bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cysteine peptidases CPA and CPB are vital for autophagy and differentiation in Leishmania mexicana
Authors: Williams Roderick A. , Tetley Laurence , Mottram Jeremy C. , Coombs Graham H. 
Published: June 2006

SummaryIn the past, ultrastructural investigations of Leishmania mexicana amastigotes revealed structures that were tentatively identified as autophagosomes. This study has now provided definitive data that autophagy occurs in the parasite during differentiation both to metacyclic promastigotes and to amastigotes, autophagosomes being particularly numerous during metacyclic to amastigote form transformation. Moreover, the results demonstrate that inhibiting two major lysosomal cysteine peptidases (CPA and CPB) or removing their genes not only interferes with the autophagy pathway but also prevents metacyclogenesis and transformation to amastigotes, thus adding support to the hypothesis that autophagy is required for cell differentiation. The study suggests that L. mexicana CPA and CPB perform similar roles to the aspartic peptidase PEP4 and the serine peptidase PRB1 in Saccharomyces cerevisiae. The results also provide an explanation for why L. mexicana CPA/CPB‐deficient mutants transform to amastigotes very poorly and lack virulence in macrophages and mice.
Lethal fragmentation of bacterial chromosomes mediated by DNA gyrase and quinolones
Authors: Malik Muhammad , Zhao Xilin , Drlica Karl 
Published: June 2006

SummaryWhen DNA gyrase is trapped on bacterial chromosomes by quinolone antibacterials, reversible complexes form that contain DNA ends constrained by protein. Two subsequent processes lead to rapid cell death. One requires ongoing protein synthesis; the other does not. The prototype quinolone, nalidixic acid, kills wild‐type Escherichia coli only by the first pathway; fluoroquinolones kill by both. Both lethal processes correlated with irreversible chromosome fragmentation, detected by sedimentation and viscosity of DNA from quinolone‐treated cells. However, only fluoroquinolones fragmented purified nucleoids when incubated with gyrase purified from wild‐type cells. A GyrA amino acid substitution (A67S) expected to perturb a GyrA–GyrA dimer interface allowed nalidixic acid to fragment chromosomes and kill cells in the absence of protein synthesis; moreover, it made a non‐inducible lexA mutant hypersusceptible to nalidixic acid, a property restricted to fluoroquinolones with wild‐type cells. The GyrA variation also facilitated immunoprecipitation of DNA fragments by GyrA antiserum following nalidixic acid treatment of cells. The ability of changes in both gyrase and quinolone structure to enhance protein synthesis‐independent lethality and chromosome fragmentation is explained by drug‐mediated destabilization of gyrase–DNA complexes. Instability of type II topoisomerase–DNA complexes may be a general phenomenon that can be exploited to kill cells.
pH‐dependent pore‐forming activity of OmpATb from Mycobacterium tuberculosis and characterization of the channel by peptidic dissection
Authors: Molle Virginie , Saint Nathalie , Campagna Sylvie , Kremer Laurent , Lea Edward , Draper Philip , Molle Gérard 
Published: June 2006

SummaryMycobacteria are characterized by an unusual cell wall that controls nutrient and small hydrophilic compound permeability. Porin‐like proteins are necessary to ensure the transport of molecules into the cell. Here, we investigated the pore‐forming properties of OmpATb, a porin from Mycobacterium tuberculosis, in lipid bilayers. Multi‐channel experiments showed an asymmetric behaviour with channel closures at negative critical voltages (Vc) and a strong decrease in Vc at acidic pH. Single‐channel experiments gave conductance values of about 850 ± 80 pS in 1 M KCl and displayed a weak cationic selectivity in 4–8 pH range. The production and characterization of a series of truncated OmpATb proteins, showed that the central domain (OmpATb73−220) was sufficient to induce the ion channel properties of the native protein in lipid bilayers, i.e. asymmetric insertion, pH‐dependent voltage closure, cationic selectivity and similar conductance values in 1 M KCl. Western blot analysis suggests that the presence of OmpATb is only restricted to certain pathogenic species. Therefore, the propensity of channels of native OmpATb to close at low pH may represent an intrinsic property allowing pathogenic mycobacteria to adapt and survive to mildly acidic conditions, such as those encountered within the macrophage phagosome.
Interaction between two murein (peptidoglycan) synthases, PBP3 and PBP1B, in Escherichia coli
Authors: Bertsche Ute , Kast Thomas , Wolf Benoît , Fraipont Claudine , Aarsman Mirjam E. G. , Kannenberg Kai , Von Rechenberg Moritz , Nguyen‐Distèche Martine , Den Blaauwen Tanneke , Höltje Joachim‐Volker , Vollmer Waldemar 
Published: June 2006

SummaryThe murein (peptidoglycan) sacculus is an essential polymer embedded in the bacterial envelope. The Escherichia coli class B penicillin‐binding protein (PBP) 3 is a murein transpeptidase and essential for cell division. In an affinity chromatography experiment, the bifunctional transglycosylase‐transpeptidase murein synthase PBP1B was retained by PBP3‐sepharose when a membrane fraction of E. coli was applied. The direct protein–protein interaction between purified PBP3 and PBP1B was characterized in vitro by surface plasmon resonance. The interaction was confirmed in vivo employing two different methods: by a bacterial two‐hybrid system, and by cross‐linking/co‐immunoprecipitation. In the bacterial two‐hybrid system, a truncated PBP3 comprising the N‐terminal 56 amino acids interacted with PBP1B. Both synthases could be cross‐linked in vivo in wild‐type cells and in cells lacking FtsW or FtsN. PBP1B localized diffusely and in foci at the septation site and also at the side wall. Statistical analysis of the immunofluorescence signals revealed that the localization of PBP1B at the septation site depended on the physical presence of PBP3, but not on the activity of PBP3. These studies have demonstrated, for the first time, a direct interaction between a class B PBP (PBP3) and a class A PBP (PBP1B) in vitro and in vivo, indicating that different murein synthases might act in concert to enlarge the murein sacculus during cell division.
Southern GEMS groups – I. Dynamical properties
Authors: Brough Sarah , Forbes Duncan A. , Kilborn Virginia A. , Couch Warrick 
Published: June 2006

Abstract
Here, we present an investigation of the properties of 16 nearby galaxy groups and their constituent galaxies. The groups are selected from the Group Evolution Multiwavelength Study (GEMS) and all have X-ray as well as wide-field neutral hydrogen (H i) observations. Group membership is determined using a friends-of-friends algorithm on the positions and velocities from the 6-degree Field Galaxy Survey and NASA/IPAC Extragalactic Database. For each group we derive their physical properties using this membership, including: velocity dispersions (σv), virial masses (MV), total K-band luminosities [LK(Tot)] and early-type fractions (fearly) and present these data for the individual groups. We find that the GEMS X-ray luminosity is proportional to the group velocity dispersions and virial masses: LX(r500) ∝σ3.11±0.59v and LX(r500) ∝M1.13±0.27V, consistent with the predictions of self-similarity between group and clusters. We also find that MV∝LK(Tot)2.0±0.9, i.e. mass grows faster than light and that the fraction of early-type galaxies in the groups is correlated with the group X-ray luminosities and velocity dispersions. We examine the brightest group galaxies (BGGs), finding that, while the luminosity of the BGG correlates with its total group luminosity, the fraction of group luminosity contained in the BGG decreases with increasing total group luminosity. This suggests that BGGs grow by mergers at early times in group evolution while the group continues to grow by accreting infalling galaxies. We form a composite galaxy group in order to examine the properties of the constituent galaxies and compare their properties with those of field galaxies. There are clear radial trends, with group galaxies becoming fainter, bluer and morphologically later types with increasing radius from the group centre, reaching field levels at radii &gt;r500(&gt;0.7r200). We divide the composite group-by-group X-ray luminosity and find that galaxies in high X-ray luminosity groups [log10LX(r500) ≥ 41.7 erg s−1] are redder with a higher giant-to-dwarf ratio and are more likely to be early-type galaxies than are those galaxies in low X-ray luminosity groups. We conclude that harassment and ram-pressure stripping processes are unlikely to cause these differences. The differences are more likely to be due to galaxy–galaxy mergers and possibly some further mechanism such as strangulation. If mergers are the dominant mechanism then the properties of galaxies in the higher X-ray luminosity groups are a result of mergers at earlier epochs in smaller mass groups that have since merged to become the structures we observe today, while lower X-ray luminosity groups are still undergoing mergers today.
The role of NADPH oxidase and MAP kinase phosphatase in UV‐B‐dependent gene expression in Arabidopsis
Authors: KALBINA IRINA , STRID ÅKE 
Published: June 2006

ABSTRACTPlant responses to supplementary UV‐B irradiation have been reported to include formation of reactive oxygen species (ROS), hydrogen peroxide, in particular, and regulation by mitogen‐activated protein kinase (MAPK) cascades which in turn are fine‐tuned by MAPK phosphatases (MKPs). Here we present direct genetic evidence for the involvement of plasma membrane NADPH oxidase, a source of superoxide and hydrogen peroxide in the apoplasts, in UV‐B signalling in Arabidopsis thaliana, by analysis of gene expression of the UV‐B molecular markers in NADPH oxidase (atrbohD, F and DF) and MAP kinase phosphatase 1 (MKP1) knockout mutants (mkp1). Whereas the NADPH oxidase mutants were affected in UV‐B‐dependent CHS, PYROA and MEB5.2 gene expression, the mkp1 mutant was affected in the general expression pattern of the pathogenesis‐related (PR) and PDF1.2 genes. The results indicate involvement of MKP1 in repressive action on gene expression of more general stress response pathways, similar to those activated by pathogen attack, while NADPH oxidase is involved in quantitative (rather than absolute) regulation of more UV‐B‐specific genes. The expressions of the molecular markers in the knockout mutant mkp1 and in its complemented lines (lines 6 and 10) were similar, as opposed to the responses of the corresponding wild‐type Wassilewskija‐4 (Ws‐4). Lines 6 and 10 showed much higher MKP1 mRNA than Ws‐4 but did not complement the mutant. This suggests a complex dependency of the MAPK phosporylation level of the PR and PDF1.2 genes. Both NADPH oxidase mutants and the mkp1 mutant phenotypically responded to UV‐B by growth retardation.
Changes in C uptake in populations of Chlamydomonas reinhardtii selected at high CO2
Authors: COLLINS SINÉAD , SÜLTEMEYER DIETER , BELL GRAHAM 
Published: June 2006

ABSTRACTEstimates of the effect of increased global atmospheric CO2 levels on oceanic primary productivity depend on the physiological responses of contemporary phytoplankton populations. However, microalgal populations will possibly adapt to rising CO2 levels in such a way that they become genetically different from contemporary populations. The unknown properties of these future populations introduce an undefined error into predictions of C pool dynamics, especially the presence and size of the biological C pump. To address the bias in predictions introduced by evolution, we measured the kinetics of CO2 uptake in populations of Chlamydomonas reinhardtii that had been selected for growth at high CO2 for 1000 generations. Following selection at high CO2, the populations were unable to induce high‐affinity CO2 uptake, and one line had a lower rate of net CO2 uptake. We attribute this to conditionally neutral mutations in genes affecting the C concentrating mechanism (CCM). Lower affinity CO2 uptake, in addition to smaller population sizes, results in a significant reduction in net CO2 uptake of about 38% relative to contemporary populations under the same conditions. This shows how predictions about the properties of communities in the future can be influenced by the effect of natural selection.
Living on the edge: feeding of subtropical open ocean copepods
Authors: Paffenhöfer Gustav‐Adolf , Mazzocchi Maria Grazia , Tzeng Mimi W. 
Published: June 2006

AbstractThe objective of this study was to provide quantitative information on environmental feeding rates of warm water oceanic epipelagic copepods. We determined clearance rates at 23 °C for various particle size ranges in shipboard studies in the western oligotrophic subtropical Atlantic Ocean for females of the calanoid species Clausocalanus furcatus and Mecynocera clausii. These in situ clearance rates were then applied to the various particle size ranges of environmental particle spectra of auto‐ and heterotrophs at different depths from three stations in the western Atlantic. After calculating the metabolic demands of each of these two copepod species and applying an assimilation efficiency of 90%, we determined that C. furcatus meets its metabolic demands in all six cases, and M. clausii in two of six cases. Clausocalanus furcatus would also meet its energy demands at 25 °C, where it is often found, while M. clausii at 20 °C, where it is regularly found, would cover its metabolic needs in four of six cases. It is hypothesized that these species, and most likely most of the other co‐occurring copepod species, are limited in their abundance by food availability, or, better said, are ‘living on the edge’ in relation to food abundance.
Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika)
Authors: Schubert Carsten J. , Durisch‐Kaiser Edith , Wehrli Bernhard , Thamdrup Bo , Lam Phyllis , Kuypers Marcel M. M. 
Published: June 2006

SummaryHere we provide the first direct evidence for the anammox process (anaerobic ammonium oxidation) in a lacustrine system, Lake Tanganyika, the second largest lake in the world. Incubations with 15N labelled nitrate showed that anammox occurred in the suboxic water layer at 100–110 m water depth. Anammox rates up to 10 nM N2 h−1 are comparable to those reported for the marine water column. Up to ∼13% of produced N2 could be attributed to the anammox process whereas the remainder was related to denitrification. Typical lipid biomarkers characteristic of anammox bacteria were found in filtered water from the depths where anammox occurred, thus supporting the presence of anammox bacteria. Further evidence is provided by fluorescence in situ hybridization (FISH), revealing up to 13 000 anammox bacteria cells per ml or 1.4% of all DAPI (4′‐6‐Diamidino‐2‐phenylindole)‐stained cells. Phylogenetic analyses of partial 16S rRNA genes indicated the presence of sequences most closely related to the known anammox bacterium Candidatus‘Scalindua brodae’ (95.7% similarity). Using the incubation results, a total loss of 0.2 Tg N2 per year linked to anammox was estimated for the Northern basin of Lake Tanganyika.
Rate‐of‐return Parity in Experimental Asset Markets*
Authors: Childs Jason , Mestelman Stuart 
Published: June 2006

AbstractThis paper applies experimental methods to evaluate the completeness of arbitrage and rate‐of‐return parity in simultaneous asset markets in which the assets are denominated in different currencies. Two assets, which return uncertain, but known, dividends in each trading period, are traded over 20 periods, after which the asset has no value. Results indicate that risk‐neutral rate‐of‐return parity is a strong predictor of relative asset prices when assets have common expected dividends and the expected dividends have common variances. The predictive power of risk‐neutral rate‐of‐return parity is reduced as the assets become differentiated.
Misleading Inferences from Panel Unit Root Tests: a Comment
Authors: Ford George S. , Jackson John D. , Kline Audrey D. 
Published: June 2006

AbstractIn their 2001 paper, Breuer, McNown, and Wallace argue that panel unit root tests are flawed in that the “all or nothing nature of these procedures may lead to serious misinterpretations of tests applied to mixed panels” (2001, p. 483). The authors propose an alternative test, the SURADF test, which allows for and estimates heterogeneous rates of convergence. We show that SURADF test results are highly sensitive to the selection of panel members. As such, application of the SURADF test seems to require a sound basis for panel member selection and a caveat that all results are panel‐specific.
Food Protection for Sale*
Authors: Lopez Rigoberto A. , Matschke Xenia 
Published: June 2006

AbstractThis article tests the Protection for Sale (PFS) model using detailed data from US food‐processing industries under alternative import‐demand specifications. All empirical results support the PFS model predictions and previous empirical work qualitatively. However, a surprising result is that we obtain weights between 2.6 and 3.6 for domestic welfare using import slopes or elasticities derived from domestic demand and supply functions. In contrast, results based on directly specified import demands (including the Armington model) yield the usual, unrealistically large estimates for the domestic welfare weight. We contend that this empirical paradox arises mainly because the explanatory variables tend to be extremely large for industries with low import ratios and/or low import elasticities (or slopes) resulting from relatively volatile import prices. The results with derived import parameters point to a much stronger role of campaign contributions within the PFS model than previously found.
Foreign Direct Investment: Flows, Volatility, and the Impact on Growth*
Authors: Lensink Robert , Morrissey Oliver 
Published: June 2006

AbstractThis paper contributes to the literature on FDI and economic growth. We deviate from previous studies by introducing measures of the volatility of FDI inflows. As introduced into the model, these are predicted to have a negative effect on growth. We estimate the standard model using cross‐section, panel data, and instrumental variable techniques. Whilst all results are not entirely robust, there is a consistent finding that volatility of FDI has a negative impact on growth. The evidence for a positive effect of FDI levels on growth is not robust, nor is that for any effect of human capital.
Making Sense of the Comparative Advantage Gains from Trade: Comment on Batra
Authors: Bernhofen Daniel M. 
Published: June 2006

AbstractThis paper addresses Ravi Batra’s (2002) criticism of the basic comparative advantage gains‐from‐trade model. While Batra’s criticism is based on the selection view interpretation of real income, the gains from trade can only be properly understood from the options view interpretation of real income. I also show how a recent empirical implementation of the gains‐from‐trade model defies Batra’s claim that “the consumption gain . . . is not subject to measurement” (2002, p. 642).
Multiple promoter elements required for leukemia inhibitory factor‐stimulated M2 muscarinic acetylcholine receptor promoter activity
Authors: Laszlo George S. , Rosoff Marc L. , Amieux Paul S. , Nathanson Neil M. 
Published: June 2006

AbstractTreatment of neuronal cells with leukemia inhibitory factor (LIF) results in increased M2 muscarinic acetylcholine receptor promoter activity. We demonstrate here that multiple promoter elements mediate LIF stimulation of M2 gene transcription. We identify a LIF inducible element (LIE) in the M2 promoter with high homology to a cytokine‐inducible ACTG‐containing sequence in the vasoactive intestinal peptide promoter. Mutagenesis of both a STAT (signal transducers and activators of transcription) element and the LIE in the M2 promoter is required to attenuate stimulation of M2 promoter activity by LIF completely. Mobility shift assays indicate that a LIF‐stimulated complex binds to a 70 base pair M2 promoter fragment. Furthermore, a STAT element within this fragment can bind to LIF‐stimulated nuclear STAT1 homodimers in vitro. Mutagenesis experiments show that cytokine‐stimulated activation of M2 promoter activity requires tyrosine residues on glycoprotein 130 (gp130) that are also required for both STAT1 and STAT3 activation. Dominant negative STAT1 or STAT3 can block LIF‐stimulated M2 promoter activity. Real‐time RT‐PCR analysis indicates that LIF‐stimulated induction of M2 mRNA is partially dependent on protein synthesis. These results show that regulation of M2 gene transcription in neuronal cells by LIF occurs through a complex novel mechanism that is dependent on LIE, STAT and de novo protein synthesis.
Trichomonas gallinae in wintering Common Wood Pigeons Columba palumbus in Spain
Authors: VILLANÚA DIEGO , HÖFLE URSULA , PÉREZ‐RODRÍGUEZ LORENZO , GORTÁZAR CHRISTIAN 
Published: June 2006

We studied the prevalence and potential subclinical effects of infestation by Trichomonas gallinae in 91 hunter‐harvested Common Wood Pigeons Columba palumbus from northern (n = 30) and southern (n = 61) Spain during the winter period. All animals were measured, sexed, aged, necropsied and their organs were weighed. Infestation with T. gallinae was diagnosed using three different methods: direct inspection for the presence of lesions, direct microscopic observation and culture. Of the sampled birds, 34.2% were positive for the presence of T. gallinae. Prevalence was significantly higher in adult Wood Pigeons than in the juvenile group, and prevalence was significantly lower in birds sampled from the north. No significant differences in prevalence were found between males and females. Culture was significantly more sensitive than the other methods of diagnosis. Parasitized birds were in poorer body condition, as revealed by their lower body mass and fat reserves. No significant variation could be detected in heart or spleen weight between parasitized and healthy birds. However, juvenile Wood Pigeons in which T. gallinae was detected had a significantly larger bursa of Fabricius. Variations in the prevalence of T. gallinae in Wood Pigeons could be related to migration as well as increased exposure through shared feed and water where these are artificially provided. We also discuss the potential effect of T. gallinae on body condition and the eventual risk for endangered predators through increased exposure to infected prey.