bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant CLE peptides from two distinct functional classes synergistically induce division of vascular cells
Authors: Whitford Ryan , Fernandez Ana , De Groodt Ruth , Ortega Esther , Hilson Pierre
Published: November 2008

The Clavata3 (CLV3)/endosperm surrounding region (CLE) signaling peptides are encoded in large plant gene families. CLV3 and the other A-type CLE peptides promote cell differentiation in root and shoot apical meristems, whereas the B-type peptides (CLE41–CLE44) do not. Instead, CLE41 inhibits the differentiation of
Zinnia elegans
tracheary elements. To test whether
CLE
genes might code for antagonistic or synergistic functions, peptides from both types were combined through overexpression within or application onto
Arabidopsis thaliana
seedlings. The CLE41 peptide (CLE41p) promoted proliferation of vascular cells, although delaying differentiation into phloem and xylem cell lineages. Application of CLE41p or overexpression of
CLE41
did not suppress the terminal differentiation of the root and shoot apices triggered by A-type CLE peptides. However, in combination, A-type peptides enhanced all of the phenotypes associated with
CLE41
gain-of-function, leading to massive proliferation of vascular cells. This proliferation relied on auxin signaling because it was enhanced by exogenous application of a synthetic auxin, decreased by an auxin polar transport inhibitor, and abolished by a mutation in the Monopteros auxin response factor. These findings highlight that vascular patterning is a process controlled in time and space by different CLE peptides in conjunction with hormonal signaling.
Antioxidants reduce endoplasmic reticulum stress and improve protein secretion
Authors: Malhotra Jyoti D. , Miao Hongzhi , Zhang Kezhong , Wolfson Anna , Pennathur Subramaniam , Pipe Steven W. , Kaufman Randal J.
Published: November 2008

Protein misfolding in the endoplasmic reticulum (ER) contributes to the pathogenesis of many diseases. Although oxidative stress can disrupt protein folding, how protein misfolding and oxidative stress impact each other has not been explored. We have analyzed expression of coagulation factor VIII (FVIII), the protein deficient in hemophilia A, to elucidate the relationship between protein misfolding and oxidative stress. Newly synthesized FVIII misfolds in the ER lumen, activates the unfolded protein response (UPR), causes oxidative stress, and induces apoptosis in vitro and in vivo in mice. Strikingly, antioxidant treatment reduces UPR activation, oxidative stress, and apoptosis, and increases FVIII secretion in vitro and in vivo. The findings indicate that reactive oxygen species are a signal generated by misfolded protein in the ER that cause UPR activation and cell death. Genetic or chemical intervention to reduce reactive oxygen species improves protein folding and cell survival and may provide an avenue to treat and/or prevent diseases of protein misfolding.
Combinatorial genetic transformation generates a library of metabolic phenotypes for the carotenoid pathway in maize
Authors: Zhu Changfu , Naqvi Shaista , Breitenbach Jürgen , Sandmann Gerhard , Christou Paul , Capell Teresa
Published: November 2008

Combinatorial nuclear transformation is a novel method for the rapid production of multiplex-transgenic plants, which we have used to dissect and modify a complex metabolic pathway. To demonstrate the principle, we transferred 5 carotenogenic genes controlled by different endosperm-specific promoters into a white maize variety deficient for endosperm carotenoid synthesis. We recovered a diverse population of transgenic plants expressing different enzyme combinations and showing distinct metabolic phenotypes that allowed us to identify and complement rate-limiting steps in the pathway and to demonstrate competition between β-carotene hydroxylase and bacterial β-carotene ketolase for substrates in 4 sequential steps of the extended pathway. Importantly, this process allowed us to generate plants with extraordinary levels of β-carotene and other carotenoids, including complex mixtures of hydroxycarotenoids and ketocarotenoids. Combinatorial transformation is a versatile approach that could be used to modify any metabolic pathway and pathways controlling other biochemical, physiological, or developmental processes.
Multitarget magnetic activated cell sorter
Authors: Adams Jonathan D. , Kim Unyoung , Soh H. Tom
Published: November 2008

Magnetic selection allows high-throughput sorting of target cells based on surface markers, and it is extensively used in biotechnology for a wide range of applications from in vitro diagnostics to cell-based therapies. However, existing methods can only perform separation based on a single parameter (i.e., the presence or absence of magnetization), and therefore, the simultaneous sorting of multiple targets at high levels of purity, recovery, and throughput remains a challenge. In this work, we present an alternative system, the multitarget magnetic activated cell sorter (MT-MACS), which makes use of microfluidics technology to achieve simultaneous spatially-addressable sorting of multiple target cell types in a continuous-flow manner. We used the MT-MACS device to purify 2 types of target cells, which had been labeled via target-specific affinity reagents with 2 different magnetic tags with distinct saturation magnetization and size. The device was engineered so that the combined effects of the hydrodynamic force produced from the laminar flow and the magnetophoretic force produced from patterned ferromagnetic structures within the microchannel result in the selective purification of the differentially labeled target cells into multiple independent outlets. We demonstrate here the capability to simultaneously sort multiple magnetic tags with >90% purity and >5,000-fold enrichment and multiple bacterial cell types with >90% purity and >500-fold enrichment at a throughput of 10
9
cells per hour.
Human multipotent stromal cells from bone marrow and microRNA: Regulation of differentiation and leukemia inhibitory factor expression
Authors: Oskowitz Adam Z. , Lu Jun , Penfornis Patrice , Ylostalo Joni , McBride Jane , Flemington Erik K. , Prockop Darwin J. , Pochampally Radhika
Published: November 2008

We observed that microRNAs (miRNAs) that regulate differentiation in a variety of simpler systems also regulate differentiation of human multipotent stromal cells (hMSCs) from bone marrow. Differentiation of hMSCs into osteoblasts and adipocytes was inhibited by using lentiviruses expressing shRNAs to decrease expression of Dicer and Drosha, two enzymes that process early transcripts to miRNA. Expression analysis of miRNAs during hMSC differentiation identified 19 miRNAs that were up-regulated during osteogenic differentiation and 20 during adipogenic differentiation, 11 of which were commonly up-regulated in both osteogenic and adipogenic differentiation. In silico models predicted that five of the up-regulated miRNAs targeted leukemia inhibitory factor (LIF) expression. The prediction was confirmed for two of the miRNAs, hsa-mir 199a and hsa-mir346, in that over-expression of the miRNAs decreased LIF secretion by hMSCs. The results demonstrate that differentiation of hMSCs is regulated by miRNAs and that several of these miRNAs target LIF.
Phage φ29 and Nf terminal protein-priming domain specifies the internal template nucleotide to initiate DNA replication
Authors: Longás Elisa , Villar Laurentino , Lázaro José M. , de Vega Miguel , Salas Margarita
Published: November 2008

Bacteriophages φ29 and Nf from
Bacillus subtilis
start replication of their linear genome at both DNA ends by a protein-primed mechanism, by which the DNA polymerase, in a template-instructed reaction, adds 5′-dAMP to a molecule of terminal protein (TP) to form the initiation product TP-dAMP. Mutational analysis of the 3 terminal thymines of the Nf DNA end indicated that initiation of Nf DNA replication is directed by the third thymine on the template, the recovery of the 2 terminal nucleotides mainly occurring by a stepwise sliding-back mechanism. By using chimerical TPs, constructed by swapping the priming domain of the related φ29 and Nf proteins, we show that this domain is the main structural determinant that dictates the internal 3′ nucleotide used as template during initiation.
Lateralization of categorical perception of color changes with color term acquisition
Authors: Franklin A. , Drivonikou G. V. , Clifford A. , Kay P. , Regier T. , Davies I. R. L.
Published: November 2008

Categorical perception (CP) of color is the faster and more accurate discrimination of two colors from different categories than two colors from the same category, even when same- and different-category chromatic separations are equated. In adults, color CP is lateralized to the left hemisphere (LH), whereas in infants, it is lateralized to the right hemisphere (RH). There is evidence that the LH bias in color CP in adults is due to the influence of color terms in the LH. Here we show that the RH to LH switch in color CP occurs when the words that distinguish the relevant category boundary are learned. A colored target was shown in either the left- or right-visual field on either the same- or different-category background, with equal hue separation for both conditions. The time to initiate an eye movement toward the target from central fixation at target onset was recorded. Color naming and comprehension was assessed. Toddlers were faster at detecting targets on different- than same-category backgrounds and the extent of CP did not vary with level of color term knowledge. However, for toddlers who knew the relevant color terms, the category effect was found only for targets in the RVF (LH), whereas for toddlers learning the color terms, the category effect was found only for targets in the LVF (RH). The findings suggest that lateralization of color CP changes with color term acquisition, and provide evidence for the influence of language on the functional organization of the brain.
Two distinct types of murine blast colony-forming cells are multipotential hematopoietic precursors
Authors: Metcalf D. , Greig K. T. , de Graaf C. A. , Loughran S. J. , Alexander W. S. , Kauppi M. , Hyland C. D. , Di Rago L. , Mifsud S.
Published: November 2008

Two types of blast colonies can be stimulated to develop in semisolid agar cultures of murine bone marrow cells. Typically, these are either multicentric colonies stimulated by stem cell factor (SCF) plus interleukin-6 (IL-6) or dispersed colonies stimulated by Flt3 ligand (FL) plus IL-6. Both types of blast colony-forming cells (BL-CFCs) can generate large numbers of lineage-committed granulocyte-macrophage progenitor cells and exhibit some capacity for self-generation and the formation of eosinophil and megakaryocyte progenitor cells. However, the two populations of BL-CFCs are largely distinct and partially separable by fluorescence-activated cell sorting and are distinguished by differing capacity to form granulocyte-committed progeny. Both types of BL-CFCs can generate dendritic cells and small numbers of lymphocytes but the FL-responsive BL-CFCs have a greater capacity to form both B and T lymphocytes. Both types of blast colonies offer remarkable opportunities to analyze multilineage commitment at a clonal level
in vitro
.
Xanthomonas axonopodis
pv.
citri
uses a plant natriuretic peptide-like protein to modify host homeostasis
Authors: Gottig Natalia , Garavaglia Betiana S. , Daurelio Lucas D. , Valentine Alex , Gehring Chris , Orellano Elena G. , Ottado Jorgelina
Published: November 2008

Plant natriuretic peptides (PNPs) are a class of extracellular, systemically mobile molecules that elicit a number of plant responses important in homeostasis and growth. The bacterial citrus pathogen,
Xanthomonas axonopodis
pv.
citri
, also contains a gene encoding a PNP-like protein, XacPNP, that shares significant sequence similarity and identical domain organization with plant PNPs but has no homologues in other bacteria. We have expressed and purified XacPNP and demonstrated that the bacterial protein alters physiological responses including stomatal opening in plants. Although
XacPNP
is not expressed under standard nutrient rich culture conditions, it is strongly induced under conditions that mimic the nutrient poor intercellular apoplastic environment of leaves, as well as in infected tissue, suggesting that
XacPNP
transcription can respond to the host environment. To characterize the role of XacPNP during bacterial infection, we constructed a
XacPNP
deletion mutant. The lesions caused by this mutant were more necrotic than those observed with the wild-type, and bacterial cell death occurred earlier in the mutant. Moreover, when we expressed
XacPNP
in
Xanthomonas axonopodis
pv.
vesicatoria
, the transgenic bacteria caused less necrotic lesions in the host than the wild-type. In conclusion, we present evidence that a plant-like bacterial PNP can enable a plant pathogen to modify host responses to create conditions favorable to its own survival.
Effects of volleyball match‐induced fatigue on knee joint position sense
Authors: Ribeiro Fernando , Santos Fernando , Gonçalves Pedro , Oliveira José
Published: November 2008

It has been suggested that a greater number of injuries during the last third of practice sessions or matches could be related to alteration of lower limb neuromuscular control due to neuromuscular fatigue. This fatigue‐related effect can be mediated by changes in joint proprioception. In athletes, the use of functional fatigue protocols could have the advantage of mimicking the demands of sporting activity, thus reflecting more specifically the changes in neuromuscular control and proprioception observed in sport settings. The purpose of the present study was to assess the effect of fatigue induced by a volleyball match on knee joint position sense in elite volleyball players. Seventeen female volleyball players aged 18.9±4.2 years from the Portuguese national team volunteered for the study. Knee joint position sense was evaluated by an open kinetic chain technique and active knee positioning, and was reported using absolute, relative, and variable angular errors. Joint position sense measures were obtained before and immediately after a simulated volleyball match of five sets. To ensure that the match was sufficiently intense to induce fatigue, the perceived exertion or exercise intensity was assessed at the end of the match using Borg’ s rating of perceived exertion (RPE) scale. All participants completed the volleyball match (90min duration), reaching or exceeding 15 on the RPE scale (15.59±0.71; range 15–17), equivalent to “hard/heavy work”. After the volleyball match, a significant increase in absolute (2.11°) and relative (1.71°) angular errors was detected. Match‐induced fatigue significantly exacerbated the overestimation of the test position. Moreover, the reliability and accuracy in estimating knee angles decreased from rest to the fatigued state, as shown by the increase (264%) in variable error. Our results show that fatigue induced by a volleyball match has a marked effect on knee joint position sense in elite female volleyball players. Knee joint position sense was less accurate and less consistent after the volleyball match. Fatigue induced by a simulated competitive volleyball match resulted in proprioceptive deficits, decreasing sensorimotor system acuity in female volleyball players.
Readability statistics of patient information leaflets in a Speech and Language Therapy Department
Authors: Pothier Louise , Day Rachael , Harris Catherine , Pothier David D.
Published: November 2008

Background: Information leaflets are commonly used in Speech and Language Therapy Departments. Despite widespread use, they can be of variable quality.

Aims: To revise current departmental leaflets using the National Health Service (NHS) Toolkit for Producing Patient Information and to test the effect that this has on the readability scores of the text.

Methods & Procedures: Twenty existing leaflets were revised with the help of the NHS Toolkit for Producing Patient Information. Readability statistics were calculated for each leaflet before and after revision.

Outcomes & Results: The mean Flesch Reading Ease (FRE) score and the Flesch–Kincaid Reading Grade Level (FKRGL) were significantly better in the revised leaflets (p<0.01 and <0.01, respectively). The variability of readability outcome measures was lower in the revised group. Only 25% of the original leaflets met recommended levels of readability, while 75% of the revised leaflets met these standards.

Conclusions: Readability is a vital component to consider in the production of information leaflets. Following simple guidelines on the production of leaflets for patients considerably improves their quality.
From hyperheavenly spaces to Walker and Osserman spaces: II
Authors: Chudecki Adam , Przanowski Maciej
Published: November 2008

Spinorial formalism employed in the weak hyperheavenly space theory is used to study Osserman spaces. General forms of metrics of signature (+ + − −) for self-dual pointwise Osserman, globally Osserman and globally Jordan–Osserman spaces admitting a two-dimensional totally null self-dual integrable distribution are found by searching for solutions to respective hyperheavenly equations with Λ. As is shown the metrics obtained describe locally all self-dual pointwise Osserman, globally Osserman and globally Jordan–Osserman spaces of types II, III, N, 0 and D (where in the case of type D one assumes that the multiple undotted Penrose spinors are real).
CRONOS: the cross-reference navigation server
Authors: Waegele Brigitte , Dunger-Kaltenbach Irmtraud , Fobo Gisela , Montrone Corinna , Mewes H.-Werner , Ruepp Andreas
Published: November 2008

Summary: Cross-mapping of gene and protein identifiers between different databases is a tedious and time-consuming task. To overcome this, we developed CRONOS, a cross-reference server that contains entries from five mammalian organisms presented by major gene and protein information resources. Sequence similarity analysis of the mapped entries shows that the cross-references are highly accurate. In total, up to 18 different identifier types can be used for identification of cross-references. The quality of the mapping could be improved substantially by exclusion of ambiguous gene and protein names which were manually validated. Organism-specific lists of ambiguous terms, which are valuable for a variety of bioinformatics applications like text mining are available for download.

Availability: CRONOS is freely available to non-commercial users at http://mips.gsf.de/genre/proj/cronos/index.html, web services are available at http://mips.gsf.de/CronosWSService/CronosWS?wsdl.

Contact:  brigitte.waegele@helmholtz-muenchen.de

Supplementary information:  Supplementary data are available at Bioinformatics online. The online Supplementary Material contains all figures and tables referenced by this article.
Align human interactome with phenome to identify causative genes and networks underlying disease families
Authors: Wu Xuebing , Liu Qifang , Jiang Rui
Published: November 2008

Motivation: Understanding the complexity in gene–phenotype relationship is vital for revealing the genetic basis of common diseases. Recent studies on the basis of human interactome and phenome not only uncovers prevalent phenotypic overlap and genetic overlap between diseases, but also reveals a modular organization of the genetic landscape of human diseases, providing new opportunities to reduce the complexity in dissecting the gene–phenotype association.

Results: We provide systematic and quantitative evidence that phenotypic overlap implies genetic overlap. With these results, we perform the first heterogeneous alignment of human interactome and phenome via a network alignment technique and identify 39 disease families with corresponding causative gene networks. Finally, we propose AlignPI, an alignment-based framework to predict disease genes, and identify plausible candidates for 70 diseases. Our method scales well to the whole genome, as demonstrated by prioritizing 6154 genes across 37 chromosome regions for Crohn's disease (CD). Results are consistent with a recent meta-analysis of genome-wide association studies for CD.

Availability: Bi-modules and disease gene predictions are freely available at the URL http://bioinfo.au.tsinghua.edu.cn/alignpi/

Contact:  ruijiang@tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors
Authors: Bateman Alex , Finn Robert D. , Sims Peter J. , Wiedmer Therese , Biegert Andreas , Söding Johannes
Published: November 2008

Motivation: Phospholipid scramblases (PLSCRs) constitute a family of cytoplasmic membrane-associated proteins that were identified based upon their capacity to mediate a Ca2+-dependent bidirectional movement of phospholipids across membrane bilayers, thereby collapsing the normally asymmetric distribution of such lipids in cell membranes. The exact function and mechanism(s) of these proteins nevertheless remains obscure: data from several laboratories now suggest that in addition to their putative role in mediating transbilayer flip/flop of membrane lipids, the PLSCRs may also function to regulate diverse processes including signaling, apoptosis, cell proliferation and transcription. A major impediment to deducing the molecular details underlying the seemingly disparate biology of these proteins is the current absence of any representative molecular structures to provide guidance to the experimental investigation of their function.

Results: Here, we show that the enigmatic PLSCR family of proteins is directly related to another family of cellular proteins with a known structure. The Arabidopsis protein At5g01750 from the DUF567 family was solved by X-ray crystallography and provides the first structural model for this family. This model identifies that the presumed C-terminal transmembrane helix is buried within the core of the PLSCR structure, suggesting that palmitoylation may represent the principal membrane anchorage for these proteins. The fold of the PLSCR family is also shared by Tubby-like proteins. A search of the PDB with the HHpred server suggests a common evolutionary ancestry. Common functional features also suggest that tubby and PLSCR share a functional origin as membrane tethered transcription factors with capacity to modulate phosphoinositide-based signaling.

Contact:  agb@sanger.ac.uk
Combining multiple positive training sets to generate confidence scores for protein–protein interactions
Authors: Yu Jingkai , Finley Russell L.
Published: November 2008

Motivation: High-throughput experimental and computational methods are generating a wealth of protein–protein interaction data for a variety of organisms. However, data produced by current state-of-the-art methods include many false positives, which can hinder the analyses needed to derive biological insights. One way to address this problem is to assign confidence scores that reflect the reliability and biological significance of each interaction. Most previously described scoring methods use a set of likely true positives to train a model to score all interactions in a dataset. A single positive training set, however, may be biased and not representative of true interaction space.

Results: We demonstrate a method to score protein interactions by utilizing multiple independent sets of training positives to reduce the potential bias inherent in using a single training set. We used a set of benchmark yeast protein interactions to show that our approach outperforms other scoring methods. Our approach can also score interactions across data types, which makes it more widely applicable than many previously proposed methods. We applied the method to protein interaction data from both Drosophila melanogaster and Homo sapiens. Independent evaluations show that the resulting confidence scores accurately reflect the biological significance of the interactions.

Contact:  rfinley@wayne.edu

Supplementary information:  Supplementary data are available at Bioinformatics Online.
Genome and proteome annotation: organization, interpretation and integration
Authors: Reeves Gabrielle A , Talavera David , Thornton Janet M
Published: November 2008

Recent years have seen a huge increase in the generation of genomic and proteomic data. This has been due to improvements in current biological methodologies, the development of new experimental techniques and the use of computers as support tools. All these raw data are useless if they cannot be properly analysed, annotated, stored and displayed. Consequently, a vast number of resources have been created to present the data to the wider community. Annotation tools and databases provide the means to disseminate these data and to comprehend their biological importance. This review examines the various aspects of annotation: type, methodology and availability. Moreover, it puts a special interest on novel annotation fields, such as that of phenotypes, and highlights the recent efforts focused on the integrating annotations.
The roles of APE1, APE2, DNA polymerase β and mismatch repair in creating S region DNA breaks during antibody class switch
Authors: Schrader Carol E , Guikema Jeroen E.J , Wu Xiaoming , Stavnezer Janet
Published: November 2008

Immunoglobulin class switch recombination (CSR) occurs by an intrachromosomal deletion requiring generation of double-stranded DNA breaks (DSBs) in immunoglobulin switch region DNA. The initial steps of DSB formation have been elucidated: cytosine deamination by activation-induced cytidine deaminase (AID) and the generation of abasic sites by uracil-DNA glycosylase (UNG). We show that abasic sites are converted into single-strand breaks (SSBs) by apurinic/apyrimidinic endonucleases (APE1 and APE2). If SSBs are near to each other on opposite strands, they will generate DSBs; but if distal from each other, mismatch repair appears to be required to generate DSBs. The resulting S region DSBs occur at dC residues that are preferentially targeted by AID. We also investigate whether DNA polymerase β, which correctly repairs SSBs resulting from APE activity, attempts to repair the breaks during CSR. We find that although polymerase β does attempt to repair S region DNA breaks in switching B cells, the frequency of AID-instigated breaks appears to outnumber the SSBs repaired correctly by polymerase β, and thus some DSBs and mutations are generated. We also show that the S region DSBs are introduced and resolved during the G1 phase of the cell cycle.
Competitive repair pathways in immunoglobulin gene hypermutation
Authors: Reynaud Claude-Agnès , Delbos Frédéric , Faili Ahmad , Guéranger Quentin , Aoufouchi Said , Weill Jean-Claude
Published: November 2008

This review focuses on the contribution of translesion DNA polymerases to immunoglobulin gene hypermutation, in particular on the roles of DNA polymerase eta (Polη) in the generation of mutations at A/T bases from the initial cytosine-targeted activation-induced cytidine deaminase (AID)-mediated deamination event, and of Polκ, an enzyme of the same polymerase family, used as a substitute when Polη is absent. The proposition that the UNG uracil glycosylase and the MSH2–MSH6 mismatch recognition complex are two competitive rather than alternative pathways in the processing of uracils generated by AID is further discussed.
Impaired ERAD and ER stress are early and specific events in polyglutamine toxicity
Authors: Duennwald Martin L. , Lindquist Susan
Published: November 2008

Protein misfolding, whether caused by aging, environmental factors, or genetic mutations, is a common basis for neurodegenerative diseases. The misfolding of proteins with abnormally long polyglutamine (polyQ) expansions causes several neurodegenerative disorders, such as Huntington’s disease (HD). Although many cellular pathways have been documented to be impaired in HD, the primary triggers of polyQ toxicity remain elusive. We report that yeast cells and neuron-like PC12 cells expressing polyQ-expanded huntingtin (htt) fragments display a surprisingly specific, immediate, and drastic defect in endoplasmic reticulum (ER)-associated degradation (ERAD). We further decipher the mechanistic basis for this defect in ERAD: the entrapment of the essential ERAD proteins Npl4, Ufd1, and p97 by polyQ-expanded htt fragments. In both yeast and mammalian neuron-like cells, overexpression of Npl4 and Ufd1 ameliorates polyQ toxicity. Our results establish that impaired ER protein homeostasis is a broad and highly conserved contributor to polyQ toxicity in yeast, in PC12 cells, and, importantly, in striatal cells expressing full-length polyQ-expanded huntingtin.
Combined Proteomic and Cytological Analysis of Ca2+-Calmodulin Regulation inPicea meyeriPollen Tube Growth
Authors: Chen Tong , Wu Xiaoqin , Chen Yanmei , Li Xiaojuan , Huang Mei , Zheng Maozhong , Baluška František , Šamaj Jozef , Lin Jinxing
Published: November 2008

Ca2+-calmodulin (Ca2+-CaM) is a critical molecule that mediates cellular functions by interacting with various metabolic and signaling pathways. However, the protein expression patterns and accompanying serial cytological responses in Ca2+-CaM signaling deficiency remain enigmatic. Here, we provide a global analysis of the cytological responses and significant alterations in protein expression profiles after trifluoperazine treatment in Picea meyeri, which abrogates Ca2+-CaM signaling. Ninety-three differentially displayed proteins were identified by comparative proteomics at different development stages and were assigned to different functional categories closely related to tip growth machinery. The inhibition of Ca2+-CaM signaling rapidly induced an increase in extracellular Ca2+ influx, resulting in dramatically increased cytosolic Ca2+ concentrations and ultrastructural abnormalities in organelles as the primary responses. Secondary and tertiary alterations included actin filament depolymerization, disrupted patterns of endocytosis and exocytosis, and cell wall remodeling, ultimately resulting in perturbed pollen tube extension. In parallel with these cytological events, time-course experiments revealed that most differentially expressed proteins showed time-dependent quantitative changes (i.e. some signaling proteins and proteins involved in organelle functions and energy production changed first, followed by alterations in proteins related to cytoskeletal organization, secretory pathways, and polysaccharide synthesis). Taken together, Ca2+-CaM dysfunction induced serial cytological responses and temporal changes in protein expression profiles, indicating the pivotal role of Ca2+-CaM in the regulation of tip growth machinery.
OsFRDL1 Is a Citrate Transporter Required for Efficient Translocation of Iron in Rice
Authors: Yokosho Kengo , Yamaji Naoki , Ueno Daisei , Mitani Namiki , Ma Jian Feng
Published: November 2008

Multidrug and toxic compound extrusion (MATE) transporters represent a large family in plants, but their functions are poorly understood. Here, we report the function of a rice (Oryza sativa) MATE gene (Os03g0216700, OsFRDL1), the closest homolog of barley (Hordeum vulgare) HvAACT1 (aluminum [Al]-activated citrate transporter 1), in terms of metal stress (iron [Fe] deficiency and Al toxicity). This gene was mainly expressed in the roots and the expression level was not affected by either Fe deficiency or Al toxicity. Knockout of this gene resulted in leaf chlorosis, lower leaf Fe concentration, higher accumulation of zinc and manganese concentration in the leaves, and precipitation of Fe in the root's stele. The concentration of citrate and ferric iron in the xylem sap was lower in the knockout line compared to the wild-type rice. Heterologous expression of OsFRDL1 in Xenopus oocytes showed transport activity for citrate. Immunostaining showed that OsFRDL1 was localized at the pericycle cells of the roots. On the other hand, there was no difference in the Al-induced secretion of citrate from the roots between the knockout line and the wild-type rice. Taken together, our results indicate that OsFRDL1 is a citrate transporter localized at the pericycle cells, which is necessary for efficient translocation of Fe to the shoot as a Fe-citrate complex.
A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance in Rice
Authors: Manosalva Patricia M. , Davidson Rebecca M. , Liu Bin , Zhu Xiaoyuan , Hulbert Scot H. , Leung Hei , Leach Jan E.
Published: November 2008

Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of pathogens and long lasting. Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. Five disease resistance QTL that colocalized with defense response genes were accumulated by marker-aided selection to develop blast-resistant varieties. One advanced backcross line carrying the major-effect QTL on chromosome (chr) 8, which included a cluster of 12 germin-like protein (OsGLP) gene members, exhibited resistance to rice (Oryza sativa) blast disease over 14 cropping seasons. To determine if OsGLP members contribute to resistance and if the resistance was broad spectrum, a highly conserved portion of the OsGLP coding region was used as an RNA interference trigger to silence a few to all expressed chr 8 OsGLP family members. Challenge with two different fungal pathogens (causal agents of rice blast and sheath blight diseases) revealed that as more chr 8 OsGLP genes were suppressed, disease susceptibility of the plants increased. Of the 12 chr 8 OsGLPs, one clustered subfamily (OsGER4) contributed most to resistance. The similarities of sequence, gene organization, and roles in disease resistance of GLP family members in rice and other cereals, including barley (Hordeum vulgare) and wheat (Triticum aestivum), suggest that resistance contributed by the chr 8 OsGLP is a broad-spectrum, basal mechanism conserved among the Gramineae. Natural selection may have preserved a whole gene family to provide a stepwise, flexible defense response to pathogen invasion.
Analysis of Intraspecies Diversity in Wheat and Barley Genomes Identifies Breakpoints of Ancient Haplotypes and Provides Insight into the Structure of Diploid and Hexaploid Triticeae Gene Pools
Authors: Wicker Thomas , Krattinger Simon G. , Lagudah Evans S. , Komatsuda Takao , Pourkheirandish Mohammad , Matsumoto Takashi , Cloutier Sylvie , Reiser Laurenz , Kanamori Hiroyuki , Sato Kazuhiro , Perovic Dragan , Stein Nils , Keller Beat
Published: November 2008

A large number of wheat (Triticum aestivum) and barley (Hordeum vulgare) varieties have evolved in agricultural ecosystems since domestication. Because of the large, repetitive genomes of these Triticeae crops, sequence information is limited and molecular differences between modern varieties are poorly understood. To study intraspecies genomic diversity, we compared large genomic sequences at the Lr34 locus of the wheat varieties Chinese Spring, Renan, and Glenlea, and diploid wheat Aegilops tauschii. Additionally, we compared the barley loci Vrs1 and Rym4 of the varieties Morex, Cebada Capa, and Haruna Nijo. Molecular dating showed that the wheat D genome haplotypes diverged only a few thousand years ago, while some barley and Ae. tauschii haplotypes diverged more than 500,000 years ago. This suggests gene flow from wild barley relatives after domestication, whereas this was rare or absent in the D genome of hexaploid wheat. In some segments, the compared haplotypes were very similar to each other, but for two varieties each at the Rym4 and Lr34 loci, sequence conservation showed a breakpoint that separates a highly conserved from a less conserved segment. We interpret this as recombination breakpoints of two ancient haplotypes, indicating that the Triticeae genomes are a heterogeneous and variable mosaic of haplotype fragments. Analysis of insertions and deletions showed that large events caused by transposable element insertions, illegitimate recombination, or unequal crossing over were relatively rare. Most insertions and deletions were small and caused by template slippage in short homopolymers of only a few base pairs in size. Such frequent polymorphisms could be exploited for future molecular marker development.
The Zeaxanthin-Independent and Zeaxanthin-Dependent qE Components of Nonphotochemical Quenching Involve Common Conformational Changes within the Photosystem II Antenna in Arabidopsis
Authors: Johnson Matthew P. , Pérez-Bueno María L. , Zia Ahmad , Horton Peter , Ruban Alexander V.
Published: November 2008

The light-harvesting antenna of higher plant photosystem II (LHCII) has the intrinsic capacity to dissipate excess light energy as heat in a process termed nonphotochemical quenching (NPQ). Recent studies suggest that zeaxanthin and lutein both contribute to the rapidly relaxing component of NPQ, qE, possibly acting in the minor monomeric antenna complexes and the major trimeric LHCII, respectively. To distinguish whether zeaxanthin and lutein act independently as quenchers at separate sites, or alternatively whether zeaxanthin fulfills an allosteric role regulating lutein-mediated quenching, the kinetics of qE and the qE-related conformational changes (ΔA  535) were compared in Arabidopsis (Arabidopsis thaliana) mutant/antisense plants with altered contents of minor antenna (kolhcb6, aslhcb4), trimeric LHCII (aslhcb2), lutein (lut2, lut2npq1, lut2npq2), and zeaxanthin (npq1, npq2). The kinetics of the two components of NPQ induction arising from zeaxanthin-independent and zeaxanthin-dependent qE were both sensitive to changes in the protein composition of the photosystem II antenna. The replacement of lutein by zeaxanthin or violaxanthin in the internal Lhcb protein-binding sites affected the kinetics and relative amplitude of each component as well as the absolute chlorophyll fluorescence lifetime. Both components of qE were characterized by a conformational change leading to nearly identical absorption changes in the Soret region that indicated the involvement of the LHCII lutein 1 domain. Based on these observations, we suggest that both components of qE arise from a common quenching mechanism based upon a conformational change within the photosystem II antenna, optimized by Lhcb subunit-subunit interactions and tuned by the synergistic effects of external and internally bound xanthophylls.
Role of the Rice HexokinasesOsHXK5andOsHXK6as Glucose Sensors
Authors: Cho Jung-Il , Ryoo Nayeon , Eom Joon-Seob , Lee Dae-Woo , Kim Hyun-Bi , Jeong Seok-Won , Lee Youn-Hyung , Kwon Yong-Kook , Cho Man-Ho , Bhoo Seong Hee , Hahn Tae-Ryong , Park Youn-Il , Hwang Ildoo , Sheen Jen , Jeon Jong-Seong
Published: November 2008

The Arabidopsis (Arabidopsis thaliana) hexokinase 1 (AtHXK1) is recognized as an important glucose (Glc) sensor. However, the function of hexokinases as Glc sensors has not been clearly demonstrated in other plant species, including rice (Oryza sativa). To investigate the functions of rice hexokinase isoforms, we characterized OsHXK5 and OsHXK6, which are evolutionarily related to AtHXK1. Transient expression analyses using GFP fusion constructs revealed that OsHXK5 and OsHXK6 are associated with mitochondria. Interestingly, the OsHXK5ΔmTP-GFP and OsHXK6ΔmTP-GFP fusion proteins, which lack N-terminal mitochondrial targeting peptides, were present mainly in the nucleus with a small amount of the proteins seen in the cytosol. In addition, the OsHXK5NLS-GFP and OsHXK6NLS-GFP fusion proteins harboring nuclear localization signals were targeted predominantly in the nucleus, suggesting that these OsHXKs retain a dual-targeting ability to mitochondria and nuclei. In transient expression assays using promoter∷luciferase fusion constructs, these two OsHXKs and their catalytically inactive alleles dramatically enhanced the Glc-dependent repression of the maize (Zea mays) Rubisco small subunit (RbcS) and rice α-amylase genes in mesophyll protoplasts of maize and rice. Notably, the expression of OsHXK5, OsHXK6, or their mutant alleles complemented the Arabidopsis glucose insensitive2-1 mutant, thereby resulting in wild-type characteristics in seedling development, Glc-dependent gene expression, and plant growth. Furthermore, transgenic rice plants overexpressing OsHXK5 or OsHXK6 exhibited hypersensitive plant growth retardation and enhanced repression of the photosynthetic gene RbcS in response to Glc treatment. These results provide evidence that rice OsHXK5 and OsHXK6 can function as Glc sensors.
Experimental Analysis of the Rice Mitochondrial Proteome, Its Biogenesis, and Heterogeneity
Authors: Huang Shaobai , Taylor Nicolas L. , Narsai Reena , Eubel Holger , Whelan James , Millar A. Harvey
Published: November 2008

Mitochondria in rice (Oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissues after anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. We have combined density gradient and surface charge purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. Quantitative comparisons of mitochondria purified by density gradients and after further surface charge purification have been used to ensure that the proteins identified copurify with mitochondria and to remove contaminants from the analysis. This rigorous approach to defining a subcellular proteome has yielded 322 nonredundant rice proteins and highlighted contaminants in previously reported rice mitochondrial proteomes. Comparative analysis with the Arabidopsis (Arabidopsis thaliana) mitochondrial proteome reveals conservation of a broad range of known and unknown function proteins in plant mitochondria, with only approximately 20% not having a clear homolog in the Arabidopsis mitochondrial proteome. As in Arabidopsis, only approximately 60% of the rice mitochondrial proteome is predictable using current organelle-targeting prediction tools. Use of the rice protein data set to explore rice transcript data provided insights into rice mitochondrial biogenesis during seed germination, leaf development, and heterogeneity in the expression of nucleus-encoded mitochondrial components in different rice tissues. Highlights include the identification of components involved in thiamine synthesis, evidence for coexpressed and unregulated expression of specific components of protein complexes, a selective anther-enhanced subclass of the decarboxylating segment of the tricarboxylic acid cycle, the differential expression of DNA and RNA replication components, and enhanced expression of specific metabolic components in photosynthetic tissues.
Protein Repairl-Isoaspartyl Methyltransferase1 Is Involved in Both Seed Longevity and Germination Vigor inArabidopsis
Authors: Ogé Laurent , Bourdais Gildas , Bove Jérôme , Collet Boris , Godin Béatrice , Granier Fabienne , Boutin Jean-Pierre , Job Dominique , Jullien Marc , Grappin Philippe
Published: November 2008

The formation of abnormal amino acid residues is a major source of spontaneous age-related protein damage in cells. The protein l-isoaspartyl methyltransferase (PIMT) combats protein misfolding resulting from l-isoaspartyl formation by catalyzing the conversion of abnormal l-isoaspartyl residues to their normal l-aspartyl forms. In this way, the PIMT repair enzyme system contributes to longevity and survival in bacterial and animal kingdoms. Despite the discovery of PIMT activity in plants two decades ago, the role of this enzyme during plant stress adaptation and in seed longevity remains undefined. In this work, we have isolated Arabidopsis thaliana lines exhibiting altered expression of PIMT1, one of the two genes encoding the PIMT enzyme in Arabidopsis. PIMT1 overaccumulation reduced the accumulation of l-isoaspartyl residues in seed proteins and increased both seed longevity and germination vigor. Conversely, reduced PIMT1 accumulation was associated with an increase in the accumulation of l-isoaspartyl residues in the proteome of freshly harvested dry mature seeds, thus leading to heightened sensitivity to aging treatments and loss of seed vigor under stressful germination conditions. These data implicate PIMT1 as a major endogenous factor that limits abnormal l-isoaspartyl accumulation in seed proteins, thereby improving seed traits such as longevity and vigor. The PIMT repair pathway likely works in concert with other anti-aging pathways to actively eliminate deleterious protein products, thus enabling successful seedling establishment and strengthening plant proliferation in natural environments.
A study of the behavior of copper electrodes in buffered borax solutions containing BTA‐type inhibitors by photoelectrochemical methods
Authors: Xu Qun‐jie , Zhou Guo‐ding
Published: November 2008

Purpose

The purpose of this paper is to provide useful information pertaining to the corrosion inhibition mechanism of BTA and its derivatives on copper.

Design/methodology/approach

The photoelectrochemical behavior of copper electrodes in buffered borax solutions (pH 9.2) containing BTA and its derivatives was comparatively studied by using a photoelectrochemical technique. It was possible to analyze the inhibition mechanism of the derivatives of BTA for copper corrosion from the photoelectrochemical results. The photoresponse of the Cu electrode in buffered borax solutions containing BTA and its derivatives was measured. Different concentrations and different kinds of inhibitors may result in different photoresponses on the Cu electrode in buffered borax solutions.

Findings

The photoresponse for copper electrodes in solutions containing a certain amount of BTA exhibits an n‐type response during anodic polarization and, the greater the n‐type photoresponse, the better the performance of the inhibitor. The photoresponse for copper electrodes in solutions containing 4CBTA, or 5CBTA, or CBT‐1, always exhibited p‐type behavior during anodic polarization, but the photoresponse changed very evidently during cathodic polarization. The larger the maximum cathodic photocurrent, then the greater was the effectiveness of the corrosion inhibitor. In consequence, it is possible to evaluate inhibitors according to ΦV and iph at more negative potentials. The more negative the ΦV and iph, the better is the inhibition. It was shown that the inhibition mechanism of the derivatives of BTA with a −COOH group was different from that occurring with ester groups. The former could make the Cu2O film on the Cu electrode thicker. The photocurrent was observed to increase when the potential was scanned to more negative potentials in the presence of certain concentrated inhibitors. It is therefore possible to evaluate the performance of inhibitors according to the value of the cathodic photocurrent. The larger the cathodic photocurrent, the better is the inhibition effect of the compound. The latter could increase the density of the polymer film on the copper electrode and prevent O2− in the solution from entering the copper surface and changing the stoichiometric ratio of Cu2O. The photocurrent type could transfer from p‐ to n‐type according to the action of certain concentrated inhibitors when the potential was scanned to more positive potentials. The value of the anodic photocurrent can be used to evaluate the effectiveness of inhibition. The larger the anodic photocurrent, the greater is the inhibition effect.

Originality/value

The paper provides useful information pertaining to the corrosion inhibition mechanism of BTA and its derivatives on copper. The photoelectrochemical technique is an effective method with which to evaluate the effectiveness of corrosion inhibitors and to investigate the mechanism of corrosion inhibition on copper.