bluuebunny/crossref_metadata_2025 huggingface dataset:
Marinobacter vinifirmus sp. nov., a moderately halophilic bacterium isolated from a wine-barrel-decalcification wastewater
Authors: Liebgott Pierre-Pol , Casalot Laurence , Paillard Sebastien , Lorquin Jean , Labat Marc
Published: November 2006

A halophilic, Gram-negative, motile, non-sporulating bacterium designated strain FB1Twas isolated from a wine-barrel-decalcification wastewater. The organism comprises straight rods and has a strictly respiratory metabolism with O2. Strain FB1Tgrows optimally at 20–30 °C and 5–6 % NaCl. The predominant fatty acids were found to be C18 : 1ω9c(30.4 %), C16 : 0(25.7 %), C12 : 03-OH (10.3 %), C16 : 1ω9c(9.7 %) and C16 : 1ω7c(8.4 %). A phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain forms a coherent cluster within the genusMarinobacter. The highest level of 16S rRNA gene sequence similarity (97.9 %) exhibited by strain FB1Twas with the type strain ofMarinobacter excellens. However, the level of DNA–DNA relatedness between the novel strain andM. excellensCIP 107686Twas only 31.2 %. The DNA G+C content of strain FB1Twas 58.7 mol%. On the basis of phenotypic and genotypic characteristics, and also phylogenetic evidence, strain FB1Tis considered to represent a novel species of the genusMarinobacter, for which the nameMarinobacter vinifirmussp. nov. is proposed. The type strain is FB1T(=DSM 17747T=CCUG 52119T).
Pseudomonas simiae sp. nov., isolated from clinical specimens from monkeys (Callithrix geoffroyi)
Authors: Vela Ana I. , Gutiérrez María C. , Falsen Enevold , Rollán Eduardo , Simarro Isabel , García Pilar , Domínguez Lucas , Ventosa Antonio , Fernández-Garayzábal José F.
Published: November 2006

An unusual Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium isolated from different clinical samples from two monkeys (Callithrix geoffroyi) was characterized by phenotypic and molecular genetic methods. The micro-organism was tentatively identified as aPseudomonasspecies on the basis of the results of cellular morphological and biochemical tests. Fatty acid studies confirmed this generic placement and comparative 16S rRNA gene sequencing studies demonstrated that the unknown isolates were phylogenetically closely related to each other (100 % sequence similarity) and were part of the ‘Pseudomonas fluorescensintrageneric cluster’. The novel bacterium, however, was distinguished from other phylogenetically related species ofPseudomonasby DNA–DNA hybridization studies and biochemical tests. On the basis of both phenotypic and phylogenetic findings, it is proposed that the novelPseudomonasisolates are classified asPseudomonas simiaesp. nov. The type strain ofP. simiaeis OLiT(=CCUG 50988T=CECT 7078T).
Brevibacillus ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field
Authors: Baek Sang-Hoon , Im Wan-Taek , Oh Hyun Woo , Lee Jung-Sook , Oh Hee-Mock , Lee Sung-Taik
Published: November 2006

A Gram-positive, rod-shaped, spore-forming bacterium, Gsoil 3088T, was isolated from soil from a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 3088Twas shown to belong to the familyPaenibacillaceae, being related toBrevibacillus centrosporus(96.6 %),Brevibacillus borstelensis(96.3 %),Brevibacillus parabrevis(96.1 %),Brevibacillus formosus(96.1 %),Brevibacillus brevis(96.1 %) andBrevibacillus laterosporus(96.0 %). The phylogenetic distances from other validly described species within the genusBrevibacilluswere greater than 4.0 % (i.e. there was less than 96.0 % similarity). The G+C content of the genomic DNA was 52.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; fatty acid profile, iso-C15 : 0, iso-C14 : 0and anteiso-C15 : 0) supported the affiliation of strain Gsoil 3088Tto the genusBrevibacillus. The results of physiological and biochemical tests allowed strain Gsoil 3088Tto be distinguished genotypically and phenotypically fromBrevibacillusspecies with validly published names. Strain Gsoil 3088T, therefore, represents a novel species of the genusBrevibacillus, for which the nameBrevibacillus ginsengisolisp. nov. is proposed. The type strain is Gsoil 3088T(=KCTC 13938T=LMG 23403T).
Paenibacillus panacisoli sp. nov., a xylanolytic bacterium isolated from soil in a ginseng field in South Korea
Authors: Ten Leonid N. , Baek Sang-Hoon , Im Wan-Taek , Lee Myungjin , Oh Hyun Woo , Lee Sung-Taik
Published: November 2006

A Gram-positive, facultatively anaerobic, motile, spore-forming bacterium, designated Gsoil 1411T, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 1411T belongs to the family Paenibacillaceae, with closest sequence similarity to the type strains of Paenibacillus xylanilyticus (95.7 %), Paenibacillus illinoisensis (95.2 %) and Paenibacillus pabuli (94.8 %). Strain Gsoil 1411T showed less than 94 % sequence similarity to the type strains of other recognized members of the genus Paenibacillus. In addition, the presence of MK-7 as the major menaquinone, anteiso-C15 : 0 as a major fatty acid (44.8 %) and the presence of PAEN513F and PAEN862F signature sequences suggest that it is affiliated to the genus Paenibacillus. The G+C content of the genomic DNA was 53.9 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 1411T is suggested to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus panacisoli sp. nov. is proposed. The type strain is Gsoil 1411T (=KCTC 13020T=LMG 23405T).
Reclassification of Lactobacillus amylophilus LMG 11400 and NRRL B-4435 as Lactobacillus amylotrophicus sp. nov.
Authors: Naser Sabri M. , Vancanneyt Marc , Snauwaert Cindy , Vrancken Gino , Hoste Bart , De Vuyst Luc , Swings Jean
Published: November 2006

The taxonomic position of six Lactobacillus amylophilus strains isolated from swine waste-corn fermentations was reinvestigated. All strains were included in a multilocus sequence analysis (MLSA) study for species identification of Lactobacillus using the genes encoding the phenylalanyl-tRNA synthase alpha subunit (pheS) and RNA polymerase alpha subunit (rpoA). Partial pheS and rpoA gene sequences showed that strains LMG 11400 and NRRL B-4435 represent a separate lineage that is distantly related to the type strain of L. amylophilus, LMG 6900T, and to three other strains of the species. The MLSA data showed that the two strains LMG 11400 and NRRL B-4435 constituted a distinct cluster, sharing 100 % pheS and rpoA gene sequence similarity. The other reference strains clustered together with the type strain of L. amylophilus, LMG 6900T, and were clearly differentiated from strains LMG 11400 and NRRL B-4435 (80 and 89 % pheS and rpoA gene sequence similarity, respectively). The 16S rRNA gene sequences of the latter two strains are 100 % identical, with the nearest phylogenetic neighbour L. amylophilus LMG 6900T showing only 97.2 % 16S rRNA gene sequence similarity. Further polyphasic taxonomic study based on whole-cell protein fingerprinting, DNA–DNA hybridization and biochemical features demonstrated that the two strains represent a single, novel Lactobacillus species, for which the name Lactobacillus amylotrophicus sp. nov. is proposed. The type strain is LMG 11400T (=NRRL B-4436T=DSM 20534T).
Selection of Appropriate Imaging Equipment and Methodology for Live Cell Imaging inDrosophila
Authors: Davis Ilan , Parton Richard M.
Published: November 2006

INTRODUCTION

The wide range of microscopy equipment and techniques are truly bewildering and ever-expanding. In the past two decades, there have been many revolutions in light microscopy techniques made possible by improvements in optics, detector technology, and computers. Furthermore, there is no indication that the rate of development of new equipment is slowing down. Here we attempt to provide an overview of available options and important considerations applicable to imagingDrosophilacells and tissues.
Live Imaging of Caenorhabditis elegans: Preparation of Samples
Authors: Podbilewicz Benjamin , Gruenbaum Yosef
Published: November 2006

INTRODUCTION

Caenorhabditis elegans, a small (adults are ~1 mm long), free-living soil nematode that feeds on bacteria, is an ideal organism for applying various live microscopy techniques. The organism is transparent, thus it is possible to microscopically analyze the whole animal throughout its entire life. Its complete cell lineage is known, making it possible to follow developmental and differentiation processes in real time. Furthermore, the development of transgenic techniques, as well as RNA interference (RNAi) methods and sophisticated genetic analyses, and the availability of a large collection of mutant lines all make C. elegans especially attractive for live microscopy. This protocol describes useful techniques for preparing C. elegans for live microscopic analysis. Details of sample preparation depend on the developmental stage of the worm to be studied.
Detection of Ubiquitylated Proteins in Mammalian Cells
Authors: Tansey William P.
Published: November 2006

INTRODUCTION

This assay is performed to detect ubiquitylated proteins in transfected mammalian cells. Twenty-four to 40 hours after transfection, cells are harvested, total ubiquitylated proteins are recovered by nickel-affinity chromatography, and specific proteins are detected by Western blotting.
Short‐term oscillations in avian molt intensity: evidence from the golden eagle Aquila chrysaetos
Authors: H. Ellis David , W. Lish James , Kéry Marc , M. Redpath Stephen
Published: November 2006

From a year‐long study of molt in the golden eagle Aquila chrysaetos, we recorded 2069 contour feathers replaced in 137 d (6 May‐19 September). Very few contour feathers were lost outside this period. From precise daily counts of feathers lost, and using time series analysis, we identified short‐term fluctuations (i.e., 19‐d subcycles) around a midsummer peak (i.e., a left‐skewed normal distribution). Because these subcycles have never before been reported and because the physiological basis for many aspects of avian molt is poorly known, we offer only hypothetical explanations for the controls responsible for the subcycles.
High JC virus load in gastric cancer and adjacent non‐cancerous mucosa
Authors: Murai Yoshihiro , Zheng Hua‐Chuan , Aziz Hekmat Osman Abdel , Mei Hong , Kutsuna Tomohiko , Nakanishi Yuko , Tsuneyama Koichi , Takano Yasuo
Published: November 2006

The JC virus (JCV) infects a large proportion of the worldwide population and approximately 90% of adults are seropositive. Recent reports have described the possibility of its oncogenetic role in several malignancies. The aim of the present study was to assess the oncogenetic significance of JCV for gastric cancer. Twenty‐two sample pairs of fresh tumor and adjacent non‐cancerous tissue (ANCT) as well as 10 normal gastric mucosa specimens were investigated on the basis of nested polymerase chain reaction (PCR) followed by Southern blotting, DNA direct sequencing, real‐time PCR, in situ PCR and immunohistochemistry. The T antigen sequence was detected in 86.4% of gastric cancers and ANCT, and in 100% of the normal mucosa samples, as for virus capsid protein, 54.1%, 68.1% and 70%, respectively. A generally low incidence was noted for agnoprotein. The JCV DNA load was approximately 10‐fold higher in both gastric cancers and paired ANCT (4784 ± 759 and 5394 ± 1466 copies/µg DNA, respectively) than in normal gastric tissue (542.4 ± 476.0 copies/µg DNA, P < 0.0001). In situ PCR revealed sporadic JCV genome‐positive cancer cells and foveolar epithelial cells. T antigen protein expression assessed by immunohistochemistry was detected only in one case (1/22; 4.5%), probably because the half life of T antigen might be short. It was concluded that the gastric epithelium in most Japanese people is infected with JCV at a low rate but levels of infection are increased markedly in both cancer cells and ANCT, indicating that multiplication of JCV copies might be a risk factor and a background for gastric carcinogenesis. (Cancer Sci 2007; 98: 25–31)
Evaluation of S100A10, annexin II and B‐FABP expression as markers for renal cell carcinoma
Authors: Domoto Tomohiro , Miyama Youko , Suzuki Hiroko , Teratani Takumi , Arai Kazumori , Sugiyama Takayuki , Takayama Tatsuya , Mugiya Soichi , Ozono Seiichiro , Nozawa Ryushi
Published: November 2006

This study aimed to analyze expression of S100A10, annexin II and B‐FABP genes in renal cell carcinoma (RCC) and their potential value as tumor markers. Furthermore, any correlation between the gene expression and prognostic indicators of RCC was analyzed. Expression of each gene was estimated by RT‐PCR in the non‐neoplastic (normal) and tumorous parts of resected kidney samples. Also, each antigen was immunostained in RCC and normal kidney tissues. Expression of the S100A10 gene averaged 2.5‐fold higher in the tumor than that in the normal tissues (n = 47), after standardization against that of β‐actin. However, expression of annexin II, a natural ligand of S100A10, was only 1.64‐fold higher. In the tissue sections of RCC, S100A10 and annexin II were immunostained in membranes. In the normal renal epithelia, however, both antigens were stained in the Bowman's capsule and the tubules from Henle's loop through the collecting duct system, but not in the proximal tubules, from where most RCC are derived. In contrast, expression of the B‐FABP gene was 20‐fold higher in the tumor. No B‐FABP was immunohistochemically detected in normal kidney sections, but it was stained in the cytoplasm of RCC tissue sections. S100A10 and B‐FABP genes were overexpressed regardless of nuclear grade and stage of RCC. Immunopositivity in RCC tissues (n = 13) was 100% for S100A10 and annexin II, and 70% for B‐FABP; however, no clear relationship was observed in either antigen with nuclear grade and stage. It was found that all three performed well as RCC markers. B‐FABP was most specific to RCC, as it was expressed little in normal kidney tissues. (Cancer Sci 2007; 98: 77–82)
Do skin prick and conjunctival provocation tests predict symptom severity in seasonal allergic rhinoconjunctivitis?
Authors: Radcliffe Michael J , Lewith George T , Prescott Philip , Church Martin K , Holgate Stephen T
Published: November 2006

Background
In the investigation of seasonal allergic rhinoconjunctivitis (SAR), quantitative skin and conjunctival allergen challenge tests are used to measure individual allergen sensitivity. These tests are reproducible and relate well to prevalence but their relationship to symptom severity is less well established.

Objective
We wished to determine if quantitative skin prick tests (QSPT) and conjunctival provocation tests (CPTs) using a single grass pollen allergen extract are reproducible and predict symptom severity in SAR.

Methods
We retrospectively analysed data from 91 participants in a previously published randomized placebo controlled study of low dosage allergen immunotherapy who were randomized to receive placebo treatment. We examined the relationship between pre‐seasonal QSPT, CPT and SAR symptoms.

Results
We found a high level of reproducibility when repeated measures were compared for both the QSPT (P<0.001) and the CPT (P<0.001) and moderate correlation (0.49) between the standard skin prick test (SPT) and the QSPT (P<0.001). We found weak negative correlation (−0.27) between the QSPT and the CPT (P<0.001). We found no correlation between seasonal symptom, use of rescue medication or quality of life (QOL) scores and pre‐seasonal QSPT or CPT.

Conclusion
In the assessment of seasonal rhinoconjunctivitis, quantitative skin and conjunctival allergen challenge tests are strongly reproducible, although there is no correlation between these tests and seasonal symptom, use of rescue medication or QOL scores.
Evidence for immunological priming and increased frequency of CD4+ CD25+ cord blood T cells in children born to mothers with type 1 diabetes
Authors: Holm B C , Svensson J , Åkesson C , Arvastsson J , Ljungberg J , Lynch K , Ivarsson S-A , Lernmark Å , Cilio C M ,   Diabetes Prediction Study in Skåne (DiPiS)
Published: November 2006

Maternal transmission of islet autoantibodies to children born to mothers with type 1 diabetes (T1D) has been shown to protect from autoantibodies and diabetes development later in life. However, the factors conferring disease protection are poorly understood. The aim of this study was to evaluate comparatively proinflammatory cytokines, autoantibodies and lymphocyte subsets in cord blood (CB) of children born to mothers with either T1D (n = 13), gestational diabetes (GDM) (n = 32) or healthy mothers (n = 81) in relation to transplacental passage of autoantibodies. The results are consistent with early priming of the fetal immune system only in children born to mothers with T1D. Levels of interleukin (IL)-1β (P = 0·022), tumour necrosis factor (TNF)-α (P = 0·002) and IL-8 (P = 0·0012), as well as the frequency of CD4+ CD25+ T cells (P < 0·01) were significantly increased, and the increased levels correlated positively with anti-GAD65 autoantibody (GADA) levels. Moreover, CD4+ CD25+ T cells of children born to T1D mothers exhibited a more pronounced memory phenotype with increased CCR4 expression and down-regulation of CD62L. These data suggest that early activation of the fetal immune system as a consequence of maternal autoimmunity and transplacental passage of GADA may influence the generation and expansion of fetal regulatory T cells. This might induce an early antigen-specific immunological tolerance that could protect against T1D later in life.
Trans-dimensional inverse problems, model comparison and the evidence
Authors: Sambridge M. , Gallagher K. , Jackson A. , Rickwood P.
Published: November 2006

In most geophysical inverse problems the properties of interest are parametrized using a fixed number of unknowns. In some cases arguments can be used to bound the maximum number of parameters that need to be considered. In others the number of unknowns is set at some arbitrary value and regularization is used to encourage simple, non-extravagant models. In recent times variable or self-adaptive parametrizations have gained in popularity. Rarely, however, is the number of unknowns itself directly treated as an unknown. This situation leads to a transdimensional inverse problem, that is, one where the dimension of the parameter space is a variable to be solved for.

This paper discusses trans-dimensional inverse problems from the Bayesian viewpoint. A particular type of Markov chain Monte Carlo (MCMC) sampling algorithm is highlighted which allows probabilistic sampling in variable dimension spaces. A quantity termed the evidence or marginal likelihood plays a key role in this type of problem. It is shown that once evidence calculations are performed, the results of complex variable dimension sampling algorithms can be replicated with simple and more familiar fixed dimensional MCMC sampling techniques. Numerical examples are used to illustrate the main points. The evidence can be difficult to calculate, especially in high-dimensional non-linear inverse problems. Nevertheless some general strategies are discussed and analytical expressions given for certain linear problems.
Management of field margins to maximize multiple ecological services
Authors: OLSON DAWN M. , WÄCKERS FELIX L.
Published: November 2006

Vegetative buffers in agricultural landscapes can provide a range of important ecological services, including conservation of native flora and fauna, enhancement of biological pest control and reduction of agrochemical drift. Typically, studies addressing the impact of such vegetative elements focus on one particular benefit. We investigated whether the benefits of field margins that had been established for conservation of northern bobwhite quail Colinus virginianus populations extended to the enhancement of biological pest control in adjacent conservation tillage cotton fields.

Densities of a selection of insect species and the predation and parasitism rates of insect pest species were measured in first‐ and second‐year field margins established for bobwhite quail as well as in an adjacent cotton crop.

Second‐year field margins yielded higher densities of all species sampled, with the exception of staphylinids and cotton aphids. Despite this, thrips and their predator, Orius insidiosus, were the only species that were also more abundant in the adjacent cotton field. Tachinids and Trichogramma and Lygus species, appeared to prefer the field margin vegetation over the cotton.

Overall, the impact of second‐year margins on the cotton crop did not significantly differ from first‐year margins with regard to pest occurrence or biological control.

Analysis of the sugar content in Meteorus autographae, a generalist parasitoid of Lepidoptera larvae, suggested that this species is severely food‐limited in the field margins established for bobwhite quail.

Synthesis and applications. This study shows that field margins designed to specifically benefit bobwhite quail may be unsuitable for providing other ecological services. By making small adjustments in the vegetative composition of these field margins, such as adding early season nectar‐producing plants, it may be feasible to combine biodiversity and pest‐control benefits and thereby optimize the overall ecological services to be gained.
SINEs of progress: Mobile element applications to molecular ecology
Authors: RAY DAVID A.
Published: November 2006

Mobile elements represent a unique and under‐utilized set of tools for molecular ecologists. They are essentially homoplasy‐free characters with the ability to be genotyped in a simple and efficient manner. Interpretation of the data generated using mobile elements can be simple compared to other genetic markers. They exist in a wide variety of taxa and are useful over a wide selection of temporal ranges within those taxa. Furthermore, their mode of evolution instills them with another advantage over other types of multilocus genotype data: the ability to determine loci applicable to a range of time spans in the history of a taxon. In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology.
Proteins encoded by the conservon of Streptomyces coelicolor A3(2) comprise a membrane‐associated heterocomplex that resembles eukaryotic G protein‐coupled regulatory system
Authors: Komatsu Mamoru , Takano Hideaki , Hiratsuka Tomonari , Ishigaki Yuji , Shimada Kyoko , Beppu Teruhiko , Ueda Kenji
Published: November 2006

Streptomyces coelicolor A3(2) retains unique conserved operons termed conservons. Here, one of the conservons (cvn9), which encodes five proteins (A9‐E9), was characterized. Mutants for cvnA9 and cvnA10 conditionally overproduced actinorhodin and performed precocious aerial growth, while a cvnE9 mutant showed the parental phenotype. Transcription of bldG, adpA and bldN was upregulated in the cvnA9 mutant. A9‐D9 were detected in the insoluble fraction of cell‐free extract of S. coelicolor by Western analysis. Biochemical analyses revealed that A9 has ATP‐hydrolysing and adenine nucleotide‐binding activities; D9 has GTP‐hydrolysing and guanine nucleotide‐binding activities; and E9 shows a typical spectrum similar to cytochrome P450. The comprehensive interaction assays demonstrated the occurrence of specific interactions between A9 and B9, A9 and C9, B9 and B9, B9 and D9, and C9 and D9. A9 associated with and dissociated from B9 (and C9) when ATP and ATP‐γ‐S were supplied in the reaction respectively. Similarly, D9 associated with and dissociated from B9 (and C9) when GTP and GTP‐γ‐S were supplied respectively. A9 and B9 were also shown for the occurrence as homocomplexes. Probably, Cvn9 proteins comprise a membrane‐associated heterocomplex resembling the eukaryotic G‐protein‐coupled receptor system, which may serve as a signal transducer that connects to the bld cascade.
Matrix metalloproteinase‐19 is highly expressed in active multiple sclerosis lesions
Authors: Van Horssen J. , Vos C. M. P. , Admiraal L. , Van Haastert E. S. , Montagne L. , Van Der Valk P. , De Vries H. E.
Published: November 2006

Matrix metalloproteinases (MMPs) are proteases known for their capacity to degrade extracellular matrix (ECM) components. MMPs have been implicated in several central nervous system (CNS) diseases, including multiple sclerosis (MS). Microarray analysis has demonstrated significant increased mRNA levels of MMP‐19 in chronic MS lesions, suggesting a role of MMP‐19 in MS pathogenesis. Therefore, in this study, we investigated the expression pattern and cellular localization of MMP‐19 protein in various well‐characterized MS lesion stages. In normal control patient white matter, MMP‐19 was constitutively expressed by microglia throughout the brain parenchyma, suggesting a physiological role for this MMP family member. Likewise, MMP‐19 was expressed by microglia in (p)reactive MS lesions, albeit more intense. In highly active demyelinating MS lesions, parenchymal and perivascular myelin‐laden macrophages were strongly immunoreactive for MMP‐19, whereas reactive astrocytes were occasionally immunopositive. Astrocytes in chronic inactive lesions were weakly stained for MMP‐19. In vitro, MMP‐19 was expressed in cultures of primary human microglia, not in astrocyte cultures. As MMP‐19 is able to degrade basement membrane constituents and other ECM proteins, it is conceivable that this relatively novel MMP family member contributes to MS pathology by remodelling the ECM of the CNS, thereby influencing leucocyte infiltration, axonal regeneration and astrogliosis.
Differential gene expression between human schwannoma and control Schwann cells
Authors: Hanemann C. O. , Bartelt‐Kirbach B. , Diebold R. , Kämpchen K. , Langmesser S. , Utermark T.
Published: November 2006

The NF2 gene encodes the tumour suppressor protein merlin. The mutation of a single allele of this gene causes the autosomal dominantly inherited disease neurofibromatosis type 2 (NF2), which is characterized mainly by vestibular schwannoma carrying a second hit mutation. Complete lack of merlin is also found in spontaneous schwannomas and meningiomas. As the events leading to schwannoma development are largely unknown we investigated the differences in gene expression between schwannoma cells from NF2 patients and normal human primary Schwann cells by cDNA array analysis. We identified 41 genes whose expression levels differed by more than factor 2. Most of these clones were corroborated by real‐time reverse transcription polymerase chain reaction analysis. By this method a total of seven genes with increased and seven genes with decreased mRNA levels in schwannoma compared with normal Schwann cells could be identified. Regulated clones, some of which not been described in Schwann cells earlier, included matrix metalloproteinase’s, growth factors, growth factor receptors and tyrosine kinases.
Are cranial germ cell tumours really tumours of germ cells?
Authors: Scotting P. J.
Published: November 2006

Germ cell tumours of the brain and those that occur in the gonads are believed to share a common origin from germ cell progenitors. This ‘germ cell theory’ rests upon similar histopathology between these tumours in different locations and the belief that endogenous somatic cells of the brain could not give rise to the range of cell types seen in germ cell tumours. An alternative ‘embryonic cell theory’ has been proposed for some classes of cranial germ cell tumours, but this still relies on the misplacement of cells in the brain (in this case the earliest embryonic stem cells) during early embryonic development. Recent evidence has demonstrated that neural stem cells of the brain can also give rise to many of the cell types seen in germ cell tumours. These data suggest that endogenous progenitor cells of the brain are a plausible alternative origin for these tumours. This idea is of central importance for studies aiming to elucidate the mechanisms of tumour development. The application of modern molecular analyses to reveal how tumour cells have altered with respect to their cell of origin relies on the certain identification of the cell from which the particular tumour arose. If the identity of this cell is mistaken, then studies to elucidate the mechanisms by which the progenitor cell has been subverted from its normal behaviour will not yield useful information. In addition, it will prove impossible to generate an appropriate animal model in which to study the underlying causes of those tumours. This article makes the case that current assumptions of the origins of cranial germ cell tumours are unreliable. It reviews the evidence in favour of the ‘germ cell theory’ and argues in favour of a ‘brain cell theory’ in which endogenous neural progenitor cells of the brain are the likely origin for these tumours. Thus, the case is made that cranial germ cell tumours, like other brain tumours, arise by the transformation of progenitor cells normally resident in the brain.
Phenotypic Analysis of IL‐10‐treated, Monocyte‐derived Dendritic Cells in Patients with Systemic Lupus Erythematosus
Authors: Figueroa‐Vega N. , Galindo‐Rodríguez G. , Bajaña S. , Portales‐Pérez D. , Abud‐Mendoza C. , Sánchez‐Torres C. , González‐Amaro R.
Published: November 2006

Dendritic cells (DC) play a dual role in the immune response, participating in its induction, and the maintenance of immune tolerance. The aim of this work was to perform a quantitative and phenotypic analysis of DC generated in vitro in the presence of IL‐10 in patients with systemic lupus erythematosus (SLE). Blood samples were obtained from 10 active and untreated patients with SLE and six controls. Monocyte‐derived DC were generated in vitro in the presence or absence of IL‐10, and a quantitative and phenotypic analysis was performed. We found that freshly isolated monocytes from SLE patients had an increased expression of CD11b. On the other hand, the efficiency of in vitro DC generation was diminished in blood samples from SLE patients for conventional DC, but not for IL‐10‐treated DC. A diminished expression of HLA‐DR, CD9 and CD86 was observed in conventional DC from SLE patients compared with controls. In contrast, enhanced levels of HLA‐DR, CD80, CD9 and CD151 tetraspanins, FN1 (a class II MHC‐tetraspanin epitope), CD85j/ILT2 and CD69 were detected in IL‐10‐treated DC from SLE patients. Accordingly, the phenotypic profile of IL‐10‐treated DC was very different in SLE and controls. However, the synthesis of IL‐10 and IL‐12 was similar in IL‐10‐treated and conventional cells in both SLE patients and controls. Our findings on the aberrant phenotype of IL‐10‐treated DC in SLE and their normal efficiency of in vitro generation may be important for the design of future therapies of this condition based on the administration of DC to induce immune tolerance.
Testing the phenotypic gambit: phenotypic, genetic and environmental correlations of colour
Authors: HADFIELD J. D. , NUTALL A. , OSORIO D. , OWENS I. P. F.
Published: November 2006

Evolutionary theory is primarily concerned with genetic processes, yet empirical testing of this theory often involves data collected on phenotypes. To make this tenable, the implicit assumption is often made that phenotypic patterns are good predictors of genetic patterns; an assumption that coined the phenotypic gambit. Although this assumption has been validated for traits with high heritability, such as morphology, its generality for traits with low heritabilities, such as life‐history and behavioural traits, remains controversial. Using a large‐scale cross‐fostering experiment, we were able to measure genetic, common environmental and phenotypic correlations between four colour traits and two skeletal traits in a wild population of passerine birds, the blue tit (Parus caeruleus). Colour traits had little heritable variation but common environment effects were found to be important; skeletal traits showed the opposite pattern. Positive correlations because of a shared natal environment were found between all traits, obscuring negative genetic correlations between some colour and skeletal traits. Consequently, phenotypic patterns were poor surrogates for genetic patterns and we suggest that this may be common if trade‐offs or substantial parental effects exist. For this group of traits, the phenotypic gambit cannot be made and we suggest caution when inferring genetic patterns from phenotypic data, especially for behavioural and life‐history traits.
Is the short‐term outcome of transurethral resection of the prostate affected by preoperative degree of bladder outlet obstruction, status of detrusor contractility or detrusor overactivity?
Authors: TANAKA YOSHINORI , MASUMORI NAOYA , ITOH NAOKI , FURUYA SEIJI , OGURA HIROSHI , TSUKAMOTO TAIJI
Published: November 2006

Aim: The aim of this study was to investigate whether the preoperative degree of bladder outlet obstruction (BOO), detrusor underactivity (DUA) or detrusor overactivity (DO) affected the short‐term outcome of transurethral resection of the prostate (TURP) for patients with lower urinary tract symptoms suggestive of benign prostatic hyperplasia (LUTS/BPH).

Methods: Ninety‐two patients with LUTS/BPH aged 50 years or older who were considered to be appropriate candidates for TURP were included in this study. Pressure‐flow study and filling cystometry were performed to determine BOO, DUA and DO before TURP. The efficacy of TURP was determined at 3 months after surgery using the efficacy criteria for treatment of BPH assessed by the International Prostate Symptom Score, QOL index, maximum flow rate and postvoid residual urine volume.

Results: On preoperative urodynamics, 60%, 40% and 48% of patients showed BOO, DUA and DO, respectively. After TURP, 76% showed ‘excellent’ or ‘good’ overall efficacy, whereas only 13% fell into the ‘poor/worse’ category. The efficacy was higher as the preoperative degree of BOO worsened. In contrast, neither DO nor DUA influenced the outcome of TURP. However, the surgery likely provided unfavorable efficacy for patients having DO but not BOO. Only 20% of the patients who had both DO and DUA but did not have BOO achieved efficacy.

Conclusions: Transurethral resection of the prostate is an effective surgical procedure for treatment of LUTS/BPH, especially for patients with BOO. DUA may not be a contraindication for TURP. The surgical indication should be circumspect for patients who do not have BOO but have DO.
Desulfurization of aromatic sulfonates by rhizosphere bacteria: high diversity of the asfA gene
Authors: Schmalenberger Achim , Kertesz Michael A.
Published: November 2006

The plant growth‐promoting effect of Pseudomonas putida S‐313 is associated with its ability to desulfurize arylsulfonates. To understand this further, other plant‐associated bacteria able to desulfurize a range of arylsulfonates were isolated from the rhizospheres of winter and spring barley. The isolates belonged to the β‐proteobacteria, including bacteria from the Variovorax paradoxus group and from the Acidovorax genus. They desulfurized toluenesulfonate to p‐cresol, and were found to contain orthologues of the P. putida S‐313 asfA gene (> 70% sequence identity to AsfA), which is required for aryldesulfonation in this species. Further putative asfA orthologues were identified in several bacteria and cyanobacteria whose genomes have been sequenced, but of these only Cupriavidus (Ralstonia) metallidurans was able to utilize arylsulfonates as sulfur source. Cultivation of V. paradoxus, C. metallidurans or P. putida S‐313 with toluenesulfonate as sulfur source led to a 100‐fold increase in expression of the asfA homologues, which was largely repressed when sulfate was added. Polymerase chain reaction with degenerate primers was used to generate asfAB clone libraries from spring‐ and winter‐barley rhizosphere DNA. Cluster analysis of 76 sequenced AsfA fragments revealed a broad diversity, with the majority of the sequences clustered together with AsfA from bacteria that are able to utilize toluenesulfonate as sulfur source. The diversity of asfA in barley rhizosphere underlines the importance of the desulfonation process for bacteria that inhabit the plant rhizosphere.
Osmoadaptative responses in the rhizobia nodulating Acacia isolated from south‐eastern Moroccan Sahara
Authors: Essendoubi Mohammed , Brhada Fatiha , Eljamali Jamal Eddine , Filali‐Maltouf Abdelkarim , Bonnassie Sylvie , Georgeault Sylvie , Blanco Carlos , Jebbar Mohamed
Published: November 2006

Four strains of rhizobia nodulating Acacia were isolated from the Moroccan desert soil by trapping with seedlings of Acacia gummifera and Acacia raddiana, and were studied for their ability to tolerate high salinity and dryness conditions. The strains MDSMC 2, MDSMC 18 and MDSMC 50 were halotolerant (they tolerated up to 1 M NaCl) and they accumulated glutamate and mannosucrose. The synthesis of the latter solute, which is the major endogenous osmolyte, is partially repressed in the presence of glycine betaine. The strain MDSMC 34 was less halotolerant (growth inhibited by a concentration greater than 0.5 M NaCl), and accumulated trehalose (as the main endogenous osmolyte) and glutamate. Rhizobia from the Moroccan desert soil were highly resistant to desiccation and their tolerance to dryness was stimulated by osmotic pretreatment. Thus, the accumulation of mannosucrose or trehalose by desert rhizobia represents both an osmoadaptative response and a part of a desiccation tolerance mechanism.
Expression of an engineered granule‐bound Escherichia coli maltose acetyltransferase in wild‐type and amf potato plants
Authors: Nazarian Firouzabadi Farhad , Vincken Jean‐Paul , Ji Qin , Suurs Luc C. J. M. , Visser Richard G. F.
Published: November 2006

Starch is used in many industrial applications, but often requires chemical derivatization to enhance its properties before use. In particular, the stability of starch polymers in solution is improved by acetylation. A drawback of this treatment is the use of pollutant chemicals. A biological alternative to chemical derivatization was investigated by the expression of an amyloplast‐targeted Escherichia coli maltose acetyltransferase (MAT) gene in tubers of wild‐type (Kardal) and mutant amylose‐free (amf) potato plants. MAT was expressed as such, or fused to the N‐ or C‐terminus of a non‐catalytic starch‐binding domain (SBD) to target the starch granule. Starch granules derived from transgenic plants were found to contain acetyl groups, although their content was low, opening up an avenue to move away from the post‐harvest chemical derivatization of starch. MAT inside starch granules was found to be active post‐harvest when supplied with acetyl‐coenzyme A and glucose or maltose, but it did not acetylate starch polymers in vitro. Starch granules from transformants in which MAT alone was expressed also showed MAT activity, indicating that MAT is accumulated in starch granules, and has affinity for starch by itself. Furthermore, starch granule morphology was altered, and fusion proteins containing MAT and SBD seemed to have a higher affinity for starch granules than two appended SBDs. These results are discussed against the background of the quaternary structure of MAT.
HRM and project intensification in R&D‐based companies: a study of Volvo Car Corporation and AstraZeneca
Authors: Bredin Karin , Söderlund Jonas
Published: November 2006

Projects have become the standard mode of organising R&D activities. The main focus of this paper is to analyse the relationship between the project operations of the R&D‐based firm and its Human Resource Management (HRM). This paper draws on a comparative case study of AstraZeneca and Volvo Car Corporation. It is argued that the project intensification currently under way has some important structural and content effects on the HRM practice of the firms. As to the content effects, we identify five critical areas within the HRM practice where special attention is needed due to project intensification. As to the structural effects, we identify two separate logics for HR specialists: the HR‐based logic and the task‐based logic. These logics give new knowledge about the design of the HR organisation and how the HR departmental structures should be adapted in a project‐intensive setting. The case studies also illustrate three alternative roles for line managers when they assume increased HR responsibility.
The front end of innovation in an era of industry convergence: evidence from nutraceuticals and functional foods
Authors: Bröring Stefanie , Martin Cloutier L. , Leker Jens
Published: November 2006

Industry convergence, defined as a ‘blurring’ of boundaries between industries, induced by converging value propositions, technologies and markets, appears to be a pervasive phenomenon leading to the emergence of inter‐industry segments. A current example of convergence can be witnessed in the nutraceuticals and functional foods sector, emerging at the boundary between the food and pharmaceutical industries. Not only technologies blur, but there is also a convergence of demand structures: consumers try to satisfy different needs in one transaction. In this context, this paper explores how actors from different industry‐specific resource backgrounds can engage in an innovative activity requiring new technological and marketing competences. Given that absorptive capacity is limited by existing competences, this paper asks how organizations with different R&D competences are able to seize opportunities for innovation emerging from convergence. Empirical findings based on primary data collected from 54 R&D projects of a nutraceutical cluster show that there are different approaches of front end decision making: while some firms follow existing processes for front end decision making, others leave existing paths and need partners to fill in gaps already identified at the front end of innovation.
Second Language Learning and Cultural Representations: Beyond Competence and Identity
Authors: Rubenfeld Sara , Clément Richard , Lussier Denise , Lebrun Monique , Auger Réjean
Published: November 2006

The socio‐contextual model of second language (L2) learning proposes that L2 learning is influenced by aspects of contact with the L2 community, L2 confidence, and identification to both the first language and L2 community (Clément, 1980; Noels & Clément, 1996). The present study examines how these aspects are linked to individuals' cultural representations, corresponding to attitudes toward the L2 community (Sperber, 1996). Respondents included Francophone (n= 50) and Anglophone (n= 50) university students with low and high ethnolinguistic vitality, respectively. Path analyses were conducted in order to examine the interrelations between aspects of the socio‐contextual model and cultural representations. These analyses revealed that, for both groups, learning an L2 leads individuals to hold more positive and accepting views of the L2 community. Implications of the findings are discussed with respect to ethnolinguistic vitality, L2 learning, and cultural representations.
Action‐oriented representation of peripersonal and extrapersonal space: Insights from manual and locomotor actions1
Authors: HIGUCHI TAKAHIRO , IMANAKA KUNIYASU , PATLA AFTAB E.
Published: November 2006

Abstract:  This paper reviews behavioral evidence demonstrating that space is accurately represented in the brain in relation to action capabilities. We initially review intriguing neuropsychological findings that show that space is differentially represented depending on whether the area is in reach of the hand (peripersonal space) or out of reach of the hand (extrapersonal space). We then review the literature on the characteristics of locomotor actions for avoiding obstacles to show that the relative dimensions of obstacles to relevant body parts are accurately represented at least one step before the obstacles are reached, i.e., while the obstacles are present in the extrapersonal space. The findings obtained from a number of studies on manual and locomotor actions will yield tentative conclusions: (a) the representation of one's body (body schema) is deeply involved in one's representation of space; (b) the representation of space is modified in response to alteration of action capabilities, although this is likely to occur only for well‐learned actions, irrespective of the type; and (c) representation of space centered on the hand somewhat differs from that centered on the whole body.
Role of stiffness in weight perception
Authors: KOIKE YASUHARU , KIM JAEHYO , DUK SHIN
Published: November 2006

Abstract:  Here, we focused on a load‐on task to clarify the judgment mechanism for weight perception. We measured hand trajectory and surface electromyography to estimate time‐varying stiffness and torque patterns in joints. Our results showed that the goal of learning motor skills under load‐on tasks is to maintain the hand position, and that humans produce force with cocontraction and increasing stiffness levels according to the weight of an object. Finally, we examined whether stiffness is an effective parameter as an efferent signal for weight perception and found that stiffness plays an important role in weight perception.
Audiotactile multisensory interactions in human information processing
Authors: KITAGAWA NORIMICHI , SPENCE CHARLES
Published: November 2006

Abstract: The last few years has seen a very rapid growth of interest in how signals from different sensory modalities are integrated in the brain to form the unified percepts that fill our daily lives. Research on multisensory interactions between vision, touch, and proprioception has revealed the existence of multisensory spatial representations that code the location of external events relative to our own bodies. In this review, we highlight recent converging evidence from both human and animal studies that has revealed that spatially‐modulated multisensory interactions also occur between hearing and touch, especially in the space immediately surrounding the head. These spatial audiotactile interactions for stimuli presented close to the head can affect not only the spatial aspects of perception, but also various other non‐spatial aspects of audiotactile information processing. Finally, we highlight some of the most important questions for future research in this area.
Dynamic spatial cognition: Components, functions, and modifiability of body schema1
Authors: SEKIYAMA KAORU
Published: November 2006

Abstract:  There has been substantial progress towards the understanding of the classical notion of “body schema,” with recent advances in experimental methodology and techniques. Mental rotation of the hands can be used as a tool to investigate body schema. Research has shown that implicit motor imagery (i.e., mental simulated movements) can be generated based on the body schema, by combining both stored and incoming sensory information. Multimodal stimulation of peripersonal space has also served as an experimental paradigm for the study of body schema. Perception of peripersonal space is based on body‐part‐centered space coding that is considered as a manifestation of the body schema, its function being to integrate visual, tactile, and proprioceptive information, and perhaps motor plans as well. By combining such experimental paradigms with neuroimaging and neurophysiological techniques, research has converged to show that the parietal association cortex and premotor cortex are important for the body schema. Multimodal perception of body parts and peripersonal space have been also studied in relation to prism adaptation and tool use effects, indicating a clear modifiability of the body schema. Following prolonged adaptation to reversed vision, a reversed hand representation can be added to the body schema like a tool. The stored component of the body schema may not be established well in young children. But once established it may not be deleted even after an arm is amputated, although it may be weakened. All of these findings help to specify properties of the body schema, its components, functions, and modifiabilities.