bluuebunny/crossref_metadata_2025 huggingface dataset:
Complete and variant forms of the ‘gonococcal genetic island’ in Neisseria meningitidis
Authors: Snyder Lori A. S. , Jarvis Stephen A. , Saunders Nigel J.
Published: December 2005

Comparative genome hybridization using the pan-Neisseriamicroarray identified genes from the gonococcal genetic island (GGI) withinNeisseria meningitidisstrains of serogroups W-135, H, and Z. While some of these strains contain nearly all of the genes of the GGI, there are differences in the presence of some of these genes between the strains, including between those of the same serogroup. Attempts were then made to determine the location of the GGI in these meningococci. Sequencing ofNeisseria gonorrhoeaestrain MS11 revealed that the GGI is a conjugative plasmid that can be chromosomally integrated at thedifsites nearungand can also be present in its circularized form. InN. meningitidis, adifsite is present in this location and also serves as the point of chromosomal integration of the GGI in this species.
Human hololactoferrin: endocytosis and use as an iron source by the parasite Entamoeba histolytica
Authors: León-Sicairos Nidia , Reyes-López Magda , Canizalez-Román Adrián , Bermúdez-Cruz Rosa María , Serrano-Luna Jesús , Arroyo Rossana , de la Garza Mireya
Published: December 2005

Entamoeba histolytica is an enteric protozoan that exclusively infects human beings. This parasite requires iron for its metabolic functions. Lactoferrin is a mammalian glycoprotein that chelates extracellular iron on mucosal surfaces, including the surface of the large intestine, where E. histolytica initiates infection. This work examined the interaction in vitro of E. histolytica trophozoites with human hololactoferrin (iron-saturated lactoferrin). A minimum concentration of 50 μM Fe from hololactoferrin supported growth of the amoeba. Amoebic binding sites for hololactoferrin were different from those for human apolactoferrin, holotransferrin and haemoglobin. One amoebic hololactoferrrin-binding polypeptide of 90 kDa was found, which was not observed after treatment of trophozoites with trypsin. Hololactoferrin-binding-protein levels increased in amoebas starved of iron, or grown in hololactoferrin. Internalization of hololactoferrin was inhibited by filipin. Endocytosed hololactoferrin colocalized with an anti-chick embryo caveolin mAb in amoebic vesicles, and lactoferrin was further detected in acidic vesicles; amoebic caveolin of 22 kDa was detected by Western blotting using this antibody. Cysteine proteases from amoebic extracts were able to cleave hololactoferrin. Together, these data indicate that E. histolytica trophozoites bind to hololactoferrin through specific membrane lactoferrin-binding proteins. This ferric protein might be internalized via caveolae-like microdomains, then used as an iron source, and degraded.
Identification of Salmonella gallinarum virulence genes in a chicken infection model using PCR-based signature-tagged mutagenesis
Authors: Shah Devendra H. , Lee Mi-jin , Park Jin-ho , Lee John-hwa , Eo Seong-kug , Kwon Jung-thek , Chae Joon-seok
Published: December 2005

Salmonella gallinarum (SG) is a non-motile host-adapted salmonella that causes fowl typhoid, a severe systemic disease responsible for significant economic losses to the poultry industry worldwide. This study describes the application of a PCR-based signature-tagged mutagenesis system to identify in vivo-essential genes of SG. Ninety-six pools representing 1152 SG mutants were screened in a natural-host chicken infection model. Twenty presumptive attenuated mutants were identified and examined further. The identity of the disrupted gene in each mutant was determined by cloning of the DNA sequences adjacent to the transposon, followed by sequencing and comparison with the bacterial genome database. In vitro and in vivo competition indices were determined for each identified mutant and a total of 18 unique, attenuating gene disruptions were identified. These mutations represented six broad genomic classes: Salmonella pathogenicity island-1 (SPI-1), SPI-2, SPI-10, SPI-13, SPI-14 and non-SPI-encoded virulence genes. SPI-13 and SPI-14 are newly identified and designated in this study. Most of the genes identified in this study were not previously believed or known to play a role in the pathogenesis of SG infection in chickens. Each STM identified mutant showed competitiveness and/or virulence defects, confirmed by in vitro and in vivo assays, and challenge tests. This study should contribute to a better understanding of the pathogenic mechanisms involved in progression of disease caused by SG, and identification of novel live vaccine candidates and new potential antibiotic targets.
In vivo cycling of the Escherichia coli transcription factor FNR between active and inactive states
Authors: Dibden David P. , Green Jeffrey
Published: December 2005

FNR proteins are transcription regulators that sense changes in oxygen availability via assembly–disassembly of [4Fe–4S] clusters. The Escherichia coli FNR protein is present in bacteria grown under aerobic and anaerobic conditions. Under aerobic conditions, FNR is isolated as an inactive monomeric apoprotein, whereas under anaerobic conditions, FNR is present as an active dimeric holoprotein containing one [4Fe–4S] cluster per subunit. It has been suggested that the active and inactive forms of FNR are interconverted in vivo, or that iron–sulphur clusters are mostly incorporated into newly synthesized FNR. Here, experiments using a thermo-inducible fnr expression plasmid showed that a model FNR-dependent promoter is activated under anaerobic conditions by FNR that was synthesized under aerobic conditions. Immunoblots suggested that FNR was more prone to degradation under aerobic compared with anaerobic conditions, and that the ClpXP protease contributes to this degradation. Nevertheless, FNR was sufficiently long lived (half-life under aerobic conditions, ∼45 min) to allow cycling between active and inactive forms. Measuring the abundance of the FNR-activated dms transcript when chloramphenicol-treated cultures were switched between aerobic and anaerobic conditions showed that it increased when cultures were switched to anaerobic conditions, and decreased when aerobic conditions were restored. In contrast, measurement of the abundance of the FNR-repressed ndh transcript under the same conditions showed that it decreased upon switching to anaerobic conditions, and then increased when aerobic conditions were restored. The abundance of the FNR- and oxygen-independent tatE transcript was unaffected by changes in oxygen availability. Thus, the simplest explanation for the observations reported here is that the FNR protein can be switched between inactive and active forms in vivo in the absence of de novo protein synthesis.
Pseudomonas aeruginosa PAO1 genes for 3-guanidinopropionate and 4-guanidinobutyrate utilization may be derived from a common ancestor
Authors: Nakada Yuji , Itoh Yoshifumi
Published: December 2005

Pseudomonas aeruginosaPAO1 utilizes 3-guanidinopropionate (3-GP) and 4-guanidinobutyrate (4-GB), which differ in one methylene group only, via distinct enzymes: guanidinopropionase (EC 3.5.3.17; thegpuAproduct) and guanidinobutyrase (EC 3.5.3.7; thegbuAproduct). The authors cloned and characterized the contiguousgpuPARgenes (in that order) responsible for 3-GP utilization, and compared the deduced sequences of their putative protein products, and the potential regulatory mechanisms ofgpuPA, with those of the correspondinggbugenes encoding the 4-GB catabolic system. GpuA and GpuR have similarity to GbuA (49 % identity) and GbuR (a transcription activator ofgbuA; 37 % identity), respectively. GpuP resembles PA1418 (58 % identity), which is a putative membrane protein encoded by a potential gene downstream ofgbuA. These features of the GpuR and GpuP sequences, and the impaired growth ofgpuRandgpuPknockout mutants on 3-GP, support the notion that GpuR and GpuP direct the 3-GP-inducible expression ofgpuA, and the uptake of 3-GP, respectively. Northern blots of mRNA from 3-GP-induced PAO1 cells revealed three transcripts ofgpuA,gpuP, andgpuPandgpuAtogether, suggesting thatgpuPandgpuAeach have a 3-GP-responsible promoter, and that some transcription from thegpuPpromoter is terminated aftergpuP, or proceeds intogpuA. Knockout ofgpuRabolished 3-GP-dependent synthesis of the transcripts, confirming that GpuR activates transcription from these promoters, with 3-GP as a specific co-inducer. The sequence conservation between the three functional pairs of the Gpu and Gbu proteins, and the absence ofgpuAPRin closely related species, imply that the triadgpugenes have co-ordinately evolved from origins common to thegbucounterparts, to establish an independent catabolic system of 3-GP inP. aeruginosa.
Medium- to large-sized xylo-oligosaccharides are responsible for xylanase induction in Prevotella bryantii B14
Authors: Miyazaki Kohji , Hirase Tatsuaki , Kojima Yoichi , Flint Harry James
Published: December 2005

Experiments were done to define the nature of the xylan-derived induction signal for xylanase activity, and evaluate which xylanase genes among the three known ones (xynA,xynBandxynC) are induced by the presence of xylan inPrevotella bryantiiB14. During the later stages of exponential growth on glucose, addition of 0·05 % water-soluble xylan (WS-X) stimulated xylanase formation within 30 min. Xylose, xylobiose, xylotriose, xylotetraose, xylopentaose, arabinose and glucuronic acid all failed to induce the xylanase activity. An acid-ethanol-soluble fraction of WS-X (approximate degree of polymerization 30) enhanced the activity significantly, whereas the acid-ethanol-insoluble fraction had no effect, unless first digested by the clonedP. bryantiiXynC xylanase. These results indicate that medium- to large-sized xylo-oligosaccharides are responsible for induction. The transcription of all three known xylanase genes fromP. bryantiiwas upregulated coordinately by addition of WS-X. There have been relatively few investigations into the regulation of xylanase activity in bacteria, and it appears to be unique that medium- to large-sized xylo-oligosaccharides are responsible for induction.
Glycogen production by different Salmonella enterica serotypes: contribution of functional glgC to virulence, intestinal colonization and environmental survival
Authors: McMeechan Alisdair , Lovell Margaret A. , Cogan Tristan A. , Marston Kerrie L. , Humphrey Tom J. , Barrow Paul A.
Published: December 2005

In enteric bacteria, the contribution of endogenous energy sources to survival both inside and outside the host is poorly understood. The contribution of glycogen production to the virulence, colonization and environmental survival of differentSalmonella entericaserotypes was assessed. Of 19 serotypes (339 strains) tested for glycogen production, 17 (256 strains) were positive. The avian-specific serovarsS. Gallinarum (62 strains) andS. Pullorum (21 strains) did not produce glycogen. The sequence ofglgCin threeS. Gallinarum strains tested revealed an identical deletion of 11 consecutive bases, which was not present inS. Pullorum, and a CCC insertion after position 597. Transduction ofS. Gallinarum andS. Pullorum to a glycogen-positive phenotype did not change the ability to colonize the intestine or affect virulence in the chicken. Mortality rates in chickens following oral infection with aS. Typhimurium glycogen mutant (glgC : : km) were not significantly reduced, although colonization of the intestine was reduced over the first 4 weeks of the trial. Growth and yield of theglgC : : km mutant were comparable to the parent. TheglgCmutant survived less well in faeces and in water at 4 °C when the strain was grown in LB broth containing 0·5 % glucose, and in saline it died off more rapidly after 7 days. The data suggest that glycogen has a complex but comparatively minor role in virulence and colonization, but a more significant role in survival.
Mutational analysis of the C-terminal domain of the Rhodobacter sphaeroides response regulator PrrA
Authors: Jones Denise F. , Stenzel Rachelle A. , Donohue Timothy J.
Published: December 2005

TheRhodobacter sphaeroidesresponse regulator PrrA directly activates transcription of genes necessary for energy conservation at low O2tensions and under anaerobic conditions. It is proposed that PrrA homologues contain a C-terminal DNA-binding domain (PrrA-CTD) that lacks significant amino acid sequence similarity to those found in other response regulators. To test this hypothesis, single amino acid substitutions were created at 12 residues in the PrrA-CTD. These mutant PrrA proteins were purified and tested for the ability to be phosphorylated by the low-molecular-mass phosphate donor acetyl phosphate, to activate transcription and to bind promoter DNA. Each mutant PrrA protein accepted phosphate from32P-labelled acetyl phosphate. At micromolar concentrations of acetyl phosphate-treated wild-type PrrA, a single 20 bp region in the PrrA-dependentcycAP2 promoter was protected from DNase I digestion. Of the mutant PrrA proteins tested, only acetyl phosphate-treated PrrA-N168A and PrrA-I177A protectedcycAP2 from DNase I digestion at similar protein concentrations compared to wild-type PrrA. The use ofin vitrotranscription assays with the PrrA-dependentcycAP2 andpucpromoters showed that acetyl phosphate-treated PrrA-N168A produced transcript levels similar to that of wild-type PrrA at comparable protein concentrations. Using concentrations of acetyl phosphate-treated PrrA that are saturating for the wild-type protein, PrrA-H170A and PrrA-I177A produced <45 % as much transcript as wild-type PrrA. Under identical conditions, the remaining mutant PrrA proteins produced little or no detectable transcripts from either promoterin vitro. Explanations are presented for why these amino acid side chains in the PrrA-CTD are important for its ability to activate transcription.
Unravelling the multiple effects of lactic acid stress on Lactobacillus plantarum by transcription profiling
Authors: Pieterse Bart , Leer Rob J. , Schuren Frank H. J. , van der Werf Mariët J.
Published: December 2005

The organic acid lactate is the predominant fermentation product of Lactobacillus plantarum. The undissociated form of this organic acid is a strong growth inhibitor for the organism. Different theories have been postulated to explain the inhibitory effects of lactic acid: (i) toxicity arising from the dissipation of the membrane potential, (ii) acidification of the cytosol, or (iii) intracellular anion accumulation. In general, organic acid stresses are complex to study, since their toxicity is highly dependent on their degree of dissociation and thus on the pH. In this study, transcription profiles of L. plantarum grown in steady-state cultures that varied in lactate/lactic acid concentration, pH, osmolarity and absolute and relative growth rate, were compared by microarray analysis. By doing so, the differential expression of multiple groups of genes could specifically be attributed to the different aspects of lactic acid stress. A highly coherent group of lactic acid-responsive, cell surface protein-encoding genes was identified, to which no function has previously been assigned. Moreover, a group of genes that showed increased expression in response to the combination of lactic acid and a lower growth rate is expected to be involved in the formation of the alternative fermentation end-products malate, acetate and ethanol. One of these pathways is the phosphoketolase by-pass that is typical for bifidobacteria.
The manganese-responsive repressor Mur of Rhizobium leguminosarum is a member of the Fur-superfamily that recognizes an unusual operator sequence
Authors: Díaz-Mireles Edit , Wexler Margaret , Todd Jonathan D. , Bellini Dominico , Johnston Andrew W. B. , Sawers R. Gary
Published: December 2005

The manganese uptake regulator Mur of Rhizobium leguminosarum is a close homologue of the global iron regulatory protein Fur. Mur represses the sitABCD operon, which encodes a Mn2+ transport system, specifically in response to Mn2+ but not Fe2+. In previous work the authors mapped the 5′ ends of two sit operon transcripts, termed TS1 and TS2, which were co-ordinately regulated by Mn2+-Mur, but this paper now shows that only TS1 is a primary transcript. DNase I protection analyses showed that purified Mur bound, with similar affinity, to two sites in the regulatory region of sitABCD, but only when Mn2+ was present in the reaction buffer. These Mn2+-Mur-binding sites, termed MRS1 and MRS2 (Mur-responsive sequence), were closely related in sequence to each other and were separated by 16 bp, spanning the transcription initiation site TS1. The extent of the protected DNA was 34 and 31 bp for MRS1 and MRS2, respectively, which is in accord with other members of the Fur family. The DNA sequences recognized by Mn2+-Mur are wholly different from conventional Fur boxes, but some similarities to a recognition sequence for the Fur regulator from Bradyrhizobium japonicum were noted. Transcription analysis of the R. leguminosarum mur gene showed its expression to be independent of Mn2+-Mur. Thus, Mur is a sequence-specific DNA-binding protein that responds in vitro to manganese, and thus can occlude RNA polymerase access to the sitABCD promoter. Moreover, Mur recognizes a DNA sequence atypical for the Fur superfamily and, like Fur from B. japonicum, defines a new subclass of Fur-like transcriptional regulators.
Differential expression of S100A2 and S100A4 in lung adenocarcinomas: Clinicopathological significance, relationship to p53 and identification of their target genes
Authors: Matsubara Daisuke , Niki Toshiro , Ishikawa Shumpei , Goto Akiteru , Ohara Etsuko , Yokomizo Takehiko , Heizmann Claus W. , Aburatani Hiroyuki , Moriyama Sachiko , Moriyama Hirokazu , Nishimura Yoshihiro , Funata Nobuaki , Fukayama Masashi
Published: December 2005

Previous studies suggest that some S100 proteins are involved in the progression of certain types of cancer. However, no comprehensive data is currently available on the expression of S100 family genes in lung adenocarcinomas. Oligonucleotide array, quantitative reverse transcription–polymerase chain reaction and western blot analyses of lung adenocarcinoma cell lines and bronchiolar epithelial cells (SAEC and NHBE) revealed that S100A2 and S100A4 were the most strikingly downregulated and upregulated members of the S100 family, respectively. Immunohistochemical analyses of 94 primary lung adenocarcinomas showed that positive S100A2 expression (33/94, 35.1%) was significantly associated with lymphatic invasion (P = 0.0233) and positive S100A4 expression (19/94, 20.2%) with vascular invasion (P = 0.0454). Interestingly, a strong inverse relationship was found between S100A4 and p53 expression (P = 0.0008). Survival analyses showed that S100A4 positivity was associated with poor patient prognosis (P = 0.042). S100A2 positivity was not associated with patient survival when the whole patient group was analyzed; however, S100A2 positivity was a favorable prognostic indicator in patients with p53‐negative tumors (P = 0.0448). Finally, we used oligonucleotide array analyses and identified potential S100A2 and S100A4 target genes involved in cancer progression: S100A2 induced RUNX3 and REPRIMO; S100A4 induced EZRIN, RUNX1 and WISP1; S100A2 repressed EGFR, NFKB2 and RELA2; and S100A4 repressed ANXA10 and IL1RN. Thus, the present study demonstrates involvement of S100A2 and S100A4 in the progression of lung adenocarcinomas and an inverse association between S100A4 and p53 expression, and provides a list of targets regulated by S100A2 and S100A4. (Cancer Sci 2005; 96: 844–857)
Helicobacter pylori infection appears essential for stomach carcinogenesis: Observations in Semarang, Indonesia
Authors: Tokudome Shinkan , Samsuria Witjitra D. , Soeripto  , Triningsih F. X. Ediati , Suzuki Sadao , Hosono Akihiro , Triono Teguh , Wijaya Indra , Sarjadi  , Miranti Ika P. , Ghadimi Reza , Moore Malcolm A.
Published: December 2005

The gastric cancer incidence in Semarang, Indonesia, is exceedingly low: only approximately 1/100th of the level in Japan. To elucidate the reason, we carried out an ecological study recruiting 69 male and 102 female participants from the general populace in January 2005. Positive urea breath tests were 0% for both men and women, and Helicobacter pylori (H. pylori) IgG antibodies were found in 2% (0–5, 95% confidence interval) of men and 2% (0–4) of women, significantly lower than the 62% (58–65) and 57% (53–60), respectively, in Japan. Furthermore, there were no positive findings with the pepsinogen tests in Semarang, again significant in comparison with the 23% (22–25) and 22% (20–23) in Japan. Variation in smoking levels and consumption of NaCl, vegetables and fruit were found, but not to an extent that would allow explanation of the major differences in gastric cancer incidence. We may conclude that the very low prevalence of H. pylori infection and thus chronic atrophic gastritis account for the rarity of stomach cancer in Semarang, Indonesia. (Cancer Sci 2005; 96: 873–875)
Heat shock protein 90 inhibitor 17‐allylamino‐17‐demethoxygeldanamycin potentiates the radiation response of tumor cells grown as monolayer cultures and spheroids by inducing apoptosis
Authors: Machida Hikaru , Nakajima Syuichi , Shikano Naoto , Nishio Junko , Okada Shinobu , Asayama Munehiko , Shirai Makoto , Kubota Nobuo
Published: December 2005

Activation of the PI3K‐Akt pathway is known to induce tumor radioresistance. In the current study, we examined the ability of 17AAG, which decreases the levels of Hsp90 client proteins including components of the PI3K‐Akt pathway, to sensitize radioresistant human squamous cell carcinoma cells to X‐irradiation. Human squamous cell carcinoma cell lines (SQ20B, SCC61 and SCC13) were incubated for 16 h at 37°C in medium containing 17AAG. Radiation sensitivity was determined by clonogenic assays, and protein levels were examined by western blotting. Apoptosis was determined in monolayer cells by AO/EB double staining and in spheroids using the TdT‐mediated dUTP nick end labeling assay. 17AAG (0.2 µM) enhanced the radiosensitivity more effectively in radioresistant SQ20B and SCC13 cells than in radiosensitive SCC61 cells. However, in all three cell lines, 17AAG increased radiation‐induced apoptosis by reducing the expression of EGFR and ErbB‐2 and inhibiting the phosphorylation of Akt. Furthermore, 17AAG (1 µM) sensitized SQ20B spheroids to radiation, and inhibition of Akt activation by 17AAG increased radiation‐induced apoptosis in spheroids. The findings suggest that 17AAG effectively sensitizes radioresistant cells to radiation by inhibiting the PI3K‐Akt pathway. Targeting the PI3K‐Akt pathway with 17AAG could be a useful strategy for radiosensitization of carcinomas. (Cancer Sci 2005; 96: 911–917)
Empirical antifungal therapy in patients with neutropenia and persistent or recurrent fever of unknown origin
Authors: Martino Rodrigo , Viscoli Claudio
Published: December 2005

Persistent or recurrent fever of unexplained origin (PFUO) in neutropenic patients receiving antibiotic therapy is commonly treated with empirical antifungal therapy (EAFT). EAFT was established as an adequate management of PFUO around 20 years ago with conventional amphotericin B deoxycholate (c‐AmB), despite its high rate of infusional and systemic toxicities. In recent years, EAFT trials for PFUO have used less toxic agents, such as the lipid formulations of AmB, the new azoles, and the echinocandin, caspofungin. In clinical trials, the lipid formulations of AmB [especially liposomal AmB (L‐AmB)] provided similar efficacy with lower toxicity but at a much higher cost. Although rarely used in clinical practice, fluconazole is equivalent to c‐AmB, provided patients at high risk of Aspergillus infections are excluded. Intravenous itraconazole was shown to be equivalent to c‐AmB, with a lower toxicity. Voriconazole did not meet non‐inferiority criteria when compared with L‐AmB. Caspofungin was shown to be non‐inferior to L‐AmB and more effective in treating baseline invasive fungal infections. To date, alternatives to AmB have shown less toxicity, but improved efficacy is less clear. This is probably because of the weakness of the indication and to the consequent difficulty in establishing objective and reproducible endpoints for comparisons. The new challenge for physicians in this field is probably presumptive antifungal therapy, an approach based on patient risk‐group stratification for developing invasive candidiasis or aspergillosis and/or the use of new diagnostic techniques to identify patients at a very early stage of infection.
Flooding, soil seed bank dynamics and vegetation resilience of a hydrologically variable desert floodplain
Authors: CAPON SAMANTHA J. , BROCK MARGARET A.
Published: December 2005

1. This paper explores soil seed bank composition and its contribution to the vegetation dynamics of a hydrologically variable desert floodplain in central Australia: the Cooper Creek floodplain. We investigated patterns in soil seed bank composition both temporally, in response to flooding (and drying), and spatially, with relation to flood frequency. Correlations between extant vegetation and soil seed bank composition are explored with respect to flooding.

2. A large and diverse germinable soil seed bank was detected comprising predominantly annual monocot and annual forb species. Soil seed bank composition did not change significantly in response to a major flood event but some spatial patterns were detected along a broad flood frequency gradient. Soil seed bank samples from frequently flooded sites had higher total germinable seed abundance and a greater abundance of annual monocots than less frequently flooded sites. In contrast, germinable seeds of perennial species belonging to the Poaceae family were most abundant in soil seed bank samples from rarely flooded sites.

3. Similarity between the composition of the soil seed bank and extant vegetation increased following flooding and was greatest in more frequently flooded areas of the floodplain, reflecting the establishment of annual species. The results indicate that persistent soil seed banks enable vegetation in this arid floodplain to respond to unpredictable patterns of flooding and drying.
Dispersal of plant fragments in small streams
Authors: RIIS TENNA , SAND‐JENSEN KAJ
Published: December 2005

1. Streams are subject to frequent natural and anthropogenic disturbances that cause sediment erosion and loss of submerged vegetation. This loss makes downstream transport and retention of vegetative propagules on the streambed very important for re‐establishing vegetation cover. We measured dispersal and retention of macrophyte stem fragments (15–20 cm long) along 300 m long reaches of four small to medium sized Danish lowland streams.

2. The number of drifting stem fragments declined exponentially with distance below the point of release. This finding makes the retention coefficient (k, m−1) in the exponential equation a suitable measure for comparisons among different macrophyte species, and between stream reaches of different hydrology and vegetation cover.

3. Buoyancy of macrophyte tissue influenced retention.Elodea canadensisstems drifted below the water surface, and were more inclined to be retained in deeper water associated with submerged plants and obstacles in the streambed.Ranunculus peltatusstems were more buoyant, drifted at the water surface, and were more inclined to be trapped in shallow water and in riparian vegetation.

4. The retention coefficient of drifting stems increased with the relative contact between the flowing water and streambed, bank and vegetation. Thus, the retention coefficients were highest (0.02–0.12 m−1) in shallow reaches with a narrow, vegetation‐free flow channel. Here there were no significant differences betweenE. canadensisandR. peltatus. Retention coefficients were lowest (0.0005–0.0135 m−1) in deeper reaches with wider vegetation‐free flow channels. Retention ofE. canadensiswas up to 16 times more likely than retention ofR. peltatus.

5. Overall, the longitudinal position in the stream system of source populations of species capable of producing numerous stems, the species‐specific retention coefficients of stems, and the retention capacity of stream reaches should be important for species distribution in perturbed stream systems. Retention of stems is probably constrained in headwaters by the small downstream flux of stem fragments because of the restricted source area, and constrained in downstream reaches by small retention coefficients. Macrophyte retention may, consequently, peak in medium‐sized streams.
Accounting for velocity anisotropy in seismic traveltime tomography: a case study from the investigation of the foundations of a Byzantine monumental building
Authors: Polymenakos L. , Tweeton D. , Papamarinopoulos S.
Published: December 2005

We estimate velocity anisotropy factors from seismic traveltime tomographic data and apply a correction for anisotropy in the inversion procedure to test possible improvements on the traveltime fit and the quality of the resulting tomographic images. We applied the anisotropy correction on a traveltime data set obtained from the investigation of the foundation structure of a monumental building: a Byzantine church from the 11th century AD, in Athens, Greece.

Vertical transverse isotropy is represented by one axis of symmetry and one anisotropy magnitude for the entire tomographic inversion grid. We choose the vertical direction for the symmetry axis by analysing the available data set and taking into account information on the character of the foundations of the church from the literature and past excavations. The anisotropy magnitude is determined by testing a series of values of anisotropy and examining their effect on the tomographic inversion results. The best traveltime fit and image quality are obtained with an anisotropy value (Vmax/Vmin) of 1.6, restricted to the high velocity structures in the subsurface. We believe that this anisotropy value, which is significantly higher than the usual values reported for near‐surface geological material, is related to the fabric of the church foundations, due to the shape of the individual stone blocks and the layout of the stonework.

Inversion results obtained with the correction for anisotropy indicate that both the traveltime fit and the image quality are improved, providing an enhanced reconstruction of the velocity field, especially for the high‐velocity features. Based on this enhanced and more reliable reconstruction of velocity distribution, an improved image of the subsurface material character was made possible. In particular, the pattern and state of the church foundations and possible weak ground material areas were revealed more clearly. This improved subsurface knowledge may assist in a better design of restoration measures for monumental buildings such as Byzantine churches.
Seismic monitoring of pressure depletion evaluated for a United Kingdom continental‐shelf gas reservoir
Authors: MacBeth Colin , Stammeijer Jan , Omerod Mark
Published: December 2005

The possibility of using 4D seismic data for monitoring pressure depletion in the low‐porosity, tight gas‐bearing Rotliegende sandstones of the UK Southern Gas Basin is investigated. The focus here is on whether fractures in the upper part of the reservoir, known to enhance productivity, can also enhance the time‐lapse seismic response. The study uses laboratory data to evaluate core‐plug stress sensitivity, published data for the stress behaviour of the fractures, followed by petro‐elastic and 4D seismic modelling of both the fractured and unfractured formation. The magnitude of the resultant 4D signatures suggests that production‐induced changes in the unfractured sands are unlikely to be observed except perhaps with highly repeatable time‐lapse surveys. On the other hand, the presence of fractures could render production effects visible in dedicated 4D acquisition or prestack parallel processed data. If present however, the signature will be sporadic, as fractures in the area are known to exist in clusters. The 4D signature may be enhanced further by certain classes of vertical geological variability and also areas of high reservoir pressure. The strongest evidence of depletion is expected to be time‐shifts seen at the base of the Rotliegende reservoir.
Mature monocyte‐derived dendritic cells respond more strongly to CCL19 than to CXCL12: consequences for directional migration
Authors: Humrich Jens Y. , Humrich Jan H. , Averbeck Marco , Thumann Peter , Termeer Christian , Kämpgen Eckhart , Schuler Gerold , Jenne Lars
Published: December 2005

The chemokine receptor CCR7 is crucial for migration of mature dendritic cells (DC) directed toward secondary lymphoid organs; however, there is little knowledge about the function of the homeostatic chemokine receptor CXCR4 in DC and its contribution to directional migration of DC during inflammation. By comparing the impact of chemokine receptor engagement on mature DC we found that the CCR7 ligand CCL19 holds a stronger chemotactic potency than the CXCR4 ligand CXCL12. Moreover, CCL19 elicited rapid, steep and long‐lasting mobilization of intracellular calcium in individual cells and induced intense phosphorylation of extracellular signal‐regulated kinase 1/2 and protein kinase B, while the intracellular signals elicited by CXCL12 were in part distinct and significantly weaker. Analysis of chemokine receptor expression revealed that although CCR7 and CXCR4 were expressed by a similar percentage of DC, the mean fluorescence intensity of CCR7 was up to six times higher, suggesting a higher receptor density. Based on these correlations we propose that the type of chemokine signal in conjunction with the expression and functional activity of the respective chemokine receptor is also determining the migration rate and potency of a chemotactic response in mature DC. In conclusion, our data support the fundamental role of CCR7 for rapidly guiding DC toward secondary lymphoid organs at an extra‐ and intracellular molecular level and on the contrary render CXCR4 a weaker contributor to directional migration of DC during inflammation.
Differential modulatory effects of Annexin 1 on nitric oxide synthase induction by lipopolysaccharide in macrophages
Authors: Smyth Tomoko , Harris Hayley J. , Brown Andrew , Tötemeyer Sabine , Farnfield Belinda A. , Maskell Duncan J. , Matsumoto Makoto , Plevin Robin , Alldridge Louise C. , Bryant Clare E.
Published: December 2005

Annexin‐1 (ANXA1) is a glucocorticoid‐regulated protein that modulates the effects of bacterial lipopolysaccharide (LPS) on macrophages. Exogenous administration of peptides derived from the N‐terminus of ANXA1 reduces LPS‐stimulated inducible nitric oxide synthase (iNOS) expression, but the effects of altering the endogenous expression of this protein are unclear. We transfected RAW264.7 murine macrophage‐like cell lines to over‐express constitutively ANXA1 and investigated whether this protein modulates the induction of iNOS, cyclooxygenase‐2 (COX‐2) and tumour necrosis factor‐α (TNF‐α) in response to LPS. In contrast to exogenous administration of N‐terminal peptides, endogenous over‐expression of ANXA1 results in up‐regulation of LPS‐induced iNOS protein expression and activity. However, levels of iNOS mRNA are unchanged. ANXA1 has no effect on COX‐2 or TNF‐α production in response to LPS. In experiments to investigate the mechanisms underlying these phenomena we observed that activation of signalling proteins classically associated with iNOS transcription was unaffected. Over‐expression of ANXA1 constitutively activates extracellular signal regulated kinase (ERK)‐1 and ERK‐2, components of a signalling pathway not previously recognized as regulating LPS‐induced iNOS expression. Inhibition of ERK activity, by the inhibitor U0126, reduced LPS‐induced iNOS expression in our cell lines. Over‐expression of ANXA1 also modified LPS‐induced phosphorylation of the ERK‐regulated translational regulation factor eukaryotic initiation factor 4E. Our data suggest that ANXA1 may modify iNOS levels by post‐transcriptional mechanisms. Thus differential effects on iNOS expression in macrophages are seen when comparing acute administration of ANXA1 peptides versus the chronic endogenous over‐expression of ANXA1.
Cytotoxic T‐lymphocyte antigen‐4 inhibits GATA‐3 but not T‐bet mRNA expression during T helper cell differentiation
Authors: Nasta Francesca , Ubaldi Vanessa , Pace Luigia , Doria Gino , Pioli Claudio
Published: December 2005

Naive CD4+ T‐cell differentiation to T helper 1 (Th1) and Th2 cells is dependent on T‐bet and GATA‐3 factors, respectively. T‐bet and GATA‐3, indeed, through chromatin remodelling allow transcriptional activation of Ifnγ and Th2 cytokine (Il4, Il5, Il13) genes, respectively. We investigated the effects of the negative costimulatory receptor cytotoxic T‐lymphocyte antigen‐4 (CTLA‐4) on GATA‐3 and T‐bet mRNA expression and Th cell differentiation in mouse naive CD4+ T cells. Our results show that CTLA‐4 inhibits GATA‐3 mRNA expression and Th2 cell differentiation. At variance, CTLA‐4 does not affect T‐bet mRNA expression and Th1 cell differentiation. GATA‐3 mRNA expression is inhibited when CD4+ cells are stimulated under both neutral (i.e. absence of cytokines) and Th2‐polarizing (i.e. presence of interleukin (IL)‐4) conditions, the effect being larger under the latter condition. Hence CTLA‐4 might affect the IL‐4/signal transducer and activator of transcription‐6 (STAT6) pathway leading to GATA‐3 mRNA up‐regulation. We found, indeed, that CTLA‐4 engagement inhibits STAT6 activation leaving unaffected the STAT6 protein level. Moreover, CTLA‐4 engagement drastically inhibits IL‐4Rα mRNA and protein up‐regulation under Th2‐polarizing conditions. Thus, CTLA‐4 exerts a tight control on Th2 cell differentiation by negatively regulating both the CD3/CD28 and the IL‐4/STAT6 pathways.
Levels and chemical speciation of arsenic in polychaetes: a review
Authors: Fattorini Daniele , Notti Alessandra , Halt Magdalena N. , Gambi Maria Cristina , Regoli Francesco
Published: December 2005

Relatively few studies have characterized basal content and variability of arsenic in polychaetes, despite the potential importance of this element as a pollutant of marine environments. Even less have investigated the chemical speciation of arsenic, occurring as inorganic and organic forms, which reflect a different biological reactivity of the element. In the present paper we integrate existing literature with new data in order to summarize the status quo on arsenic bioaccumulation in polychaetes. We consider species with different trophic habits, phylogenetic relationships, geographic distribution and ecology. Reported data indicate a high variability in arsenic concentration with levels ranging from <1 μg·g−1 to more than 2500 μg·g−1 in different species; some additional species analyzed in this work confirm species‐specific characteristics which are not easily explained by biological or ecological factors. The profile of arsenic compounds in polychaetes is different to that of most aquatic organisms. Typically this element occurs in non‐toxic organic forms, however several polychaete species have been shown to accumulate relatively toxic molecules and subsequently biotransform them by processes such as methylation. Conclusions from the literature review reveal a complex array of arsenic actions in the environment and suggest a biological role of this element in the life history of some polychaete species.
Peripheral nerve avulsion injuries as experimental models for adult motoneuron degeneration
Authors: Watabe Kazuhiko , Hayashi Yuichi , Kawazoe Yoko
Published: December 2005

We have used adult rat peripheral nerve avulsion models to evaluate the effects of neuroprotective molecules on motoneuron degeneration. The right facial nerves of adult Fischer 344 male rats were avulsed and adenoviral vectors encoding glial cell line‐derived neurotrophic factor (GDNF), brain‐derived neurotrophic factor (BDNF), transforming growth factor‐β2 (TGFβ2), and growth inhibitory factor (GIF) were injected into the facial canal. The treatment with the vectors significantly prevented the loss of lesioned facial motoneurons, improved choline acetyltransferase (ChAT) immunoreactivity and suppressed the induction of nitric oxide synthase activity in these neurons. In separate experiments, animals were orally administered a solution of a neuroprotective compound T‐588 after avulsion. Both free oral administration and oral tube administration of T‐588 improved the survival of injured motoneurons and ameliorated their ChAT immunoreactivity. These results indicate that the gene transfer of GDNF, BDNF, TGFβ2, and GIF and oral administration of T‐588 may prevent the degeneration of motoneurons in adult humans with motoneuron injury and motor neuron diseases.
Illustration of dynamic changes in Alzheimer pathology: From mild cognitive impairment to terminal stage
Authors: Yamaguchi Haruyasu
Published: December 2005

It is quite important to examine the neuropathology of large numbers of brains from non‐demented as well as demented subjects to elucidate the pathogenesis of dementia. Such a study, “power neuropathology” reveals the temporal profile of the disease, and results in the development of the treatment and the prevention of dementia.
Spatial patterns of the pathological changes in the temporal lobe of patients with neuronal intermediate filament inclusion disease
Authors: Cairns Nigel J. , Armstrong Richard A.
Published: December 2005

Neuronal intermediate filament inclusion disease (NIFID) is a new neurodegenerative disease characterized histologically by the presence of neuronal cytoplasmic inclusions (NI) immunopositive for intermediate filament proteins, neuronal loss, swollen achromatic neurons (SN), and gliosis. We studied the spatial patterns of these pathological changes parallel to the pia mater in gyri of the temporal lobe in four cases of NIFID. Both the NI and SN occurred in clusters that were regularly distributed parallel to the pia mater, the cluster sizes of the SN being significantly greater than those of the NI. In a significant proportion of areas studied, there was a spatial correlation between the clusters of NI and those of the SN and with the density of the surviving neurons. In addition, the clusters of surviving neurons were negatively correlated (out of phase) with the clusters of glial cell nuclei. The pattern of clustering of these histological features suggests that there is degeneration of the cortico‐cortical projections in NIFID leading to the formation of NI and SN within the same vertical columns of cells. The glial cell reaction may be a response to the loss of neurons rather than to the appearance of the NI or SN.
Stripping torque as a predictor of successful internal fracture fixation
Authors: Edwards Thomas R. , Tevelen Greg , English Hugh , Crawford Ross
Published: December 2005

Background:  Internal fixation of fractures using plates and screws is a common method of treatment. Occasionally the internal fixation fails prior to fracture healing. This often requires revision surgery. Determining the force that internal fixation needs to withstand postoperatively would enable this force to be applied intraoperatively as a test to predict successful fixation. The purpose of the present paper was to determine the minimum stripping torque needed to predict successful internal fixation strength.

Methods:  The pull‐out strength and stripping torque relationships of 4.5‐mm cortical bone screws in Sawbones polyurethane foam were determined. Screw forces were directly measured using an LCM load cell washer on a model intertrochanteric neck of femur fracture fixed with 135° 4‐hole pin and plate loaded to single leg stance conditions. Additionally a 135° 4‐hole pin and plate was mounted on foam blocks and loaded until failure of the shaft screws from the foam occurred. Predicted stripping torque/yield load was determined.

Results:  Pull‐out strength and stripping torque of 4.5‐mm cortical bone screws in polyurethane foam have a high degree of linear correlation R2 = 0.95. Direct measurement of shaft screw forces at single leg stance conditions were 585−686 N. This correlated with a stripping torque of 0.9 Nm. Load to yield testing at single leg stance conditions corresponded to a stripping torque of 1.8 Nm.

Conclusion:  Withstanding 0.9−1.8 Nm of torque during insertion of the femoral shaft screws of a 135° 4‐hole pin and plate predicts that the construct will successfully withstand single leg stance.
Fournier's gangrene: a retrospective clinical study on forty‐one patients
Authors: Ayan Fadil , Sunamak Oguzhan , Paksoy Sabri M. , Polat Semra S. , As Abdullah , Sakoglu Nevin , Cetinkale Oguz , Sirin Feridun
Published: December 2005

Background:  Fournier's gangrene, first described by Dr Jean Alfred Fournier in 1883, still has a high mortality rate. The prognosis and outcome of such patients were analysed.

Methods:  Forty‐one patients with Fournier's gangrene were reviewed on the parameters of age, sex, aetiological agents, predisposing factors, treatment modalities and outcomes.

Results:  Although early intervention and careful treatment was carried out, nine of 41 patients (21.9%) died as a result of complications of septicemia. Among the treatment modalities, there were extensive debridement, drainage, excisions of the skin and fascia, colostomy procedure, extensive antibiotic treatment and hyperbaric oxygen therapy. Although a combination of different treatment modalities were used, the mortality rate was 21.9%.

Conclusions:  Fournier's gangrene is still a severe disease. Today, hyperbaric oxygen treatment is very effective in the treatment of this disease.
Unsaturated phosphatidylcholine and its application in surgical adhesion
Authors: Chen Yi , Hills Brian A. , Hills Yvette C.
Published: December 2005

Background:  It has been confirmed that surface‐active phospholipid (SAPL), or surfactant, lines the surface of peritoneum and serves as a release and lubricating agent. The most important component in SAPL is phosphatidylcholine. A previous animal study showed that a saturated phosphatidylcholine, dipalmitoyl‐phosphatidylcholine, reduced the formation of surgical adhesion. Latest studies have indicated that the dominant SAPL species at some sites outside the lung are not saturated phosphatidylcholine but, rather, are unsaturated phosphatidylcholine

Methods:  High performance liquid chromatography was used to analyse the phosphatidylcholine profile of dialysate samples obtained from peritoneal dialysis patients. Friction tests were performed on dipalmitoyl‐phosphatidylcholine and selected unsaturated phosphatidylcholine.

Results:  It was discovered that unsaturated phosphatidylcholine was the dominant SAPL species inside the peritoneal cavity. They are palmitoyl‐linoleoyl‐phosphatidylcholine, palmitoyl‐oleoylphosphatidylcholine and stearoylarachidonoylphosphatidylcholine. Most interestingly, there was no dipalmitoyl‐phosphatidylcholine detected from these dialysate samples. The coefficients of static and dynamic friction from palmitoyllinoleoyl‐phosphatidylcholine and palmitoyloleoyl‐phosphatidylcholine were measured and found to be lower than that of dipalmitoyl‐phosphatidylcholine.

Conclusion:  The results from the current study reveal that unsaturated phosphatidylcholine is the endogenous species inside the peritoneal cavity. This discovery offers further evidence that the dominant SAPL species at non‐lung sites are unsaturated phosphatidylcholine, not saturated phosphatidylcholine, strongly indicating the difference between phosphatidylcholine species distribution at lung and non‐lung sites. Unsaturated phosphatidylcholine has better anti‐friction and lubrication properties than dipalmitoyl‐phosphatidylcholine. Unsaturated phosphatidylcholine‐based SAPL pharmaceutical products should be developed and evaluated.