bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SCABRA3 Nuclear Gene Encodes the Plastid RpoTp RNA Polymerase, Which Is Required for Chloroplast Biogenesis and Mesophyll Cell Proliferation in Arabidopsis
Authors: Hricová Andrea , Quesada Victor , Micol José Luis 
Published: May 2006

Abstract
In many plant species, a subset of the genes of the chloroplast genome is transcribed by RpoTp, a nuclear-encoded plastid-targeted RNA polymerase. Here, we describe the positional cloning of the SCABRA3 (SCA3) gene, which was found to encode RpoTp in Arabidopsis (Arabidopsis thaliana). We studied one weak (sca3-1) and two strong (sca3-2 and sca3-3) alleles of the SCA3 gene, the latter two showing severely impaired plant growth and reduced pigmentation of the cotyledons, leaves, stem, and sepals, all of which were pale green. The leaf surface was extremely crumpled in the sca3 mutants, although epidermal cell size and morphology were not perturbed, whereas the mesophyll cells were less densely packed and more irregular in shape than in the wild type. A significant reduction in the size, morphology, and number of chloroplasts was observed in homozygous sca3-2 individuals whose photoautotrophic growth was consequently perturbed. Microarray analysis showed that several hundred nuclear genes were differentially expressed in sca3-2 and the wild type, about one-fourth of which encoded chloroplast-targeted proteins. Quantitative reverse transcription-PCR analyses showed that the sca3-2 mutation alters the expression of the rpoB, rpoC1, clpP, and accD plastid genes and the SCA3 paralogs RpoTm and RpoTmp, which respectively encode nuclear-encoded mitochondrion or dually targeted RNA polymerases. Double-mutant analysis indicated that RpoTmp and SCA3 play redundant functions in plant development. Our findings support a role for plastids in leaf morphogenesis and indicate that RpoTp is required for mesophyll cell proliferation.
Identification of a Mung Bean Arabinofuranosyltransferase That Transfers Arabinofuranosyl Residues onto (1, 5)-Linked α-l-Arabino-Oligosaccharides
Authors: Konishi Teruko , Ono Hiroshi , Ohnishi-Kameyama Mayumi , Kaneko Satoshi , Ishii Tadashi 
Published: May 2006

Abstract
Arabinofuranosyltransferase activity was identified in Golgi membranes obtained from mung bean (Vigna radiata) hypocotyls. The enzyme transfers the arabinofuranosyl (Araf) residue from UDP-β-l-arabinofuranose to exogenous (1, 5)-linked α-l-arabino-oligosaccharides labeled at their reducing ends with 2-aminobenzamide. The transferred residue was shown, using 1H-nuclear magnetic resonance spectroscopy and α-l-arabinofuranosidase treatment, to be α-l-Araf and to be linked to O-5 of the nonreducing terminal Araf residue of the acceptor oligosaccharide. The enzyme was nonprocessive because only a single Araf residue was added to the acceptor molecule. Arabino-oligosaccharides with a degree of polymerization between 3 and 8 were acceptor substrates. The 2-aminobenzamide-labeled arabino-tetra- and pentasaccharides were the most effective acceptor substrates analyzed. The enzyme has a pH optimum between 6.5 and 7.0 and its activity is stimulated by Mn2+ and Co2+ ions. The apparent Km and Vmax values of the arabinofuranosyltransferase for UDP-arabinofuranose are 243 μm and 243 pmol min−1 mg protein−1, respectively. The highest enzyme activity was detected in the elongating regions of mung bean hypocotyls. The data show that UDP-arabinofuranose is the donor molecule for the generation of arabino-oligosaccharides composed of Araf residues.
A Suppressor of fab1 Challenges Hypotheses on the Role of Thylakoid Unsaturation in Photosynthetic Function
Authors: Barkan Lenore , Vijayan Perumal , Carlsson Anders S. , Mekhedov Sergei , Browse John 
Published: May 2006

Abstract
Leaf membrane lipids of the Arabidopsis (Arabidopsis thaliana) fatty acid biosynthesis 1 (fab1) mutant contain a 35% to 40% increase in the predominant saturated fatty acid 16:0, relative to wild type. This increase in membrane saturation is associated with loss of photosynthetic function and death of mutant plants at low temperatures. We have initiated a suppressor screen for mutations that allow survival of fab1 plants at 2°C. Five suppressor mutants identified in this screen all rescued the collapse of photosynthetic function observed in fab1 plants. While fab1 plants died after 5 to 7 weeks at 2°C, the suppressors remained viable after 16 weeks in the cold, as judged by their ability to resume growth following a return to 22°C and to subsequently produce viable seed. Three of the suppressors had changes in leaf fatty acid composition when compared to fab1, indicating that one mechanism of suppression may involve compensating changes in thylakoid lipid composition. Surprisingly, the suppressor phenotype in one line, S31, was associated with a further substantial increase in lipid saturation. The overall leaf fatty acid composition of S31 plants contained 31% 16:0 compared with 23% in fab1 and 17% in wild type. Biochemical and genetic analysis showed that S31 plants contain a new allele of fatty acid desaturation 5 (fad5), fad5-2, and are therefore partially deficient in activity of the chloroplast 16:0 Δ7 desaturase. A double mutant produced by crossing fab1 to the original fad5-1 allele also remained alive at 2°C, indicating that the fad5-2 mutation is the suppressor in the S31 (fab1 fad5-2) line. Based on the biophysical characteristics of saturated and unsaturated fatty acids, the increased 16:0 in fab1 fad5-2 plants would be expected to exacerbate, rather than ameliorate, low-temperature damage. We propose instead that a change in shape of the major thylakoid lipid, monogalactosyldiacylglycerol, mediated by the fad5-2 mutation, may compensate for changes in lipid structure resulting from the original fab1 mutation. Our identification of mutants that suppress the low-temperature phenotype of fab1 provides new tools to understand the relationship between thylakoid lipid structure and photosynthetic function.
Surface Position, Not Signaling from Surrounding Maternal Tissues, Specifies Aleurone Epidermal Cell Fate in Maize
Authors: Gruis Darren (Fred) , Guo Hena , Selinger David , Tian Qing , Olsen Odd-Arne 
Published: May 2006

AbstractMaize (Zea mays) endosperm consists of an epidermal-like surface layer of aleurone cells, an underlying body of starchy endosperm cells, and a basal layer of transfer cells. To determine whether surrounding maternal tissues perform a role in specifying endosperm cell fates, a maize endosperm organ culture technique was established whereby the developing endosperm is completely removed from surrounding maternal tissues. Using cell type-specific fluorescence markers, we show that aleurone cell fate specification occurs exclusively in response to surface position and does not require specific, continued maternal signal input. The starchy endosperm and aleurone cell fates are freely interchangeable throughout the lifespan of the endosperm, with internalized aleurone cells converting to starchy endosperm cells and with starchy endosperm cells that become positioned at the surface converting to aleurone cells. In contrast to aleurone and starchy endosperm cells, transfer cells fail to develop in in vitro-grown endosperm, supporting earlier indications that maternal tissue interaction is required to fully differentiate this cell type. Several parameters confirm that the maize endosperm organ cultures described herein retain the main developmental features of in planta endosperm, including fidelity of aleurone mutant phenotypes, temporal and spatial control of cell type-specific fluorescent markers, specificity of cell type transcripts, and control of mitotic cell divisions.
Early Steps in the Biosynthesis of NAD in Arabidopsis Start with Aspartate and Occur in the Plastid
Authors: Katoh Akira , Uenohara Kazuya , Akita Mitsuru , Hashimoto Takashi 
Published: May 2006

Abstract
NAD is a ubiquitous coenzyme involved in oxidation-reduction reactions and is synthesized by way of quinolinate. Animals and some bacteria synthesize quinolinate from tryptophan, whereas other bacteria synthesize quinolinate from aspartate (Asp) using l-Asp oxidase and quinolinate synthase. We show here that Arabidopsis (Arabidopsis thaliana) uses the Asp-to-quinolinate pathway. The Arabidopsis l-Asp oxidase or quinolinate synthase gene complemented the Escherichia coli mutant defective in the corresponding gene, and T-DNA-based disruption of either of these genes, as well as of the gene coding for the enzyme quinolinate phosphoribosyltransferase, was embryo lethal. An analysis of functional green fluorescent protein-fused constructs and in vitro assays of uptake into isolated chloroplasts demonstrated that these three enzymes are located in the plastid.
Carbon Balance and Circadian Regulation of Hydrolytic and Phosphorolytic Breakdown of Transitory Starch
Authors: Weise Sean E. , Schrader Stephen M. , Kleinbeck Kyle R. , Sharkey Thomas D. 
Published: May 2006

Abstract
Transitory starch is formed in chloroplasts during the day and broken down at night. Transitory starch degradation could be regulated by light, circadian rhythms, or carbon balance. To test the role of these potential regulators, starch breakdown rates and metabolites were measured in bean (Phaseolus vulgaris) and Arabidopsis (Arabidopsis thaliana) plants. In continuous light, starch and maltose levels oscillated in a circadian manner. Under photorespiratory conditions, transitory starch breakdown occurred in the light faster than at night and glucose-6-P (G6P) was elevated. Nonaqueous fractionation showed that the increase in G6P occurred in the chloroplast. When Arabidopsis plants lacking the plastidic starch phosphorylase enzyme were placed under photorespiratory conditions, G6P levels remained constant, indicating that the increased chloroplastic G6P resulted from phosphorolytic starch degradation. Maltose was increased under photorespiratory conditions in both wild type and plants lacking starch phosphorylase, indicating that regulation of starch breakdown may occur at a point preceding the division of the hydrolytic and phosphorolytic pathways. When bean leaves were held in N2 to suppress photosynthesis and Suc synthesis without increasing photorespiration, starch breakdown did not occur and maltose and G6P levels remained constant. The redox status of the chloroplasts was found to be oxidized under conditions favoring starch degradation.
SCARFACEEncodes an ARF-GAP That Is Required for Normal Auxin Efflux and Vein Patterning inArabidopsis
Authors: Sieburth Leslie E. , Muday Gloria K. , King Edward J. , Benton Geoff , Kim Sun , Metcalf Kasee E. , Meyers Lindsay , Seamen Emylie , Van Norman Jaimie M. 
Published: May 2006

AbstractTo identify molecular mechanisms controlling vein patterns, we analyzed scarface (sfc) mutants. sfc cotyledon and leaf veins are largely fragmented, unlike the interconnected networks in wild-type plants. SFC encodes an ADP ribosylation factor GTPase activating protein (ARF-GAP), a class with well-established roles in vesicle trafficking regulation. Quadruple mutants of SCF and three homologs (ARF-GAP DOMAIN1, 2, and 4) showed a modestly enhanced vascular phenotype. Genetic interactions between sfc and pinoid and between sfc and gnom suggest a possible function for SFC in trafficking of auxin efflux regulators. Genetic analyses also revealed interaction with cotyledon vascular pattern2, suggesting that lipid-based signals may underlie some SFC ARF-GAP functions. To assess possible roles for SFC in auxin transport, we analyzed sfc roots, which showed exaggerated responses to exogenous auxin and higher auxin transport capacity. To determine whether PIN1 intracellular trafficking was affected, we analyzed PIN1:green fluorescent protein (GFP) dynamics using confocal microscopy in sfc roots. We found normal PIN1:GFP localization at the apical membrane of root cells, but treatment with brefeldin A resulted in PIN1 accumulating in smaller and more numerous compartments than in the wild type. These data suggest that SFC is required for normal intracellular transport of PIN1 from the plasma membrane to the endosome.
γ-Tubulin Is Essential for Microtubule Organization and Development inArabidopsis
Authors: Pastuglia Martine , Azimzadeh Juliette , Goussot Magali , Camilleri Christine , Belcram Katia , Evrard Jean-Luc , Schmit Anne-Catherine , Guerche Philippe , Bouchez David 
Published: May 2006

AbstractThe process of microtubule nucleation in plant cells is still a major question in plant cell biology. γ-Tubulin is known as one of the key molecular players for microtubule nucleation in animal and fungal cells. Here, we provide genetic evidence that in Arabidopsis thaliana, γ-tubulin is required for the formation of spindle, phragmoplast, and cortical microtubule arrays. We used a reverse genetics approach to investigate the role of the two Arabidopsis γ-tubulin genes in plant development and in the formation of microtubule arrays. Isolation of mutants in each gene and analysis of two combinations of γ-tubulin double mutants showed that the two genes have redundant functions. The first combination is lethal at the gametophytic stage. Disruption of both γ-tubulin genes causes aberrant spindle and phragmoplast structures and alters nuclear division in gametophytes. The second combination of γ-tubulin alleles affects late seedling development, ultimately leading to lethality 3 weeks after germination. This partially viable mutant combination enabled us to follow dynamically the effects of γ-tubulin depletion on microtubule arrays in dividing cells using a green fluorescent protein marker. These results establish the central role of γ-tubulin in the formation and organization of microtubule arrays in Arabidopsis.
ArabidopsisPASTICCINO2 Is an Antiphosphatase Involved in Regulation of Cyclin-Dependent Kinase A
Authors: Da Costa Marco , Bach Liên , Landrieu Isabelle , Bellec Yannick , Catrice Olivier , Brown Spencer , De Veylder Lieven , Lippens Guy , Inzé Dirk , Faure Jean-Denis 
Published: May 2006

AbstractPASTICCINO2 (PAS2), a member of the protein Tyr phosphatase-like family, is conserved among all eukaryotes and is characterized by a mutated catalytic site. The cellular functions of the Tyr phosphatase-like proteins are still unknown, even if they are essential in yeast and mammals. Here, we demonstrate that PAS2 interacts with a cyclin-dependent kinase (CDK) that is phosphorylated on Tyr and not with its unphosphorylated isoform. Phosphorylation of the conserved regulatory Tyr-15 is involved in the binding of CDK to PAS2. Loss of the PAS2 function dephosphorylated Arabidopsis thaliana CDKA;1 and upregulated its kinase activity. In accordance with its role as a negative regulator of the cell cycle, overexpression of PAS2 slowed down cell division in suspension cell cultures at the G2-to-M transition and early mitosis and inhibited Arabidopsis seedling growth. The latter was accompanied by altered leaf development and accelerated cotyledon senescence. PAS2 was localized in the cytoplasm of dividing cells but moved into the nucleus upon cell differentiation, suggesting that the balance between cell division and differentiation is regulated through the interaction between CDKA;1 and the antiphosphatase PAS2.
Nuclear and cytoplasmic Maspin expression in primary non-small cell lung cancer
Authors: Woenckhaus Matthias , Bubendorf Lukas , Dalquen Peter , Foerster Julia , Blaszyk Hagen , Mirlacher Martina , Soler Markus , Dietmaier Wolfgang , Sauter Guido , Hartmann Arndt , Wild Peter J 
Published: May 2006

Aim:To investigate whether nuclear and cytoplasmic Maspin expression is associated with distinct clinicopathological parameters and TP53 expression in a representative series of primary non-small cell lung cancer (NSCLC).Methods:Tissue microarrays (n = 487) were used to immunohistochemically analyse expression of Maspin and TP53. Cytoplasmic and nuclear expression of Maspin was scored on the basis of the percentage of positive tumour cells. Univariate analysis of clinicopathological variables potentially affecting tumour-specific survival was performed.Results:Immunohistochemical Maspin expression (nuclear and cytoplasmic) was informative in 72.3% (352/487) of cases. Cytoplasmic and nuclear Maspin immunoreactivity in ⩾10% of tumour cells was detected in 37.8% (133/352) and 65.3% (230/352) of informative cases, respectively. Nuclear and cytoplasmic Maspin staining was observed more frequently in primary squamous cell carcinomas than in other lung cancer types. Only nuclear Maspin immunoreactivity was significantly associated with positive TP53 staining. Cytoplasmic or nuclear Maspin expression was not associated with tumour-specific survival.Conclusion:Maspin expression was found both in the nucleus and the cytoplasm of NSCLC, more frequently in squamous cell carcinomas. However, no association with tumour-specific survival could be demonstrated.
Examination of peripheral blood films using automated microscopy; evaluation of Diffmaster Octavia and Cellavision DM96
Authors: Ceelie H , Dinkelaar R B , van Gelder W 
Published: May 2006

Background:Differential counting of peripheral blood cells is an important diagnostic tool. Yet, this technique requires highly trained staff, is labour intensive and has limited statistical reliability. A recent development in this field was the introduction of automated peripheral blood differential counting systems. These computerised systems provide an automated morphological analysis of peripheral blood films, including a preclassification of both red and white cells (RBCs and WBCs, respectively).Aims:To investigate the ability of two automated microscopy systems to examine peripheral blood smears.Methods:Two automated microscopy systems, the Cellavision Diffmaster Octavia (Octavia) and Cellavision DM96 (DM96), were evaluated.Results:The overall preclassification accuracy values for the Octavia and the DM96 systems were 87% and 92%, respectively. Evaluation of accuracy (WBC analysis) showed good correlation for both automated systems when compared with manual differentiation. Total analysis time (including post classification) was 5.4 min/slide for the Octavia and 3.2 min/slide for the DM96 (100 WBC/slide) system. The DM96 required even less time than manual differentiation by an experienced biomedical scientist.Conclusions:The Octavia and the DM96 are automated cell analysis systems capable of morphological classification of RBCs and WBCs in peripheral blood smears. Classification accuracy depends on the type of pathological changes in the blood sample. Both systems operate most effectively in the analysis of non-pathological blood samples.
Expression of peroxisome proliferator activated receptor γ and cyclo-oxygenase 2 in primary and recurrent ovarian carcinoma
Authors: Stadlmann Sylvia , Gueth Uwe , Wight Edward , Kunz-Schughart Leoni A , Hartmann Arndt , Singer Gad 
Published: May 2006

Aim:Peroxisome proliferator-activated receptor γ (PPARγ) has emerged as a potential therapeutic target in several types of cancer. In ovarian carcinomas, limited and conflicting data on PPARγ protein expression have been reported.Methods:The immunoexpression of PPARγ and its putative target cyclo-oxygenase 2 (COX2) was investigated in tumour tissues from 80 patients with primary and corresponding recurrent ovarian serous carcinomas after conventional platinum-based chemotherapy.Results:PPARγ expression was observed in 29% of primary and recurrent carcinomas. In the recurrent tumours, PPARγ expression inversely correlated with COX2 overexpression in both chemosensitive (p = 0.02) and chemoresistant (p = 0.04) carcinomas.Conclusions:The data indicate that PPARγ may represent a potential target for second-line treatment in ovarian cancers.
Construction and validation of a bone marrow tissue microarray
Authors: Zimpfer Annette , Schönberg Sharon , Lugli Alessandro , Agostinelli Claudio , Pileri Stefano A , Went Philip , Dirnhofer Stephan 
Published: May 2006

Background:The use of tissue microarrays (TMAs) is now a generally accepted method for the investigation of solid tumours. However, little is known about the applicability of the TMA technique for analysis of patients with acute leukaemia. A bone marrow (BM)-TMA analysis with 15 different immunohistochemical markers was performed. The TMA was validated by comparison with the corresponding full tissue sections.Materials and methods:A BM-TMA comprising 148 cases of acute leukaemia, including 115 acute myeloid leukaemia (AML) and 33 acute lymphoblastic leukaemia (ALL) cases, was constructed. Expression of CD3, CD10, CD15, CD20, CD34, CD61, CD68, CD79a, CD99, CD117, CD138, myeloperoxidase, haemoglobin A1, glycophorin and terminal deoxynucleotidyl transferase was immunohistochemically analysed. 50 cases of the TMA were directly compared with the corresponding full tissue section to validate the results.Results:Morphologically and immunohistochemically, 6 (4%) of 148 cases and 765 (11%) cores of 6912 individual analyses were not evaluable. A direct comparison of TMA cases with conventional full sections showed a concordance of the results of 100%.Conclusions:The small size of bone-marrow biopsies and the presence of bony trabeculae do not preclude construction and analysis of acute leukaemia TMAs. Acute leukaemia cases on TMA displayed the characteristic phenotypic profiles expected in different AML and ALL subtypes. Therefore, the TMA technique is also a promising method for high-throughput analysis of combined marker expression and clinicopathological correlations in patients with leukaemia.
Presence of mouse mammary tumour-like virus gene sequences may be associated with morphology of specific human breast cancer
Authors: Lawson J S , Tran D D , Carpenter E , Ford C E , Rawlinson W D , Whitaker N J , Delprado W 
Published: May 2006

Background:Mouse mammary tumour virus (MMTV) has a proven role in breast carcinogenesis in wild mice and genetically susceptible in-bred mice. MMTV-likeenvgene sequences, which indicate the presence of a replication-competent MMTV-like virus, have been identified in some human breast cancers, but rarely in normal breast tissues. However, no evidence for a causal role of an MMTV-like virus in human breast cancer has emerged, although there are precedents for associations between specific histological characteristics of human cancers and the presence of oncogenic viruses.Aim:To investigate the possibility of an association between breast cancer and MMTV-like viruses.Methods:Histological characteristics of invasive ductal human breast cancer specimens were compared with archival MMTV-associated mammary tumours from C3H experimental mice. The presence of MMTV-likeenvDNA sequences in the human breast cancer specimens was determined by polymerase chain reaction and confirmed by Southern hybridisation.Results:MMTV-likeenvgene sequences were identified in 22 of 59 (37.3%) human breast cancer specimens. Seventeen of 43 (39.5%) invasive ductal carcinoma breast cancer specimens and 4 of 16 (25%) ductal carcinoma in situ specimens had some histological characteristics, which were similar to MMTV-associated mouse mammary tumours. However, these similarities were not associated with the presence or absence of MMTV-like gene sequences in the human breast tumour specimens. A significant (p = 0.05) correlation was found between the grade of the human breast cancer and similarity to the mouse mammary tumours. The lower the grade, the greater the similarity.Conclusion:Some human breast cancer specimens, in which MMTV-likeenvDNA sequences have been identified, were shown to have histological characteristics (morphology) similar to MMTV-associated mouse mammary tumours. These observations are compatible with, but not conclusive of, an association between the presence of MMTV-likeenvDNA sequences and some human breast cancers.