bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of NtrC in biofilm formation via controlling expression of the gene encoding an ADP‐glycero‐manno‐heptose‐6‐epimerase in the pathogenic bacterium, Vibrio vulnificus
Authors: Kim Han‐Suk , Lee Mi‐Ae , Chun Se‐Jin , Park Soon‐Jung , Lee Kyu‐Ho 
Published: December 2006

SummaryTo identify the genetic elements required for biofilm formation, we screened a pool of random Vibrio vulnificus mutants for their ability to form biofilms. One mutant displaying significantly decreased biofilm‐forming activity was found to contain a transposon insertion in the ntrC gene. The ntrC gene encodes a well‐known transcriptional activator. We examined how this regulator modulates a biofilm‐forming process in V. vulnificus by searching for NtrC target gene(s). Comparison of the proteomes of ntrC mutant and wild‐type strains grown under planktonic and biofilm stages revealed that synthesis of the protein homologous to GmhD (ADP‐glycero‐manno‐heptose‐6‐epimerase) was elevated during the growth period for biofilm formation and was strongly influenced by NtrC. A luxAB‐transcriptional fusion with the gmhD promoter region indicated that gmhD expression was positively regulated by both NtrC and RpoN. The function of the gmhD gene product in V. vulnificus was assessed by constructing and phenotypic analyses of an isogenic mutant. The gmhD mutant was defective in production of mature lipopolysaccharide (LPS) and exopolysaccharides (EPS), and demonstrated an attenuated ability to form a biofilm. These results suggest that NtrC acts as a key regulator of both LPS and EPS biosyntheses and, thereby, modulates critical steps in biofilm development of V. vulnificus.
Topology‐dependent transcription in linear and circular plasmids of the segmented genome of Borrelia burgdorferi
Authors: Beaurepaire Cécile , Chaconas George 
Published: December 2006

SummaryThe segmented genome of Borrelia burgdorferi, a causative agent of Lyme disease, contains a mixture of over 20 linear and circular plasmids. Genes encoding five paralogous families of plasmid replication proteins are located on both circular and linear DNA molecules. The effect of DNA topology on the transcription of replication proteins from two B. burgdorferi plasmids, cp9 and lp17, was examined using quantitative reverse transcription polymerase chain reaction. Circular to linear conversion of a cp9‐derived plasmid resulted in a 160‐fold decrease in transcript levels of bbc01, believed to encode the replication initiator. A 14.9‐fold reduction in plasmid copy number was also observed, resulting in a net 10.7‐fold lower transcription level per gene copy on a linear versus a circular plasmid. In contrast, expression of the bbd14 replication initiator for the linear plasmid lp17 was 7.2 times higher per gene copy on a linear versus a circular plasmid. Topology‐dependent transcription of these genes may help to block topological interconversions during genome evolution, offers a new avenue for global gene regulation and also has important implications for the design of genetic complementation experiments in B. burgdorferi.
Leaf growth rate per unit thermal time follows QTL‐dependent daily patterns in hundreds of maize lines under naturally fluctuating conditions
Authors: SADOK WALID , NAUDIN PHILIPPE , BOUSSUGE BENOIT , MULLER BERTRAND , WELCKER CLAUDE , TARDIEU FRANCOIS 
Published: December 2006

ABSTRACTWe have analysed daily patterns of leaf elongation rate (LER) in large data sets with 318 genotypes placed in naturally fluctuating temperature and evaporative demand, and examined the effect of targeted alleles on these patterns. The method consisted, firstly, in expressing elongation rate per unit thermal time, so it became temperature independent; secondly, in a joint analysis of diurnal fluctuations of elongation rate and of micrometeorological conditions in several experiments, and finally, in a comparison of daily patterns between groups of genotypes possessing targeted alleles. (1) Conditions for using thermal time at a time step of 15 min were first tested successfully in 318 recombinant inbred lines (RILs) of three mapping populations. (2) An analysis of 1989 time courses revealed a robust daily pattern of LER per unit thermal time (LERth) over several experiments. LERth was constant during the night and was reproducible (for a given RIL) over up to 10 consecutive nights in different experiments. It declined rapidly during the early morning, closely following the daily pattern of transpiration rate. (3) Groups of RILs carrying alleles conferring a high response to temperature had markedly higher night‐time plateau of LER than those with low responses. Groups of RILs with high response to evaporative demand had rapid decreases in elongation rate at the transition between night and day, while this decrease was slower in groups of RILs with low response. These results open the way for using kinetics of responses to environmental stimuli as a phenotyping tool in genetic analyses.
Calmodulin‐binding protein phosphatase PP7 is involved in thermotolerance in Arabidopsis
Authors: LIU HONG‐TAO , LI GUO‐LIANG , CHANG HUI , SUN DA‐YE , ZHOU REN‐GANG , LI BING 
Published: December 2006

ABSTRACTPP7 is the first protein Ser/Thr phosphatase to be found to interact with calmodulin (CaM) in plants. The T‐DNA insertion AtPP7 knockout line and AtPP7 overexpression lines were employed to study the specific function of AtPP7. The AtPP7 knockout impaired the thermotolerance of Arabidopsis seedlings while the overexpression of AtPP7 resulted in plants with increased thermotolerance. Results from real‐time polymerase chain reaction (PCR) showed that the expression of AtHSP70 and AtHSP101 genes was up‐regulated in AtPP7 overexpression lines after heat shock (HS) at 37 °C for 1 h. Protein gel blot analysis showed that HSP70 protein levels increased in AtPP7 overexpression lines after HS at 37 °C for 2 h. The expression of the AtPP7 gene was also induced by HS at 37 °C in wild‐type Arabidopsis. Using a yeast two‐hybrid screen, we showed an interaction between AtPP7 and CaM. In addition, we found that AtPP7 interacts with an HS transcription factor (HSF), suggesting a possible role for AtPP7 in regulating the expression of heat shock protein (HSP) genes.
Warm and cold parental reproductive environments affect seed properties, fitness, and cold responsiveness in Arabidopsis thaliana progenies
Authors: BLÖDNER C. , GOEBEL C. , FEUSSNER I. , GATZ C. , POLLE A. 
Published: December 2006

ABSTRACTConditions in the parental environment during reproduction can affect the performance of the progenies. The goals of this study were to investigate whether warm or cold temperatures in the parental environment during flowering and seed development affect Arabidopsis thaliana seed properties, growth performance, reproduction and stress tolerance of the progenies, and to find candidate genes for progeny‐related differences in stress responsiveness. Parental plants were raised at 20 °C and maintained from bolting to seed maturity at warm (25 °C) or cold (15 °C) temperatures. Analysis of seed properties revealed significant increases in nitrogen in seeds from warm temperature and significant increases in lipids and in the ratio of α‐linolenic to oleic acid in seeds from the cold parental environment. Progenies of the warm parental environment showed faster germination rates, faster root elongation growth, higher leaf biomass and increased seed production at various temperatures compared with those from the cold parental environment. This indicates that under stable environmental conditions, progenies from warm parental environments had a clear adaptive advantage over those from cold parental environments. This parental effect was presumably transmitted by the higher nitrogen content of the seeds developed in warm conditions. When offspring from parents grown at different temperatures were exposed to chilling or freezing stress, photosynthetic yield recovered faster in progenies originating from cold parental environments. Cold acclimation involved up‐regulation of transcripts of flavanone 3‐hydroxylase (F3H) and pseudo response regulator 9 (PRR9) and down‐regulation of growth‐associated transcription factors (TFs) NAP and AP2domain containing RAP2.3. NAP, a regulator of senescence, and PRR9, a temperature‐sensitive modulator of the circadian clock, were probably involved in mediating parent‐of‐origin effects, because they showed progeny‐related expression differences under chilling. Because low temperatures also delay senescence, cold responsiveness of NAP suggests that this factor is linked with the regulatory network that is important for environmental acclimation of plants.
A novel non‐invasive optical method for quantitative visualization of pH dynamics in the rhizosphere of plants
Authors: BLOSSFELD STEPHAN , GANSERT DIRK 
Published: December 2006

ABSTRACTA novel optical method for non‐invasive, quantitative and high‐resolution imaging of spatial and temporal pH dynamics in soils mediated by plant roots is introduced. This method overcomes present limitations of measurement of pH, mainly short‐term and punctiform measurements, by recording long‐term dynamics of the micro‐pattern of pH in the root–soil interface without disturbance of the biological and physico‐chemical conditions. Juncus effusus L., rooting in a permanently flooded rhizotron, was selected as the test organism for qualifying the technique. The measurements showed pronounced diurnal variations of pH along the roots, particularly along the elongation zone. Diurnal oscillation of pH caused by the roots reached up to 0.5 units. Long‐term records at 4 s intervals over more than 8 weeks revealed considerable spatial and temporal patterns of pH dynamics in the rhizosphere of about 10% of the pH scale (pH 7.0–8.5). The measured data were validated by the use of pH electrodes. Concomitantly measured oxygen concentration showed hypoxic conditions around root tips (10–70 µmol O2 L−1) and almost anoxic conditions (0.9 µmol O2 L−1) in the bulk soil. The present study qualifies this novel pH‐sensing technique as a powerful analytical tool for quantitative visualization of undisturbed bioprocess dynamics.
Phosphate in the arbuscular mycorrhizal symbiosis: transport properties and regulatory roles
Authors: JAVOT HÉLÈNE , PUMPLIN NATHAN , HARRISON MARIA J. 
Published: December 2006

ABSTRACTIn response to the colonization by arbuscular mycorrhizal (AM) fungi, plants reprioritize their phosphate (Pi)‐uptake strategies to take advantage of nutrient transfer via the fungus. The mechanisms underlying Pi transport are beginning to be understood, and recently, details of the regulation of plant and fungal Pi transporters in the AM symbiosis have been revealed. This review summarizes recent advances in this area and explores current data and hypotheses of how the plant Pi status affects the symbiosis. Finally, suggestions of an interrelationship of Pi and nitrogen (N) in the AM symbiosis are discussed.
Carbonate dissolution revealed by silt grain‐size distribution: comparison of Holocene and Last Glacial Maximum sediments from the pelagic South Atlantic
Authors: FRENZ MICHAEL , HENRICH RÜDIGER 
Published: December 2006

AbstractThe current issue of global warming and the role of the ocean in global exchange of CO2 increases the interest in solid budgets of marine carbonate production and dissolution. The present study utilizes grain‐size composition of pelagic sediments in order to trace spatial and temporal variability of carbonate sedimentation in the South Atlantic for the Holocene and Last Glacial Maximum (LGM, 19–23 cal kyr BP). A decrease in grain size (e.g. sand content, mean grain size of coarse carbonate silt) indicates increased carbonate dissolution as a result of increased fragmentation of calcareous microfossils. The spatial grain‐size pattern suggests a threshold water depth below which a gradual grain‐size decrease becomes increasingly rapid. This water depth is considered as the sedimentary lysocline. For the Holocene time slice, a constant, gradual decrease of foraminifer carbonate of about 5–10% per 1000 m water depth above the lysocline gives evidence for supra‐lysoclinal dissolution. The water depth of the lysocline for the Holocene is tied to the interface of North Atlantic Deep Water and Antarctic Bottom Water (AABW) (ca 4100 m). Submarine ridges which restrict intrusion of AABW into the Angola Basin cause an asymmetry in carbonate preservation across the Mid‐Atlantic Ridge. The lysocline was reconstructed at ca 3100 m for the LGM. These data suggest that the ca 1000 m rise of the lysocline eradicated the Holocene east–west asymmetry.
Association between Messinian drainage network formation and major tectonic activity in the Marche Apennines (Italy)
Authors: Scarselli Sonia , Simpson Guy D. H. , Allen Philip A. , Minelli Giorgio , Gaudenzi Lorenzo 
Published: December 2006

AbstractThe Marche Apennines (Italy) offer an excellent opportunity to constrain the temporal and spatial relationships between drainage network formation and tectonic activity. Using a combination of field data, seismic lines and boreholes we show that the main deformation phase took place during the Messinian when the area, affected by the Messinian sea level drop, emerged and evolved from marine to continental conditions. The results highlight that during the Messinian emersion a drainage network developed contemporaneously with an increase in tectonic activity that could be related to sea level fall and river erosion. The present‐day river system, which is dominated by transverse rivers that cut straight across the tectonic grain, is located in older Messinian palaeovalleys, even though the region was subsequently covered by water until the late Pliocene–early Pleistocene.
A simple and reliable assay for detecting specific nucleotide sequences in plants using optical thin‐film biosensor chips
Authors: Bai Su‐Lan , Zhong Xiaobo , Ma Ligeng , Zheng Wenjie , Fan Liu‐Min , Wei Ning , Deng Xing Wang 
Published: December 2006

SummaryHere we report the adaptation and optimization of an efficient, accurate and inexpensive assay that employs custom‐designed silicon‐based optical thin‐film biosensor chips to detect unique transgenes in genetically modified (GM) crops and SNP markers in model plant genomes. Briefly, aldehyde‐attached sequence‐specific single‐stranded oligonucleotide probes are arrayed and covalently attached to a hydrazine‐derivatized biosensor chip surface. Unique DNA sequences (or genes) are detected by hybridizing biotinylated PCR amplicons of the DNA sequences to probes on the chip surface. In the SNP assay, target sequences (PCR amplicons) are hybridized in the presence of a mixture of biotinylated detector probes and a thermostable DNA ligase. Only perfect matches between the probe and target sequences, but not those with even a single nucleotide mismatch, can be covalently fixed on the chip surface. In both cases, the presence of specific target sequences is signified by a color change on the chip surface (gold to blue/purple) after brief incubation with an anti‐biotin IgG horseradish peroxidase (HRP) to generate a precipitable product from an HRP substrate. Highly sensitive and accurate identification of PCR targets can be completed within 30 min. This assay is extremely robust, exhibits high sensitivity and specificity, and is flexible from low to high throughput and very economical. This technology can be customized for any nucleotide sequence‐based identification assay and widely applied in crop breeding, trait mapping, and other work requiring positive detection of specific nucleotide sequences.
Characterization of the centromere and peri‐centromere retrotransposons inBrassica rapaand their distribution in relatedBrassicaspecies
Authors: Lim Ki‐Byung , Yang Tae‐Jin , Hwang Yoon‐Jung , Kim Jung Sun , Park Jee‐Young , Kwon Soo‐Jin , Kim JinA , Choi Beom‐Soon , Lim Myung‐Ho , Jin Mina , Kim Ho‐Il , de Jong Hans , Bancroft Ian , Lim YongPyo , Park Beom‐Seok 
Published: December 2006

SummaryWe report the identification and characterization of the major repeats in the centromeric and peri‐centromeric heterochromatin ofBrassica rapa.The analysis involved the characterization of 88 629 bacterial artificial chromosomes (BAC) end sequences and the complete sequences of two BAC clones. We identified centromere‐specific retrotransposons ofBrassica(CRB) and various peri‐centromere‐specific retrotransposons (PCRBr). Three copies of the CRB were identified in one BAC clone as nested insertions within a tandem array of 24 copies of a 176 bp centromeric repeat, CentBr. A complex mosaic structure consisting of nine PCRBr elements and large blocks of 238 bp degenerate tandem repeats (TR238) were found in or near a derivative of 5S–25S rDNA sequences. The chromosomal positions of selected repeats were determined usingin situhybridization. These revealed that CRB is a major component of all centromeres in three diploidBrassicaspecies and their allotetraploid relatives. However, CentBr was not detected in the most distantly related of the diploid species analyzed,B. nigra. PCRBr and TR238 were found to be major components in the peri‐centromeric heterochromatin blocks of four chromosomes ofB. rapa.These repetitive elements were not identified inB. oleraceaorB. nigra, indicating that they are A‐genome‐specific.
The petunia restorer of fertility protein is part of a large mitochondrial complex that interacts with transcripts of the CMS‐associated locus
Authors: Gillman Jason D. , Bentolila Stéphane , Hanson Maureen R. 
Published: December 2006

SummaryA class of nuclear genes termed ‘restorers of fertility’ (Rf) acts to suppress the expression of abnormal mitochondrial genes associated with cytoplasmic male sterility (CMS). In petunia, both the nuclear Rf gene and mitochondrial CMS‐associated gene have previously been identified. The CMS‐associated gene is an aberrant chimera in which portions of several mitochondrially encoded genes are fused to an unknown reading frame. The dominant Rf allele reduces the CMS‐associated protein to nearly undetectable levels and alters the RNA population derived from the CMS locus, but its mechanism of action has not been determined. The petuniaRf gene is a member of the pentatricopeptide repeat gene family (PPR), an unusually large gene family in Arabidopsis (approximately 450 genes) compared with yeast (five genes) and mammalian genomes (six genes). The PPR gene family has been implicated in the control of organelle gene expression. To gain insight into the mode of action of PPR genes, we generated transgenic petunia plants expressing a functional tagged version of Rf. Analysis of the restorer protein revealed that it is part of a soluble mitochondrial inner‐membrane‐associated, RNase‐sensitive high‐molecular‐weight protein complex. The complex is associated with mRNA derived from the CMS locus.
BIOMARKER: Phosphatidylethanol as a sensitive and specific biomarker—comparison with gamma‐glutamyl transpeptidase, mean corpuscular volume and carbohydrate‐deficient transferrin
Authors: Hartmann Susanne , Aradottir Steina , Graf Marc , Wiesbeck Gerhard , Lesch Otto , Ramskogler Katrin , Wolfersdorf Manfred , Alling Christer , Wurst Friedrich Martin 
Published: December 2006

ABSTRACTPhosphatidylethanol (PEth), a direct ethanol metabolite, is detectable in blood for more than 2 weeks after sustained ethanol intake. Our aim was to assess the usefulness of PEth [comparing sensitivity, specificity and the area under the curve (AUC)] as compared with carbohydrate‐deficient transferrin (CDT), gamma‐glutamyl transpeptidase (GGT) and mean corpuscular volume (MCV), calculating the results from sober patients against those from alcohol‐dependent patients during withdrawal. Fifty‐six alcohol‐dependent patients (ICD‐10 F 10.25) in detoxification, age 43 years, GGT 81 U/l, MCV 96.4 fl, %CDT 4.2, 1400 g ethanol intake in the last 7 days (median), were included in the study. Over the time of 1 year, 52 samples from 35 sober forensic psychiatric addicted in‐patients [age 34 years, GGT 16 U/l, MCV 91 fl, CDT 0.5 (median)] in a closed ward were drawn and used for comparison . PEth was measured in heparinized whole blood with a high‐performance liquid chromatography method. GGT, MCV and %CDT were measured using routine methods. A receiver operating characteristic curve analysis was carried out, with ‘current drinking status’ (sober/drinking) as the state variable and PEth, MCV, GGT and CDT as test variables. The resulting AUC was 0.974 (P < 0.0001, confidence interval 0.932–1.016) for PEth. At a cut‐off of 0.36 µmol/l, the sensitivity was 94.5% and specificity 100%. The AUC for CDT, GGT and MCV were 0.931, 0.894 and 0.883, respectively. A significant Spearman’s rank correlation was found between PEth and GGT (r = 0.739), CDT (r = 0.643), MVC (r = 0.639) and grams of ethanol consumed in the last 7 days (r = 0.802). Our data suggest that PEth has potential to be a sensitive and specific biomarker, having been found in previous studies to indicate longer lasting intake of higher amounts of alcohol.
PRECLINICAL STUDY: Ghrelin administration into tegmental areas stimulates locomotor activity and increases extracellular concentration of dopamine in the nucleus accumbens
Authors: Jerlhag Elisabet , Egecioglu Emil , Dickson Suzanne L. , Douhan Annika , Svensson Lennart , Engel Jörgen A. 
Published: December 2006

ABSTRACTGhrelin stimulates appetite, increases food intake and causes adiposity by mechanisms that include direct actions on the brain. Previously, we showed that intracerebroventricular administration of ghrelin has stimulatory and dopamine‐enhancing properties. These effects of ghrelin are mediated via central nicotine receptors, suggesting that ghrelin can activate the acetylcholine–dopamine reward link. This reward link consists of cholinergic input from the laterodorsal tegmental area (LDTg) to the mesolimbic dopamine system that originates in the ventral tegmental area (VTA) and projects to the nucleus accumbens. Given that growth hormone secretagogue receptors (GHSR‐1A) are expressed in the VTA and LDTg, brain areas involved in reward, the present series of experiments were undertaken to examine the hypothesis that these regions may mediate the stimulatory and dopamine‐enhancing effects of ghrelin, by means of locomotor activity and in vivo microdialysis in freely moving mice. We found that local administration of ghrelin into the VTA (1 µg in 1 µl) induced an increase in locomotor activity and in the extracellular concentration of accumbal dopamine. In addition, local administration of ghrelin into the LDTg (1 µg in 1 µl) caused a locomotor stimulation and an increase in the extracellular levels of accumbal dopamine. Taken together, this indicates that ghrelin might, via activation of GHSR‐1A in the VTA and LDTg, stimulate the acetylcholine–dopamine reward link, implicating that ghrelin is a part of the neurochemical overlap between the reward systems and those that regulate energy balance.