystem II destroy the proposed oxygen, water and proton pathways. Then oxygen has direct access to P
+
680
Pheo
–
, singlet oxygen will be produced and may successively oxidize specific amino acids of the phosphorylated D1 protein of photosystem II dimers that are confined to appressed granal domains, thereby targeting D1 protein for eventual degradation and replacement in non–appressed thylakoid domains.
What is β–carotene doing in the photosystem II reaction centre?
Authors: Telfer Alison
Published: November 2002

During photosynthesis carotenoids normally serve as antenna pigments, transferring singlet excitation energy to chlorophyll, and preventing singlet oxygen production from chlorophyll triplet states, by rapid spin exchange and decay of the carotenoid triplet to the ground state. The presence of two β–carotene molecules in the photosystem II reaction centre (RC) now seems well established, but they do not quench the triplet state of the primary electron–donor chlorophylls, which are known as P680. The β–carotenes cannot be close enough to P680for triplet quenching because that would also allow extremely fast electron transfer from β–carotene to P+680, preventing the oxidation of water. Their transfer of excitation energy to chlorophyll, though not very efficient, indicates close proximity to the chlorophylls ligated by histidine 118 towards the periphery of the two main RC polypeptides. The primary function of the β–carotenes is probably the quenching of singlet oxygen produced after charge recombination to the triplet state of P680. Only when electron donation from water is disturbed does β–carotene become oxidized. One β–carotene can mediate cyclic electron transfer via cytochromeb559. The other is probably destroyed upon oxidation, which might trigger a breakdown of the polypeptide that binds the cofactors that carry out charge separation.
Biogenesis, assembly and turnover of photosystem II units
Authors: Baena–González Elena , Aro Eva–Mari
Published: November 2002

Assembly of photosystem II, a multiprotein complex embedded in the thylakoid membrane, requires stoichiometric production of over 20 protein subunits. Since part of the protein subunits are encoded in the chloroplast genome and part in the nucleus, a signalling network operates between the two genetic compartments in order to prevent wasteful production of proteins. Coordinated synthesis of proteins also takes place among the chloroplast–encoded subunits, thus establishing a hierarchy in the protein components that allows a stepwise building of the complex. In addition to this dependence on assembly partners, other factors such as the developmental stage of the plastid and various photosynthesis–related parameters exert a strict control on the accumulation, membrane targeting and assembly of the PSII subunits. Here, we briefly review recent results on this field obtained with three major approaches: biogenesis of photosystem II during the development of chloroplasts from etioplasts, use of photosystem II–specific mutants and photosystem II turnover during its repair cycle.
The mechanism for proton–coupled electron transfer from tyrosine in a model complex and comparisons with Y
Z
oxidation in photosystem II
Authors: Sjödin Martin , Styring Stenbjörn , Åkermark Björn , Sun Licheng , Hammarström Leif
Published: November 2002

In the water–oxidizing reactions of photosystem II (PSII), a tyrosine residue plays a key part as an intermediate electron–transfer reactant between the primary donor chlorophylls (the pigment P
680
) and the water–oxidizing Mn cluster. The tyrosine is deprotonated upon oxidation, and the coupling between the proton reaction and electron transfer is of great mechanistic importance for the understanding of the water–oxidation mechanism. Within a programme on artificial photosynthesis, we have made and studied the proton–coupled tyrosine oxidation in a model system and been able to draw mechanistic conclusions that we use to interpret the analogous reactions in PSII.
Functional implications on the mechanism of the function of photosystem II including water oxidation based on the structure of photosystem II
Authors: Fromme Petra , Kern Jan , Loll Bernhard , Biesiadka Jaceck , Saenger Wolfram , Witt Horst T. , Krauss Norbert , Zouni Athina
Published: November 2002

The structure of photosystem I at 3.8 Å resolution illustrated the main structural elements of the water–oxidizing photosystem II complex, including the constituents of the electron transport chain. The location of the Mn cluster within the complex has been identified for the first time to our knowledge. At this resolution, no individual atoms are visible, however, the electron density of the Mn cluster can be used to discuss both the present models of the Mn cluster as revealed from various spectroscopic methods and the implications for the mechanisms of water oxidation. Twenty–six chlorophylls from the antenna system of photosystem II have been identified. They are arranged in two layers, one close to the stromal side and one close to the lumenal side. Comparing the structure of the antenna system of photosystem II with the chlorophyll arrangement in photosystem I, which was recently determined at 2.5 Å resolution shows that photosystem II lacks the central domain of the photosystem I antenna, which is discussed in respect of the repair cycle of photosystem II due to photoinhibition.
Simulations of the
1
H electron spin echo–electron nuclear double resonance and
2
H electron spin echo envelope modulation spectra of exchangeable hydrogen nuclei coupled to the S
2
–state photosystem II manganese cluster
Authors: Aznar Constantino P. , Britt R. David
Published: November 2002

The pulsed EPR methods of electron spin echo envelope modulation (ESEEM) and electron spin echo–electron nuclear double resonance (ESE–ENDOR) are used to investigate the proximity of exchangeable hydrogens around the paramagnetic S
2
–state Mn cluster of the photosystem II oxygen–evolving complex. Although ESEEM and ESE–ENDOR are both pulsed electron paramagnetic resonance techniques, the specific mechanisms by which nuclear spin transitions are observed are quite different. We are able to generate good simulations of both
1
H ESE–ENDOR and
2
H ESEEM signatures of exchangeable hydrogens at the S
2
–state cluster. The convergence of simulation parameters for both methods provides a high degree of confidence in the simulations. Several exchangeable protons–deuterons with strong dipolar couplings are observed. In the simulations, two of the close (≈2.5 Å) hydrogen nuclei exhibit strong isotropic couplings and are therefore most probably associated with direct substrate ligation to paramagnetic Mn. Another two of the close (≈2.7 Å) hydrogen nuclei show no isotropic couplings and are therefore most probably not contained in Mn ligands. We suggest that these proximal hydrogens may be associated with a Ca
2+
–bound substrate, as indicated in recent mechanistic proposals for O
2
formation.
The role of inactive photosystem–II–mediated quenching in a last–ditch community defence against high light stressin vivo
Authors: Soon Chow Wah , Lee Hae–Youn , Park Youn–Il , Park Yong–Mok , Hong Yong–Nam , Anderson Jan M.
Published: November 2002

Photoinactivation of photosystem II (PSII), the light–induced loss of ability to evolve oxygen, is an inevitable event during normal photosynthesis, exacerbated by saturating light but counteracted by repair via new protein synthesis. The photoinactivation of PSII is dependent on the dosage of light: in the absence of repair, typically one PSII is photoinactivated per 107photons, although the exact quantum yield of photoinactivation is modulated by a number of factors, and decreases as fewer active PSII targets are available. PSII complexes initially appear to be photoinactivated independently; however, when less than 30% functional PSII complexes remain, they seem to be protected by strongly dissipative PSII reaction centres in several plant species examined so far, a mechanism which we term ‘inactive PSII–mediated quenching‘. This mechanism appears to require a pH gradient across the photosynthetic membrane for its optimal operation. The residual fraction of functional PSII complexes may, in turn, aid in the recovery of photoinactivated PSII complexes when conditions become less severe. This mechanism may be important for the photosynthetic apparatus in extreme environments such as those experienced by over–wintering evergreen plants, desert plants exposed to drought and full sunlight and shade plants in sustained sunlight.