bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma and hepatic tissue levels of thrombomodulin, tissue factor, NFκB and nitric oxide in responders and nonresponders to IFNα therapy
Authors: George M. , Baluch M. , Van Thiel D. H. 
Published: September 2003

Summary. Hepatitis C virus (HCV) infects hepatocytes and utilizes the hepatocyte to replicate. In so doing, many hepatocyte activities are shifted from their native state to one reflecting liver cell stress. Thrombomodulin and tissue factor are endothelial cell proteins that are expressed as a result of tissue injury or stress. Urokinase is a serine protease, which has been implicated in a number of physiologic and pathologic processes related to cellular stress and or injury. Nitric oxide is produced by cells in response to injury and functions both as a vasodilator and as an activator of a large number of cytokine cascades. NFκB is a transcription factor that forms one of the first lines of cellular defense against infection and hepatocellular stress.The levels of these four factors in plasma, hepatocyte cytosol and hepatocyte nuclear extracts provide a precise panoramic measure of cellular stress. Plasma, hepatocyte cytosol and nuclear extracts of hepatocytes were assayed for these four factors in 17 patients treated with αIFN for chronic hepatitis C. Five of the 17 were responders while 12 were nonresponders. Ten normal controls and 1 normal control liver were assayed also for each parameter.Nonresponders had 2x the plasma urokinase levels of responders and normals. The cytosol prepared from hepatocytes of nonresponders had a urokinase level 15‐fold that of the controls and responders to IFN therapy. Plasma thrombomodulin levels in nonresponders were sixfold greater than those of responders and controls. The levels of all of the other measures in plasma, cytosol and nuclear extracts of liver tissue varied minimally between responders and nonresponders and the normal controls.These data demonstrate that: (i) urokinase levels in plasma and more clearly in cytosol are greater in nonresponders than responders, and (ii) plasma thrombomodulin levels in nonresponders are sixfold greater than those of responders and controls. These data suggest that urokinase and thrombomodulin may be unique markers of cellular and endothelial stress present in individuals with chronic hepatitis C. These markers might be useful during the clinical course of chronic hepatitis C, as a means of gauging the tissue response to therapy.
Hepatitis C virus infection: prevalence, predictor variables and prevention opportunities among drug users in Italy
Authors: Quaglio G. L. , Lugoboni F. , Pajusco B. , Sarti M. , Talamini G. ,   GICS, Mezzelani P. , Des Jarlais D. C. 
Published: September 2003

Summary. The study assessed rates and predictor variables of hepatitis C virus (HCV) infection among drug users receiving pharmacological treatment for opiates addiction.There was a large cohort study in 16 public centres for drug users in north‐eastern Italy, with data collected by standardized face‐to‐face interviews between February 2001 and August 2001.Of 1095 participants, 74.2% were HCV seropositive. Anti‐HCV status was independently associated with duration of drug use of over 10 years, injecting as a route of drug administration, and hepatitis B virus (HBV) and human immunodeficiency virus (HIV) seropositivity. Further statistical analysis was conducted by dividing the subjects on the basis of the duration of heroin use: more or <10 years. In the multivariate analyses, route of drug administration and HBV status were associated with HCV seropositivity among both groups. Less education was associated with HCV among the shorter term drug users. HIV status and having a sexual partner with a history of drug use were associated with HCV seropositivity among the longer term drug users.Half of the short‐term heroin users were still HCV seronegative when starting treatment, suggesting opportunities for reducing new HCV infections. Remarkable was the relationship between vaccination for hepatitis B and HCV serostatus. Being HBV seropositive was strongly associated with being HCV seropositive. But heroin users who had been vaccinated for HBV were not significantly more likely to be HCV seropositive than heroin users who were HBV seronegative. HBV vaccination does not provide biological protection against HCV; however, vaccinating heroin users against HBV may help to create a stronger pro‐health attitude among heroin users, leading to a reduction in HCV risk behaviour.
Rapid and proven production of transplastomic tobacco plants by restoration of pigmentation and photosynthesis
Authors: Klaus Sebastian M. J. , Huang Fong‐Chin , Eibl Christian , Koop Hans‐Ulrich , Golds Timothy J. 
Published: September 2003

SummaryTobacco chloroplast transformation is typically achieved using dominant, selectable antibiotic resistance genes such as aadA, nptII and aphA‐6. An improvement would be the combination of such a marker with a visual screening system for the early and conclusive detection of plastid transformants. As such, we investigated the use of three photosynthesis‐deficient plastid mutants, ΔpetA, Δycf3 and ΔrpoA, for the development of a phenotypic selection system. Mutant plants were used as an alternative to the wild‐type as source tissue for transformation, re‐introducing deleted plastid sequences and using the aphA‐6 gene as a selection marker. The reconstitution of the deleted genes in transformed regenerants resulted in shoots with a visually distinct phenotype comparable to the wild‐type. This transformation/selection system overcomes the common problems associated with plastid transformation, e.g. the recovery of spontaneous mutants or nuclear insertions. In addition to the benefits offered by phenotypic selection, phenotype reconstitution leads to restoration of photosynthesis, which we assume drives reconstituted plants rapidly towards homoplasmy. As such, repeated cycles of regeneration in the presence of an antibiotic selection agent are no longer required.
Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress
Authors: Maathuis Frans J. M. , Filatov Victor , Herzyk Pawel , C. Krijger Gerard , B. Axelsen Kristian , Chen Sixue , Green Brian J. , Li Yi , Madagan Kathryn L. , Sánchez‐Fernández Rocío , Forde Brian G. , Palmgren Michael G. , Rea Philip A. , Williams Lorraine E. , Sanders Dale , Amtmann Anna 
Published: September 2003

SummaryPlant nutrition critically depends on the activity of membrane transporters that translocate minerals from the soil into the plant and are responsible for their intra‐ and intercellular distribution. Most plant membrane transporters are encoded by multigene families whose members often exhibit overlapping expression patterns and a high degree of sequence homology. Furthermore, many inorganic nutrients are transported by more than one transporter family. These considerations, coupled with a large number of so‐far non‐annotated putative transporter genes, hamper our progress in understanding how the activity of specific transporters is integrated into a response to fluctuating conditions. We designed an oligonucleotide microarray representing 1096 Arabidopsis transporter genes and analysed the root transporter transcriptome over a 96‐h period with respect to 80 mm NaCl, K+ starvation and Ca2+ starvation. Our data show that cation stress led to changes in transcript level of many genes across most transporter gene families. Analysis of transcriptionally modulated genes across all functional groups of transporters revealed families such as V‐type ATPases and aquaporins that responded to all treatments, and families – which included putative non‐selective cation channels for the NaCl treatment and metal transporters for Ca2+ starvation conditions – that responded to specific ionic environments. Several gene families including primary pumps, antiporters and aquaporins were analysed in detail with respect to the mRNA levels of different isoforms during ion stress. Cluster analysis allowed identification of distinct expression profiles, and several novel putative regulatory motifs were discovered within sets of co‐expressed genes.
Misregulation of tetrapyrrole biosynthesis in transgenic tobacco seedlings expressing mammalian biliverdin reductase
Authors: Franklin Keara A. , Linley Philip J. , Montgomery Beronda L. , Lagarias J. Clark , Thomas Brian , Jackson Stephen D. , Terry Matthew J. 
Published: September 2003

SummaryPrevious studies have established that the expression of mammalian biliverdin IXα reductase (BVR) in transgenic tobacco (Nicotiana tabacum cv. Maryland Mammoth) resulted in the loss of photoregulatory activity of all phytochromes together with a pronounced chlorophyll deficiency. This study was undertaken to assess the contribution of BVR‐mediated alteration of tetrapyrrole metabolism to the observed phenotypes of BVR transgenic plants. BVR expression in dark‐grown plants led to the reduced accumulation of protochlorophyllide and transcripts for the two committed enzymes for 5‐aminolevulinic acid (ALA) synthesis despite the marked increased capacity for synthesis of ALA. Together with the observation that Mg‐porphyrin accumulation in dark‐grown seedlings treated with an iron chelator was unaffected by BVR expression, these results indicate that BVR diverts tetrapyrrole metabolism toward heme synthesis while also reducing heme levels to de‐repress ALA synthesis. By contrast with dark‐grown seedlings, light‐grown BVR plants showed a marked inhibition of ALA synthesis compared with wild‐type plants – a result that was correlated with the disappearance of the CHL I subunit of Mg‐chelatase and an increase in heme oxygenase protein levels. As transcript levels of all tetrapyrrole biosynthetic genes tested were not strongly affected by BVR expression, these results implicate misregulated tetrapyrrole metabolism to be a major mechanism for BVR‐dependent inhibition of chlorophyll biosynthesis in light‐grown plants.
The biosynthesis of the branched‐chain sugar d‐apiose in plants: functional cloning and characterization of a UDP‐d‐apiose/UDP‐d‐xylose synthase from Arabidopsis
Authors: Mølhøj Michael , Verma Rajeev , Reiter Wolf‐Dieter 
Published: September 2003

Summary d‐Apiose is a plant‐specific branched‐chain monosaccharide found in rhamnogalacturonan II (RG‐II), apiogalacturonan, and several apioglycosides. Within RG‐II, d‐apiose serves as the binding site for borate, which leads to the formation of cross‐links within the wall. Biochemical studies in duckweed and parsley have established that uridine 5′‐diphospho‐d‐apiose (UDP‐d‐apiose) is formed from UDP‐d‐glucuronate by decarboxylation and re‐arrangement of the carbon skeleton, leading to ring contraction and branch formation. The enzyme catalyzing this reaction also forms UDP‐d‐xylose by decarboxylation of UDP‐d‐glucuronate, and has therefore been named UDP‐d‐apiose/UDP‐d‐xylose synthase. Using a bioinformatics approach, we identified a candidate gene (AXS1) for this enzyme in Arabidopsis and functionally expressed its cDNA in Escherichia coli. The recombinant enzyme catalyzed the conversion of UDP‐d‐glucuronate to a mixture of UDP‐d‐apiose and UDP‐d‐xylose with a turnover number of 0.3 min‐1. AXS1 required NAD+ for enzymatic activity, and was strongly inhibited by UDP‐d‐galacturonate. It was highly expressed in all plant organs consistent with a function in synthesizing an essential cell wall precursor. Database searches indicated the presence of closely related sequences in a variety of crop plants. The cloning of the AXS1 gene will help to investigate the biosynthesis of RG‐II, and permit insights into the mechanism by which d‐apiose and other branched monosaccharides are formed.
Deletion of the tobacco plastid psbA gene triggers an upregulation of the thylakoid‐associated NAD(P)H dehydrogenase complex and the plastid terminal oxidase (PTOX)
Authors: Baena‐González Elena , Allahverdiyeva Yagut , Svab Zora , Maliga Pal , Josse Eve‐Marie , Kuntz Marcel , Mäenpää Pirkko , Aro Eva‐Mari 
Published: September 2003

SummaryWe have constructed a tobacco psbA
gene deletion mutant that is devoid of photosystem II (PSII) complex. Analysis of thylakoid membranes revealed comparable amounts, on a chlorophyll basis, of photosystem I (PSI), the cytochrome b6f complex and the PSII light‐harvesting complex (LHCII) antenna proteins in wild‐type (WT) and ΔpsbA leaves. Lack of PSII in the mutant, however, resulted in over 10‐fold higher relative amounts of the thylakoid‐associated plastid terminal oxidase (PTOX) and the NAD(P)H dehydrogenase (NDH) complex. Increased amounts of Ndh polypeptides were accompanied with a more than fourfold enhancement of NDH activity in the mutant thylakoids, as revealed by in‐gel NADH dehydrogenase measurements. NADH also had a specific stimulating effect on P700+ re‐reduction in the ΔpsbA thylakoids. Altogether, our results suggest that enhancement of electron flow via the NDH complex and possibly other alternative electron transport routes partly compensates for the loss of PSII function in the ΔpsbA mutant. As mRNA levels were comparable in WT and ΔpsbA plants, upregulation of the alternative electron transport pathways (NDH complex and PTOX) occurs apparently by translational or post‐translational mechanisms.
Architecture and transcriptional activity of the initiator element of the TATA‐less RPL21 gene
Authors: Achard Patrick , Lagrange Thierry , El‐Zanaty Abdel‐Fattah , Mache Régis 
Published: September 2003

SummaryThe nuclear RPL21 gene coding for the plastid ribosomal protein L21 is a TATA‐less gene that is overexpressed in a leaf‐dependent manner by the specific usage of a strong initiator called P1. We have previously shown that the RPL21 core promoter spanning from −23 to +104 relative to P1 start site activates transcription in the same manner as does the full promoter. Here, we present results of experiments aimed at deciphering the RPL21 core promoter architecture. Results of transient expression using various 5′ deletions of the core promoter fused to a chloramphenicol acetyl transferase (CAT) reporter gene show that 34 bp encompassing the P1 initiation site (from −23 to +11) are required for full transcription activation. Gel‐shift analysis shows that five DNA/protein complexes (C1–C5) are formed on this 34‐bp fragment with protein extracts from green tissues. C1 is the major complex present during seed germination. The other complexes are present in young leaf tissues suggesting a role in transcription activation. Linker scanning mutagenesis experiments show that the five complexes form two independent groups: I (C1–C3) and II (C4 and C5), with a common binding site located on P1. Using transgenic plants, we show that three nucleotides encompassing the P1 start site and three trinucleotides necessary for group I binding are determinant for RPL21 activation. These results identify an unusually compact core structure, which is centred on P1 initiation site and is responsible for transcription activation. A model of the architecture of this region is presented.
The HECT ubiquitin‐protein ligase (UPL) family in Arabidopsis: UPL3 has a specific role in trichome development
Authors: Downes Brian P. , Stupar Robert M. , Gingerich Derek J. , Vierstra Richard D. 
Published: September 2003

SummaryAttachment of one or more ubiquitins (Ubs) to various intracellular proteins has a number of roles in plants including the selective removal of regulatory proteins by the 26S proteasome. The final step in this modification is performed by ubiquitin‐protein ligases (E3s) that promote Ub transfer to appropriate targets. One important family of E3s is defined by the presence of a HECT domain, an active site first found at the C‐terminus of the human E3 (E6‐AP). Using a consensus HECT domain as the query, we identified a family of seven HECT‐containing ubiquitin‐protein ligases (UPL1–UPL7) in Arabidopsis thaliana that can be grouped into four subfamilies. The UPL3 and UPL4 subfamily encodes approximately 200‐kDa proteins with four Armadillo repeats similar to those in the nuclear pore protein importin‐α, suggesting that these E3s identify their targets through binding to nuclear localization sequences. Although T‐DNA disruptions of the UPL3 locus do not affect overall growth and development of Arabidopsis, the mutants show aberrant trichome morphology. Instead of developing three branches, many upl3 trichomes contain five or more branches. The upl3 trichomes also often undergo an additional round of endoreplication resulting in enlarged nuclei with ploidy levels of up to 64C. upl3 plants are hypersensitive to gibberellic acid‐3 (GA3), consistent with the role of gibberellins in trichome development. The phenotype of upl3 mutants is similar to that of kaktus, a previously described set of trichome mutants with supernumerary branches. Genetic analyses confirmed that upl3 mutants and kaktus‐2 are allelic with kaktus‐2 plants harboring a splice‐site mutation within the UPL3‐transcribed region. Collectively, the data indicate that the ubiquitination of one or more activator proteins by UPL3 is necessary to repress excess branching and endoreplication of Arabidopsis trichomes.
Identification of functional lox sites in the plastid genome
Authors: Corneille Sylvie , Lutz Kerry A. , Azhagiri Arun K. , Maliga Pal 
Published: September 2003

SummaryOur objective was to test whether or not cyclization recombination (CRE), the P1 phage site‐specific recombinase, induces genome rearrangements in plastids. Testing was carried out in tobacco plants in which a DNA sequence, located between two inversely oriented locus of X‐over of P1 (loxP) sites, underwent repeated cycles of inversions as a means of monitoring CRE activity. We report here that CRE mediates deletions between loxP sites and plastid DNA sequences in the 3′rps12 gene leader (lox‐rps12) or in the psbA promoter core (lox‐psbA). We also observed deletions between two directly oriented lox‐psbA sites, but not between lox‐rps12 sites. Deletion via duplicated rRNA operon promoter (Prrn) sequences was also frequent in CRE‐active plants. However, CRE‐mediated recombination is probably not directly involved, as no recombination junction between loxP and Prrn could be observed. Tobacco plants carrying deleted genomes as a minor fraction of the plastid genome population were fertile and phenotypically normal, suggesting that the absence of deleted genome segments was compensated by gene expression from wild‐type copies. The deleted plastid genomes disappeared in the seed progeny lacking CRE. Observed plastid genome rearrangements are specific to engineered plastid genomes, which contain at least one loxP site or duplicated psbA promoter sequences. The wild‐type plastid genome is expected to be stable, even if CRE is present in the plastid.
Expression of a stress‐induced hemoglobin affects NO levels produced by alfalfa root cultures under hypoxic stress
Authors: Dordas Christos , Hasinoff Brian B. , Igamberdiev Abir U. , Manac'h Nathalie , Rivoal Jean , Hill Robert D. 
Published: September 2003

SummaryTransgenic alfalfa root cultures expressing sense and antisense barley hemoglobin transcripts were examined under varying levels of atmospheric oxygen. Root cultures overexpressing the hemoglobin gene (Hb+) maintained root growth when placed under 3% oxygen, whereas control cultures or cultures underexpressing hemoglobin (Hb−) experienced 30–70% declines in growth under the same conditions. ATP levels and ATP/ADP ratios for Hb+ lines did not significantly differ in 40 and 3% oxygen, whereas the ATP levels and ATP/ADP ratios in control and Hb− lines were significantly lower under 3% oxygen. Large increases in the production of nitric oxide (NO) were measured in root cultures grown under hypoxic conditions compared to aerobic conditions. The amount of NO accumulated in an Hb− line was 2.5‐fold higher than that in the Hb+ line. Treatment of transgenic root lines under 40% oxygen with NO resulted in significant declines in the ATP levels and ATP/ADP ratio of an Hb− line and the control line, with no significant change in an Hb+ line. The root cell structure of an Hb− line showed evidence of cell breakdown under hypoxic growth, whereas an Hb+ line had no evidence of cell breakdown under similar growth conditions. These results lead us to hypothesize that NO is involved in the response of plants to hypoxia and that hemoglobin modulates the levels of NO in the hypoxic cell.
The transcriptional response of Arabidopsis to genotoxic stress – a high‐density colony array study (HDCA)
Authors: Chen I‐Peng , Haehnel Urs , Altschmied Lothar , Schubert Ingo , Puchta Holger 
Published: September 2003

SummaryA genome‐wide transcription profiling of Arabidopsis upon genotoxic stress has been performed using a high‐density colony array (HDCA). The array was based on a library of 27 000 cDNA clones derived from Arabidopsis cells challenged with bleomycin plus mitomycin C. The array covers more than 10 000 individual genes (corresponding to at least 40% of Arabidopsis genes). After hybridisation of the HDCA with labelled cDNA probes obtained from genotoxin‐treated (bleomycin plus mitomycin C, 6 h) and untreated seedlings, 39 genes revealed an increased and 24 genes a decreased expression among the 3200 highly expressed clones (representing approximately 1200 individual genes because of redundancy of the cDNA library). Of the 4900 clones with a low transcriptional level, the expression of 500 clones was found to be altered and 57 genes with increased and 22 genes with decreased expression were identified by sequence analysis of 135 identified clones. The HDCA results were validated by real‐time PCR analysis. For about 80% of genes (34 out of 42), alteration in expression was confirmed, indicating the reliability of the HDCA for transcription profiling. DNA damage and stress‐responsive genes encoding, for instance transcription factors (myb protein and WRKY1), the ribonucleotide reductase small subunit (RNR2), thymidine kinase (TK), an AAA‐type ATPase, the small subunit of a DNA polymerase and a calmodulin‐like protein were found to be strongly upregulated. Also, several genes involved in cell cycle regulation revealed significant alteration in transcription, as detected by real‐time PCR analysis, suggesting disturbance of cell cycle progression by mutagen treatment.
IMB1, a bromodomain protein induced during seed imbibition, regulates ABA‐ and phyA‐mediated responses of germination in Arabidopsis
Authors: Duque Paula , Chua Nam‐Hai 
Published: September 2003

SummaryWe report the characterization of a plant gene encoding a member of the BET subgroup of bromodomain proteins, a novel class of putative transcription factors. Imbibition‐inducible 1 (IMB1) appears to be a nuclear protein as suggested by subcellular localization in onion epidermal cells using an IMB1–yellow fluorescent protein (YFP) fusion protein. In Arabidopsis thaliana, IMB1 is expressed at very low levels in dry seeds, but is markedly induced during seed imbibition. In addition, IMB1 transcript levels are down regulated during germination. Seeds of a loss‐of‐function mutant allele, imb1, show impaired cotyledon greening during germination in abscisic acid (ABA) and express higher levels of ABI5 protein than the wild type. Moreover, imb1 seeds are deficient in the phytochrome A (phyA)‐mediated very‐low‐fluence response of germination. Microarray analysis revealed that genes included in different functional categories, such as cell‐wall metabolism or plastid function, are repressed in imbibed imb1 seeds. Mutant imb1 plants appear normal, indicating that IMB1 is involved in regulating a specific developmental stage. Taken together, these results show that IMB1 plays a role in the promotion of seed germination by both negatively and positively regulating the ABA and phyA transduction pathways, respectively. In imbibed seeds, IMB1 modulates the transcription of a battery of genes, providing clues on its mode of action.