bluuebunny/crossref_metadata_2025_split huggingface dataset:
B-Bolivia, an Allele of the Maize b1 Gene with Variable Expression, Contains a High Copy Retrotransposon-Related Sequence Immediately Upstream
Authors: Selinger David A. , Chandler Vicki L. 
Published: July 2002

Abstract
The maize (Zea mays) b1 gene encodes a transcription factor that regulates the anthocyanin pigment pathway. Of the b1 alleles with distinct tissue-specific expression,B-Peru and B-Bolivia are the only alleles that confer seed pigmentation. B-Bolivia produces variable and weaker seed expression but darker, more regular plant expression relative to B-Peru. Our experiments demonstrated that B-Bolivia is not expressed in the seed when transmitted through the male. When transmitted through the female the proportion of kernels pigmented and the intensity of pigment varied. Molecular characterization of B-Boliviademonstrated that it shares the first 530 bp of the upstream region with B-Peru, a region sufficient for seed expression. Immediately upstream of 530 bp, B-Bolivia is completely divergent from B-Peru. These sequences share sequence similarity to retrotransposons. Transient expression assays of various promoter constructs identified a 33-bp region inB-Bolivia that can account for the reduced aleurone pigment amounts (40%) observed with B-Bolivia relative to B-Peru. Transgenic plants carrying theB-Bolivia promoter proximal region produced pigmented seeds. Similar to native B-Bolivia, some transgene loci are variably expressed in seeds. In contrast to nativeB-Bolivia, the transgene loci are expressed in seeds when transmitted through both the male and female. Some transgenic lines produced pigment in vegetative tissues, but the tissue-specificity was different from B-Bolivia, suggesting the introduced sequences do not contain theB-Bolivia plant-specific regulatory sequences. We hypothesize that the chromatin context of the B-Boliviaallele controls its epigenetic seed expression properties, which could be influenced by the adjacent highly repeated retrotransposon sequence.
Expression of bar in the Plastid Genome Confers Herbicide Resistance
Authors: Lutz Kerry A. , Knapp Jane E. , Maliga Pal 
Published: July 2002

Abstract
Phosphinothricin (PPT) is the active component of a family of environmentally safe, nonselective herbicides. Resistance to PPT in transgenic crops has been reported by nuclear expression of abar transgene encoding phosphinothricin acetyltransferase, a detoxifying enzyme. We report here expression of a bacterial bar gene (b-bar1) in tobacco (Nicotiana tabacum cv Petit Havana) plastids that confers field-level tolerance to Liberty, an herbicide containing PPT. We also describe a second bacterial bar gene (b-bar2) and a codon-optimized syntheticbar (s-bar) gene with significantly elevated levels of expression in plastids (&gt;7% of total soluble cellular protein). Although these genes are expressed at a high level, direct selection thus far did not yield transplastomic clones, indicating that subcellular localization rather than the absolute amount of the enzyme is critical for direct selection of transgenic clones. The codon-modified s-bar gene is poorly expressed in Escherichia coli, a common enteric bacterium, due to differences in codon use. We propose to use codon usage differences as a precautionary measure to prevent expression of marker genes in the unlikely event of horizontal gene transfer from plastids to bacteria. Localization of the bar gene in the plastid genome is an attractive alternative to incorporation in the nuclear genome since there is no transmission of plastid-encoded genes via pollen.
Unsaturated Fatty Acids in Membrane Lipids Protect the Photosynthetic Machinery against Salt-Induced Damage inSynechococcus
Authors: Allakhverdiev Suleyman I. , Kinoshita Mikio , Inaba Masami , Suzuki Iwane , Murata Norio 
Published: July 2002

Abstract
In this study, the tolerance to salt stress of the photosynthetic machinery was examined in relation to the effects of the genetic enhancement of the unsaturation of fatty acids in membrane lipids in wild-type and desA + cells ofSynechococcus sp. PCC 7942. Wild-type cells synthesized saturated and mono-unsaturated fatty acids, whereasdesA + cells, which had been transformed with the desA gene for the Δ12 acyl-lipid desaturase ofSynechocystis sp. PCC 6803, also synthesized di-unsaturated fatty acids. Incubation of wild-type anddesA + cells with 0.5 m NaCl resulted in the rapid loss of the activities of photosystem I, photosystem II, and the Na+/H+ antiport system both in light and in darkness. However,desA + cells were more tolerant to salt stress and osmotic stress than the wild-type cells. The extent of the recovery of the various photosynthetic activities from the effects of 0.5 m NaCl was much greater indesA + cells than in wild-type cells. The photosystem II activity of thylakoid membranes fromdesA + cells was more resistant to 0.5m NaCl than that of membranes from wild-type cells. These results demonstrated that the genetically engineered increase in unsaturation of fatty acids in membrane lipids significantly enhanced the tolerance of the photosynthetic machinery to salt stress. The enhanced tolerance was due both to the increased resistance of the photosynthetic machinery to the salt-induced damage and to the increased ability of desA + cells to repair the photosynthetic and Na+/H+ antiport systems.
Hydraulic Conductance and Mercury-Sensitive Water Transport for Roots of Opuntia acanthocarpa in Relation to Soil Drying and Rewetting
Authors: Martre Pierre , North Gretchen B. , Nobel Park S. 
Published: July 2002

Abstract
Drought-induced changes in root hydraulic conductance (L P) and mercury-sensitive water transport were examined for distal (immature) and mid-root (mature) regions ofOpuntia acanthocarpa. During 45 d of soil drying,L P decreased by about 67% for distal and mid-root regions. After 8 d in rewetted soil,L P recovered to 60% of its initial value for both regions. Axial xylem hydraulic conductivity was only a minor limiter of L P. Under wet conditions, HgCl2 (50 μm), which is known to block membrane water-transport channels (aquaporins), decreasedL P and the radial hydraulic conductance for the stele (L R, S) of the distal root region by 32% and 41%, respectively; both L P andL R, S recovered fully after transfer to 2-mercaptoethanol (10 mm). In contrast, HgCl2 did not inhibit L P of the mid-root region under wet conditions, although it reducedL R, S by 41%. Under dry conditions, neitherL P nor L R, S of the two root regions was inhibited by HgCl2. After 8 d of rewetting, HgCl2 decreased L Pand L R, S of the distal region by 23% and 32%, respectively, but L P andL R, S of the mid-root region were unaltered. Changes in putative aquaporin activity accounted for about 38% of the reduction in L P in drying soil and for 61% of its recovery for the distal region 8 d after rewetting. In the stele, changes in aquaporin activity accounted for about 74% of the variable L R, S during drought and after rewetting. Thus, aquaporins are important for regulating water movement for roots of O. acanthocarpa.
Mutational Analysis of Branching in Pea. Evidence ThatRms1 and Rms5 Regulate the Same Novel Signal
Authors: Morris Suzanne E. , Turnbull Colin G.N. , Murfet Ian C. , Beveridge Christine A. 
Published: July 2002

Abstract
The fifth increased branching ramosus(rms) mutant, rms5, from pea (Pisum sativum), is described here for phenotype and grafting responses with four other rms mutants. Xylem sap zeatin riboside concentration and shoot auxin levels inrms5 plants have also been compared withrms1 and wild type (WT). Rms1 andRms5 appear to act closely at the biochemical or cellular level to control branching, because branching was inhibited in reciprocal epicotyl grafts between rms5 orrms1 and WT plants, but not inhibited in reciprocal grafts between rms5 and rms1 seedlings. The weakly transgressive or slightly additive phenotype of therms1 rms5 double mutant provides further evidence for this interaction. Like rms1, rms5rootstocks have reduced xylem sap cytokinin concentrations, andrms5 shoots do not appear deficient in indole-3-acetic acid or 4-chloroindole-3-acetic acid. Rms1 andRms5 are similar in their interaction with otherRms genes. Reciprocal grafting studies withrms1, rms2, and rms5, together with the fact that root xylem sap cytokinin concentrations are reduced in rms1 and rms5 and elevated inrms2 plants, indicates that Rms1 andRms5 may control a different pathway than that controlled by Rms2. Our studies indicate thatRms1 and Rms5 may regulate a novel graft-transmissible signal involved in the control of branching.
Chloroplast Protein Translocon Components atToc159 and atToc33 Are Not Essential for Chloroplast Biogenesis in Guard Cells and Root Cells
Authors: Yu Tien-Shin , Li Hsou-min 
Published: July 2002

Abstract
Protein import into chloroplasts is mediated by a protein import apparatus located in the chloroplast envelope. Previous results indicate that there may be multiple import complexes in Arabidopsis. To gain further insight into the nature of this multiplicity, we analyzed the Arabidopsis ppi1 and ppi2 mutants, which are null mutants of the atToc33 and atToc159 translocon proteins, respectively. In the ppi2 mutant, in contrast to the extremely defective plastids in mesophyll cells, chloroplasts in guard cells still contained starch granules and thylakoid membranes. The morphology of root plastids in both mutants was similar to that in wild type. After prolonged light treatments, root plastids of both mutants and the wild type differentiated into chloroplasts. Enzymatic assays indicated that the activity of a plastid enzyme was reduced only in leaves but not in roots. These results indicated that both theppi1 and ppi2 mutants had functional root and guard cell plastids. Therefore, we propose that import complexes are cell type specific rather than substrate or plastid specific.
Solution structure and backbone dynamics of the DNA‐binding domain of mouse Sox‐5
Authors: Cary Peter D. , Read Christopher M. , Davis Ben , Driscoll Paul C. , Crane‐Robinson Colyn 
Published: July 2002

AbstractThe fold of the murine Sox‐5 (mSox‐5) HMG box in free solution has been determined by multidimensional NMR using 15N‐labeled protein and has been found to adopt the characteristic twisted L‐shape made up of two wings: the major wing comprising helix 1 (F10–F25) and helix 2 (N32–A43), the minor wing comprising helix 3 (P51–Y67) in weak antiparallel association with the N‐terminal extended segment. 15N relaxation measurements show considerable mobility (reduced order parameter, S2) in the minor wing that increases toward the amino and carboxy termini of the chain. The mobility of residues C‐terminal to Q62 is significantly greater than the equivalent residues of non‐sequence‐specific boxes, and these residues show a weaker association with the extended N‐terminal segment than in non‐sequence boxes. Comparison with previously determined structures of HMG boxes both in free solution and complexed with DNA shows close similarity in the packing of the hydrophobic cores and the relative disposition of the three helices. Only in hSRY/DNA does the arrangement of aromatic sidechains differ significantly from that of mSox‐5, and only in rHMG1 box 1 bound to cisplatinated DNA does helix 1 have no kink. Helix 3 in mSox‐5 is terminated by P68, a conserved residue in DNA sequence‐specific HMG boxes, which results in the chain turning through ∼90°.
Crystal structure of an archaeal DNA sliding clamp: Proliferating cell nuclear antigen from Pyrococcus furiosus
Authors: Matsumiya Shigeki , Ishino Yoshizumi , Morikawa Kosuke 
Published: July 2002

AbstractThe proliferating cell nuclear antigen (PCNA) is now recognized as one of the key proteins in DNA metabolic events because of its direct interactions with many proteins involved in important cellular processes. We have determined the crystal structure of PCNA from a hyperthermophilic archaeon, Pyrococcus furiosus (PfuPCNA), at 2.1 Å resolution. PfuPCNA forms a toroidal, ring‐shaped structure consisting of homotrimeric molecules, which is also observed in the PCNA crystals from human and yeast. The overall structure of PfuPCNA is highly conserved with other PCNA proteins, as well as with the bacterial β clamp and the bacteriophage gp45. This result shows that the three‐dimensional structure of the sliding clamp is conserved in the three domains of life. PfuPCNA has two remarkable features compared with the human and yeast PCNA molecules: it has more ion pairs and fewer intermolecular main chain hydrogen bonds. The former may contribute to the thermal stability of PfuPCNA, and the latter may be the cause of the stimulatory effect of PfuPCNA on the DNA synthesizing activity of P. furiosus DNA polymerases in the absence of the clamp loader replication factor C in vitro.
Open‐and‐shut cases in coiled‐coil assembly: α‐sheets and α‐cylinders
Authors: Walshaw John , Woolfson Derek N. 
Published: July 2002

AbstractThe coiled coil is a ubiquitous protein‐folding motif. It generally is accepted that coiled coils are characterized by sequence patterns known as heptad repeats. Such patterns direct the formation and assembly of amphipathic α‐helices, the hydrophobic faces of which interface in a specific manner first proposed by Crick and termed “knobs‐into‐holes packing”. We developed software, socket, to recognize this packing in protein structures. As expected, in a trawl of the protein data bank, we found examples of canonical coiled coils with a single contiguous heptad repeat. In addition, we identified structures with multiple, overlapping heptad repeats. This observation extends Crick's original postulate: Multiple, offset heptad repeats help explain assemblies with more than two helices. Indeed, we have found that the sequence offset of the multiple heptad repeats is related to the coiled‐coil oligomer state. Here we focus on one particular sequence motif in which two heptad repeats are offset by two residues. This offset sets up two hydrophobic faces separated by ≈150°–160° around the α‐helix. In turn, two different combinations of these faces are possible. Either similar or opposite faces can interface, which leads to open or closed multihelix assemblies. Accordingly, we refer to these two forms as α‐sheets and α‐cylinders. We illustrate these structures with our own predictions and by reference to natural variants on these designs that have recently come to light.
Ligand binding to the inhibitory and stimulatory GTP cyclohydrolase I/GTP cyclohydrolase I feedback regulatory protein complexes
Authors: Yoneyama Toshie , Hatakeyama Kazuyuki 
Published: July 2002

AbstractGTP cyclohydrolase I feedback regulatory protein (GFRP) mediates feedback inhibition of GTP cyclohydrolase I activity by 6R‐l‐erythro‐5,6,7,8‐tetrahydrobiopterin (BH4), which is an essential cofactor for key enzymes producing catecholamines, serotonin, and nitric oxide as well as phenylalanine hydroxylase. GFRP also mediates feed‐forward stimulation of GTP cyclohydrolase I activity by phenylalanine at subsaturating GTP levels. These ligands, BH4 and phenylalanine, induce complex formation between one molecule of GTP cyclohydrolase I and two molecules of GFRP. Here, we report the analysis of ligand binding using the gel filtration method of Hummel and Dreyer. BH4 binds to the GTP cyclohydrolase I/GFRP complex with a Kd of 4 μM, and phenylalanine binds to the protein complex with a Kd of 94 μM. The binding of BH4 is enhanced by dGTP. The binding stoichiometrics of BH4 and phenylalanine were estimated to be 10 molecules of each per protein complex, in other words, one molecule per subunit of protein, because GTP cyclohydrolase I is a decamer and GFRP is a pentamer. These findings were corroborated by data from equilibrium dialysis experiments. Regarding ligand binding to free proteins, BH4 binds weakly to GTP cyclohydrolase I but not to GFRP, and phenylalanine binds weakly to GFRP but not to GTP cyclohydrolase I. These results suggest that the overall structure of the protein complex contributes to binding of BH4 and phenylalanine but also that each binding site of BH4 and phenylalanine may be primarily composed of residues of GTP cyclohydrolase I and GFRP, respectively.
Observation of the closing of individual hydrogen bonds during TFE–induced helix formation in a peptide
Authors: Jaravine Victor A. , Alexandrescu Andrei T. , Grzesiek Stephan 
Published: July 2002

AbstractHelix formation of an S‐peptide analog, comprising the first 20 residues of Ribonuclease A and two additional N‐terminal residues, was studied by measuring hydrogen bond (H‐bond) h3JNC′ scalar couplings as a function of 2,2,2‐trifluoroethanol (TFE) concentration. The h3JNC′ couplings give direct evidence for the closing of individual backbone N‐H•••O = C H‐bonds during the TFE‐induced formation of secondary structure. Whereas no h3JNC′ correlations could be detected without TFE, α‐helical (i,i +4) H‐bond correlations were observed for the amides of residues A5 to M15 in the presence of TFE. The analysis of individual coupling constants indicates that α‐helix formation starts at the center of the S‐peptide around residue E11 and proceeds gradually from there to both peptide ends as the TFE concentration is increased. At 60% to 90% TFE, well‐formed α‐helical H‐bonds were observed for the amides hydrogens of residues K9 to Q13, whereas H‐bonds of residues T5 to A8, H14, and M15 are affected by fraying. No intramolecular backbone H‐bonds are present at and beyond the putative helix stop signal D16. As the h3JNC′ constants represent ensemble averages and the dependence of h3JNC′ on H‐bond lengths is very steep, the size of the individual h3JNC′ coupling constants can be used as a measure for the population of a closed H‐bond. These individual populations are in agreement with results derived from the Lifson‐Roig theory for coil‐to‐helix transitions. The present work shows that the closing of individual H‐bonds during TFE‐induced helix formation can be monitored by changes in the size of H‐bond scalar couplings.
Performance of a Foil-Magnetic Hybrid Bearing
Authors: Swanson E. E. , Heshmat H. , Walton J. 
Published: July 2002

Abstract
To meet the advanced bearing needs of modern turbomachinery, a hybrid foil-magnetic hybrid bearing system was designed, fabricated, and tested in a test rig designed to simulate the rotor dynamics of a small gas turbine engine (31 kN to 53 kN thrust class). This oil-free bearing system combines the excellent low and zero-speed capabilities of the magnetic bearing with the high-load capacity and high-speed performance of the compliant foil bearing. An experimental program is described which documents the capabilities of the bearing system for sharing load during operation at up to 30,000 rpm and the foil bearing component’s ability to function as a backup in case of magnetic bearing failure. At an operating speed of 22,000 rpm, loads exceeding 5300 N were carried by the system. This load sharing could be manipulated by an especially designed electronic control algorithm. In all tests, rotor excursions were small and stable. During deliberately staged magnetic bearing malfunctions, the foil bearing proved capable of supporting the rotor during continued operation at full load and speed, as well as allowing a safe rotor coastdown. The hybrid system tripled the load capacity of the magnetic bearing alone and can offer a significant reduction in total bearing weight compared to a comparable magnetic bearing.
Investigation of SiO2 plasma enhanced chemical vapor deposition through tetraethoxysilane using attenuated total reflection Fourier transform infrared spectroscopy
Authors: Deshmukh Shashank C. , Aydil Eray S. 
Published: July 2002

In situ attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was used to study surface processes during plasma enhanced chemical vapor deposition (PECVD) of silicon dioxide through tetraethoxysilane (TEOS) and oxygen. ATR-FTIR studies were conducted on thin (about 50 Å) silicon dioxide films deposited on GaAs. This approach allowed us to obtain the infrared spectrum of TEOS adsorbed on SiO2 in the spectral region 4000–770 cm−1 and to determine the surface species and their relative surface concentrations as a function of deposition conditions in a helical resonator plasma reactor. Studies were conducted where the SiO2 surface was exposed to TEOS and O2 plasma sequentially and/or simultaneously. Surface processes were studied as a function of exposure to TEOS and substrate temperature. In situ ATR-FTIR studies of adsorption of TEOS on the SiO2 surface show that TEOS adsorbs chemically and irreversibly onto the SiO2 surface above 100 °C. SiO2 growth was found to occur even without an oxygen plasma at temperatures as low as 200 °C, albeit very slowly. Below 100 °C TEOS was also found to adsorb physically: The extent of the physically adsorbed state was found to increase with decreasing temperature. Hence, during PECVD of SiO2 below 100 °C, physically adsorbed TEOS can be trapped in the growing oxide giving rise to increased ethoxy and OH species which in turn adversely affect the film integrity and quality.
The ATR-FTIR studies of the surface exposed to TEOS at various temperatures indicate that the chemical adsorption of TEOS onto SiO2 proceeds through a precursor-mediated adsorption mechanism where the precursor is a physically adsorbed TEOS molecule. Exposure of adsorbed TEOS to O atoms (oxygen plasma) removed the ethoxy ligands of the surface ethoxysiloxanes, produced surface SiOH species as reaction product, and resulted in deposition of SiO2. In situ and real time studies of the actual PECVD process revealed that water and SiOH species are formed as intermediate surface reaction products and subsequent reaction and elimination of the silanol species can become the rate limiting step (as far as SiOH incorporation in the film is concerned) if the deposition rate is too high.
Effect of Subinhibitory Concentrations of Macrolides on Expression of Flagellin inPseudomonas aeruginosaandProteus mirabilis
Authors: Kawamura-Sato Kumiko , Iinuma Yoshitsugu , Hasegawa Tadao , Horii Toshinobu , Yamashino Takafumi , Ohta Michio 
Published: July 2002

ABSTRACTIn the present study we showed by molecular analysis that the inhibition of motility by macrolides inProteus mirabilisandPseudomonas aeruginosawas well correlated with the loss of the expression of flagellin. Erythromycin, clarithromycin, and azithromycin at subinhibitory concentrations (sub-MICs) suppressed the expression of flagellin dose dependently. Azithromycin had the strongest inhibitory effect on the expression ofP. aeruginosaflagellin, whereas 16-membered rokitamycin had only a weak inhibitory effect. These results indicate the potential effectiveness of sub-MICs of erythromycin, clarithromycin, and azithromycin for the treatment of patients withP. mirabilisandP. aeruginosainfections.