bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary Radiation Pattern of Novel Protein Phosphatases Revealed by Analysis of Protein Data from the Completely Sequenced Genomes of Humans, Green Algae, and Higher Plants
Authors: Kerk David , Templeton George , Moorhead Greg B.G. 
Published: December 2007

AbstractIn addition to the major serine/threonine-specific phosphoprotein phosphatase, Mg2+-dependent phosphoprotein phosphatase, and protein tyrosine phosphatase families, there are novel protein phosphatases, including enzymes with aspartic acid-based catalysis and subfamilies of protein tyrosine phosphatases, whose evolutionary history and representation in plants is poorly characterized. We have searched the protein data sets encoded by the well-finished nuclear genomes of the higher plants Arabidopsis (Arabidopsis thaliana) and Oryza sativa, and the latest draft data sets from the tree Populus trichocarpa and the green algae Chlamydomonas reinhardtii and Ostreococcus tauri, for homologs to several classes of novel protein phosphatases. The Arabidopsis proteins, in combination with previously published data, provide a complete inventory of known types of protein phosphatases in this organism. Phylogenetic analysis of these proteins reveals a pattern of evolution where a diverse set of protein phosphatases was present early in the history of eukaryotes, and the division of plant and animal evolution resulted in two distinct sets of protein phosphatases. The green algae occupy an intermediate position, and show similarity to both plants and animals, depending on the protein. Of specific interest are the lack of cell division cycle (CDC) phosphatases CDC25 and CDC14, and the seeming adaptation of CDC14 as a protein interaction domain in higher plants. In addition, there is a dramatic increase in proteins containing RNA polymerase C-terminal domain phosphatase-like catalytic domains in the higher plants. Expression analysis of Arabidopsis phosphatase genes differentially amplified in plants (specifically the C-terminal domain phosphatase-like phosphatases) shows patterns of tissue-specific expression with a statistically significant number of correlated genes encoding putative signal transduction proteins.
Dual Targeting of Arabidopsis HOLOCARBOXYLASE SYNTHETASE1: A Small Upstream Open Reading Frame Regulates Translation Initiation and Protein Targeting
Authors: Puyaubert Juliette , Denis Laurence , Alban Claude 
Published: December 2007

Abstract
Protein biotinylation is an original and very specific posttranslational modification, compartmented in plants, between mitochondria, plastids, and the cytosol. This reaction modifies and activates few carboxylases committed in key metabolisms and is catalyzed by holocarboxylase synthetase (HCS). The molecular bases of this complex compartmentalization and the relative function of each of the HCS genes, HCS1 and HCS2, identified in Arabidopsis (Arabidopsis thaliana) are mainly unknown. Here, we showed by reverse genetics that the HCS1 gene is essential for plant viability, whereas disruption of the HCS2 gene in Arabidopsis does not lead to any obvious phenotype when plants are grown under standard conditions. These findings strongly suggest that HCS1 is the only protein responsible for HCS activity in Arabidopsis cells, including the cytosolic, mitochondrial, and plastidial compartments. A closer study of HCS1 gene expression enabled us to propose an original mechanism to account for this multiplicity of localizations. Located in the HCS1 messenger RNA 5′-untranslated region, an upstream open reading frame regulates the translation initiation of HCS1 and the subsequent targeting of HCS1 protein. Moreover, an exquisitely precise alternative splicing of HCS1 messenger RNA can regulate the presence and absence of this upstream open reading frame. The existence of these complex and interdependent mechanisms creates a rich molecular platform where different parameters and factors could control HCS targeting and hence biotin metabolism.
Arabidopsis GenesAS1,AS2, andJAGNegatively Regulate Boundary-Specifying Genes to Promote Sepal and Petal Development
Authors: Xu Ben , Li Ziyu , Zhu Yan , Wang Hua , Ma Hong , Dong Aiwu , Huang Hai 
Published: December 2007

AbstractBoundary formation is crucial for organ development in multicellular eukaryotes. In higher plants, boundaries that separate the organ primordia from their surroundings have relatively low rates of cell proliferation. This cellular feature is regulated by the actions of certain boundary-specifying genes, whose ectopic expression in organs can cause inhibition of organ growth. Here, we show that the Arabidopsis thaliana ASYMMETRIC LEAVES1 and 2 (AS1 and AS2) and JAGGED (JAG) genes function in the sepal and petal primordia to repress boundary-specifying genes for normal development of the organs. Loss-of-function as1 jag and as2 jag double mutants produced extremely tiny sepals and petals. Analysis of a cell-cycle marker HISTONE4 revealed that cell division in sepal primordia of the double mutant was inhibited. Moreover, these abnormal sepals and petals exhibited ectopic overexpression of the boundary-specifying genes PETAL LOSS (PTL) and CUP-SHAPED COTYLEDONS1 and 2 (CUC1 and CUC2). Loss of PTL or CUC1 and CUC2 functions in the as1 jag background could partially rescue the tiny sepal and petal phenotypes, supporting the model that the tiny sepal/petal phenotypes are caused, at least in part, by ectopic expression of boundary-specifying genes. Together, our data reveal a previously unrecognized fundamental regulation by which AS1, AS2, and JAG act to define sepal and petal from their boundaries.
Systemic and Intracellular Responses to Photooxidative Stress inArabidopsis
Authors: Rossel Jan Bart , Wilson Pip B. , Hussain Dawar , Woo Nick S. , Gordon Matthew J. , Mewett Osman P. , Howell Katharine A. , Whelan Jim , Kazan Kemal , Pogson Barry J. 
Published: December 2007

AbstractAs the sun tracks daily through the sky from east to west, different parts of the canopy are exposed to high light (HL). The extent of and mechanisms by which a systemic acquired acclimation (SAA) response might preacclimate shaded leaves that will be subsequently exposed to full sunlight is largely undefined. We investigated the role of an Arabidopsis thaliana zinc finger transcription factor, ZAT10, in SAA. ZAT10 overexpression resulted in enhanced tolerance to photoinhibitory light and exogenous H2O2, increased expression of antioxidative genes whose products are targeted to multiple subcellular compartments. Partial HL exposure of a leaf or leaves rapidly induced ZAT10 mRNA in distal, shaded photosynthetic tissues, including the floral stem, cauline leaves, and rosette, but not in roots. Fully 86% of fivefold HL-upregulated and 71% of HL-downregulated genes were induced and repressed, respectively, in distal, shaded leaves. Between 15 and 23% of genes whose expression changed in the HL and/or distal tissues were coexpressed in the ZAT10 overexpression plants, implicating ZAT10 in modulating the expression of SAA-regulated genes. The SAA response was detectable in plants with mutations in abscisic acid, methyl jasmonate, or salicylic acid synthesis or perception, and systemic H2O2 diffusion was not detected. Hence, SAA is distinct from pathogen-stimulated systemic acquired resistance and apparently involves a novel signal or combination of signals that preacclimate photosynthetic tissues to HL.
An Endoplasmic Reticulum Stress Response in Arabidopsis Is Mediated by Proteolytic Processing and Nuclear Relocation of a Membrane-Associated Transcription Factor, bZIP28
Authors: Liu Jian-Xiang , Srivastava Renu , Che Ping , Howell Stephen H. 
Published: December 2007

Abstract
Stresses leading to the accumulation of misfolded proteins in the endoplasmic reticulum (ER) elicit a highly conserved ER stress response in plants called the unfolded protein response (UPR). While the response itself is well documented in plants, the components of the signaling pathway are less well known. We have identified three membrane-associated basic domain/leucine zipper (bZIP) factors in Arabidopsis thaliana that are candidates for ER stress sensors/transducers. One of these factors, bZIP28, an ER-resident transcription factor, is activated in response to treatment by tunicamycin (TM), an agent that blocks N-linked protein glycosylation. Following TM treatment, bZIP28 is processed, releasing its N-terminal, cytoplasm-facing domain, which is translocated to the nucleus. Expression of a truncated form of bZIP28, containing only the cytoplasmic domain of the protein, upregulated the expression of ER stress response genes in the absence of stress conditions. Thus, bZIP28 serves as a sensor/transducer in Arabidopsis to mediate ER stress responses related to UPR.
P-Glycoprotein4 Displays Auxin Efflux Transporter–Like Action in Arabidopsis Root Hair Cells and Tobacco Cells
Authors: Cho Misuk , Lee Sang Ho , Cho Hyung-Taeg 
Published: December 2007

Abstract
ATP binding cassette (ABC) transporters transport diverse substrates across membranes in various organisms. However, plant ABC transporters have only been scantily characterized. By taking advantage of the auxin-sensitive Arabidopsis thaliana root hair cell and tobacco (Nicotiana tabacum) suspension cell systems, we show here that Arabidopsis P-glycoprotein4 (PGP4) displays auxin efflux activity in plant cells. Root hair cell–specific overexpression of PGP4 (PGP4ox) and known auxin efflux transporters, such as PGP1, PGP19, and PIN-FORMEDs, decreased root hair elongation, whereas overexpression of the influx transporter AUXIN-RESISTANT1 enhanced root hair length. PGP4ox-mediated root hair shortening was rescued by the application of auxin or an auxin efflux inhibitor. These results indicate that the increased auxin efflux activity conferred by PGP4 reduces auxin levels in the root hair cell and consequently inhibits root hair elongation. PGP4ox in tobacco suspension cells also increased auxin efflux. PGP4 proteins were targeted to the plasma membrane of Arabidopsis root hair cells and tobacco cells without any clear subcellular polarity. Brefeldin A partially interfered with the trafficking of PGP4 reversibly, and this was rescued by pretreatment with auxin. These results suggest that PGP4 is an auxin efflux transporter in plants and that its trafficking to the plasma membrane involves both BFA-sensitive and -insensitive pathways.
RAR1 and HSP90 Form a Complex with Rac/Rop GTPase and Function in Innate-Immune Responses in Rice
Authors: Thao Nguyen Phuong , Chen Letian , Nakashima Ayako , Hara Shin-ichiro , Umemura Kenji , Takahashi Akira , Shirasu Ken , Kawasaki Tsutomu , Shimamoto Ko 
Published: December 2007

Abstract
A rice (Oryza sativa) Rac/Rop GTPase, Os Rac1, is involved in innate immunity, but its molecular function is largely unknown. RAR1 (for required for Mla12 resistance) and HSP90 (a heat shock protein 90 kD) are important components of R gene–mediated disease resistance, and their function is conserved in several plant species. HSP90 has also recently been shown to be important in mammalian innate immunity. However, their functions at the molecular level are not well understood. In this study, we examined the functional relationships between Os Rac1, RAR1, and HSP90. Os RAR1-RNA interference (RNAi) rice plants had impaired basal resistance to a compatible race of the blast fungus Magnaporthe grisea and the virulent bacterial blight pathogen Xanthomonas oryzae. Constitutively active Os Rac1 complemented the loss of resistance, suggesting that Os Rac1 and RAR1 are functionally linked. Coimmunoprecipitation experiments with rice cell culture extracts indicate that Rac1 forms a complex with RAR1, HSP90, and HSP70 in vivo. Studies with Os RAR1-RNAi and treatment with geldanamycin, an HSP90-specific inhibitor, showed that RAR1 and HSP90 are essential for the Rac1-mediated enhancement of pathogen-associated molecular pattern–triggered immune responses in rice cell cultures. Furthermore, the function of HSP90, but not RAR1, may be essential for their association with the Rac1 complex. Os Rac1 also regulates RAR1 expression at both the mRNA and protein levels. Together, our results indicate that Rac1, RAR1, HSP90, and HSP70 form one or more protein complexes in rice cells and suggest that these proteins play important roles in innate immunity in rice.
Regulation of Rice NADPH Oxidase by Binding of Rac GTPase to Its N-Terminal Extension
Authors: Wong Hann Ling , Pinontoan Reinhard , Hayashi Kokoro , Tabata Ryo , Yaeno Takashi , Hasegawa Kana , Kojima Chojiro , Yoshioka Hirofumi , Iba Koh , Kawasaki Tsutomu , Shimamoto Ko 
Published: December 2007

Abstract
Reactive oxygen species (ROS) produced by NADPH oxidase play critical roles in various cellular activities, including plant innate immunity response. In contrast with the large multiprotein NADPH oxidase complex of phagocytes, in plants, only the homologs of the catalytic subunit gp91phox and the cytosolic regulator small GTPase Rac are found. Plant homologs of the gp91phox subunit are known as Rboh (for respiratory burst oxidase homolog). Although numerous Rboh have been isolated in plants, the regulation of enzymatic activity remains unknown. All rboh genes identified to date possess a conserved N-terminal extension that contains two Ca2+ binding EF-hand motifs. Previously, we ascertained that a small GTPase Rac (Os Rac1) enhanced pathogen-associated molecular pattern–induced ROS production and resistance to pathogens in rice (Oryza sativa). In this study, using yeast two-hybrid assay, we found that interaction between Rac GTPases and the N-terminal extension is ubiquitous and that a substantial part of the N-terminal region of Rboh, including the two EF-hand motifs, is required for the interaction. The direct Rac–Rboh interaction was supported by further studies using in vitro pull-down assay, a nuclear magnetic resonance titration experiment, and in vivo fluorescence resonance energy transfer (FRET) microscopy. The FRET analysis also suggests that cytosolic Ca2+ concentration may regulate Rac–Rboh interaction in a dynamic manner. Furthermore, transient coexpression of Os Rac1 and rbohB enhanced ROS production in Nicotiana benthamiana, suggesting that direct Rac–Rboh interaction may activate NADPH oxidase activity in plants. Taken together, the results suggest that cytosolic Ca2+ concentration may modulate NADPH oxidase activity by regulating the interaction between Rac GTPase and Rboh.
Tuthillia, a new Neotropical psyllid genus (Homoptera: Psylloidea)
Authors: HODKINSON I. D. , BROWN R. G. , BURCKHARDT D. 
Published: January 2008

Abstract Tuthillia gen.n. (Homoptera: Psylloidea) is erected for four Neotropical species: canabina sp.n. (the type‐species from Belize and Panama), cognata sp.n. (Brazil), latipennis sp.n. (Panama) and iuncta sp.n. (Brazil). It is suggested that Tuthillia forms a monophyletic group with the ciriacremine genera Ciriacremum, Kleiniella and Pal‐mapenna. However, only iuncta possesses an R‐M cross vein in the forewing, a character which has been used to define the ciriacremines in the past. It seems, therefore, that this character is unstable and alternative synapomorphies are discussed. The genital morphology of Tuthillia is similar to that found in both Ciriacreminae and Diaphorininae (Aphalaridae). It is speculated that these subfamilies represent previously unrecognized sister groups defined using the genital characters as synapomorphies.
REVERSIBLE PHOTODIMERIZATION OF ANTHRACENE AND TETRACENE
Authors: Wei Kei Sin , Livingston Robert 
Published: January 2008

Abstract— Dianthracene is efficiently photodissociated, forming anthracene with a quantum yield of about 0.63. Like anthracene, tetracene undergoes a reversible photochemical reaction, the product of which appears to be di‐tetracene. In dilute, deoxygenated solutions the of quantum yeild for the formation of di‐tetracene is directly proportional to the concentration of the monomer ødim = 2.2 (T̃). The quantum yield for the reverse reaction is approximately 0.74When dilute deaerated solutions of anthracene are irradiated with the unfiltered radiation from a quartz‐mercury arc, a degradation product is formed. Unlike the dimer, this product cannot be converted into anthracene either by heating it to 200d̀C or by irradiating it in solution with light of 254 nm. This degradation product appears to be the compound or compounds which Birks et al. believed to be dianthracene. Irradiation of deaerated solutions of anthracene (or tetracene) with light of wavelenghts longer than 300 nm produces only the dimer, which has an absorption spectrum similar to that reported by Coulson et al.
SOLVENT EFFECTS ON THE SPECTRA OF RETINAL SCHIFF BASES—I. MODELS FOR THE BATHOCHROMIC SHIFT OF THE CHROMOPHORE SPECTRUM IN VISUAL PIGMENTS*
Authors: Kliger D. S. , Milder S. J. , Dratz E. A. 
Published: January 2008

Abstract— Retinylidine Schiff base spectra have been investigated in a variety of solvents that were chosen primarily to mimic possible environments of the chromophore in visual pigments. These studies have identified particular amino acid side chains which can have important influences on visual pigment spectra. Most amino acid side chain analogues or solvents which mimic the peptide bond environment have little effect on retinylidine Schiff base spectra. Tyrosine, tryptophan, and cysteine analogues and ionized aspartic and glutamic acid analogues produce pronounced red shifts in the spectra. As is explained in more detail in the following paper the presence of these amino acids in the chromophore “pocket” of the protein is sufficient to account for the spectra of many visual pigments. Calculations of the spectra of protonated Schiff bases under a variety of conditions have been considered in conjunction with the spectral data to provide a model for the nature of the chromophore interactions with its environment.In solution and in rhodopsin the protonated Schiff base linkage is likely to be associated with an anion. The presence of certain amino acid side chains along the remainder of the retinal chain in the protein can modify the spectrum by altering the polarizability and polarity of the environment. The polarity in the region of the ionone ring appears to be particularly important for shifting the spectrum. In solution the nucleophilicity of the solvent also has an important influence on the anion‐protonated Schiff base region of the chromophore.
THE ROLE OF BIRADICALOID GEOMETRIES IN ORGANIC PHOTOCHEMISTRY
Authors: Michl Josef 
Published: January 2008

Abstract— Excited molecules tend to return to the ground state at biradicaloid geometries, i.e. those for which the simple MO description yields two non‐bonding orbitals occupied by only two electrons in the ground state. The nature of electronic states at these geometries and the consequences for the course of photochemical reactions are summarized, using the cases of H2 and H4 as simple models. Several aspects of classification schemes for photochemical reactions are discussed.Detailed mechanisms of photocycloaddition, of adiabatic photochemical rearrangement of Dewar aromatics, and of luminol chemiluminescence are considered as examples.
ON THE GENERATION OF THE HYDROXYLATION AGENT FROM SUPEROXIDE RADICAL. CAN THE HABER–WEISS REACTION BE THE SOURCE OF OH RADICALS?
Authors: Czapski Gidon , Ilan Yael A. 
Published: January 2008

Abstract— In many biological systems, the role of O2‐ in hydroxylation and toxic processes was assumed to be due to the formation of OH radicals. The Haber‐Weiss reaction (Haber and Weiss, 1934)—(H2O2+ O2‐→ OH + OH‐+ O2) was suggested as the origin of this activity.In this study it is shown that this reaction pathway is too slow, and that OH is probably formed from the reaction of complexed superoxide with H2O2 or/and from the reduction of Fe(III), bound to biological compounds, by O2‐; the reduced Fe(II) can then react with H2O2 as a Fenton reagent, to yield OH.It is also shown that singlet oxygen cannot be formed in these biological systems neither from the dismutation of OJ nor from the reaction of O2‐ with OH. Singlet oxygen may be formed from the reduction of metal complexes by O2‐.
PHOTOELECTROCHEMICAL STUDY OF CHLOROPHYLL‐a MULTILAYERS ON SnO2 ELECTRODE
Authors: Miyasaka Tsutomu , Watanabe Tadashi , Fijjishima Akira , Honda Kenichi 
Published: January 2008

Abstract—Photoelectrochemical behaviour of Chl‐a multilayers, built up on SnO2 optically transparent electrode by means of the Langmuir technique, was investigated in an electrolyte solution with or without hydroquinone as a reducing agent. Quantum efficiencies of the anodic photocurrents in the presence of hydroquinone tended to decrease with increasing number of layers. In the electrolyte without hydroquinone, the cathodic photocurrents were observed in the presence of dissolved oxygen. A possibility of a reaction of water with the oxidized Chl‐a is suggested.
THE BLUE ANOMALOUS EMISSION OF LARGE AND SMALL PHYTOCHROME*
Authors: Holzwarth Alfred R. , Braslavsky Silvia E. , Culshaw Stephen , Schaffner Kurt 
Published: January 2008

Abstract–Small and immunoaffinity‐purified large phytochrome (Pr and Pfr) show a so‐called anomalous fluorescence with λemmax= 470 and 440 nm, respectively, when irradiated within the blue absorption band. Model studies indicate that this emission arises from a dipyrromethenone partial structure produced by a nucleophilic addition to the central carbon C‐10 of the bilindione chromophore. The anomalous emitter of phytochrome is thus similar to one bilirubin conformer which has previously been found to contribute to the absorption and emission of the bile pigment.
PHOTOSENSITIZED LYSIS OF LIPOSOMES BY HEMATOPORPHYRIN DERIVATIVE
Authors: Grossweiner Leonard I. , Goyal Greesh C. 
Published: January 2008

AbstractThe spectral properties and efficiency for photosensitizing the lysis of phosphatidylcholine liposomes have been measured for the components of hematoporphyrin derivative (Hpd) after alkaline hydrolysis and fractionation by polyacrylamidc gel chromatography. Two major and two minor Hpd fractions have been identified whose spectral properties correlate with the anoxic sensitizing efficiency and the oxygen enhancement ratio (OER). The fastest moving fraction, which is the putative biologically active component, comprised one‐third of the starting material and had OER = 2.7. Liposome lysis by this fraction was inhibited in the presence of human serum albumin at concentration ratios comparable to those employed for photoradiation therapy. The present results show that Hpd can act as an oxic and anoxic photosensitizer of a model biomembrane and suggest that separation from serum proteins is required for in vivo photosensitization.