bluuebunny/crossref_metadata_2025 huggingface dataset:
The temperature response of photosynthesis in tobacco with reduced amounts of Rubisco
Authors: KUBIEN DAVID S. , SAGE ROWAN F.
Published: January 2008

The reasons for the decline in net CO2 assimilation (A) above its thermal optimum are controversial. We tested the hypothesis that increasing the ratio of Rubisco activase to Rubisco catalytic site concentration would increase the activation state of Rubisco at high temperatures. We measured photosynthetic gas exchange, in vivo electron transport (J) and the activation state of Rubisco between 15 and 45 °C, at 38 and 76 Pa ambient CO2, in wild‐type (WT) and anti‐rbcS tobacco. The Rubisco content of the anti‐rbcS lines was 30% (S7‐1) or 6% (S7‐2) of WT, but activase levels were the same in the three genotypes. Anti‐rbcS plants had lower A than WT at all temperatures, but had a similar thermal optimum for photosynthesis as WT at both CO2 levels. In WT plants, Rubisco was fully activated at 32 °C, but the activation state declined to 64% at 42 °C. By contrast, the activation state of Rubisco was above 90% in the S7‐1 line, between 15 and 42 °C. Both A and J declined about 20% from Topt to the highest measurement temperatures in WT and the S7‐1 line, but this was fully reversed after a 20 min recovery at 35 °C. At 76 Pa CO2, predicted rates of RuBP regeneration‐limited photosynthesis corresponded with measured A in WT tobacco at all temperatures, and in S7‐1 tobacco above 40 °C. Our observations are consistent with the hypothesis that the high temperature decline in A in the WT is because of an RuBP regeneration limitation, rather than the capacity of Rubisco activase to maintain high Rubisco activation state.
Deposition and localization of lipid polyester in developing seeds of Brassica napus and Arabidopsis thaliana
Authors: Molina Isabel , Ohlrogge John B. , Pollard Mike
Published: January 2008

Mature seeds of Arabidopsis thaliana and Brassica napus contain complex mixtures of aliphatic monomers derived from non‐extractable lipid polyesters. Most of the monomers are deposited in the seed coat, and their compositions suggest the presence of both cutin and suberin layers. The location of these polyesters within the seed coat, and their contributions to permeability of the seed coat and other functional properties are unknown. Polyester deposition was followed over Brassica seed development and distinct temporal patterns of monomer accumulation were observed. Octadecadiene‐1,18‐dioate, the major leaf cutin monomer, was transiently deposited. In contrast, the saturated dicarboxylates maintained a constant level during seed desiccation, whereas the fatty alcohols and saturated ω‐hydroxy fatty acids continually increased. Dissection and analysis of Brassica seed coats showed that suberization is not specific to the chalaza. Analysis of the Arabidopsis ap2‐7 mutant suggested that suberin monomers are preferentially associated with the outer integument. Several Arabidopsis knockout mutant lines for genes involved in polyester biosynthesis (att1, fatB and gpat5) were examined for seed monomer load and composition. The variance in polyester monomers of these mutants is correlated with dye penetration assays. Furthermore, stable transgenic plants expressing promoter::YFP fusions showed ATT1 promoter activity in the inner integument, whereas GPAT5 promoter is active in the outer integument. Together, the Arabidopsis data indicated that there is a suberized layer associated with the outer integument and a cutin‐like polyester layer associated with the inner seed coat.
Rapid spatiotemporal patterning of cytosolic Ca2+ underlies flagellar excision in Chlamydomonas reinhardtii
Authors: Wheeler Glen L. , Joint Ian , Brownlee Colin
Published: January 2008

Ca2+‐dependent signalling processes are implicated in many aspects of flagella function in the green alga, Chlamydomonas. In this study, we examine the spatiotemporal dynamics of cytosolic Ca2+ ([Ca2+]cyt) in single Chlamydomonas cells during the process of flagellar excision, using biolistically loaded calcium‐responsive dyes. Acid‐induced deflagellation occurred in parallel with a single transient elevation in whole‐cell [Ca2+]cyt, which was absent in the acid deflagellation‐deficient adf1 mutant. Deflagellation could also be induced by elevated external Ca2+ ([Ca2+]ext), which promoted very rapid spiking of [Ca2+]cyt across the whole cell and in the flagella. We also detected very rapid apically localised Ca2+ signalling events with an approximate duration of 500 msec. Ninety‐seven per cent of deflagellation events coincided with a rapid elevation in [Ca2+]cyt in the apical region of the cell, either in the form of a whole cell or an apically localised increase, indicating that [Ca2+]cyt elevations in the apical region play an underlying role in deflagellation. Our data indicate that elevated [Ca2+]ext acts to disrupt Ca2+ homeostasis which induces deflagellation by both Adf1‐dependent and Adf1‐independent mechanisms. Elevated [Ca2+]ext also results in further [Ca2+]cyt elevations after the main period of whole cell spiking which are very strongly associated with deflagellation, exhibit a high degree of apical localisation and are largely absent in the adf1 mutant. We propose that these later elevations may act as specific signals for deflagellation.
Phylogenetic footprints in fern spore‐ and seed‐specific gene promoters
Authors: Schallau Anna , Kakhovskaya Irina , Tewes Anne , Czihal Andreas , Tiedemann Jens , Mohr Michaela , Grosse Ivo , Manteuffel Renate , Bäumlein Helmut
Published: January 2008

Spermatophyte seed‐storage proteins have descended from a group of proteins involved in cellular desiccation/hydration processes. Conserved protein structures are found across all plant phyla and in the fungi andArchaea. We investigated whether conservation in the coding region sequence is paralleled by common gene regulatory processes. Seed‐ and spore‐specific gene promoters of three phylogenetically diverse plants were analysed by transient and transgenic expression inArabidopsis thalianaand tobacco. The transcription factors FUS3 and ABI3, which are central regulators of seed maturation processes, interact withcis‐motifs of seed‐specific promoters from distantly related plants. The promoter of a fern spore‐specific gene encoding a seed‐storage globulin‐like protein exhibits strong seed‐specific activity in both Arabidopsis and tobacco. The existence of phylogenetic footprints indicates good conservation of regulatory pathways controlling gene expression in fern spores and in gymnosperm and angiosperm seeds, reflecting the concerted evolution of coding and regulatory regions.
TECHNICAL ADVANCE: Induction of phenotypic variation by activation of genes harbouring a maize Spm element in their promoter regions using a TnpA–VP16 fusion protein
Authors: Sorokin Alexander P. , Walsh Sean , Baumann Kim , Nichols John , Bevan Michael , Jones Jonathan D.G. , Martin Cathie , Clarke Jonathan H.
Published: January 2008

For many crops, a narrowing genetic base is becoming an increasingly significant problem for improvements made through breeding. Commonly used breeding procedures systematically reduce genetic diversity within elite gene pools. Here we describe a new technique for activation of genes in lines carrying Spm or dSpm transposon insertions. Activation of genes in Arabidopsis harbouring Spm or dSpm insertions in their promoters can be induced by over‐expression of the TnpA–VP16 fusion protein, which binds Spm ends and activates local transcription. As a result, a variety of phenotypes are recovered from multiple‐copy Spm lines in Arabidopsis. Application of this technique to a number of Spm insertion collections in Arabidopsis provides a valuable approach for new insights into plant gene functions. It also provides a proof‐of‐principle demonstration that the method could be used to generate new variation in elite lines of maize.
The gibberellin biosynthetic genes AtGA20ox1 and AtGA20ox2 act, partially redundantly, to promote growth and development throughout the Arabidopsis life cycle
Authors: Rieu Ivo , Ruiz‐Rivero Omar , Fernandez‐Garcia Nieves , Griffiths Jayne , Powers Stephen J. , Gong Fan , Linhartova Terezie , Eriksson Sven , Nilsson Ove , Thomas Stephen G. , Phillips Andrew L. , Hedden Peter
Published: January 2008

The activity of the gibberellin (GA) biosynthetic enzymes GA 20‐oxidases (GA20ox) is of particular importance in determining GA concentration in many plant species. In Arabidopsis these enzymes are encoded by a family of five genes: AtGA20ox1–AtGA20ox5. Transcript analysis indicated that they have different expression patterns and may thus participate differentially in GA‐regulated developmental processes. We have used reverse genetics to determine the physiological roles of AtGA20ox1 and AtGA20ox2, the most highly expressed GA20ox genes during vegetative and early reproductive development. AtGA20ox1 and AtGA20ox2 act redundantly to promote hypocotyl and internode elongation, flowering time, elongation of anther filaments, the number of seeds that develop per silique and elongation of siliques, with AtGA20ox1 making the greater contribution to internode and filament elongation, and AtGA20ox2 making the greater contribution to flowering time and silique length. Pollination of the double mutant with wild‐type pollen indicated that the GA promoting silique elongation is of maternal origin. The ga20ox2 phenotype revealed that GA promotes the number of stem internodes that elongate upon bolting, and does so independently of its effect on internode elongation. Comparison of the phenotype of the double mutant with that of the highly GA‐deficient ga1‐3 mutant indicates that other GA20ox genes contribute to all the developmental processes examined, and, in some cases such as root growth and leaf expansion, make major contributions, as these processes were unaffected in the double mutant. In addition, the effects of the mutations are mitigated by the homeostatic mechanism that acts on expression of other GA dioxygenase and GID1 receptor genes.
Phytochromes and cryptochromes regulate the differential growth of Arabidopsis hypocotyls in both a PGP19‐dependent and a PGP19‐independent manner
Authors: Nagashima Akitomo , Suzuki Genki , Uehara Yukiko , Saji Kensuke , Furukawa Toshiko , Koshiba Tomokazu , Sekimoto Masayo , Fujioka Shozo , Kuroha Takeshi , Kojima Mikiko , Sakakibara Hitoshi , Fujisawa Noriko , Okada Kiyotaka , Sakai Tatsuya
Published: January 2008

Photoreceptors, phytochromes and cryptochromes regulate hypocotyl growth under specific conditions, by suppressing negative gravitropism, modulating phototropism and inhibiting elongation. Although these effects seem to be partially caused via the regulation of the phytohormone auxin, the molecular mechanisms underlying this process are still poorly understood. In our present study, we demonstrate that the flabby mutation enhances both phytochrome‐ and cryptochrome‐inducible hypocotyl bending in Arabidopsis. The FLABBY gene encodes the ABC‐type auxin transporter, PGP19, and its expression is suppressed by the activation of phytochromes and cryptochromes. Our current results therefore indicate that the phytochromes and cryptochromes have at least two effects upon the tropic responses of the hypocotyls in Arabidopsis: the enhancement of hypocotyl bending through the suppression of PGP19, and a PGP19‐independent mechanism that induces hypocotyl bending. By the using an auxin polar transport assay and DR5:GUS expression analysis, we further find that the phytochromes inhibit basipetal auxin transport, and induce the asymmetric distribution of auxin in the hypocotyls. These data suggest that the control of auxin transport by phytochromes and cryptochromes is a critical regulatory component of hypocotyl growth in response to light.
Anthranilate N‐methyltransferase, a branch‐point enzyme of acridone biosynthesis
Authors: Rohde Britta , Hans Joachim , Martens Stefan , Baumert Alfred , Hunziker Peter , Matern Ulrich
Published: January 2008

Acridone alkaloids formed by acridone synthase in Ruta graveolens L. are composed of N‐methylanthraniloyl CoA and malonyl CoAs. A 1095 bp cDNA from elicited Ruta cells was expressed in Escherichia coli, and shown to encode S‐adenosyl‐l‐methionine‐dependent anthranilate N‐methyltransferase. SDS–PAGE of the purified enzyme revealed a mass of 40 ± 2 kDa, corresponding to 40 059 Da for the translated polypeptide, whereas the catalytic activity was assigned to a homodimer. Alignments revealed closest relationships to catechol or caffeate O‐methyltransferases at 56% and 55% identity (73% similarity), respectively, with little similarity (∼20%) to N‐methyltransferases for purines, putrescine, glycine, or nicotinic acid substrates. Notably, a single Asn residue replacing Glu that is conserved in caffeate O‐methyltransferases determines the catalytic efficiency. The recombinant enzyme showed narrow specificity for anthranilate, and did not methylate catechol, salicylate, caffeate, or 3‐ and 4‐aminobenzoate. Moreover, anthraniloyl CoA was not accepted. As Ruta graveolens acridone synthase also does not accept anthraniloyl CoA as a starter substrate, the anthranilate N‐methylation prior to CoA activation is a key step in acridone alkaloid formation, channelling anthranilate from primary into secondary branch pathways, and holds promise for biotechnological applications. RT‐PCR amplifications and Western blotting revealed expression of the N‐methyltransferase in all organs of Ruta plants, particularly in the flower and root, mainly associated with vascular tissues. This expression correlated with the pattern reported previously for expression of acridone synthase and acridone alkaloid accumulation.
Reactive oxygen species mediate Na+‐inducedSOS1mRNA stability in Arabidopsis
Authors: Chung Jung‐Sung , Zhu Jian‐Kang , Bressan Ray A. , Hasegawa Paul M. , Shi Huazhong
Published: January 2008

Salt Overly Sensitive 1 (SOS1), a plasma membrane Na+/H+antiporter in Arabidopsis, is a salt tolerance determinant crucial for the maintenance of ion homeostasis in saline stress conditions.SOS1mRNA is unstable at normal growth conditions, but its stability is substantially increased under salt stress and other ionic and dehydration stresses. In addition, H2O2treatment increases the stability ofSOS1mRNA.SOS1mRNA is inherently unstable and rapidly degraded with a half‐life of approximately 10 min. Rapid decay ofSOS1mRNA requires new protein synthesis. Stress‐inducedSOS1mRNA stability is mediated by reactive oxygen species (ROS). NADPH oxidase is also involved in the upregulation ofSOS1mRNA stability, presumably through the control of extracellular ROS production. Thecis‐element required forSOS1mRNA instability resides in the 500‐bp region within the 2.2 kb at the 3′ end of theSOS1mRNA. Furthermore, mutations in theSOS1gene rendersos1mutants more tolerant to paraquat, a non‐selective herbicide causing oxidative stress, indicating that SOS1 plays negative roles in tolerance of oxidative stress. A hypothetical model for the signaling pathway involving SOS1‐mediated pH changes, NADPH oxidase activation, apoplastic ROS production and downstream signaling transduction is proposed, and the biological significance of ROS‐mediated induction ofSOS1mRNA stability is discussed.
Redundant cis‐acting determinants of 3′ processing and RNA stability in the chloroplast rbcL mRNA of Chlamydomonas
Authors: Goldschmidt‐Clermont Michel , Rahire Michèle , Rochaix Jean‐David
Published: January 2008

We have designed a screen for mutants affected in 3′ maturation of the chloroplast rbcL mRNA in Chlamydomonas reinhardtii. We inserted a spectinomycin resistance cassette, 5′atpA::aadA::3′rbcL, in a peripheral domain of tscA, the gene for a small non‐coding RNA involved in trans‐splicing of psaA. Depending on the orientation of the cassette, a polar effect was observed which was due to processing at the 3′rbcL element: the chimeric tscA RNA was truncated and splicing of psaA was blocked. We selected phenotypic revertants of this insertion mutant that restored psaA splicing, which correlated with the presence of chimeric transcripts that regained the 3′ part of tscA. We analyzed two nuclear and six chloroplast suppressors. Five chloroplast mutations altered a short element in the center of the second inverted repeat in the 3′rbcL (IR2), and one deleted a larger region including this element. These mutations revealed a cis‐acting element in IR2 which is required for 3′ processing. When the same mutations were inserted in the 3′ untranslated region (UTR) of the native rbcL gene, the rbcL mRNA accumulated to normal levels, but in strong alleles its 3′ end was located upstream, near the end of the first inverted repeat (IR1). Deletion of either IR1 or IR2 allowed stable accumulation of rbcL mRNA, but deletion of both resulted in its complete absence. This indicated that the two inverted repeats function as redundant mRNA stability determinants in the 3′ UTR of rbcL.
Use of Phadiatop® Infant in diagnosis of specific sensitization in young children with wheeze or eczema
Authors: Lau Susanne , Nilsson Monika , Sulser Claudia , Schulz Gabriele , Borres Magnus P , Wahn Ulrich
Published: January 2008

Wheezing and eczema are common symptoms in young children and it is important to disclose sensitization for correct management. The objective of this study was to assess the diagnostic values of Phadiatop Infant, an in vitro test for graded determination of immunoglobulin E (IgE) antibodies to food and inhalant allergens. One‐hundred and forty‐nine children (median age 1.4 yr) with symptoms of wheezing (51%) eczema (28%) or a combination of both (21%) were classified as atopic or non‐atopic based on case history, atopic history, physical examination and determination of IgE antibodies. The clinical performance of Phadiatop Infant was evaluated for 145 children against this classification in a blinded manner to the allergist. Fifty‐one children were classified as atopic of which Phadiatop Infant identified 49. Ninety‐four were non‐atopic of which the test identified 90. This resulted in a sensitivity of 96%, a specificity of 96%, a positive and a negative predictive value of 94% and 98%, respectively. Logistic regression showed that probability had to be assessed as atopic increased with increasing Phadiatop Infant values. These results suggest that Phadiatop Infant can be recommended as an adjunct to the clinical information in the differential diagnosis on IgE‐mediated allergy in young children. The test thus provides an opportunity for early correct diagnosis and identification of subjects at risk for whom intervention may be necessary.
Obesity and the prevalence of allergic diseases in schoolchildren
Authors: Kusunoki Takashi , Morimoto Takeshi , Nishikomori Ryuta , Heike Toshio , Ito Masatoshi , Hosoi Susumu , Nakahata Tatsutoshi
Published: January 2008

Although the association between obesity and bronchial asthma (BA) has been gaining more attention, few studies have been conducted concerning the relationship between obesity and other allergic diseases. The objective of this study was to determine whether and how childhood obesity is associated with allergic diseases other than BA, such as atopic dermatitis (AD), allergic rhinitis (AR), allergic conjunctivitis (AC), and either AR or AC (AR/AC). A questionnaire was administered to the parents of 50,086 Japanese schoolchildren. Associations between childhood obesity and the various allergic diseases were evaluated by univariate and multivariate logistic models. Significant associations were found between higher body mass index (BMI) and AD (p = 0.03), and lower BMI and AC (p < 0.0001), and AR/AC (p < 0.0001). There was a significantly higher prevalence of BA in girls with obesity (p = 0.009) than in those without obesity. Significantly lower prevalence of AC (p = 0.01) and AR/AC (p = 0.002) among children with obesity, and AR (p = 0.04) and AR/AC (p = 0.0004) among boys with obesity were observed than those without obesity. Those who were obese and had AD were significantly more likely to have severe symptoms (p = 0.01). Overall, childhood obesity has positive associations with BA prevalence and AD severity, whereas it has negative associations with AR and AC prevalence, especially among boys. Changes in the immunologic balance accompanied by obesity might have different effects on each type of allergic disease. Exploring the mechanisms by which childhood obesity affects allergic status should lead to new management options for childhood allergy.
An Ultrastructural Characterization of the Ooplasm in Ovarian Follicles of the Immature Ostrich (Struthio camelus)
Authors: Madekurozwa M.‐C. , Kimaro W. H.
Published: January 2008

Primordial, pre‐vitellogenic and vitellogenic follicles were present in the ovary of the immature ostrich. The oocytes of these follicles were composed of a nucleus surrounded by ooplasm. Central, intermediate and cortical regions formed the ooplasm. The organelles present in these ooplasmic regions varied depending on the stage of follicular development. In primordial and small pre‐vitellogenic (100–150 μm in diameter) follicles the central region of the ooplasm was dominated by an accumulation of organelles, which formed Balbiani’s vitelline body. In contrast, the central region in vitellogenic follicles was filled with numerous large yolk spheres, many of which contained lining bodies. Numerous lipid droplets interspersed with mitochondria and small yolk spheres formed the intermediate ooplasmic region in primordial and small pre‐vitellogenic follicles. In large pre‐vitellogenic (150–400 μm in diameter) and vitellogenic follicles the intermediate region contained a greater density of mitochondria and small yolk spheres. Small yolk spheres were observed in the cortical region of pre‐vitellogenic follicles. An interesting feature of the cortical region in vitellogenic follicles was the frequent occurrence of Golgi complexes. The results of the study indicate that although the ovarian follicles in the immature ostrich are not ovulated, the components and composition of the ooplasm are similar to those observed in the mature follicles of other avian species.
Bilateral Lymphangiomatous Testicular Lesions in a Lamb
Authors: Brown P , Smith K , Bazely K , Glover M , Barr F
Published: January 2008

Contents

Bilateral testicular enlargement was recognized in a young lamb; both gonads were largely replaced by a mass composed of multiple cystic spaces. Positive immunohistochemical staining for factor VIII‐related protein indicated that the cysts were lined by endothelial cells. The precise nature and origin of the lesions is unclear; they might represent hamartomas or benign tumours or may be a result of lymphatic obstruction.
Significance of nitric oxide and its modulation mechanisms by endogenous nitric oxide synthase inhibitors and arginase in the micturition disorders and erectile dysfunction
Authors: Masuda Hitoshi
Published: January 2008

Abstract:  Evidence indicates that nitric oxide (NO) deficiency contributes to micturition disorders, especially in the afferent pathway and erectile dysfunction (ED). Two possible causes of NO deficiency are substrate (l‐arginine) limitation and increased levels of endogenous inhibitors of NO synthase (particularly asymmetric dimethylarginine: ADMA) in plasma and tissues. Elevated tissues of ADMA and NG‐monomethyl‐L‐arginine (L‐NMMA) have been reported to be associated with impaired NO‐mediated urethral, trigonal and cavernosal relaxations by pelvic ischemia. Also, plasma ADMA may help to identify underlying cardiovascular disease in men with ED. Decreased l‐arginine availability to NO synthase is due to the shunting of l‐arginine into other pathways such as arginase. Interaction between NO synthase and arginase has been reported to be involved in NO‐mediated urethral and prostatic relaxations. Also, increased arginase activity in cavernosal tissues likely contributes to the ED that accompanies diabetes mellitus and aging. Therefore, arginase inhibition has been reported to enhance the NO‐dependent physiological process for erectile function.
EhaA is a novel autotransporter protein of enterohemorrhagic Escherichia coli O157:H7 that contributes to adhesion and biofilm formation
Authors: Wells Timothy J. , Sherlock Orla , Rivas Lucy , Mahajan Arvind , Beatson Scott A. , Torpdahl Mia , Webb Richard I. , Allsopp Luke P. , Gobius Kari S. , Gally David L. , Schembri Mark A.
Published: January 2008

Autotransporter (AT) proteins have been identified in many Gram‐negative pathogens and are unique in that their primary sequence is sufficient to direct their transport across the bacterial membrane system. Where characterized they are uniformly associated with virulence. Using conserved AT motifs as a search tool, four putative AT proteins were identified in the Enterohemorrhagic Escherichia coli O157:H7 EDL933 genome. The genes encoding these proteins (z0402/ehaA, z0469/ehaB, z3487/ehaC and z3948/ehaD) were PCR amplified, cloned and expressed in an E. coli K‐12 MG1655flu background. Preliminary characterization revealed that ehaA, ehaB and ehaD encode proteins associated with increased biofilm formation. One of these genes (ehaA) resides on a genomic island in E. coli O157:H7 strains EDL933 and Sakai. Over‐expression of EhaA in E. coli K‐12 demonstrated it is located at the cell surface and resulted in the formation of large cell aggregates, promoted significant biofilm formation and mediated adhesion to primary epithelial cells of the bovine terminal rectum. The expression of ehaA was demonstrated in E. coli EDL933 by RT‐PCR. An EhaA‐specific antibody revealed the EhaA protein was expressed in 24/50 generic Shiga toxin‐producing E. coli (STEC) strains of various serotypes including O157:H7. However, the deletion of ehaA from E. coli EDL933 and a STEC strain from serotype O111:H– did not affect biofilm growth. Our results suggest that EhaA may contribute to adhesion, colonization and biofilm formation by E. coli O157:H7 and possibly other STEC serotypes.
Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology
Authors: Cava Felipe , De Pedro Miguel Angel , Blas‐Galindo Emilio , Waldo Geoffrey S. , Westblade Lars F. , Berenguer José
Published: January 2008

Superfolder GFP (sGFP) is a variant of the Green Fluorescent Protein that folds efficiently when fused to poorly folded proteins. In this study, we show that sGFP, but not enhanced GFP, is functional in vivo at 70°C in the extreme thermophile Thermus thermophilus (Tth); thus, permitting the use of sGFP as a localization tag in vivo. We created a suite of plasmids that allow the expression of carboxy‐terminal sGFP fusion proteins in both Escherichia coli and Tth. In order to demonstrate the facility of sGFP as an in vivo localization tag in Tth, we tagged GroES (the small subunit of the bacterial GroES/GroEL chaperone), NarC (a membrane component of the nitrate respiration apparatus) and PhoA (a TAT‐secreted periplasmic protein), and visualized the distribution of the sGFP fusion proteins using confocal microscopy. Fusions to NarC and PhoA produced enzymatically active proteins that complemented both the narC and the phoA strains respectively. Observation of the distribution of the GroES‐sGFP protein by confocal microscopy revealed a homogeneous fluorescence in the cells, which is in full agreement with the cytoplasmic nature of GroES, whereas the NarC‐sGFP protein was localized to the membrane. Finally, a combination of confocal microscopy and biochemistry revealed that PhoA is localized in the periplasm. We suggest that sGFP will be broadly applicable in characterizing various extreme thermophile systems.
Global features of the Alcanivorax borkumensis SK2 genome
Authors: Reva Oleg N. , Hallin Peter F. , Willenbrock Hanni , Sicheritz‐Ponten Thomas , Tümmler Burkhard , Ussery David W.
Published: January 2008

The global feature of the completely sequenced Alcanivorax borkumensis SK2 type strain chromosome is its symmetry and homogeneity. The origin and terminus of replication are located opposite to each other in the chromosome and are discerned with high signal to noise ratios by maximal oligonucleotide usage biases on the leading and lagging strand. Genomic DNA structure is rather uniform throughout the chromosome with respect to intrinsic curvature, position preference or base stacking energy. The orthologs and paralogs of A. borkumensis genes with the highest sequence homology were found in most cases among γ‐Proteobacteria, with Acinetobacter and P. aeruginosa as closest relatives. A. borkumensis shares a similar oligonucleotide usage and promoter structure with the Pseudomonadales. A comparatively low number of only 18 genome islands with atypical oligonucleotide usage was detected in the A. borkumensis chromosome. The gene clusters that confer the assimilation of aliphatic hydrocarbons, are localized in two genome islands which were probably acquired from an ancestor of the Yersinia lineage, whereas the alk genes of Pseudomonas putida still exhibit the typical Alcanivorax oligonucleotide signature indicating a complex evolution of this major hydrocarbonoclastic trait.
The characterization of functions involved in the establishment and maturation of Klebsiella pneumoniae in vitro biofilm reveals dual roles for surface exopolysaccharides
Authors: Balestrino Damien , Ghigo Jean‐Marc , Charbonnel Nicolas , Haagensen Janus A. J. , Forestier Christiane
Published: January 2008

The ability to form biofilm is seen as an increasingly important colonization strategy among both pathogenic and environmental Klebsiella pneumoniae strains. The aim of the present study was to identify abiotic surface colonization factors of K. pneumoniae using different models at different phases of biofilm development. A 2200 K. pneumoniae mutant library previously obtained by signature‐tagged mutagenesis was screened in static and dynamic culture models to detect clones impaired at early and/or mature stages of biofilm formation. A total of 28 mutants were affected during late phases of biofilm formation, whereas 16 mutants displayed early adhesion defect. These mutants corresponded to genes involved in potential cellular and DNA metabolism pathways and to membrane transport functions. Eight mutants were deficient in capsule or LPS production. Gene disruption and microscopic analyses showed that LPS is involved in initial adhesion on both glass and polyvinyl‐chloride and the capsule required for the appropriate initial coverage of substratum and the construction of mature biofilm architecture. These results give new insight into the bacterial factors sequentially associated with the ability to colonize an abiotic surface and reveal the dual roles played by surface exopolysaccharides during K. pneumoniae biofilm formation.
Co‐occurrence of β‐N‐methylamino‐l‐alanine, a neurotoxic amino acid with other cyanobacterial toxins in British waterbodies, 1990–2004
Authors: Metcalf James S. , Banack Sandra Anne , Lindsay Jaime , Morrison Louise F. , Cox Paul Alan , Codd Geoffrey A.
Published: January 2008

The neurotoxic amino acid, β‐N‐methylamino‐l‐alanine, was found to be present in all of 12 analysed samples of cyanobacterial blooms, scums and mats, which had been collected in seven years between 1990 and 2004 inclusive and stored at −20°C. BMAA identification was by high performance liquid chromatography with fluorescence detection and by triple quadrapole mass spectrometry after derivatization. The samples originated from 11 freshwater lakes and 1 brackish waterbody, used either for drinking water, recreation, or both. BMAA was present at between 8 and 287 μg g−1 cyanobacterial dry weight and was present as both the free amino acid and associated with precipitated proteins. Ten of the samples contained additional cyanotoxins (including microcystins, anatoxin‐a, nodularin and saxitoxin) at the time of sample collection. Five of the samples were associated with animal deaths, attributable at the time of sample collection, to microcystins, nodularin or anatoxin‐a. The data demonstrate the presence of BMAA by high performance liquid chromatography and mass spectrometry in a diverse range of cyanobacterial bloom samples from high resource waterbodies. Furthermore, samples collected over several years shows that BMAA can co‐occur with other known cyanotoxins in such waterbodies. Health risk assessment of cyanobacterial BMAA in waterbodies is suggested.
Major differences of bacterial diversity and activity inside and outside of a natural iron‐fertilized phytoplankton bloom in the Southern Ocean
Authors: West Nyree J. , Obernosterer Ingrid , Zemb Olivier , Lebaron Philippe
Published: January 2008

One of the first comparisons of a natural iron fertilized bloom with a high‐nutrient low‐chlorophyll (HNLC) site was undertaken during the Kerguelen ocean and plateau compared study (KEOPS) cruise. To understand better the bacteria–phytoplankton relationship in the context of natural iron fertilization, bacterial diversity and activity was investigated in the bloom and in the adjacent HNLC region by 16S rDNA clone libraries and by single strand conformation polymorphism (SSCP) analysis. Both libraries were dominated by Alphaproteobacteria, Gammaproteobacteria and the Cytophaga‐Flavobacteria‐Bacteroides group. Cluster analysis at 99% sequence similarity yielded several microdiverse clusters and revealed striking differences between the two libraries. In the bloom, the dominant operational taxonomic units (OTUs) were the Roseobacter NAC11‐7 cluster, SAR92 and a Cytophaga‐Flavobacteria‐Bacteroides cluster related to the agg58 group, whereas in the HNLC region, SAR11, Roseobacter RCA and Polaribacter dominated. SSCP analysis of 16S rDNA and 16S rRNA revealed contrasting dynamics of three different Roseobacter OTUs. Roseobacter NAC11‐7 and NAC11‐6 had higher relative abundances and activities in the bloom compared with the HNLC site and NAC11‐6 was only detected at the decline of the bloom concomitant with a shift in phytoplankton composi tion. In contrast, Roseobacter RCA was relatively abundant and active both inside and outside of the bloom. These results suggest that the different OTUs within the Roseobacter group represent functional groups that each play an important role in the cycling of carbon.
Think big – giant genes in bacteria
Authors: Reva Oleg , Tümmler Burkhard
Published: January 2008

Long genes should be rare in archaea and eubacteria because of the demanding costs of time and resources for protein production. The search in 580 sequenced prokaryotic genomes, however, revealed 0.2% of all genes to be longer than 5 kb (absolute number: 3732 genes). Eighty giant bacterial genes of more than 20 kb in length were identified in 47 taxa that belong to the phyla Thermotogae (1), Chlorobi (3), Planctomycetes (1), Cyanobacteria (2), Firmicutes (7), Actinobacteria (9), Proteobacteria (23) or Euryarchaeota (1) (number of taxa in brackets). Giant genes are strain‐specific, differ in their tetranucleotide usage from the bulk genome and occur preferentially in non‐pathogenic environmental bacteria. The two longest bacterial genes known to date were detected in the green sulfur bacterium Chlorobium chlorochromatii CaD3 encoding proteins of 36 806 and 20 647 amino acids, being surpassed in length only by the human titin coding sequence. More than 90% of bacterial giant genes either encode a surface protein or a polyketide/non‐ribosomal peptide synthetase. Most surface proteins are acidic, threonine‐rich, lack cystein and harbour multiple amino acid repeats. Giant proteins increase bacterial fitness by the production of either weapons towards or shields against animate competitors or hostile environments.
Phenazines and biosurfactants interact in the biological control of soil‐borne diseases caused by Pythium spp.
Authors: Perneel Maaike , D'hondt Liesbet , De Maeyer Katrien , Adiobo Amayana , Rabaey Korneel , Höfte Monica
Published: January 2008

In this study, the putative role of phenazines and rhamnolipid‐biosurfactants, antagonistic metabolites produced by Pseudomonas aeruginosa PNA1, was tested in the biological control of Pythium splendens on bean (Phaseolus vulgaris L) and Pythium myriotylum on cocoyam (Xanthosoma sagittifolium L Schott). A rhamnolipid‐deficient and a phenazine‐deficient mutant of PNA1 were used either separately or jointly in plant experiments. When the mutants were applied separately, no disease‐suppressive effect was observed, although both mutants still produced one of the antagonistic compounds (phenazines or rhamnolipids). When the mutants were concurrently introduced in the soil, the biocontrol activity was restored to wild‐type levels. Bean seeds developed significantly less pre‐emergence damping‐off caused by P. splendens when treated with a mixture of purified phenazine‐1‐carboxamide and rhamnolipids than with any of the chemicals alone. When phenazines and rhamnolipids were combined at concentrations that had no observable effects when the metabolites were applied separately, mycelial growth of P. myriotylum was significantly reduced. In addition, microscopic analysis revealed substantial vacuolization and disintegration of Pythium hyphae after incubation in liquid medium amended with both metabolites. Results of this study indicate that phenazines and biosurfactants are acting synergistically in the control of Pythium spp.
Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol
Authors: De La Torre José R. , Walker Christopher B. , Ingalls Anitra E. , Könneke Martin , Stahl David A.
Published: January 2008

The widespread occurrence and diversity of ammonia oxidizing Archaea suggests their contribution to the nitrogen cycle is of global significance. Their distribution appeared limited to low‐ and moderate‐temperature environments until the recent finding of a diagnostic membrane lipid, crenarchaeol, in terrestrial hot springs. We report here the cultivation of a thermophilic nitrifier (‘Candidatus Nitrosocaldus yellowstonii’), an autotrophic crenarchaeote growing up to 74°C by aerobic ammonia oxidation. The major core lipid of this archaeon growing at 72°C is crenarchaeol, providing the first direct evidence for its synthesis by a thermophile. These findings greatly extend the upper temperature limit of nitrification and document that the capacity for ammonia oxidation is broadly distributed among the Crenarchaeota.
Ecology of type II secretion in marine gammaproteobacteria
Authors: Evans Flavia F. , Egan Suhelen , Kjelleberg Staffan
Published: January 2008

Compelling findings on the direct association of the type II secretion (T2S) system with different ecological functions in marine bacteria have challenged the traditional view of the T2S pathway, the function of which has been mostly studied in pathogenic bacteria. The availability of a number of whole‐genome sequence data sets enabled the analysis of the genetic composition of the T2S system across a number of Vibrios and Alteromonads. The widespread Gammaproteobacteria, in particular the Alteromonadales and the Vibrionales group, are recognized to play significant roles in the cycling of nutrients in coastal and pelagic marine ecosystems and are also found associated with marine eukaryotes. The combined analysis of the role and the genetic composition of the T2S system in Gammaproteobacteria provides important evidence for the significance of the T2S pathway in the ecology of environmental bacteria.
Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names
Authors: Bertrand Yann , Härlin Mikael
Published: January 2008

When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon namedoes notprimarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.
The Effect of the Size of the Military on Stock Market Performance in the United States and the UK
Authors: DiPietro William R. , Anoruo Emmanuel , Sawhney Bansi
Published: January 2008

This paper uses regression analysis to investigate the relationship between military expenditure and stock market performance for the United States and the United Kingdom. Specifically, the study applies the Bierens‐Guo unit root procedures to ascertain the time series properties of the variables in the study. The standard OLS technique is employed to determine the influence of military expenditure on stock markets for the period 1914 through 2001. The results from the unit root tests indicate that the military expenditure, military personnel, stock market, and energy consumption series are level stationary. The results from the OLS equations suggest that military expenditure has significantly positive effect on stock market performance for the United States and the United Kingdom. The implication of this finding is that high‐income class and people in power are less likely to oppose increases in military spending even though such expenditures are not in the best interest of the society.
Is Contemporary Interest Rate in Conflict with Islamic Ethics?
Authors: Kula Erhun
Published: January 2008

This paper considers whether the modern interest rate theory is in conflict with Islamic values. Unfortunately, the issue is not sufficiently debated in economic and cognate literature and thus a mist surrounds the Islamic concept of interest (riba) and its use in the Moslem world that contains about 1.3 billion people and hundreds of billions of dollars of surplus funds. A substantial part of this money has not been made available to the commercial banking system as Islamists in particular keep their savings in the form of gold, precious stones or durable foreign currency, in residential or other safe places, believing that earning interest on savings is against the principles of Islam. This attitude by creating a shortage of funds for investment projects is hampering the economic development of many Moslem countries where standards of living are generally low. The finding of the paper is that only one component part of the time preference rate, namely pure time discount, may be objectionable from the Islamic as well as from secular viewpoints; the rest does not appear to be against Muslim ethics. However, a truly competitive financial market structure is likely to wipe away the excessive pure time discount rate leaving the market interest rate free from any objectionable parameter.
Macro‐Determinants of Gambling in Industrialized Nations
Authors: Pryor Frederic L.
Published: January 2008

This study investigates some of the macro‐determinants of commercial gambling in 21 industrialized nations. Of the possible economic determinants, two seem particularly important: the per capita income of the country since gambling represents a larger share of the income of low‐income people than high‐income people; and the general uncertainty of the economic environment, as measured by annual fluctuations in the GDP. Of the possible cultural determines, two also seem particularly important: the values held by the population, as measured by a factor analysis of a number of questions from the World Value Study; and the degree to which the society insures against risk through social welfare expenditures. For the OECD nations in the early part of the 21st century, all four variables prove to be significantly related to the ratio of gambling expenditures to disposable income.
On the Shortest Queue Version of the Erlang Loss Model
Authors: Yao Haishen , Knessl Charles
Published: January 2008

We consider two parallel M/M/N/N queues. Thus there are N servers in each queue and no waiting line(s). The network is fed by a single Poisson arrival stream of rate λ, and the 2N servers are identical exponential servers working at rate μ. A new arrival is routed to the queue with the smaller number of occupied servers. If both have the same occupancy then the arrival is routed randomly, with the probability of joining either queue being 1/2. This model may be viewed as the shortest queue version of the classic Erlang loss model. If all 2N servers are occupied further arrivals are turned away and lost. We let ρ=λ/μ and a=N/ρ=Nμ/λ. We study this model both numerically and asymptotically. For the latter we consider heavily loaded systems (ρ→∞) with a comparably large number of servers (N→∞ with a=O(1)). We obtain asymptotic approximations to the joint steady state distribution of finding m servers occupied in the first queue and n in the second. We also consider the marginal distribution of the number of occupied servers in the second queue, as well as some conditional distributions. We show that aspects of the solution are much different according as a > 1/2, a≈ 1/2, 1/4 < a < 1/2, a≈ 1/4 or 0 < a < 1/4. The asymptotic approximations are shown to be quite accurate numerically.
EVALUATION OF POLICE SERVICES IN MEDIUM‐SIZED CITIES
Authors: BAKER RALPH , MEYER FRED A. , CORBETT A. M. , RUDONI DOROTHY
Published: January 2008

Citizen evaluations of police services in four medium‐sized cities are investigated in this article. Socioeconomic characteristics as well as police attitudes and political attitudes were found not to be good predictors of citizen evaluation. Complaint efficacy was found to be the best predictor of citizen satisfaction with police services.
THE U.S. CIRCUIT JUDGE NOMINATING COMMISSION
Authors: SLOTNICK ELLIOT E.
Published: January 2008

This article examines the institution of the U.S. Circuit Judge Nominating Commission as a new actor in the recruitment process to the federal judiciary. The mandate and operation of the commission are examined and, through the utilization of mailed questionnaires, the research attempts to tap the decisional criteria employed by commission members. Criticisms of the commission and its operation are developed utilizing questionnaire responses as well as documents comprising the commission mandate. The implications of “merit” recruitment for both the district and appeals courts are examined.
THE STICK, THE CARROT, AND OTHER STRATEGIES: A Theoretical Analysis of Governmental Intervention
Authors: BALCH GEORGE I.
Published: January 2008

This article considers four strategies that a government agency might use to change the behavior of individuals: (1) informing target individuals of benefits; (2) facilitating the change for individuals; (3) requiring such change, with penalties for noncompliance; and (4) making the change more attractive. Two complementary theoretical perspectives—learning theory (Skinner) and utility theory (Schultze) —are used to analyze the strategies. Information and facilitation work best on “motivated” people. Regulation works best for strongly desired, discrete, detectable goals achievable in few ways; but it requires much monitoring and may promote undesired reactions. Incentives are the basis of the most reliable, efficient strategies, especially if the change is continuous, detectable, and achievable in many ways.
PUBLIC PARTICIPATION IN TRIAL COURT ELECTIONS: Possibilities for Accentuating the Positive and Eliminating the Negative
Authors: DUBOIS PHILIP L.
Published: January 2008

A large part of the debate over state judicial selection has focused upon the lack of voter interest in and knowledge about judicial elections. This study investigates voter participation in the contested nonpartisan elections for California Superior Court judge from 1958–1978. Focusing upon the variations among and within the state's counties, the analysis attempts to assess the contributions of sociological, environmental, and institutional variables to the level of participation. An exploration of the policy implications of the findings suggests, among other things, that judicial elections in large metropolitan areas might well be abandoned and replaced with some system of gubernatorial appointment and reappointment of judges.