bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk-sharing and social differentiation of demand in land-tenancy markets in southern Portugal, seventeenth–nineteenth centuries
Authors: SANTOS RUI
Published: October 2006

Theoretical debates about the efficiency of sharecropping discuss risk-sharing in relation to farmers' wealth and credit, as one explanatory factor. This perspective is explored here in the southern Portuguese province of Alentejo, from the seventeenth to the mid-nineteenth century. Three points are made: (1) leasing and sharecropping coexisted on the same land; (2) there was no unequivocal relationship between risk sharing, on the one hand, and the contractual mode of tenancy (fixed-rent or sharecropping), on the other; and (3) relating risk-sharing, defined as a continuous variable, with social differentiation of demand for tenancies provides a rationale for a hypothetical long-term shift in contracts, from medieval sharecropping to fixed-rent tenancies with sharecrop subletting in the nineteenth century.
Environmental policy, comparative advantage, and welfare for a developing economy
Authors: BELADI HAMID , CHAO CHI-CHUR
Published: October 2006

This paper investigates the effects of pollution taxation for a dual developing economy with a separate abatement sector. Due to the real rigidity of the urban wage, pollution taxes raise the cost of the urban good and hence its relative price. This suggests that because of flexible rural wages, the developing economy tends to have a comparative advantage in the rural good which may be less polluting. Moreover, the higher price of the urban good worsens the urban unemployment ratio. The optimal tax on pollution is thus lower than the marginal environmental damage to the economy.
Mixing economic and administrative instruments: the case of shrimp aquaculture in Thailand
Authors: BLUFFSTONE RANDALL A. , ANANTANASUWONG DARARATT , RUZICKA IVAN
Published: October 2006

Economic instruments offer the potential to reach pre-determined environmental goals at a lower aggregate cost than less incentive-based measures, but administrative underpinnings crucial to the effective functioning of economic instruments may be lacking in developing countries. For this reason, pragmatic analysts and policymakers often advocate the use of so-called ‘mixed’ instruments that combine incentive mechanisms with improved administrative arrangements. This paper explores such possibilities with reference to intensive shrimp aquaculture, which dominates shrimp farming and is an important economic sector in Thailand. This activity has been cited as a major contributor to environmental degradation in Thailand and several other countries through destruction of mangrove forests, salinization of land, sludge disposal, and, in particular, water pollution. An analytical model is presented that highlights some of the key opportunities and limitations of mixed instruments applied to shrimp aquaculture. Mixed instruments are then proposed and evaluated.
Meridional overturning circulation in the South Atlantic at the last glacial maximum
Authors: Lynch‐Stieglitz Jean , Curry William B. , Oppo Delia W. , Ninneman Ulysses S. , Charles Christopher D. , Munson Jenna
Published: October 2006

The geostrophic shear associated with the meridional overturning circulation is reflected in the difference in density between the eastern and western margins of the ocean basin. Here we examine how the density difference across 30°S in the upper 2 km of the Atlantic Ocean (and thus the magnitude of the shear associated with the overturning circulation) has changed between the last glacial maximum and the present. We use oxygen isotope measurements on benthic foraminifera to reconstruct density. Today, the density in upper and intermediate waters along the eastern margin in the South Atlantic is greater than along the western margin, reflecting the vertical shear associated with the northward flow of surface and intermediate waters and the southward flowing North Atlantic Deep Waters below. The greater density along the eastern margin is reflected in the higher δ18O values for surface sediment benthic foraminifera than those found on the western margin for the upper 2 km. For the last glacial maximum the available data indicate that the eastern margin foraminifera had similar δ18O to those on the western margin between 1 and 2 km and that the gradient was reversed relative to today with the higher δ18O values in the western margin benthic foraminifera above 1 km. If this reversal in benthic foraminifera δ18O gradient reflects a reversal in seawater density gradient, these data are not consistent with a vigorous but shallower overturning cell in which surface waters entering the Atlantic basin are balanced by the southward export of Glacial North Atlantic Intermediate Water.
Quasi‐stationary jets transporting surface warm waters across the transition zone between the subtropical and the subarctic gyres in the North Pacific
Authors: Isoguchi Osamu , Kawamura Hiroshi , Oka Eitarou
Published: October 2006

Surface flow jets and associated sea surface temperature (SST) distribution are investigated in the northwestern North Pacific, using satellite‐derived surface currents and SST data that can resolve fine spatial scale structure. The combined use of these data reveals warm tongue phenomena driven by surface geostrophic jets, which extend northeastward in the Kuroshio‐Oyashio transition area. They roughly coincide with the Subarctic Front (SAF) defined as the 4°C isotherm at 100 m depth. The phenomena appear throughout the year with seasonal cycles, which do not correspond with that of the subarctic North Pacific. Their positions are affected by bottom topography so that their quasi‐stationary and consistent features are suggested. Thus it is implied that these jets play an important role in transporting warm waters toward the subarctic region. The time series of SST and current fields describe the jets' year‐to‐year variability involving some changes in strength and connections with the Kuroshio Extension (KE), and demonstrate the effects of advection by the jets on SST fields. When KE extends northward at its crests for 1999–2002, one of the jets along SAF simultaneously strengthens, resulting in high SST region directly over and along the south side of the jet. Hydrographic data show warm, saline water intrusions along the jets. Their mean fields also reveal that these jets are vertically well‐developed, forming a boundary between the subtropical and subarctic gyres in the North Pacific.
Observational evidence for a cross frontal heat pump in the Southern Ocean
Authors: Ansorge I. J. , Lutjeharms J. R. E. , Swart N. C. , Durgadoo J. V.
Published: October 2006

Transient eddies in the Southern Ocean play a central role in the global thermohaline circulation. Meridional exchange of heat and salt is not geographically uniformly distributed, but may be concentrated in a number of specific regions where high levels of mesoscale turbulence are generated. We have identified a powerful example of such a region at the South‐West Indian Ridge in which cross‐ACC heat transport is dependent on eddy shedding. We show that Antarctic eddies are shed across the APF into the Subantarctic at an average of 3 a year and that they have a longevity of 11 months. Furthermore, we calculate the meridional heat and salt deficit of −5.6 ± 1.5 × 1019 J and −8.1 ± 1.5 × 1011 kg relative to the surrounding Subantarctic waters of one such eddy. Despite the importance of this process, eddy heat transport remains one of the most poorly observed quantities in the Southern Ocean.
The event that produced heat shield rock and its implications for the Martian atmosphere
Authors: Chappelow J. E. , Sharpton V. L.
Published: October 2006

Methods developed in previous work were used to estimate the mass, trajectory, and atmospheric conditions that produced Heat Shield Rock, the iron meteorite discovered on Mars by the Opportunity rover in January, 2005. We find that Heat Shield Rock encountered Mars at high speed and shallow entry angle, probably at a time when the planet possessed a thicker atmosphere. It entered the atmosphere with a mass of more than 60 kg, underwent significant ablation during atmospheric passage, and ricocheted across the surface upon impact. We conclude that Heat Shield Rock probably represents physical evidence that Mars once had a denser atmosphere.
A trajectory study into the origin of spring time Arctic boundary layer ozone depletion
Authors: Bottenheim Jan W. , Chan Elton
Published: October 2006

In polar regions, severe marine boundary layer ozone depletion episodes (ODEs) are a yearly recurring phenomenon in the spring. Using 9 years of 10‐day three‐dimensional trajectory calculations, the origin of ODEs at three Arctic observatories is investigated. The analysis indicates that marginal ice zones are potential source regions of ODEs. Those regions do broadly correspond to areas where increased levels of bromine oxide (BrO), an indicator of ozone depletion chemistry, are observed by the GOME satellite. The source region of ODEs, observed at Barrow, Alaska, is found to be about 1 day's travel upwind, in agreement with expectations based on the rate at which O3 depletion chemistry occurs. In contrast, the likely source region for ODEs observed at Alert, Canada, and Zeppelinfjellet, Norway, appears to be located several days' travel upwind, off the Siberian coast. This result may reflect the absence of favorable ice conditions for O3 depletion chemistry nearer those sites. Assuming that O3 depletion occurs at those regions, this implies that air parcels without O3 remain that way for several days or the depletion is slower than current understanding of the O3 depletion chemistry suggests. Rapid changes in O3 mole fractions at those measurement sites appears not to be an indication of fast chemical destruction of ozone but rather are due to abrupt air mass changes. Data for September indicate a much narrower distribution of ozone mole fractions and no particular pattern linking a preferred area with lower mole fractions.
A Study of the Logic of Empirical Arguments in Psychological Research: “The Automaticity of Social Behavior” as a Case Study
Authors: Katzko Michael W.
Published: October 2006

This article describes the logical structure of one type of empirical argument commonly used in psychological research. A characteristic flaw in its application is identified and illustrated with an analysis of a number of experiments. Intraindividual as well as social factors that contribute to the flaw's occurrence are discussed. The operation of the social factor is explored with an analysis of citation patterns in the literature. The citation analysis reveals the degree to which the flaw goes unnoticed, in deference to building a consensus of support for broad theoretical claims. The article closes with an outline of the decisions involved in choosing a research strategy and indicates the epistemic consequences of these choices.
Intellectual Competence and the Intelligent Personality: A Third Way in Differential Psychology
Authors: Chamorro-Premuzic Tomas , Furnham Adrian
Published: October 2006

This article conceptualizes the construct of the intelligent personality as an indicator of intellectual competence in an attempt to expand the traditional concept of intelligence and account for both ability and nonability determinants of academic performance. Theoretical implications are discussed with regard to recent attempts to (a) explain correlations between personality and intelligence measures, (b) conceptualize novel constructs that may bridge the gap between intelligence and personality, and (c) develop a conceptual model for understanding the relationship among individual differences underlying human performance in real-world settings. Practical implications are also considered, in particular with regard to the validity of the intelligent personality as a predictor of future achievement.
Why Doesn't the Writing Cure Help Poets?
Authors: Kaufman James C. , Sexton Janel D.
Published: October 2006

This paper examines the literature on creative writing and mental illness and relates it to the “writing cure” research that shows that expressive writing improves health. There is an abundance of evidence that professional poets have poorer health outcomes relative to both other writers and to the population at large. Why doesn't the writing cure help them? The formation of a narrative, an element often missing in poetry, may provide the answer. Other possible explanations are that poets may be more depressed to begin with and may be even worse off if they did not write. For female poets, they may be subject to stereotypic expectations about writing themes, which may put them at further risk. Those seeking improvements in health through writing are advised to adopt a narrative style.
Human inhibitor of apoptosis proteins: why XIAP is the black sheep of the family
Authors: Eckelman Brendan P , Salvesen Guy S , Scott Fiona L
Published: October 2006

Several of the inhibitor of apoptosis protein (IAP) family members regulate apoptosis in response to various cellular assaults. Some members are also involved in cell signalling, mitosis and targeting proteins to the ubiquitin‐proteasome degradation machinery. The most intensively studied family member, X‐linked IAP (XIAP), is a potent inhibitor of caspase activity; hence, it is generally assumed that direct caspase inhibition is an important conserved function of most members of the family. Biochemical and structural studies have precisely mapped the elements of XIAP required for caspase inhibition. Intriguingly, these elements are not conserved among IAPs. Here, we review current knowledge of the caspase‐inhibitory potential of the human IAPs and show that XIAP is probably the only bona fide caspase inhibitor, suggesting that the other family members never gained the ability to directly inhibit caspase activity.
Entering neurons: botulinum toxins and synaptic vesicle recycling
Authors: Verderio Claudia , Rossetto Ornella , Grumelli Carlotta , Frassoni Carolina , Montecucco Cesare , Matteoli Michela
Published: October 2006

Botulinum toxins are metalloproteases that act inside nerve terminals and block neurotransmitter release through their cleavage of components of the exocytosis machinery. These toxins are used to treat human diseases that are characterized by hyperfunction of cholinergic terminals. Recently, evidence has accumulated that gangliosides and synaptic vesicle proteins cooperate to mediate toxin binding to the presynaptic terminal. The differential distribution of synaptic vesicle protein receptors, gangliosides and toxin substrates in distinct neuronal populations opens up the possibility of using different serotypes of botulinum toxins for the treatment of central nervous system diseases caused by altered activity of selected neuronal populations.
Human α-defensins neutralize toxins of the mono-ADP-ribosyltransferase family
Authors: Kim Chun , Slavinskaya Zoya , Merrill A. Rod , Kaufmann Stefan H. E.
Published: October 2006

Various bacterial pathogens secrete toxins, which are not only responsible for fatal pathogenesis of disease, but also facilitate evasion of host defences. One of the best-known bacterial toxin groups is the mono-ADP-ribosyltransferase family. In the present study, we demonstrate that human neutrophil α-defensins are potent inhibitors of the bacterial enzymes, particularly against DT (diphtheria toxin) and ETA (Pseudomonas exotoxin A). HNP1 (human neutrophil protein 1) inhibited DT- or ETA-mediated ADP-ribosylation of eEF2 (eukaryotic elongation factor 2) and protected HeLa cells against DT- or ETA-induced cell death. Kinetic analysis revealed that inhibition of DT and ETA by HNP1 was competitive with respect to eEF2 and uncompetitive against NAD+ substrates. Our results reveal that toxin neutralization represents a novel biological function of HNPs in host defence.
Structure-guided design of a novel class of benzyl-sulfonate inhibitors for influenza virus neuraminidase
Authors: Platis Dimitris , Smith Brian J. , Huyton Trevor , Labrou Nikolaos E.
Published: October 2006

Influenza NA (neuraminidase) is an antiviral target of high pharmaceutical interest because of its essential role in cleaving sialic acid residues from cell surface glycoproteins and facilitating release of virions from infected cells. The present paper describes the use of structural information in the progressive design from a lead binding ion (a sulfate) to a potent submicromolor inhibitor (Ki 0.13 μM). Structural information derived from the X-ray structure of an NA complexed with several sulfate ions, in combination with results derived from affinity labelling and molecular modelling studies, was used to guide design of potent sulfonic acid-based inhibitors. These inhibitors are structural fragments of the polysulfonate triazine dye Cibacron Blue 3GA and represent novel lead scaffolds for designing non-carbohydrate inhibitors for influenza neuraminidases.
Conformational transitions induced in heparin octasaccharides by binding with antithrombin III
Authors: Guerrini Marco , Guglieri Sara , Beccati Daniela , Torri Giangiacomo , Viskov Christian , Mourier Pierre
Published: October 2006

The present study deals with the conformation in solution of two heparin octasaccharides containing the pentasaccharide sequence GlcNNAc,6S-GlcA-GlcNNS,3,6S-IdoA2S-GlcNNS,6S [AGA*IA; where GlcNNAc,6S is N-acetylated, 6-O-sulfated α-D-glucosamine, GlcNNS,3,6S is N,3,6-O-trisulfated α-D-glucosamine and IdoA2S is 2-O-sulfated IdoA (α-L-iduronic acid)] located at different positions in the heparin chain and focuses on establishing geometries of IdoA residues (IdoA2S and IdoA) both inside and outside the AGA*IA sequence. AGA*IA constitutes the active site for AT (antithrombin) and is essential for the expression of high anticoagulant and antithrombotic activities. Analysis of NMR parameters [NOEs (nuclear Overhauser effects), transferred NOEs and coupling constants] for the two octasaccharides indicated that between the 1C4 and 2S0 conformations present in dynamic equilibrium in the free state for the IdoA2S residue within AGA*IA, AT selects the 2S0 form, as previously shown [Hricovini, Guerrini, Bisio, Torri, Petitou and Casu (2001) Biochem. J. 359, 265–272]. Notably, the 2S0 conformation is also adopted by the non-sulfated IdoA residue preceding AGA*IA that, in the absence of AT, adopts predominantly the 1C4 form. These results further support the concept that heparin-binding proteins influence the conformational equilibrium of iduronic acid residues that are directly or indirectly involved in binding and select one of their equi-energetic conformations for best fitting in the complex. The complete reversal of an iduronic acid conformation preferred in the free state is also demonstrated for the first time. Preliminary docking studies provided information on the octasaccharide binding location agreeing most closely with the experimental data. These results suggest a possible biological role for the non-sulfated IdoA residue preceding AGA*IA, previously thought not to influence the AT-binding properties of the pentasaccharide. Thus, for each AT binding sequence longer than AGA*IA, the interactions with the protein could differ and give to each heparin fragment a specific biological response.
Hepatocyte nuclear factor-4α contributes to carbohydrate-induced transcriptional activation of hepatic fatty acid synthase
Authors: Adamson Aaron W. , Suchankova Gabriela , Rufo Caterina , Nakamura Manabu T. , Teran-Garcia Margarita , Clarke Steven D. , Gettys Thomas W.
Published: October 2006

Refeeding a carbohydrate-rich meal after a fast produces a co-ordinated induction of key glycolytic and lipogenic genes in the liver. The transcriptional response is mediated by insulin and increased glucose oxidation, and both signals are necessary for optimal induction of FAS (fatty acid synthase). The glucose-regulated component of FAS promoter activation is mediated in part by ChREBP [ChoRE (carbohydrate response element)-binding protein], which binds to a ChoRE between −7300 and −7000 base-pairs in a carbohydrate-dependent manner. Using in vivo footprinting with nuclei from fasted and refed rats, we identify an imperfect DR-1 (direct repeat-1) element between −7110 and −7090 bp that is protected upon carbohydrate refeeding. Electrophoretic mobility-shift assays establish that this DR-1 element binds HNF-4α (hepatocyte nuclear factor 4α), and chromatin immunoprecipitation establishes that HNF-4α binding to this site is increased approx. 3-fold by glucose refeeding. HNF-4α transactivates reporter constructs containing the distal FAS promoter in a DR-1-dependent manner, and this DR-1 is required for full glucose induction of the FAS promoter in primary hepatocytes. In addition, a 3-fold knockdown of hepatocyte HNF-4α by small interfering RNA produces a corresponding decrease in FAS gene induction by glucose. Co-immunoprecipitation experiments demonstrate a physical interaction between HNF-4α and ChREBP in primary hepatocytes, further supporting an important complementary role for HNF-4α in glucose-induced activation of FAS transcription. Taken together, these observations establish for the first time that HNF-4α functions in vivo through a DR-1 element in the distal FAS promoter to enhance gene transcription following refeeding of glucose to fasted rats. The findings support the broader view that HNF-4α is an integral component of the hepatic nutrient sensing system that co-ordinates transcriptional responses to transitions between nutritional states.
Increased protein glycation in fructosamine 3-kinase-deficient mice
Authors: da-Cunha Maria VEIGA , Jacquemin Patrick , Delpierre Ghislain , Godfraind Catherine , Théate Ivan , Vertommen Didier , Clotman Frédéric , Lemaigre Frédéric , Devuyst Olivier , Van Schaftingen Emile
Published: October 2006

Amines, including those present on proteins, spontaneously react with glucose to form fructosamines in a reaction known as glycation. In the present paper, we have explored, through a targeted gene inactivation approach, the role of FN3K (fructosamine 3-kinase), an intracellular enzyme that phosphorylates free and protein-bound fructose-ϵ-lysines and which is potentially involved in protein repair. Fn3k−/− mice looked healthy and had normal blood glucose and serum fructosamine levels. However, their level of haemoglobin-bound fructosamines was approx. 2.5-fold higher than that of control (Fn3k+/+) or Fn3k+/− mice. Other intracellular proteins were also significantly more glycated in Fn3k−/− mice in erythrocytes (1.8–2.2-fold) and in brain, kidney, liver and skeletal muscle (1.2–1.8-fold), indicating that FN3K removes fructosamines from intracellular proteins in vivo. The urinary excretion of free fructose-ϵ-lysine was 10–20-fold higher in fed mice compared with mice starved for 36 h, and did not differ between fed Fn3k+/+ and Fn3k−/− mice, indicating that food is the main source of urinary fructose-ϵ-lysine in these mice and that FN3K does not participate in the metabolism of food-derived fructose-ϵ-lysine. However, in starved animals, the urinary excretion of fructose-ϵ-lysine was 2.5-fold higher in Fn3k−/− mice compared with Fn3k+/+ or Fn3k+/− mice. Furthermore, a marked increase (5–13-fold) was observed in the concentration of free fructose-ϵ-lysine in tissues of fed Fn3k−/− mice compared with control mice, indicating that FN3K participates in the metabolism of endogenously produced fructose-ϵ-lysine. Taken together, these data indicate that FN3K serves as a protein repair enzyme and also in the metabolism of endogenously produced free fructose-ϵ-lysine.
Aldolase potentiates DIDS activation of the ryanodine receptor in rabbit skeletal sarcoplasmic reticulum
Authors: Seo In-Ra , Moh Sang Hyun , Lee Eun Hui , Meissner Gerhard , Kim Do Han
Published: October 2006

DIDS (4,4′-di-isothiocyanostilbene-2,2′-disulfonate), an anion channel blocker, triggers Ca2+ release from skeletal muscle SR (sarcoplasmic reticulum). The present study characterized the effects of DIDS on rabbit skeletal single Ca2+-release channel/RyR1 (ryanodine receptor type 1) incorporated into a planar lipid bilayer. When junctional SR vesicles were used for channel incorporation (native RyR1), DIDS increased the mean Po (open probability) of RyR1 without affecting unitary conductance when Cs+ was used as the charge carrier. Lifetime analysis of single RyR1 activities showed that 10 μM DIDS induced reversible long-lived open events (Po=0.451±0.038) in the presence of 10 μM Ca2+, due mainly to a new third component for both open and closed time constants. However, when purified RyR1 was examined in the same condition, 10 μM DIDS became considerably less potent (Po=0.206±0.025), although the caffeine response was similar between native and purified RyR1. Hence we postulated that a DIDS-binding protein, essential for the DIDS sensitivity of RyR1, was lost during RyR1 purification. DIDS-affinity column chromatography of solubilized junctional SR, and MALDI–TOF (matrix-assisted laser-desorption ionization–time-of-flight) MS analysis of the affinity-column-associated proteins, identified four major DIDS-binding proteins in the SR fraction. Among them, aldolase was the only protein that greatly potentiated DIDS sensitivity. The association between RyR1 and aldolase was further confirmed by co-immunoprecipitation and aldolase-affinity batch-column chromatography. Taken together, we conclude that aldolase is physically associated with RyR1 and could confer a considerable potentiation of the DIDS effect on RyR1.
Characterization of a novel cAMP-binding, cAMP-specific cyclic nucleotide phosphodiesterase (TcrPDEB1) from Trypanosoma cruzi
Authors: Díaz-Benjumea Rocío , Laxman Sunil , Hinds Thomas R. , Beavo Joseph A. , Rascón Ana
Published: October 2006

Trypanosoma cruzi, the causative agent of Chagas disease, encodes a number of different cAMP-specific PDE (phosphodiesterase) families. Here we report the identification and characterization of TcrPDEB1 and its comparison with the previously identified TcrPDEB2 (formerly known as TcPDE1). These are two different PDE enzymes of the TcrPDEB family, named in accordance with the recent recommendations of the Nomenclature Committee for Kinetoplast PDEs [Kunz, Beavo, D'Angelo, Flawia, Francis, Johner, Laxman, Oberholzer, Rascon, Shakur et al. (2006) Mol. Biochem. Parasitol. 145, 133–135]. Both enzymes show resistance to inhibition by many mammalian PDE inhibitors, and those that do inhibit do so with appreciable differences in their inhibitor profiles for the two enzymes. Both enzymes contain two GAF (cGMP-specific and -stimulated phosphodiesterases, Anabaena adenylate cyclases and Escherichia coliFhlA) domains and a catalytic domain highly homologous with that of the T. brucei TbPDE2/TbrPDEB2 family. The N-terminus+GAF-A domains of both enzymes showed significant differences in their affinities for cyclic nucleotide binding. Using a calorimetric technique that allows accurate measurements of low-affinity binding sites, the TcrPDEB2 N-terminus+GAF-A domain was found to bind cAMP with an affinity of ∼500 nM. The TcrPDEB1 N-terminus+GAF-A domain bound cAMP with a slightly lower affinity of ∼1 μM. The N-terminus+GAF-A domain of TcrPDEB1 did not bind cGMP, whereas the N-terminus+GAF-A domain of TcrPDEB2 bound cGMP with a low affinity of ∼3 μM. GAF domains homologous with those found in these proteins were also identified in related trypanosomatid parasites. Finally, a fluorescent cAMP analogue, MANT-cAMP [2′-O-(N-methylanthraniloyl)adenosine-3′,5′-cyclic monophosphate], was found to be a substrate for the TcPDEB1 catalytic domain, opening the possibility of using this molecule as a substrate in non-radioactive, fluorescence-based PDE assays, including screening for trypanosome PDE inhibitors.
A protein extension to shorten RNA: elongated elongation factor-Tu recognizes the D-arm of T-armless tRNAs in nematode mitochondria
Authors: Sakurai Masayuki , Watanabe Yoh-ichi , Watanabe Kimitsuna , Ohtsuki Takashi
Published: October 2006

Nematode mitochondria possess extremely truncated tRNAs. Of 22 tRNAs, 20 lack the entire T-arm. The T-arm is necessary for the binding of canonical tRNAs and EF (elongation factor)-Tu (thermo-unstable). The nematode mitochondrial translation system employs two different EF-Tu factors named EF-Tu1 and EF-Tu2. Our previous study showed that nematode Caenorhabditis elegans EF-Tu1 binds specifically to T-armless tRNA. C. elegans EF-Tu1 has a 57-amino acid C-terminal extension that is absent from canonical EF-Tu, and the T-arm-binding residues of canonical EF-Tu are not conserved. In this study, the recognition mechanism of T-armless tRNA by EF-Tu1 was investigated. Both modification interference assays and primer extension analysis of cross-linked ternary complexes revealed that EF-Tu1 interacts not only with the tRNA acceptor stem but also with the D-arm. This is the first example of an EF-Tu recognizing the D-arm of a tRNA. The binding activity of EF-Tu1 was impaired by deletion of only 14 residues from the C-terminus, indicating that the C-terminus of EF-Tu1 is required for its binding to T-armless tRNA. These results suggest that C. elegans EF-Tu1 recognizes the D-arm instead of the T-arm by a mechanism involving its C-terminal region. This study sheds light on the co-evolution of RNA and RNA-binding proteins in nematode mitochondria.
Structure, function and mechanism of exocyclic DNA methyltransferases
Authors: Bheemanaik Shivakumara , Reddy Yeturu V. R. , Rao Desirazu N.
Published: October 2006

DNA MTases (methyltransferases) catalyse the transfer of methyl groups to DNA from AdoMet (S-adenosyl-L-methionine) producing AdoHcy (S-adenosyl-L-homocysteine) and methylated DNA. The C5 and N4 positions of cytosine and N6 position of adenine are the target sites for methylation. All three methylation patterns are found in prokaryotes, whereas cytosine at the C5 position is the only methylation reaction that is known to occur in eukaryotes. In general, MTases are two-domain proteins comprising one large and one small domain with the DNA-binding cleft located at the domain interface. The striking feature of all the structurally characterized DNA MTases is that they share a common core structure referred to as an ‘AdoMet-dependent MTase fold’. DNA methylation has been reported to be essential for bacterial virulence, and it has been suggested that DNA adenine MTases (Dams) could be potential targets for both vaccines and antimicrobials. Drugs that block Dam could slow down bacterial growth and therefore drug-design initiatives could result in a whole new generation of antibiotics. The transfer of larger chemical entities in a MTase-catalysed reaction has been reported and this represents an interesting challenge for bio-organic chemists. In general, amino MTases could therefore be used as delivery systems for fluorescent or other reporter groups on to DNA. This is one of the potential applications of DNA MTases towards developing non-radioactive DNA probes and these could have interesting applications in molecular biology. Being nucleotide-sequence-specific, DNA MTases provide excellent model systems for studies on protein–DNA interactions. The focus of this review is on the chemistry, enzymology and structural aspects of exocyclic amino MTases.
Mannitol is required for asexual sporulation in the wheat pathogen Stagonospora nodorum (glume blotch)
Authors: Solomon Peter S. , Waters Ormonde D. C. , Jörgens Cordula I. , Lowe Rohan G. T. , Rechberger Judith , Trengove Robert D. , Oliver Richard P.
Published: October 2006

The physiological role of the mannitol cycle in the wheat pathogen Stagonospora nodorum (glume blotch) has been investigated by reverse genetics and metabolite profiling. A putative mannitol 2-dehydrogenase gene (Mdh1) was cloned by degenerate PCR and disrupted. The resulting mutated mdh1 strains lacked all detectable NADPH-dependent mannitol dehydrogenase activity. The mdh1 strains were unaffected for mannitol production but, surprisingly, were still able to utilize mannitol as a sole carbon source, suggesting a hitherto unknown mechanism for mannitol catabolism. The mutant strains were not compromised in their ability to cause disease or sporulate. To further our understanding of mannitol metabolism, a previously developed mannitol-1-phosphate dehydrogenase (gene mpd1) disruption construct [Solomon, Tan and Oliver (2005) Mol. Plant–Microbe Interact. 18, 110–115] was introduced into the mutated mdh1 background, resulting in a strain lacking both enzyme activities. The mpd1mdh1 strains were unable to grow on mannitol and produced only trace levels of mannitol. The double-mutant strains were unable to sporulate in vitro when grown on minimal medium for extended periods. Deficiency in sporulation was correlated with the depletion of intracellular mannitol pools. Significantly sporulation could be restored with the addition of mannitol. Pathogenicity of the double mutant was not compromised, although, like the previously characterized mpd1 mutants, the strains were unable to sporulate in planta. These findings not only question the currently hypothesized pathways of mannitol metabolism, but also identify for the first time that mannitol is required for sporulation of a filamentous fungus.
Divertor interferometer diagnostic for ITER
Authors: Brower D. L. , Deng B. H. , Ding W. X.
Published: October 2006

In the harsh environment of the divertor region in ITER, plasmas spanning a huge density range from 1019to1022m−3 are anticipated making measurement of the electron density particularly challenging. For any reasonable wavelength choice, the total phase measured by a conventional two-color interferometer system is always ⪢2π and therefore subject to fringe counting errors. This problem can be remedied by adding a polarimeter capability whereby the Cotton-Mouton effect is measured or by employing differential interferometry. Using either approach, the total phase is always ⪡2π. The conceptual design of an interferometer system along with possible wavelength choices will be explored.
Signal processing techniques for lithium beam polarimetry on DIII-D
Authors: Thomas D. M. , Leonard A. W.
Published: October 2006

On the DIII-D tokamak the LIBEAM diagnostic provides precise measurements of the local magnetic field direction by combined polarimetry/ spectroscopy of the Zeeman-split 2S-2P lithium resonance line. Using these measurements we are able to determine the behavior of the edge toroidal current density jϕ(r), a parameter of critical interest for edge stability and performance. For a successful measurement, analysis of the polarization state of the spectrally filtered fluorescence must be done with high precision in the presence of nonideal filtering, beam intensity evolution, and dynamically varying background light. This is accomplished by polarization modulation of the collected emission, followed by digital demodulation at various harmonics of the modulation frequency. Either lock-in or fast Fourier transform techniques can be used to determine the various Stokes parameters and reconstruct the field directions based on accurate spatial and polarization efficiency calibrations. Details of the specific techniques used to analyze various DIII-D discharges are described, along with a discussion of the present limitations and some possible avenues towards improving the analysis.
“Sometimes a Community and Sometimes a Battlefield”: From the Comedic Public Sphere to the Commons of Speakers' Corner
Authors: Cooper Davina
Published: October 2006

Speakers' Corner in London is perceived as a space in which people speak freely without state interference; it is also popularly known as a place in which eccentrics and others, without access to mainstream media, orate. In this paper I explore Speakers' Corner as a discursive space, seeking to find a way through its polarised representations as a free space of serious and important deliberation and as a degraded trivial public sphere. I do so through the concept of the comedic public, which loosely draws upon Bakhtin's work on the carnival but also differs in significant ways. At the same time I argue that Speakers' Corner should not just be read or evaluated in terms of the public speech generated; the Corner is also a place in which communities form and strangers interact with others in counternormative ways. I argue that these social dimensions, often neglected, constitute an important aspect of the Corner's practice; they are also dimensions generated and incited by the Corner's discursive qualities. To illustrate this further I consider the expression of emotion, engagement in combative debate, and heckling as junctures through which social interactions arise. Finally, I suggest the social dimension to the Corner might productively be understood through the concept of the commons.
Embodied Geographies, Naturalised Boundaries, and Uncritical Geopolitics in La Frontière Invisible
Authors: Fall Juliet J
Published: October 2006

In this paper I explore embodiment and spatiality by discussing the example of a conflict between competing representations of landscapes and the female body in the two volumes of the comic books La Frontière Invisible. This piece of fiction deals specifically and explicitly with a reassessment of the gaze in the production of knowledge by examining maps as tools of power, control, and colonisation. However, despite an apparent desire to reject reactionary political approaches, the authors seem to associate the naturalised (female) body with (naturalised) geopolitical scenarios by fetishising the body through complex discursive transcodings between women and nature. In contrast to this, in this paper I suggest considering the body as a site and space of resistance to (political) imposition. Drawing on both feminist geography and critical geopolitics, I suggest an alternative way of considering the consequences of embodied geographies for cartography by examining the links between naturalised bodies and naturalised political boundaries. The main argument is that the body, by posing an uncontrollable, unpredictable threat to regular ways of producing cartographic knowledge, entails the possibility of a counterstrategic reinscription of spatial discourses and the creation of an alternative, more ethical cartography. This ethical cartography is rooted in embodied recalcitrance to imposed inscriptions associated with hegemonic positions.
A Place of Sense: A Kinaesthetic Ethnography of Cyclists on Mont Ventoux
Authors: Spinney Justin
Published: October 2006

In this paper I explore the notion that our movements in and through a place define our engagement with it and help to constitute it as a place. Concepts and concomitant interpretations of place as a ‘situated’ and contemplative experience have to date received much cultural geographical attention. In increasingly mobile societies, however, I argue that mobility should be central to the ways in which we conceptualise and understand the character and meanings of different spaces and places. Although geographical exploration has begun concerning the politics and power relations of the mobile subject, little attention has yet been paid to the experiences and spatialities generative of the body-subject in mobility. Whilst acknowledging the importance of representations in directing action, I strategically emphasise and explore the notion that we create meaning and belong in a place according to how we are in a place. Drawing upon ethnographic work with racing and touring cyclists in the United Kingdom and France, I consider how the conjoining of the person and bike and the resulting embodied rhythms and kinaesthetic sensations of the movement of cycling are constitutive of the character and meanings of particular places. Ultimately, in this paper I point to an understanding of the kinaesthetic and sensuous experiences of the hybrid subject–object (in this instance ‘the cyclist’) as fundamental in rethinking how people live, feel, and ultimately create meaningful spatial relations.
Structure–function relationships of the plant cuticle and cuticular waxes — a smart material?
Authors: Bargel Hendrik , Koch Kerstin , Cerman Zdenek , Neinhuis Christoph
Published: October 2006

The cuticle is the main interface between plants and their environment. It covers the epidermis of all aerial primary parts of plant organs as a continuous extracellular matrix. This hydrophobic natural composite consists mainly of the biopolymer, cutin, and cuticular lipids collectively called waxes, with a high degree of variability in composition and structure. The cuticle and cuticular waxes exhibit a multitude of functions that enable plant life in many different terrestrial habitats and play important roles in interfacial interactions. This review highlights structure–function relationships that are the subjects of current research activities. The surface waxes often form complex crystalline microstructures that originate from self-assembly processes. The concepts and results of the analysis of model structures and the influence of template effects are critically discussed. Recent investigations of surface waxes by electron and X-ray diffraction revealed that these could be assigned to three crystal symmetry classes, while the background layer is not amorphous, but has an orthorhombic order. In addition, advantages of the characterisation of formation of model wax types on a molecular scale are presented. Epicuticular wax crystals may cause extreme water repellency and, in addition, a striking self-cleaning property. The principles of wetting and up-to-date concepts of the transfer of plant surface properties to biomimetic technical applications are reviewed. Finally, biomechanical studies have demonstrated that the cuticle is a mechanically important structure, whose properties are dynamically modified by the plant in response to internal and external stimuli. Thus, the cuticle combines many aspects attributed to smart materials.
Dynamic susceptibility contrast-enhanced perfusion magnetic resonance (MR) imaging combined with contrast-enhanced MR imaging in the follow-up of immunogene-treated glioblastoma multiforme
Authors: Stenberg L. , Englund E. , Wirestam R. , Siesjö P. , Salford L. G. , Larsson E.-M.
Published: October 2006

Purpose: To assess the value of the combined use of dynamic susceptibility contrast-enhanced perfusion magnetic resonance imaging (MRI) and conventional contrast-enhanced MRI for the follow-up of treatment of glioblastoma multiforme (GBM).

Material and Methods: 79 examinations were performed in six surgically and immunogene-treated patients and two surgically treated patients. Ratios of the relative cerebral blood volume (rCBV) in lesions and in the contralateral normal-appearing white matter were calculated. The regions with elevated rCBV were compared with those with contrast enhancement. Tissue specimens from surgical biopsies and autopsies were studied histopathologically.

Results: The lesion-to-normal rCBV ratios were high in the tumors prior to operation (7.3 to 18.2) as well as in the recurrent tumors (1.6 to 13.2). The volumes of the regions with elevated rCBV were similar to those with contrast enhancement in 63 of the 79 examinations. However, in 11 of 79 examinations, the regions with high rCBV were smaller than the regions with contrast enhancement (“mismatch”). In two samples from the immunogene-treated patients this was correlated with the histopathological finding of malignant tumor with numerous proliferating GBM vessels with multiple minimal lumina, sometimes thrombotized or ruptured. These vessels may have increased permeability with contrast enhancement not accompanied by increased microvascular volume.

Conclusion: 1) Elevated rCBV on perfusion MRI corresponding to the contrast-enhancing lesion supports the diagnosis of recurrent malignant tumor. 2) A mismatch showing a volume of rCBV elevation smaller than that of contrast enhancement can be seen in particularly aggressive tumor growth and is thus not always a sign of reactive non-tumor changes. 3) The combination of perfusion MRI and conventional contrast MRI provides useful information in the follow-up of glioblastoma multiforme treatment.
Caudal regression syndrome with sacral rib: MRI features
Authors: Shah J. R. , Sainani N. , Patkar D. P.
Published: October 2006

Caudal regression syndrome (CRS) involves improper and incomplete development of distal spinal segments. Sacral rib is an unusual entity, where an accessory rib arises from the sacral vertebral segments. Very few cases have been described in the English literature. We present the case of a 3-year-old girl presenting with urinary and bowel incontinence and difficulties in walking with left-sided sacral rib, terminal cord syrinx, and caudal regression syndrome, involving sacrococcygeal segments, diagnosed on MRI. The association is not well illustrated in previous reports.
A prospective comparison of duplex ultrasonography, captopril renography, MRA, and CTA in assessing renal artery stenosis
Authors: Eklöf H. , Ahlström H. , Magnusson A. , Andersson L.-G. , Andrén B. , Hägg A. , Bergqvist D. , Nyman R.
Published: October 2006

Purpose: To prospectively compare the diagnostic accuracy of duplex ultrasonography, captopril renography, computed tomography angiography (CTA), and 3D Gd magnetic resonance angiography (MRA) in diagnosing hemodynamically significant renal artery stenosis (RAS).

Material and Methods: The standard of reference was measurement of transstenotic pressure gradient. Fifty-eight hypertensive patients with suspicion of RAS were evaluated, when possible, by all five techniques. Sensitivity and specificity to detect RAS were compared for each technique on both a patient and kidney basis. Discrepancies were evaluated separately and classified as borderline, method dependent, or operator dependent.

Results: The prevalence of RAS was 77%. The sensitivity/specificity of ultrasonography, captopril renography, CTA, and MRA in detecting kidneys with RAS was 73/71%, 52/63%, 94/62%, and 93/91%, respectively. Ultrasonography had a significantly lower sensitivity than CTA and MRA ( P<0.001) but higher than captopril renography ( P = 0.013). Borderline RAS was the main cause for discrepancies.

Conclusion: MRA and CTA were significantly better than duplex ultrasonography and captopril renography in detecting hemodynamically significant RAS. The ultrasonography criteria for RAS based on the evaluation of renal peak systolic velocity and renal/aortic ratio are questionable. Captopril renography cannot be recommended for assessing RAS.
Demystifying the Niger Delta conflict: Towards an integrated explanation
Authors: Idemudia Uwafiokun , Ite Uwem
                      E.
Published: October 2006

The conflict in the Niger Delta region in Nigeria has lasted for more than a decade, with little or no attempt at an analytical explanation. As a result, the situation has made effective conflict resolution difficult, and perpetuated the confusion of fiction over fact. This paper sets out to correct the shortcomings in existing literature by proffering an integrated explanation of various factors responsible for the conflict. The paper concludes that political and economic factors are the root causes of conflict in the Niger Delta, with environmental and social factors as the proximate and trigger causes, respectively. Given the nature of the relationship among the myriad factors responsible for the conflict, what is required is a comprehensive approach to conflict resolution that pursues development in the Niger Delta on the basis and principles of social, economic and environmental sustainability.