bluuebunny/crossref_metadata_2025_split huggingface dataset:
PsbP Protein, But Not PsbQ Protein, Is Essential for the Regulation and Stabilization of Photosystem II in Higher Plants
Authors: Ifuku Kentaro , Yamamoto Yumiko , Ono Taka-aki , Ishihara Seiko , Sato Fumihiko 
Published: October 2005

Abstract
PsbP and PsbQ proteins are extrinsic subunits of photosystem II (PSII) and participate in the normal function of photosynthetic water oxidation. Both proteins exist in a broad range of the oxygenic photosynthetic organisms; however, their physiological roles in vivo have not been well defined in higher plants. In this study, we established and analyzed transgenic tobacco (Nicotiana tabacum) plants in which the levels of PsbP or PsbQ were severely down-regulated by the RNA interference technique. A plant that lacked PsbQ showed no specific phenotype compared to a wild-type plant. This suggests that PsbQ in higher plants is dispensable under the normal growth condition. On the other hand, a plant that lacked PsbP showed prominent phenotypes: drastic retardation of growth, pale-green-colored leaves, and a marked decrease in the quantum yield of PSII evaluated by chlorophyll fluorescence. In PsbP-deficient plant, most PSII core subunits were accumulated in thylakoids, whereas PsbQ, which requires PsbP to bind PSII in vitro, was dramatically decreased. PSII without PsbP was hypersensitive to light and rapidly inactivated when the repair process of the damaged PSII was inhibited by chloramphenicol. Furthermore, thermoluminescence studies showed that the catalytic manganese cluster in PsbP-deficient leaves was markedly unstable and readily disassembled in the dark. The present results demonstrated that PsbP, but not PsbQ, is indispensable for the normal PSII function in higher plants in vivo.
Overexpression of AtCpNifS Enhances Selenium Tolerance and Accumulation in Arabidopsis
Authors: Van Hoewyk Douglas , Garifullina Gulnara F. , Ackley Ashley R. , Abdel-Ghany Salah E. , Marcus Matthew A. , Fakra Sirine , Ishiyama Keiki , Inoue Eri , Pilon Marinus , Takahashi Hideki , Pilon-Smits Elizabeth A.H. 
Published: October 2005

Abstract
Selenium (Se) is an essential element for many organisms but is toxic at higher levels. CpNifS is a chloroplastic NifS-like protein in Arabidopsis (Arabidopsis thaliana) that can catalyze the conversion of cysteine into alanine and elemental sulfur (S0) and of selenocysteine into alanine and elemental Se (Se0). We overexpressed CpNifS to investigate the effects on Se metabolism in plants. CpNifS overexpression significantly enhanced selenate tolerance (1.9-fold) and Se accumulation (2.2-fold). CpNifS overexpressors showed significantly reduced Se incorporation into protein, which may explain their higher Se tolerance. Also, sulfur accumulation was enhanced by approximately 30% in CpNifS overexpressors, both on media with and without selenate. Root transcriptome changes in response to selenate mimicked the effects observed under sulfur starvation. There were only a few transcriptome differences between CpNifS-overexpressing plants and wild type, besides the 25- to 40-fold increase in CpNifS levels. Judged from x-ray analysis of near edge spectrum, both CpNifS overexpressors and wild type accumulated mostly selenate (SeVI). In conclusion, overexpression of this plant NifS-like protein had a pronounced effect on plant Se metabolism. The observed enhanced Se accumulation and tolerance of CpNifS overexpressors show promise for use in phytoremediation.
Plant-Derived Transfer DNAs
Authors: Rommens Caius M. , Bougri Oleg , Yan Hua , Humara Jaime M. , Owen Joanna , Swords Kathy , Ye Jingsong 
Published: October 2005

Abstract
The transfer of DNA from Agrobacterium to plant cell nuclei is initiated by a cleavage reaction within the 25-bp right border of Ti plasmids. In an effort to develop all-native DNA transformation vectors, 50 putative right border alternatives were identified in both plant expressed sequence tags and genomic DNA. Efficacy tests in a tobacco (Nicotiana tabacum) model system demonstrated that 14 of these elements displayed at least 50% of the activity of conventional Agrobacterium transfer DNA borders. Four of the most effective plant-derived right border alternatives were found to be associated with intron-exon junctions. Additional elements were embedded within introns, exons, untranslated trailers, and intergenic DNA. Based on the identification of a single right border alternative in Arabidopsis and three in rice (Oryza sativa), the occurrence of this motif was estimated at a frequency of at least 0.8×10−8. Modification of plasmid DNA sequences flanking the alternative borders demonstrated that both upstream and downstream sequences play an important role in initiating DNA transfer. Optimal DNA transfer required the elements to be preceded by pyrimidine residues interspaced by AC-rich trinucleotides. Alteration of this organization lowered transformation frequencies by 46% to 93%. Despite their weaker resemblance with left borders, right border alternatives also functioned effectively in terminating DNA transfer, if both associated with an upstream A[C/T]T[C/G]A[A/T]T[G/T][C/T][G/T][C/G]A[C/T][C/T][A/T] domain and tightly linked cytosine clusters at their junctions with downstream DNA. New insights in border region requirements were used to construct an all-native alfalfa (Medicago sativa) transfer DNA vector that can be used for the production of intragenic plants.
Identification of Three Urease Accessory Proteins That Are Required for Urease Activation in Arabidopsis
Authors: Witte Claus-Peter , Rosso Mario G. , Romeis Tina 
Published: October 2005

Abstract
Urease is a nickel-containing urea hydrolase involved in nitrogen recycling from ureide, purine, and arginine catabolism in plants. The process of urease activation by incorporation of nickel into the active site is a prime example of chaperone-mediated metal transfer to an enzyme. Four urease accessory proteins are required for activation in Klebsiella aerogenes. In plants urease accessory proteins have so far been only partially defined. Using reverse genetic tools we identified four genes that are necessary for urease activity in Arabidopsis (Arabidopsis thaliana; ecotypes Columbia and Nössen). Plants bearing T-DNA or Ds element insertions in either the structural gene for urease or in any of the three putative urease accessory genes AtureD, AtureF, and AtureG lacked the corresponding mRNAs and were defective in urease activity. In contrast to wild-type plants, the mutant lines were not able to support growth with urea as the sole nitrogen source. To investigate whether the identified accessory proteins would be sufficient to support eukaryotic urease activation, the corresponding cDNAs were introduced into urease-negative Escherichia coli. In these bacteria, urease activity was observed only when all three plant accessory genes were coexpressed together with the plant urease gene. Remarkably, plant urease activation occurred as well in cell-free E. coli extracts, but only in extracts from cells that had expressed all three accessory proteins. The future molecular dissection of the plant urease activation process may therefore be performed in vitro, providing a powerful tool to further our understanding of the biochemistry of chaperone-mediated metal transfer processes in plants.
Maize rough sheath2 and ItsArabidopsisOrthologue ASYMMETRIC LEAVES1 Interact with HIRA, a Predicted Histone Chaperone, to MaintainknoxGene Silencing and Determinacy during Organogenesis
Authors: Phelps-Durr Tara L. , Thomas Julie , Vahab Phil , Timmermans Marja C.P. 
Published: October 2005

AbstractPlant shoots are characterized by indeterminate growth resulting from the action of a population of stem cells in the shoot apical meristem (SAM). Indeterminacy within the SAM is specified in part by the class I knox homeobox genes. The myb domain proteins rough sheath2 (RS2) and ASYMMETRIC LEAVES1 (AS1) from maize (Zea mays) and Arabidopsis thaliana, respectively, are required to establish determinacy during leaf development. These proteins are part of a cellular memory system that in response to a stem cell–derived signal keeps knox genes in an off state during organogenesis. Here, we show that RS2/AS1 can form conserved protein complexes through interaction with the DNA binding factor ASYMMETRIC LEAVES2, a predicted RNA binding protein (RIK, for RS2-Interacting KH protein), and a homologue of the chromatin-remodeling protein HIRA. Partial loss of HIRA function in Arabidopsis results in developmental defects comparable to those of as1 and causes reactivation of knox genes in developing leaves, demonstrating a direct role for HIRA in knox gene repression and the establishment of determinacy during leaf formation. Our data suggest that RS2/AS1 and HIRA mediate the epigenetic silencing of knox genes, possibly by modulating chromatin structure. Components of this process are conserved in animals, suggesting the possibility that a similar epigenetic mechanism maintains determinacy during both plant and animal development.
Cell Cycle Progression in the Pericycle Is Not Sufficient for SOLITARY ROOT/IAA14-Mediated Lateral Root Initiation inArabidopsis thaliana
Authors: Vanneste Steffen , De Rybel Bert , Beemster Gerrit T.S. , Ljung Karin , De Smet Ive , Van Isterdael Gert , Naudts Mirande , Iida Ryusuke , Gruissem Wilhelm , Tasaka Masao , Inzé Dirk , Fukaki Hidehiro , Beeckman Tom 
Published: October 2005

AbstractTo study the mechanisms behind auxin-induced cell division, lateral root initiation was used as a model system. By means of microarray analysis, genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the auxin/indole-3-acetic acid (AUX/IAA) signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation.
Solution structure of Archaeglobus fulgidis peptidyl‐tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes
Authors: Powers Robert , Mirkovic Nebojsa , Goldsmith‐Fischman Sharon , Acton Thomas B. , Chiang Yiwen , Huang Yuanpeng J. , Ma Lichung , Rajan P.K. , Cort John R. , Kennedy Michael A. , Liu Jinfeng , Rost Burkhard , Honig Barry , Murray Diana , Montelione Gaetano T. 
Published: October 2005

AbstractThe solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123‐residue (13.6‐kDa) protein, has been determined by NMR methods. The structure of AF2095 is comprised of four α‐helices and a mixed β‐sheet consisting of four parallel and anti‐parallel β‐strands, where the α‐helices sandwich the β‐sheet. Sequence and structural comparison of AF2095 with proteins from Homo sapiens, Methanocaldococcus jannaschii, and Sulfolobus solfataricus reveals that AF2095 is a peptidyl‐tRNA hydrolase (Pth2). This structural comparison also identifies putative catalytic residues and a tRNA interaction region for AF2095. The structure of AF2095 is also similar to the structure of protein TA0108 from archaea Thermoplasma acidophilum, which is deposited in the Protein Data Bank but not functionally annotated. The NMR structure of AF2095 has been further leveraged to obtain good‐quality structural models for 55 other proteins. Although earlier studies have proposed that the Pth2 protein family is restricted to archeal and eukaryotic organisms, the similarity of the AF2095 structure to human Pth2, the conservation of key active‐site residues, and the good quality of the resulting homology models demonstrate a large family of homologous Pth2 proteins that are conserved in eukaryotic, archaeal, and bacterial organisms, providing novel insights in the evolution of the Pth and Pth2 enzyme families.
Crystal structure of the E230Q mutant of cAMP‐dependent protein kinase reveals an unexpected apoenzyme conformation and an extended N‐terminal A helix
Authors: Wu Jian , Yang Jie , Kannan Natarajan , Madhusudan  , Xuong Nguyen‐Huu , Ten Eyck Lynn F. , Taylor Susan S. 
Published: October 2005

AbstractGlu230, one of the acidic residues that cluster around the active site of the catalytic subunit of cAMP‐dependent protein kinase, plays an important role in substrate recognition. Specifically, its side chain forms a direct salt‐bridge interaction with the substrate's P‐2 Arg. Previous studies showed that mutation of Glu230 to Gln (E230Q) caused significant decreases not only in substrate binding but also in the rate of phosphoryl transfer. To better understand the importance of Glu230 for structure and function, we solved the crystal structure of the E230Q mutant at 2.8 Å resolution. Surprisingly, the mutant preferred an open conformation with no bound ligands observed, even though the crystals were grown in the presence of MgATP and the inhibitor peptide, IP20. This is in contrast to the wild‐type protein that, under the same conditions, prefers the closed conformation of a ternary complex. The structure highlights the importance of the electrostatic surface not only for substrate binding and catalysis, but also for the mechanism for closing the active site cleft. This surface mutation clearly disrupts the recognition and binding of substrate peptide so that the enzyme prefers an open conformation that cannot trap ATP. This is consistent with the reinforcing concepts of conformational dynamics and the synergistic binding of ATP and substrate peptide. Another unusual feature of the structure is the observation of the entire N terminus (Gly1–Thr32) assumes an extended α‐helix conformation. Finally, based on temperature factors, this mutant structure is more stable than the wild‐type C‐subunit in the apo state.
Intestinal fluid volumes and transit of dosage forms as assessed by magnetic resonance imaging
Authors: SCHILLER C. , FRÖHLICH C.‐P. , GIESSMANN T. , SIEGMUND W. , MÖNNIKES H. , HOSTEN N. , WEITSCHIES W. 
Published: October 2005

SummaryAim : The gastrointestinal transit of sequentially administered capsules was investigated in relation to the availability of fluid along the intestinal lumen by magnetic resonance imaging.Methods : Water‐sensitive magnetic resonance imaging was performed on 12 healthy subjects during fasting and 1 h after a meal. Specifiable non‐disintegrating capsules were administered at 7, 4 and 1 h prior to imaging.Results : While food intake reduced the mean fluid volumes in the small intestine (105 ± 72 mL vs. 54 ± 41 mL, P < 0.01) it had no significant effect on the mean fluid volumes in the colon (13 ± 12 mL vs. 18 ± 26 mL). The mean number of separated fluid pockets increased in both organs after meal (small intestine: 4 vs. 6, P < 0.05; large intestine: 4 vs. 6, P < 0.05). The distribution of capsules between the small and large intestine was strongly influenced by food (colon: 3 vs. 17 capsules, P < 0.01).Conclusions : The results show that fluid is not homogeneously distributed along the gut, which likely contributes to the individual variability of drug absorption. Furthermore, transport of fluid and solids through the ileocaecal valve is obviously initiated by a meal‐induced gastro‐ileocaecal reflex.
Helicobacter pylori first‐line treatment and rescue options in patients allergic to penicillin
Authors: GISBERT J. P. , GISBERT J. L. , MARCOS S. , OLIVARES D. , PAJARES J. M. 
Published: October 2005

SummaryBackground : Helicobacter pylori eradication is a challenge in patients allergic to penicillin, especially those who have failed a first‐eradication trial.Aim : To assess the efficacy and tolerability of H. pylori first‐line treatment and rescue options in patients allergic to penicillin.Methods : Prospective single centre study including 40 consecutive treatments administered to patients allergic to penicillin. Therapy regimens: First‐line (12 patients) omeprazole, clarithromycin and metronidazole for 7 days; second‐line (17 patients) ranitidine bismuth citrate, tetracycline and metronidazole for 7 days; third‐line (nine patients) rifabutin, clarithromycin and omeprazole for 10 days; and fourth‐line (two patients) levofloxacin, clarithromycin and omeprazole for 10 days. Outcome variable: a negative 13C‐urea breath test 8 weeks after completion of treatment.Results : Per‐protocol/intention‐to‐treat eradication rates were: first‐line (64/58%); second‐line (ranitidine bismuth citrate; 53/47%); third‐line (rifabutin; 17/11%) and fourth‐line regimen (levofloxacin; 100/100%). Compliance with treatment was generally good, except with the rifabutin‐based regimen, which presented adverse effects in 89% of the patients, including four cases of myelotoxicity.Conclusions : H. pylori‐infected patients who are allergic to penicillin may be treated with a first‐line treatment combining a proton‐pump inhibitor, clarithromycin and metronidazole. Rescue options may include a regimen with ranitidine bismuth citrate, tetracycline and metronidazole. A levofloxacin‐based rescue regimen (with proton‐pump inhibitor and clarithromycin) may also represent an alternative, even when two or more consecutive eradication treatments have previously failed. However, rifabutin + clarithromycin + proton‐pump inhibitor regimen is ineffective and poorly tolerated.
Did intense adverse media publicity impact on prescribing of paroxetine and the notification of suspected adverse drug reactions? Analysis of routine databases, 2001–2004
Authors: Martin Richard M. , May Margaret , Gunnell David 
Published: October 2005

AimTo document the impact on clinical practice in England of media attention around possible adverse effects of paroxetine.DesignAnalysis of national selective serotonin reuptake inhibitor (SSRI) prescribing trends and yellow‐card adverse drug reaction reports, 2001–2004.ResultsFrom a steady state in 2001, paroxetine prescribing declined sharply from April 2002, coinciding with a USA regulatory action; the subsequent decline in paroxetine prescribing was 1.87% per month (95% confidence interval − 2.06, −1.68). Other SSRI prescribing increased by 1% per month until a major UK review of SSRIs in children in December 2003, after which prescribing plateaued. Media publicity was associated with short‐term peaks in yellow‐card reports related to paroxetine.ConclusionFalls in paroxetine and other SSRI prescribing in the UK coincided, respectively, with regulatory communications from the USA and the UK, but associations may have noncausal or other explanations. Reports of adverse reactions to paroxetine appeared to increase after adverse media publicity about the drug.
The BRAFV600E mutation is not associated with poor prognostic factors in Korean patients with conventional papillary thyroid microcarcinoma
Authors: Kim Tae Yong , Kim Won Bae , Song Ja Young , Rhee Yoon Soo , Gong Gyungyub , Cho Yong Mee , Kim Sang Yoon , Kim Seong Chul , Hong Suck Joon , Shong Young Kee 
Published: October 2005

SummaryBackground  The BRAFV600E mutation, the most common genetic alteration reported in papillary thyroid carcinoma, has been associated with poor prognostic factors.Aim  To determine whether the presence of the BRAFV600E mutation is associated with poor prognosis in Korean patients with conventional papillary thyroid microcarcinoma (micro‐PTC).Patients and methods  DNA was extracted from paraffin‐embedded thyroid tumour specimens taken from 60 patients with conventional micro‐PTC, as well as from nine patients with follicular variant papillary carcinoma, six with nodular hyperplasia, four with follicular carcinoma (including one with Hürthle cell carcinoma), four with follicular adenoma (including two with Hürthle cell adenoma) and one each with medullary carcinoma, poorly differentiated carcinoma and anaplastic carcinoma. The presence of the BRAFV600E mutation was determined by polymerase chain reaction (PCR) amplification of exon 15 followed by direct sequencing.Results  The BRAFV600E mutation was detected in tumour samples from 31 of 60 conventional micro‐PTC patients (52%), but was not detected in patients with other types of thyroid tumours. The age distribution, tumour size, extrathyroid extension, multifocality and staging did not differ significantly between patients with and without the BRAFV600E mutation.Conclusion  In Korean patients with conventional micro‐PTC, the presence of the BRAFV600E mutation was not significantly associated with prognostic factors.
Hyporesponsiveness to erythropoietic therapy due to chronic inflammation
Authors: Macdougall I. C. , Cooper A. C. 
Published: October 2005

AbstractThe anaemia associated with chronic renal failure is multi‐factorial. Although a relative erythropoietin deficiency is a major factor, it has also been recognized in recent times that uraemia is a chronic inflammatory state, and thus patients with renal failure also develop anaemia due to mechanisms associated with chronic inflammation. Thus, patients with chronic renal failure have activation of various immune cells, both monocytes and T‐cells. These mononuclear cells have also been shown to release pro‐inflammatory cytokines such as IL‐1, IL‐6, TNF‐alfa and interferon gamma. These cytokines, particularly TNF‐alfa and interferon gamma, are known to cause significant suppression of erythropoiesis. The exact molecular mechanism for this effect is not yet clear, but interferon gamma is an important stimulator of apoptosis in various cell types, including erythroid progenitor cells. This effect may be potentiated by other cytokines such as TNF‐alfa, and this might then antagonise the anti‐apoptotic action of erythropoietin on erythroid progenitors cells, thus reducing responsiveness to exogenous erythropoietic therapy. Chronic renal failure is also associated with increased hepcidin production which may also exacerbate the anaemia by inducing a functional iron deficiency in such patients.
Benefits and risks of iron therapy for chronic anaemias
Authors: Weiss G. , Gordeuk V. R. 
Published: October 2005

AbstractIron is used widely for the treatment of anaemias with iron‐restricted erythropoiesis. This intervention can be both beneficial and detrimental depending on the type of the underlying process. While in iron deficiency anaemia (IDA), the most frequent anaemia in the world, iron is the therapy of choice, this intervention can be harmful in the anaemia of chronic disease or anaemia associated with renal failure, the most common anaemias in hospitalized adult patients in Western countries. Iron is able to negatively affect cell‐mediated immune effector mechanisms directed against invading microorganisms and tumour cells while at the same time, as an essential nutrient, it can stimulate the proliferation of these unwanted cells. In addition, iron catalyses the formation of toxic radicals leading to tissue damage or the promotion of cardiovascular events. Thus, it is essential to correctly diagnose the precise cause of anaemia and to consider the benefits and hazards of targeted iron therapy.