bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel Discrete Micellar Cubic Phase From a Mixture of GMO/Ethanol/Water
Authors: Efrat Rivka , Aserin Abraham , Danino Dganit , Wachtel Ellen J. , Garti Nissim
Published: December 2005

During the reconstruction the ternary phase diagram of glycerol monooleate (GMO)/ethanol/water, we detected a novel structure not previously seen. The new phase, denoted QL (micellar cubic liquid), is located within the 49–54 wt.-% water/41–33 wt.-% GMO binary mixture line and at 10–13 wt.-% EtOH in a small island within the phase diagram close to the cubic liquid-crystalline phase region. The QL phase is transparent (not tinted), of a low viscosity (36.6 Pa s), non-birefringent, and stable at room temperature. Evidence from severe centrifugation, synchrotron small-angle X-ray scattering (SAXS) measurements, and rheological behavior revealed that the sample is a single phase. SAXS reflections suggest that two types of domain may coexist. The symmetry of the QL phase is Pm3n. A cubic micellar structure is the dominant mesostructure of this unique sample. Cryo-TEM images show highly ordered domains with cubic symmetry, of lattice parameter 103 ± 2 Å. A possible transformation pathway to the QL phase is a ‘rupture and refusion’ mechanism, as the phase seems to have discontinuous symmetry.
Preparation, Characterization, and Electrical Properties of a Self-Assembled meso-Pyridyl Porphyrin Monolayer on Gold Surfaces
Authors: Sathyapalan Amarchand , Lohani Anup , Santra Sangita , Goyal Saurabh , Ravikanth M. , Mukherji Soumyo , Rao V. Ramgopal
Published: December 2005

A meso-pyridyl porphyrin, 5-(4-(2-(4-(S-acetylthiomethyl)phenyl)ethynyl)phenyl)-10,15,20-tris(4-pyridyl) porphyrin was synthesized by coupling of 5-{4-ethynyl}phenyl-10,15,20-tris(4-pyridyl) porphyrin with 4-(S-acetylthiomethyl)-4-iodobenzene under mild palladium coupling conditions. The meso-pyridyl porphyrin was used for the preparation of self assembled monolayers on gold substrates. The gold substrates were made by the thermal evaporation of gold on oxidized Si(100) surfaces. The self-assembled monolayers (SAMs) were characterized using ground state UV absorption and X-ray photoelectron spectroscopic (XPS) techniques and also by scanning probe microscopy (SPM) techniques. The UV-absorption spectra of the porphyrin monolayer exhibited a 10 nm red shift in the Soret band compared to the porphyrin in CHCl3 solution. This indicates that the porphyrin molecules are aligned on the gold substrate in a side-by-side orientation. The typical shifts in the binding energy by XPS revealed that the chemisorption of the thiolate species of the porphyrin to the surface occurs through a strong sulfur–gold bonding mechanism. Basic hexagonal (√3×√3) R 30° well ordered self-assembled monolayers of meso-pyridyl porphyrin was observed by molecular-resolution atomic force microscopy (AFM). Room temperature current–voltage (I–V) spectra by scanning tunneling spectroscopy (STS) at varying set point current were collected to study the electronic transport properties of the monolayers on the gold surface.
Microstructure and water retention of Oxisols in Thailand
Authors: Tawornpruek S. , Kheoruenromne I. , Suddhiprakarn A. , Gilkes R. J.
Published: December 2005

The moisture characteristics and related pore size distributions of Thai Oxisols were determined for 11 representative pedons. These soils are Kandiustox and Kandiudox located in the North-east Plateau, South-east Coast, and Peninsular Thailand. They are generally acidic (pH 5–6), clayey, have low cation exchange capacity (5–15 cmolc/kg) and have low bulk densities (0.77–1.36 Mg/m3). The microstructures of these soils are mostly granular with compound packing 10–1500 μm voids between aggregates. Water retention curves for all soils are similar with amounts of water retained at 33 kPa (field capacity) ranging from 22 to 43 (%weight) and 1500 kPa (permanent wilting point) ranging from 17 to 34%. Water available to plants is 3–12%. There is a strongly bimodal pore size distribution with the modal macropore and micropore diameters calculated from the soil moisture retention characteristic curves being about 100 μm and 0.02 μm. The pore size distribution determined by N2-BET method indicates a modal micropore of about 0.01 μm. The total volume of pores >5 μm estimated by image analysis of scanning electron micrographs ranges from 20 to 50% with most of the variation in porosity being due to large differences in macropore (>75 μm) volume.
RHL1 is an essential component of the plant DNA topoisomerase VI complex and is required for ploidy-dependent cell growth
Authors: Sugimoto-Shirasu Keiko , Roberts Gethin R. , Stacey Nicola J. , McCann Maureen C. , Maxwell Anthony , Roberts Keith
Published: December 2005

How cells achieve their final sizes is a pervasive biological question. One strategy to increase cell size is for the cell to amplify its chromosomal DNA content through endoreduplication cycles. Although endoreduplication is widespread in eukaryotes, we know very little about its molecular mechanisms. Successful progression of the endoreduplication cycle in
Arabidopsis
requires a plant homologue of archaeal DNA topoisomerase (topo) VI. To further understand how DNA is endoreduplicated and how this process is regulated, we isolated a dwarf
Arabidopsis
mutant,
hyp7
(
hypocotyl 7
), in which various large cell types that in the wild type normally endoreduplicate multiple times complete only the first two rounds of endoreduplication and stall at 8C.
HYP7
encodes the RHL1 (ROOT HAIRLESS 1) protein, and sequence analysis reveals that RHL1 has similarity to the C-terminal domain of mammalian DNA topo IIα, another type II topo that shares little sequence homology with topo VI. RHL1 shows DNA binding activity
in vitro
, and we present both genetic and
in vivo
evidence that RHL1 forms a multiprotein complex with plant topo VI. We propose that RHL1 plays an essential role in the topo VI complex to modulate its function and that the two distantly related topos, topo II and topo VI, have evolved a common domain that extends their function. Our data suggest that plant topo II and topo VI play distinct but overlapping roles during the mitotic cell cycle and endoreduplication cycle.
Modulation of neuropeptide Y expression in adult mice does not affect feeding
Authors: Marie Linda Ste. , Luquet Serge , Cole Toby B. , Palmiter Richard D.
Published: December 2005

Despite numerous experiments showing that administration of neuropeptide Y (NPY) to rodents stimulates feeding and obesity, whereas acute interference with NPY signaling disrupts feeding and promotes weight loss, NPY-null mice have essentially normal body weight regulation. These conflicting observations suggest that chronic lack of NPY during development may lead to compensatory changes that normalize regulation of food intake and energy expenditure in the absence of NPY. To test this idea, we used gene targeting to introduce a doxycycline (Dox)-regulated cassette into the
Npy
locus, such that NPY would be expressed until the mice were given Dox, which blocks transcription. Compared with wild-type mice, adult mice bearing this construct expressed ≈4-fold more
Npy
mRNA, which fell to ≈20% of control values within 3 days after treatment with Dox. NPY protein also fell ≈20-fold, but the half-life of ≈5 days was surprisingly long. The biological effectiveness of these manipulations was demonstrated by showing that overexpression of NPY protected against kainate-induced seizures. Mice chronically overexpressing NPY had normal body weight, and administration of Dox to these mice did not suppress feeding. Furthermore, the refeeding response of these mice after a fast was normal. We conclude that, if there is compensation for changes in NPY levels, then it occurs within the time it takes for Dox treatment to deplete NPY levels. These observations suggest that pharmacological inhibition of NPY signaling is unlikely to have long-lasting effects on body weight.
VIS-O-BAC: exploratory visualization of functional genome studies from bacteria
Authors: Dieterich Guido , Kärst Uwe , Wehland Jürgen , Jänsch Lothar
Published: December 2005

Summary: The visualization-aided exploration of complex datasets will allow the research community to formulate novel functional hypotheses leading to a better understanding of biological processes at all levels. Therefore, we have developed a web resource termed VIS-O-BAC designed for the functional investigation of expression data for model systems, such as bacterial pathogens based on a graphical display. Genome-scale datasets derived from typical ‘omic’ approaches can directly be explored with respect to three biologically relevant aspects, the genome structure (operon organization), the organization of genes in pathways (KEGG) and the gene function with Gene Ontology (GO) terms. The integrated viewers can be used in parallel and combine expression data and functional annotations from different external data repositories. The graphical visualizations evidently accelerate both the validation of regulatory information and the detection of affected biological processes.

Availability:  

Contact:  lja@gbf.de

Supplementary information: Supplementary data are available at Bioinformatics online.
SubLoc: a server/client suite for protein subcellular location based on SOAP
Authors: Chen Hu , Huang Ni , Sun Zhirong
Published: December 2005

Summary: Based on SOAP(Simple Object Access Protocol) technology, the SubLoc server/client suite offers a user-friendly interface for searching and predicting protein subcellular location.

Availability:SubLoc SOAP server is available through HTTP protocol at . The client software can be downloaded at . More information is given at .

Contact:  sunzhr@mail.tsinghua.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.
Differential regulation of urease activity in Helicobacter hepaticus and Helicobacter pylori
Authors: Belzer Clara , Stoof Jeroen , Beckwith Catherine S. , Kuipers Ernst J. , Kusters Johannes G. , van Vliet Arnoud H. M.
Published: December 2005

Helicobacter hepaticus is a pathogen of rodents, which causes diverse enteric and hepatic inflammatory diseases and malignancies. The urease enzyme is an important colonization factor of gastric Helicobacter species like Helicobacter pylori, but little is known about the role and regulation of urease in enterohepatic Helicobacter species. Here it is reported that urease activity of H. hepaticus does not contribute to acid resistance, and that it is nickel-responsive at the post-translational level. H. hepaticus strain ATCC 51449 did not grow or survive at pH 3·0, and supplementation with urea or NiCl2 did not abrogate this acid sensitivity. Furthermore, urease enzyme activity of H. hepaticus was acid-independent, which contrasts with the acid-induced urease system of H. pylori. Nickel supplementation of Brucella medium resulted in a tenfold increase in urease activity in both H. hepaticus and H. pylori, but the maximum level of urease activity in H. hepaticus was still three- to fivefold lower when compared to H. pylori in the same conditions. The increase in urease activity of H. hepaticus was not associated with elevation of urease mRNA or protein levels. Inhibition of protein synthesis by chloramphenicol did not affect nickel-responsive induction of urease activity in H. hepaticus, and confirmed that nickel induction occurs at the post-translational level, probably by activation of preformed apo-enzyme. In conclusion, both the role of the urease enzyme and the regulation of urease activity differ between the enterohepatic pathogen H. hepaticus and the gastric pathogen H. pylori.
Phylogeny of Wolbachia pipientis based on gltA, groEL and ftsZ gene sequences: clustering of arthropod and nematode symbionts in the F supergroup, and evidence for further diversity in the Wolbachia tree
Authors: Casiraghi M. , Bordenstein S. R. , Baldo L. , Lo N. , Beninati T. , Wernegreen J. J. , Werren J. H. , Bandi C.
Published: December 2005

Current phylogenies of the intracellular bacteria belonging to the genus Wolbachia identify six major clades (A–F), termed ‘supergroups’, but the branching order of these supergroups remains unresolved. Supergroups A, B and E include most of the wolbachiae found thus far in arthropods, while supergroups C and D include most of those found in filarial nematodes. Members of supergroup F have been found in arthropods (i.e. termites), and have previously been detected in the nematode Mansonella ozzardi, a causative agent of human filariasis. To resolve the phylogenetic positions of Wolbachia from Mansonella spp., and other novel strains from the flea Ctenocephalides felis and the filarial nematode Dipetalonema gracile, the authors generated new DNA sequences of the Wolbachia genes encoding citrate synthase (gltA), heat-shock protein 60 (groEL), and the cell division protein ftsZ. Phylogenetic analysis confirmed the designation of Wolbachia from Mansonella spp. as a member of the F supergroup. In addition, it was found that divergent lineages from Dip. gracile and Cte. felis lack any clear affiliation with known supergroups, indicating further genetic diversity within the Wolbachia genus. Finally, although the data generated did not permit clear resolution of the root of the global Wolbachia tree, the results suggest that the transfer of Wolbachia spp. from arthropods to nematodes (or vice versa) probably occurred more than once.
Four molecules of the 33 kDa haemagglutinin component of the Clostridium botulinum serotype C and D toxin complexes are required to aggregate erythrocytes
Authors: Mutoh Shingo , Suzuki Tomonori , Hasegawa Kimiko , Nakazawa Yozo , Kouguchi Hirokazu , Sagane Yoshimasa , Niwa Koichi , Watanabe Toshihiro , Ohyama Tohru
Published: December 2005

Normally, large-sized botulinum toxin complexes (L-TC) of serotype C and D are composed of a single neurotoxin, a single non-toxic non-haemagglutinin, two HA-70 molecules, four HA-33 molecules and four HA-17 molecules that assemble to form a 650 kDa L-TC. The 540 and 610 kDa TC species (designated here as L-TC2and L-TC3, respectively) were purified in addition to the 650 kDa L-TC from the culture supernatants of serotype D strains (D-4947 and D-CB16) and serotype C strains (C-6814 and C-Yoichi). The 650 kDa L-TC from D-4947, D-CB16 and C-6814 showed haemagglutination and erythrocyte-binding activity, but their L-TC2and L-TC3species had only binding activity. In contrast, every TC species from C-Yoichi having the C-terminally truncated variant of HA-33 exhibited neither haemagglutination activity nor erythrocyte-binding activity. Four strain-specific HA-33/HA-17 complexes were isolated from the 650 kDa L-TC of each strain. The 650 kDa HA-hybrid L-TCs were reconstituted by various combinations of isolated HA-33/HA-17 complexes and haemagglutination-negative L-TC2or L-TC3from each strain. HA-hybrid 650 kDa L-TC, including at least one HA-33/HA-17 complex derived from C-Yoichi, lost haemagglutination activity, leading to the conclusion that the binding of four HA-33 molecules is required for haemagglutination activity of botulinum L-TC. The results of the modelling approach indicated that the structure of a variant C-Yoichi HA-33 molecule reveals clear deformation of theβ-trefoil domain responsible for the carbohydrate recognition site.
Contribution of a PerR-like regulator to the oxidative-stress response and virulence of Enterococcus faecalis
Authors: Verneuil Nicolas , Rincé Alain , Sanguinetti Maurizio , Posteraro Brunella , Fadda Giovanni , Auffray Yanick , Hartke Axel , Giard Jean-Christophe
Published: December 2005

PerR is one of the most important transcriptional regulators involved in the oxidative-stress response in Bacillus subtilis. Here, the homologous gene in Enterococcus faecalis, ranked among the leading causes of nosocomial infection, was characterized and analysed. Phenotype analysis showed that the perR mutant was significantly more resistant to H2O2 challenge (P<0·05). Expression of eight genes with potential roles in the oxidative-stress response was determined in the wild-type and perR-mutant strains by real-time quantitative PCR. Surprisingly, low quantitative differences in the transcriptional activity of these genes in the mutant versus wild-type were observed. Likewise, this locus was not involved in survival within murine macrophages, but in the mouse peritonitis model, the perR mutant appeared less lethal than the JH2-2 wild-type strain. The combined results show that PerR affects E. faecalis virulence and that its implication in the transcriptional regulation in this bacterium deviates from the B. subtilis model.
Transcription and autoregulation of the Rv3134c-devR-devS operon of Mycobacterium tuberculosis
Authors: Bagchi Gargi , Chauhan Santosh , Sharma Deepak , Tyagi Jaya Sivaswami
Published: December 2005

DevR is a transcriptional regulator that mediates the genetic response of Mycobacterium tuberculosis to oxygen limitation and nitric oxide exposure. devR is co-transcribed along with devS, which encodes its cognate sensor kinase, and an upstream gene, Rv3134c. The transcriptional activity of this operon was characterized by primer extension, transcriptional fusion and electrophoretic mobility shift assays (EMSAs) under aerobic conditions. Transcription start points (Tsps) were detected upstream of both Rv3134c and devR, and the major transcript was derived from upstream of Rv3134c. Sequences with similarity to sigma factor consensus elements and to DevR-binding motifs were detected in the vicinity of the Tsps by in silico analysis. EMSAs with promoter regions and DevR protein showed that DevR binds to its own promoters in a sequence-specific manner with differing affinities. Consistent with the primer extension and EMSA data, Rv3134c promoters, and not devR promoters, were determined to be the principal promoters of this operon using reporter assays performed in Mycobacterium smegmatis and Escherichia coli. Furthermore, DevR modulated the activity of both devR and Rv3134c promoters. From these findings it is inferred that the Rv3134c-devR-devS operon is transcribed from multiple promoters and is autoregulated.
Analysis of differential protein expression during growth states of Ferroplasma strains and insights into electron transport for iron oxidation
Authors: Dopson Mark , Baker-Austin Craig , Bond Philip L.
Published: December 2005

To investigate the metabolic biochemistry of iron-oxidizing extreme acidophiles, a proteomic analysis of chemomixotrophic and chemo-organotrophic growth, as well as protein expression in the absence of organic carbon, was carried out in Ferroplasma species. Electron transport chain inhibitor studies, spectrophotometric analysis and proteomic results suggest that oxidation of ferrous iron may be mediated by the blue copper-haem protein sulfocyanin and the derived electron passes to a cbb
3 terminal electron acceptor. Despite previous suggestions of a putative carbon dioxide fixation pathway, no up-regulation of proteins typically associated with carbon dioxide fixation was evident during incubation in the absence of organic carbon. Although a lack of known carbon dioxide fixation proteins does not constitute proof, the results suggest that these strains are not autotrophic. Proteins putatively involved in central metabolic pathways, a probable sugar permease and flavoproteins were up-regulated during chemo-organotrophic growth in comparison to the protein complement during chemomixotrophic growth. These results reflect a higher energy demand to be derived from the organic carbon during chemo-organotrophic growth. Proteins with suggested function as central metabolic enzymes were expressed at higher levels during chemomixotrophic growth by Ferroplasma acidiphilum YT compared to ‘Ferroplasma acidarmanus’ Fer1. This study addresses some of the biochemical and bioenergetic questions fundamental for survival of these organisms in extreme acid-leaching environments.
Cloning and characterization of the goadsporin biosynthetic gene cluster from Streptomyces sp. TP-A0584
Authors: Onaka Hiroyasu , Nakaho Mizuho , Hayashi Keiko , Igarashi Yasuhiro , Furumai Tamotsu
Published: December 2005

The biosynthetic gene cluster of goadsporin, a polypeptide antibiotic containing thiazole and oxazole rings, was cloned from Streptomyces sp. TP-A0584. The cluster contains a structural gene, godA, and nine god (goadsporin) genes involved in post-translational modification, immunity and transcriptional regulation. Although the gene organization is similar to typical bacteriocin biosynthetic gene clusters, each goadsporin biosynthetic gene shows low homology to these genes. Goadsporin biosynthesis is initiated by the translation of godA, and the subsequent cyclization, dehydration and acetylation are probably catalysed by godD, godE, godF, godG and godH gene products. godI shows high similarity to the 54 kDa subunit of the signal recognition particle and plays an important role in goadsporin immunity. Furthermore, four goadsporin analogues were produced by site-directed mutagenesis of godA, suggesting that this biosynthesis machinery is used for the heterocyclization of peptides.
bph genes of the thermophilic PCB degrader, Bacillus sp. JF8: characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC
Authors: Mukerjee-Dhar Gouri , Shimura Minoru , Miyazawa Daisuke , Kimbara Kazuhide , Hatta Takashi
Published: December 2005

Bacillussp. JF8 is a thermophilic polychlorinated biphenyl (PCB) degrader, which utilizes biphenyl and naphthalene. A thermostable, Mn-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase, BphC_JF8, has been characterized previously. Upstream ofbphCare five ORFs exhibiting low homology with, and a different gene order from, previously characterizedbphgenes. From the 5′ to 3′ direction the genes are: a putative regulatory gene (bphR), a hydrolase (bphD), the large and small subunits of a ring-hydroxylating dioxygenase(bphA1A2), and acis-diol dehydrogenase (bphB). Hybridization studies indicate that the genes are located on a plasmid. Ring-hydroxylating activity of recombinant BphA1A2_JF8 towards biphenyl, PCB, naphthalene and benzene was observed inEscherichia colicells, with complementation of non-specific ferredoxin and ferredoxin reductase by host cell proteins. PCB degradation by recombinant BphA1A2_JF8 showed that the congener specificity of the recombinant enzyme was similar toBacillussp. JF8. BphD_JF8, with an optimum temperature of 85 °C, exhibited a narrow substrate preference for 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. The Arrhenius plot of BphD_JF8 was biphasic, with two characteristic energies of activation and a break point at 47 °C.
Phase I study of radioimmunotherapy with an anti‐CD20 murine radioimmunoconjugate (90Y‐ibritumomab tiuxetan) in relapsed or refractory indolent B‐cell lymphoma
Authors: Watanabe Takashi , Terui Shoji , Itoh Kuniaki , Terauchi Takashi , Igarashi Tadahiko , Usubuchi Noriko , Nakata Masanobu , Nawano Shigeru , Sekiguchi Naohiro , Kusumoto Shigeru , Tanimoto Kazuki , Kobayashi Yukio , Endo Keigo , Seriu Taku , Hayashi Masaki , Tobinai Kensei
Published: December 2005

We conducted a phase I study to evaluate the safety and efficacy of radioimmunotherapy with yttrium‐90‐ibritumomab tiuxetan (Y2B8) in Japanese patients with relapsed or refractory indolent B‐cell lymphoma. Indium‐111‐labeled ibritumomab tiuxetan (In2B8; 3.5 or 5 mCi [129.5 or 185 MBq]) was administered on day 1, followed by serial gamma‐camera imaging to investigate the distribution of In2B8 in the whole body of patients and to judge the feasibility of Y2B8 administration. Y2B8 with a dose of 0.3 mCi/kg (11.1 MBq/kg) or 0.4 mCi/kg (14.8 MBq/kg) was administered on day 8. Grade 4 neutropenia and grade 3 thrombocytopenia were observed in three of nine of the patients evaluated for safety. Critical toxicities (prolonged thrombocytopenia or severe non‐hematological toxicities) were observed in two of six patients in the 0.4 mCi/kg (14.8 MBq/kg) dose group but were not seen in any of the three patients in the 0.3 mCi/kg (11.1 MBq/kg) dose group. The non‐hematological toxicities of the nine patients were of grade 2 or less, except in two patients who had been heavily treated previously. They experienced critical toxicities such as infection, diarrhea, hyponatremia and prolonged thrombocytopenia, as well as other frequent grade 2 non‐hematological toxicities. Although the pharmacokinetic profiles were similar to those in the US study, one of the two patients was clarified retrospectively as showing abnormal biodistribution of In2B8 in the bone marrow, as judged by an independent third party panel of radiologists. Five of the 10 participants achieved complete responses or unconfirmed complete responses and two partial responses. In conclusion, the recommended dose of Y2B8 for the subsequent phase II study for Japanese patients is 0.4 mCi/kg (14.8 MBq/kg). This dose of radioimmunotherapy was feasible when patients with altered biodistribution of In2B8 were excluded, and it was highly effective. (Cancer Sci 2005; 96: 903–910)
Important prognostic histological parameters for patients with invasive ductal carcinoma of the pancreas
Authors: Mitsunaga Shuichi , Hasebe Takahiro , Iwasaki Motoki , Kinoshita Taira , Ochiai Atsushi , Shimizu Nobuyoshi
Published: December 2005

For clinicians, the orthodox histological investigation of patients with invasive ductal carcinoma (IDC) remains important for predicting prognoses. The purpose of the present study was to determine the most important of the known prognostic histological parameters (including fibrotic focus and tumor necrosis), enabling the outcomes of 101 patients with IDC of the pancreas to be predicted accurately. Furthermore, we established a scoring classification consisting of important prognostic histological parameters examined in this study. Multivariate survival analyses showed that invasive tumor size of more than 3 cm, the presence of tumor necrosis, the presence of nerve plexus invasion and lymph vessel invasion scores of 2 or 3 were important prognostic factors. Our scoring classification, consisting of the above four parameters, accurately classified the outcome of patients independent of the invasive tumor size of IDC. We concluded that invasive tumor size of 3 cm or more, the presence of tumor necrosis, the presence of nerve plexus invasion and lymph vessel invasion scores of 2 or 3 are important histological prognostic parameters for patients with IDC of the pancreas. Furthermore, the scoring system consisting of the above four histological parameters is probably a very useful prognostic histological classification for patients with IDC of the pancreas. (Cancer Sci2005; 96: 858–865)
Helicobacter pylori CagA: a new paradigm for bacterial carcinogenesis
Authors: Hatakeyama Masanori , Higashi Hideaki
Published: December 2005

Infection with cagA‐positive Helicobacter pylori is associated with the development of gastric adenocarcinoma. The cagA gene product CagA is injected directly from the bacterium into the bacterium‐attached gastric epithelial cells via the type‐IV secretion system. Upon membrane localization and subsequent tyrosine phosphorylation by Src family kinases, CagA functions as a scaffolding adaptor and interacts with a number of host proteins that regulate cell growth, cell motility and cell polarity in both CagA phosphorylation‐dependent and phosphorylation‐independent manners. Of special interest is the interaction of CagA with the SHP‐2 tyrosine phosphatase, gain‐of‐function mutations that of which have recently been found in a variety of human malignancies. The CagA–SHP‐2 interaction is entirely dependent on CagA tyrosine phosphorylation and, through the complex formation, SHP‐2 is catalytically activated and induces morphological transformation with elevated cell motility. Intriguingly, structural diversity of the tyrosine phosphorylation sites of CagA accounts for the differential activity of individual CagA to bind and activate SHP‐2. Deregulation of SHP‐2 and other intracellular signaling molecules by H. pylori CagA may predispose cells to accumulate multiple genetic and epigenetic changes involved in gastric carcinogenesis. Furthermore, the differential potential of individual CagA to disturb cellular functions indicates that H. pylori strains carrying biologically more active CagA are more virulent than those with less active CagA and are more closely associated with gastric carcinoma. (Cancer Sci 2005; 96: 835–843)
Competition between perch (Perca fluviatilis) and ruffe (Gymnocephalus cernuus): the advantage of turning night into day
Authors: SCHLEUTER D. , ECKMANN R.
Published: December 2005

1. The outcome of interspecific competition for food resources depends both on the competitors’ sensory abilities and on environmental conditions. In laboratory experiments we tested the influence of daylight and darkness on feeding behaviour and specific growth rate (SGR) of two species with different sensory abilities.

2. We used perch (Perca fluviatilis) as a visually orientated, and ruffe (Gymnocephalus cernuus) as a mechano‐sensory oriented predator and tested their growth rates and behaviour under conditions of interspecific and intraspecific competition. Three different foraging conditions were used: food supplied (i) only during the day, (ii) only during the night or (iii) during both day and night.

3. In perch neither SGR nor feeding behaviour were influenced substantially by interspecific competition during daylight. During darkness their foraging behaviour changed markedly and their access to the food source as well as their SGR were negatively affected by the presence of ruffe.

4. Ruffe's foraging behaviour did not change during either day or night with interspecific competition. During the night ruffe's SGR was higher with interspecific competition, probably because of a release from intraspecific competition and the competitive inferiority of perch during the night.

5. Because of its seonsory abilities ruffe feeds predominantly at night, thereby reducing competitive interference from perch.
Time‐lapse seismic analysis of pressure depletion in the Southern Gas Basin
Authors: Hall Stephen A. , MacBeth Colin , Stammeijer Jan , Omerod Mark
Published: December 2005

In the Southern Gas Basin (SGB) of the North Sea there are many mature gas fields where time‐lapse monitoring could be very beneficial in extending production life. However, the conditions are not immediately attractive for time‐lapse seismic assessment. This is primarily because the main production effect to be assessed is a pore pressure reduction and frame stiffening because of gas production in tight sandstone reservoirs that also have no real seismic direct hydrocarbon indicators. Modelling, based on laboratory measurements, has shown that such an effect would be small and difficult to detect in seismic data. This paper makes two main contributions. Firstly, this is, to our knowledge, the first time‐lapse study in the SGB and involves a real‐data assessment of the viability for detecting production in such an environment. Secondly, the feasibility of using markedly different legacies of data in such a study is addressed, including an assessment of the factors influencing the crossmatching. From the latter, it is found that significant, spatially varying time shifts need to be, and are successfully, resolved through 3‐D warping. After the warping, the primary factors limiting the crossmatching appear to be residual local phase variations, possibly induced by the differing migration strategies, structure, reverberations and different coherencies of the volumes, caused by differences in acquisition‐structure azimuth and acquisition fold. Despite these differences, a time‐lapse amplitude signature is observed that is attributable to production. The character of the 4‐D amplitude anomalies may also indicate variations in stress sensitivity, e.g. because of zones of fracturing. Additionally, warping‐derived time attributes have been highlighted as a potential additional avenue for detection of pressure depletion in such reservoirs. Although the effects are subtle, they may indicate changes in stress/pressure in and around the reservoir because of production. However, to fully resolve the subtle time‐lapse effects in such a reservoir, the data differences need to be better addressed, which may be possible by full re‐processing and pre‐stack analysis, but more likely dedicated 4‐D acquisition would be required.
Magnetic data analysis at low latitudes using magnitude transforms
Authors: Gerovska Daniela , Stavrev Petar
Published: December 2005

Magnitude transforms include magnitude magnetic anomalies (MMA), their gradients and Laplacians. They can be calculated from the total magnetic anomalies or other component anomalies. Magnitude magnetic anomalies have a space distribution different from that of the component anomalies. Their values are non‐negative and their respective patterns are similar to the positive gravity anomalies. Magnitude transforms are an effective tool for magnetic data analysis due to their simplified pattern and direct correlation with the space location of the source. They have advantages over the traditionally used reduction‐to‐the‐pole (RTP) transform, especially at low magnetic latitudes. The calculation of magnitudes of the anomalous field requires the total field data to be transformed into the component anomalies, while the reduction‐to‐the‐pole transform also includes a rotation of the magnetization vector, the orientation of which is usually assumed. For equal latitudes, the transfer functions of component‐component transforms in the frequency domain show better stability than the component‐component‐rotation transfer function. This is illustrated by a comparison of analytical expressions, and synthetic models of magnetic fields. The Dixon seamount case shows the possibilities for an improved data analysis and more confident source recognition at low latitudes using magnetic transforms.
Induction of autoimmunity by immunization with hapten‐modified hen egg lysozyme in hen egg lysozyme‐transgenic mice
Authors: Kang Hee‐Kap , Chung Yun Jo , Park Chung Ung , Jang Yong‐Suk , Kim Byung S.
Published: December 2005

To understand the mechanism of autoimmunity induction, hen egg lysozyme (HEL)‐transgenic (Tg) C57BL/6 (B6) mice were immunized with HEL or phosphorylcholine‐conjugated HEL (PC‐HEL). Repeated immunization of HEL‐Tg mice with native HEL failed to induce the antibody response against HEL. However, immunization with PC‐HEL generated a significant anti‐HEL antibody response. Immunization of the Tg mice with dominant (HEL74−88) or cryptic (HEL47−61) T‐cell epitope peptide stimulated the corresponding T‐cell response and similarly yielded the anti‐HEL antibody response. Predominance of immunoglobulin G1 (IgG1) anti‐HEL antibody response in the HEL‐Tg mice and preferential IL‐4 production by HEL‐specific T cells suggested the dependency of the antibody response to the presence of T helper 2. HEL‐Tg mice received HEL‐primed B6 T cells, but not HEL‐primed Tg T cells, were able to generate anti‐HEL antibody response following PC‐HEL immunization. The pattern and the level of epitope peptides generated by splenic antigen‐presenting cells indicated that PC‐HEL results in much more efficient processing as compared to HEL. These results strongly suggest that the enhancement of antigen processing by hapten (PC) conjugation to the antigen facilitates more efficient stimulation of T cells reactive to self antigen, HEL in HEL‐Tg mice resulting in the production of anti‐self HEL antibody.
Inbreeding, outbreeding and environmental effects on genetic diversity in 46 walleye (Sander vitreus) populations
Authors: CENA CHRISTOPHER J. , MORGAN GEORGE E. , MALETTE MICHAEL D. , HEATH DANIEL D.
Published: December 2005

Genetic diversity is recognized as an important population attribute for both conservation and evolutionary purposes; however, the functional relationships between the environment, genetic diversity, and fitness‐related traits are poorly understood. We examined relationships between selected lake parameters and population genetic diversity measures in 46 walleye (Sander vitreus) populations across the province of Ontario, Canada, and then tested for relationships between six life history traits (in three categories: growth, reproductive investment, and mortality) that are closely related to fitness, and genetic diversity measures (heterozygosity, d2, and Wright's inbreeding coefficient). Positive relationships were observed between lake surface area, growing degree days, number of species, and hatchery supplementation versus genetic diversity. Walleye early growth rate was the only life history trait significantly correlated with population heterozygosity in both males and females. The relationship between FIS and male early growth rate was negative and significant (P < 0.01) and marginally nonsignificant for females (P = 0.06), consistent with inbreeding depression effects. Only one significant relationship was observed for d2: female early growth rate (P < 0.05). Stepwise regression models showed that surface area and heterozygosity had a significant effect on female early growth rate, while hatchery supplementation, surface area and heterozygosity had a significant effect on male early growth rate. The strong relationship between lake parameters, such as surface area, and hatchery supplementation, versus genetic diversity suggests inbreeding and outbreeding in some of the populations; however, the weak relationships between genetic diversity and life history traits indicate that inbreeding and outbreeding depression are not yet seriously impacting Ontario walleye populations.
Phylogenetic relationship of LumbricalusFrame, 1992 (Polychaeta: Lumbrineridae), with ecological and distribution data
Authors: Carrera‐Parra Luis F.
Published: December 2005

This study is the first phylogenetic reconstruction of the eight Lumbricalus species, using parsimony analysis of 11 morphological characters. Following previous higher‐level phylogenetic analysis, Kuwaita magnaMohammad, 1973 was selected as outgroup. The analysis yielded one most parsimonious tree of 18 steps, consistency index of 0.7222, homoplasy index of 0.2778, and retention index of 0.6875. The topology of this tree revealed the separation of the genus in four groups, (i) L. foresti, L. adriatica, L. harrisae and L. aotearoae; (ii) L. composita and L. vossae; (iii) L. januarii; and (iv) L. vivianneae. Furthermore, ecological and distribution data on the genus are provided, and a possible explanation of the discontinuous distribution of L. januarii is provided.
The inferential basis of species hypotheses: the solution to defining the term ‘species’
Authors: Fitzhugh Kirk
Published: December 2005

A formal definition of the term ‘species’ is presented that is logically consistent with the inferential structures that lead to other taxonomic categories in biological systematics. A species name denotes an explanatory hypothesis that accounts for specified intrinsic or relational properties of organisms that can be accounted for by way of past tokogenetic,i.e., reproductive events. The inference of species hypotheses involves a form of non‐deductive reasoning known as abduction. Hypotheses in other taxonomic categories, such as ‘semaphoronts’ (sensuW. Hennig,Phylogenetic Systematics, University of Illinois Press, Urbana, 1966), genera, families,etc., exhibit the same abductive form. The differences between semaphoront, species, and supraspecific hypotheses is in the causal theories applied to infer each – these theories being ontogenetic, tokogenetic, and phylogenetic, respectively. By formally defining the term species as an explanatory hypothesis accounting for properties of organisms by way of tokogeny, there are several distinct consequences: (1) species cannot have the ontological status of individuals, and it would be inaccurate to reduce them to class constructs; (2) acknowledging species as representative of explanatory hypotheses leaves available a variety of tokogenetic theories, such as asexual, sexual, and metagenetic reproductive processes to account for relevant organismal properties; (3) removal of species hypotheses from consideration, as in the ‘least inclusive taxonomic unit’ concept of Pleijel & Rouse [Proceedings of the Royal Society of London, Series B267(2000) 627;Zoologica Scripta29(2000) 157] is nihilistic; and (4) advocating the reduction of inferences of species hypotheses to one class of characters,e.g., ‘DNA barcoding,’ would be irrational.
Another diet of worms: the applicability of polychaete feeding guilds as a useful conceptual framework and biological variable
Authors: Pagliosa Paulo Roberto
Published: December 2005

A fundamental question in guild studies is how to separate species into guilds. In a seminal manuscript, Fauchald & Jumars [Oceanography and Marine Biology Annual Review17 (1979) 193] summarized polychaete feeding biology and proposed a conceptual framework to test hypotheses on the sympatric occurrence of congeners with limited morphological differentiation. Twenty‐six years after this publication, few studies have tested the validity and practical functioning of this scheme of polychaete feeding guilds and then only using part of the classification. The objective of the present study was to analyze the applicability of polychaete feeding guilds to ecological and environment assessments. Two data sets from Santa Catarina Island Bay, southern Brazil, were used. The first data set deals with spatial distribution of natural polychaete assemblages along the bay. The second data set treats fauna in urbanized versus relatively pristine mangroves. Multivariate analysis showed similar patterns in sample groups formed using guilds or densities and composition data. The role of feeding guilds in benthic systems was assessed through comparison with environmental variables. The polychaete assemblage from the Bay was related to sediment type. Motile and discretely motile carnivores and herbivores with jawed probosces matched coarse sands; surface deposit feeders and filter feeders were found in fine sands; and surface and subsurface deposit feeders and carnivores, all with soft probosces matched silt and clay sediments. The data analyses in mangroves showed surface deposit feeders and filter feeders in undisturbed sites and omnivorous species in disturbed ones. The polychaete feeding guilds appear relevant to assembly rules based on resource availability, to resource partitioning and to interspecific competition.
The seasonal dynamics of six species of Dorvilleidae (Polychaeta) in the harbour of La Spezia (Italy)
Authors: Prevedelli D. , Massamba N'Siala G. , Simonini R.
Published: December 2005

In the harbour of La Spezia (Italy) six polychaete species belonging to the family Dorvilleidae are present. The population dynamics of Dinophilus gyrociliatus, Ophryotrocha hartmanni, O. japonica, O. labronica, O. puerilis and Schistomeringos rudolphii has been studied from August 2002 to August 2003. The density of each species was considerably different and during the year there was a species succession that alternated in dominating the community. The role of the life‐history characteristics of each species and environmental conditions in determining the population dynamics are discussed.
The publications of Kristian Fauchald and the polychaete taxa named in those works
Authors: Ward Linda A.
Published: December 2005

Between 1961 and 2002, Kristian Fauchald produced, 72 single and co‐authored publications and named three families, thirty four genera and 256 species of polychaetes. A bibliography of his publications, excluding abstracts, book reviews, thesis and dissertation, along with a list of the polychaete taxa named in these works are given here.
Pineal germinoma associated with multiple congenital melanocytic nevi: A unique presentation
Authors: Aker Fügen V. , Berkman Zafer M. , Aydıngöz İkbal , Hakan Tayfun , Toksoy Güven
Published: December 2005

Intracranial germ cell tumors are rarely seen and typically localize in the pineal or suprasellar region. The largest category of germ cell tumors is the germinoma. There have been reported associations of malignant tumors and chromosomal abnormalities in germ cell tumors. In this study, we present a 22‐year‐old man with multiple congenital melanocytic nevi in association with pineal tumor. Congenital melanocytic lesions greater than 2 cm were counted to be 54 in number, and those smaller than 1 cm in diameter were found to be 25 in number. The pathological diagnosis of the pineal tumors was germinoma, and the lesions located in the occipital region and trunk were compound congenital nevi. To our knowledge, a relationship between multiple congenital melanocytic nevi and germ cell tumors has not been reported before. The connection between them remains to be clarified.
Epithelioid malignant peripheral nerve sheath tumor involving maxillary sinus
Authors: Izycka‐Swieszewska Ewa , Drogoszewska Barbara , Filipowicz Joanna , Szurowska Edyta , Kaminski Maciej , Jaskiewicz Kazimierz
Published: December 2005

We present a case of epithelioid malignant peripheral nerve sheath tumor (MPNST) located in the maxillary sinus region in a young man. The clinical history was short, but at admission the neoplastic infiltration was so extensive that only diagnostic biopsy was performed. The patient received palliative treatment and died 6 months later. Histologically, the neoplasm had a predominant epithelioid component. Neoplastic tissue was vimentin, S‐100, Cam 5.2 and neuron‐specific enolase positive. P53 protein reaction was found in 6% of the cells and the proliferation index assessed with Ki‐67 was 52%. An appropriate immunohistochemical  panel  was  essential  for  the  final  diagnosis  of this epithelioid malignant tumor, with the location rather unusual for MPNST.
Autopsy case of hereditary spastic paraplegia with thin corpus callosum showing severe gliosis in the cerebral white matter
Authors: Kuru Satoshi , Sakai Motoko , Konagaya Masaaki , Yoshida Mari , Hashizume Yoshio
Published: December 2005

We report an autopsy case of a 51‐year‐old man clinically diagnosed with a complicated type of hereditary spastic paraplegia. His sister showed similar manifestations. Gait disturbance was manifested at 14 years of age. Subsequently, slowly progressive spastic tetraplegia developed with mental deterioration, neuropathy and amyotrophy. Marked cerebral atrophy with thin corpus callosum was shown by cranial MRI. Autopsy revealed a severely atrophic brain with extreme thinning of the whole corpus callosum. Microscopically, neurodegeneration was found in the corticospinal tract, thalamus, cerebral white matter and substantia nigra, as well as in the anterior horn and posterior column of the spinal cord. The remaining neurons contained large amounts of lipofuscin and eosinophilic granules. Unique to this patient was the severe gliosis in the cerebral white matter and substantia nigra, suggesting that sufficient development had been established when the degenerative process occurred. The predominant feature of the present case is the neurodegeneration process rather than hypoplasia.