bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in nematode communities after manuring in millet fields in Senegal
Authors: Villenave Cécile , Oliver Robert , Fernandes Paula , Ekschmitt Klemens , Bongers Tom
Published: September 2003

Changes in the soil nematofauna community structure were followed in nine millet fields on seven farms in two villages in Senegal during one cropping cycle. Cultivation practices were done by field owners. One plot in each field was divided into two subplots; in one of these, manure (20 t ha-1) was added at sowing. Before the manure input, at mid-cycle and at millet harvest, the structure of the nematode fauna was studied. Soil physico-chemical characteristics, microbial carbon and plant production were measured at sowing and at millet harvest. In the sub-plots where manure was added, millet yield increased by 155%, the mineral nitrogen content of the soil increased by about 45%, while nitrogen flux increased by 150% and microbial biomass by 65%. The significant enrichment of soil by manure led to a 75% increase in total nematode population density at mid-cycle and to a 30% increase at harvest time. The density of opportunistic bacterial-feeding and fungal-feeding nematodes was significantly larger with than without manure. This result is similar to those of comparable studies in temperate areas; however the relative abundance of enrichment opportunists was extremely low with regard to that found under similar conditions in temperate ecosystems. Furthermore, the abundance of the c-p 2 bacterialfeeding nematodes, belonging mainly to the family Cephalobidae, was strongly correlated with soil microbial biomass. The other c-p feeding guilds showed no correlation with nitrogen flux, or soil microbial biomass.
Production and characterisation of monoclonal antibodies to antigens from Xiphinema index
Authors: Lamberti Franco , Curtis Rosane , Brown Derek , Jones John , Moens Maurice , Chen Qing
Published: September 2003

When feeding, Xiphinema index induces remarkable cellular modifications at the feeding site in the root tips of its hosts, similar to those induced by root endoparasites such as Meloidogyne spp. The large size of X. index enables direct analysis of their proteins. Following immunisation of a mouse with macerated extracts of X. index bodies, a panel of monoclonal antibodies (MAbs) was obtained against this nematode. The MAbs were used in immunolocalisation studies and antibodies recognising epitopes present at the surface coat, inner cuticle, dorsal gland cell and dorsal duct, body wall muscle fibres, nervous system and reproductive system were identified. These antibodies provide useful tools for studying plant-nematode interactions.
Heterorhabditis baujardi sp. n. (Rhabditida: Heterorhabditidae) from Vietnam and morphometric data for H. indica populations
Authors: Nguyen Ngoc Chau , Phan Ke Long , Moens Maurice , Subbotin Sergei
Published: September 2003

A survey of entomopathogenic nematodes in Vietnam yielded several Heterorhabditis isolates. The majority belonged to H. indica; their morphometrics are given in this paper. Three isolates collected in forests in Backan, Ninhbinh and Kontum provinces, Vietnam are here described as a new species Heterorhabditis baujardi sp. n. The new species is distinguished from the other ten valid Heterorhabditis species by a combination of morphological, morphometrical, and DNA characters. Heterorhabditis baujardi sp. n. is morphometrically similar to H. indica, but can be separated from this species by the shape of the gubernaculum and the number of normal pairs of genital papillae. The gubernaculum of H. baujardi sp. n. with the proximal end ventrally curved resembles that of H. bacteriophora. Heterorhabditis baujardi sp. n. can be separated from this latter species by a shorter body length of infective juveniles and longer spicules, longer gubernaculum, and a higher spicule length to anal body diameter ratio of males. The canonical discriminant analysis of morphometrical characters of both infective juveniles and males failed to discriminate Heterorhabditis baujardi sp. n. from H. indica. However, the new species was easily distinguished from H. downesi, H. marelatus, H. megidis and H. bacteriophora. Heterorhabditis baujardi sp. n. was slightly separated from H. bacteriophora by variables of the infective juveniles, but was clearly distinguished by variables of the males. Cross-breeding tests using isolates of the new species and H.indica did not yield fertile progeny. Analysis of the ITS1 sequence of rDNA of H. baujardi sp. n. revealed substantial differences with other known ITS1 Heterorhabditis sequences. Phylogenetic relationships between Heterorhabditis species and the usefulness of morphological and molecular characters for identification of species from this group are discussed.
Characterisation of virulence in populations of Meloidogyne chitwoodi and evidence for a resistance gene in pepper Capsicum annuum L. line PM 217
Authors: Berthou François , Palloix Alain , Mugniéry Didier
Published: September 2003

Doubled haploid lines of pepper from the F1 hybrid of PM 217 × Yolo Wonder were tested for their resistance to different populations of Meloidogyne chitwoodi. PM 217 has the Me1 gene for resistance to Meloidogyne incognita, M. arenaria, M. javanica and Me2 gene for resistance to M. hispanica. With two European populations a clear segregation was observed. The necrotic reactions and the resistant: susceptible segregation of 1 : 1 suggested the occurrence of a major gene, different from but close to Me1. With another European population of M. chitwoodi and with M. fallax, no resistance was observed. Two American and two southern European M. chitwoodi populations were totally avirulent to the two pepper parents. These results demonstrate the existence of great polymorphism in M. chitwoodi populations and of a major gene in pepper controlling a specific resistance against some populations.
A review of plant-parasitic and soil nematodes in Slovenia
Authors: Karssen Gerrit , Širca Saša , Urek Gregor
Published: September 2003

An overview is presented of all plant parasitic and soil inhabiting nematodes found in Slovenia. Most of the nearly 50 records, representing 115 nematode genera and 112 different species, have been published in national journals or technical reports and are therefore not directly available. These records include plant- and animal-parasitic nematodes, free-living nematodes and marine nematodes. The greater part of them was isolated from agricultural areas, while others were found in natural areas such as the Adriatic sea and caves.
Baujardia mirabilis gen. n., sp. n. from pitcher plants and its phylogenetic position within Panagrolaimidae (Nematoda: Rhabditida)
Authors: Van Driessche Rita , De Ley Irma Tandingan , De Ley Paul , Segers Hendrik , Bert Wim
Published: September 2003

Measurements, line drawings and scanning electromicrographs are provided of Baujardia mirabilis gen. n., sp. n., isolated from pitcher fluid of Nepenthes mirabilis from Thailand. The new genus differs from all known nematodes in having two opposing and offset spermatheca-like pouches at the junction of oviduct and uterus. It also differs from most known Rhabditida in having four cephalic setae instead of papillae. Phylogenetic analysis of small subunit rDNA sequence data robustly places the new genus within Panagrolaimidae as a sister taxon to Panagrellus. These unusual nematodes resemble Panagrellus in body size (1.8-2.7 mm in females, 1.3-1.9 mm in males) and in the monodelphic, prodelphic female reproductive system with thickened vaginal walls and prominent postvulval sac. However, they differ from Panagrellus in the characters mentioned above, in their comparatively longer stegostom and in the shape of the male spicules. Because of its aberrant characters, inclusion of this new genus in Panagrolaimidae requires changes to the family diagnosis.
An in vitro examination of the feeding behaviour of Paratrichodorus anemones (Nematoda: Trichodoridae), with comments on the ability of the nematode to acquire and transmit Tobravirus particles
Authors: Brown Derek , Karanastasi Eirini , Wyss Urs
Published: September 2003

The plant-parasitic nematode Paratrichodorus anemones efficiently transmits tobacco rattle virus that causes substantial economic damage to vegetable and ornamental flower-bulb crops. The nematode acquires and transmits virus particles when feeding on plant roots, but previous studies on feeding by trichodorid nematodes suggested that the nematodes destroyed the cells upon which they fed. For successful establishment of virus infection in a plant, virus particles would have to be introduced by the nematode into root cells that would remain fully functional. Consequently, the efficient transmission of the genus Tobravirus by trichodorids could not occur where the majority of attacked root cells become irreversibly damaged and, therefore, unsuitable for establishment of virus infection. Live specimens of P. anemones feeding on Nicotiana tabacum seedlings growing in agar were examined in real time using videoenhanced interference light microscopy to determine how trichodorids acquire and transmit Tobravirus particles. The feeding cycle of P. anemones had four distinct phases: i) root exploration, ii) cell exploration, iii) cell sampling, and iv) cell feeding, followed by a quiescent period. Preceding the initiation of phase iv) an average of four cells, which had been perforated by the nematode onchiostyle, were immediately abandoned and thus remained fully functional. Also, during this phase, about 5% of the perforated cells remained alive and fully functional, providing a suitable environment for the establishment of virus infection. Each feed on a single cell was similar to that previously observed with Trichodorus similis, being in four phases, i.e., cell wall perforation, salivation, ingestion and withdrawal.
Tylenchomorpha (Nematoda: Tylenchina) in Belgium, an updated list
Authors: Bert Wim , Coomans August , Geraert Etienne , Claerbout Frederik , Borgonie Gaëtan
Published: September 2003

The list of Tylenchomorpha known from Belgium is updated with observations from 32 locations. Forty two species are added, of which 11 are new records for the Belgium nematofauna. Five nominal species are removed because of synonymy and the list of 161 species is presented nomenclaturally.
Nacobbus aberrans (Thorne, 1935) Thorne & Allen, 1944 (Nematoda: Pratylenchidae); a nascent species complex revealed by RFLP analysis and sequencing of the ITS-rDNA region
Authors: Hunt David , Manzanilla-López Rosa , Reid Alex
Published: September 2003

Twelve populations of Nacobbus aberrans, sensu lato, from Mexico, Bolivia, Peru, Ecuador and Argentina were subjected to molecular analysis of their genetic variability. RFLP banding patterns revealed three groups: i) Mexico, Ecuador and Argentina 1 populations; ii) Bolivia and Peru populations; iii) Argentina 2 population. These differences were confirmed by sequencing the ITS rDNA region. Depth of branching was strongly supportive of the presence of three separate species, thus supporting the hypothesis that N. aberrans s.l. is indeed a species complex. The populations from Mexico, Ecuador and Argentina 1 are attributed to N. aberrans s.s., although this requires confirmation by molecular characterisation of N. aberrans from the type locality in the USA; those from Bolivia and Peru are attributed to N. bolivianus Lordello, Zamith & Boock, 1961 with Argentina 2 regarded as representing another taxon. Nacobbus serendipiticus and N. batatiformis are removed from synonymy under N. aberrans s.l . and regarded as species inquirendae . Consistent minor banding patterns in the RFLP profiles may indicate that the genus reproduces predominantly by parthenogenesis.
Three species of the Xiphinema americanum lineage (Nematoda: Longidoridae) from Iran
Authors: Fadaei Ali Akbar , Coomans August , Kheiri Ahmad
Published: September 2003

Soil samples collected from different regions of Iran contained Xiphinema oxycaudatum Lamberti & Bleve-Zacheo, 1979, X. rivesi Dalmasso, 1969 and X. pachtaicum (Tulaganov, 1938) Kirjanova, 1951. The first two species are reported for the first time from Iran. The latter species was previously reported from vineyards in Iran (Mojtahedi et al., 1980), but the Iranian specimens were not described. Populations on different hosts are compared. Special attention was given to the structure of the odontostyle bases and that of the reproductive system because of their possible importance in species differentiation.
Effect of biotic and abiotic factors on the morphometric variability of Paratrichodorus rhodesiensis (Nematoda: Trichodoridae) from Senegal
Authors: Wondirad Mandefro , Decraemer Wilfrida , Baujard Pierre
Published: September 2003

Effects of temperature, humidity, temperature and humidity interaction and host on morphometric variability of Paratrichodorus rhodesiensis were studied. Nematode cultures were established in a glasshouse under controlled environments. Amongst the factors investigated, host was found to be the most influential on both sexes (P < 0.05) affecting all characters in females and eight out of 11 characters in males. Ratios b and c were found to be highly variable and hence their use is not suggested. On the contrary, ratio a was found to be a good indicator of nematode condition, particularly in association with hosts. Vulva position (V) was found to be the most stable character. Paratrichodorus rhodesiensis was affected by higher temperatures of 34 and 36°C. Change in humidity did not show a demonstrable trend on morphometric characters in both sexes. Interaction effect of temperature and humidity resulted in a significant effect on body length and body diameter in females and on ratio b and c, pharynx, onchiostyle and tail length in males.
Playing Language Games and Performing Rituals: Religious Studies as Ideological State Apparatus
Authors: Fitzgerald Timothy
Published: September 2003

The Wittgensteinian philosophy of language games in the service of "religion" is circular and closed from criticism, and this generates the illusion that "religion" is compellingly universal. Also some historians, while attempting to uncover the specific and localized origins of the modern category "religion" in early modern Europe, simultaneously and unwittingly reconstruct the assumed universality of the category by uncritically using the problematized word in a description of societies in which the modern category, according to their own research findings, did not yet exist. These techniques suggest an unacknowledged ideological field lying behind the usages of the category. I argue that "religion" is one of a pair, the other half being "non-religion" or "the secular". The formation of the modern notion of religion needs to be seen initially in relation to privatized Protestant piety and the separation of church and state, whereby an apparently demystified human nature and fully rational modern civil society was made possible. But the application of the religion-secular distinction to an increasing number of colonies has resulted in "religion" becoming a catch-all container for indigenous institutions and practices that impede progress (i.e., impede realization of secular rationality by the natives). Debates about the logic of the religion-secular category can only become fruitful when we analyze the way in which they each construct their other half. However, the way "religion" is institutionalized and investigated in the academy elides its function in the invention and legitimation of the modern Euro-American secular, for it is treated as though it stands alone, either as a category in its own right or as a natural reality corresponding to that category.
Discursive Study of Religion: From States of the Mind to Communication and Action
Authors: von Stuckrad Kocku
Published: September 2003

This article addresses the predicament of the academic study of religions and directs the debate into more fruitful fields of research. After a brief account of the most important problems - identified as the "crisis of representation", the "situated observer", and the "dilemma of essentialism and relativism" - I argue that, in order to cope with these afflictions, we should scrutinize religions as systems of communication and action and not as systems of (unverifiable) belief. Not inner states of the mind or speculations about the transcendent are our issue, but the analysis of publicly communicated constructions. The term "fields of discourse" is introduced to denote both the coherence of these cultural arenas and the "recursive" involvement of scholars who are themselves actors in them. As a meta-theoretical instrument, the ideal type of "discourse" makes visible multiple perspectives on religious phenomena and - although the analysis' contingency and ethnocentricity is acknowledged - allows for the description of long-lasting traditions.
Primitive Texts, Savage Contexts: Contextualizing the Study of Religion in Colonial Situations
Authors: Chidester David
Published: September 2003

write about the cultural, social, and political history of the study of religion.
Clonal evolution and lack of cytogenetic response are adverse prognostic factors for hematologic relapse of chronic phase CML patients treated with imatinib mesylate
Authors: O'Dwyer Michael E. , Mauro Michael J. , Blasdel Carolyn , Farnsworth Melanie , Kurilik Gwen , Hsieh Yi-Ching , Mori Motomi , Druker Brian J.
Published: September 2003

We followed 141 patients treated with imatinib mesylate (> 300 mg) for chronicphase chronic myelogenous leukemia (CML) following failure of treatment with interferon. During 12 months from the start of imatinib mesylate treatment, 96.5% achieved a complete hematologic response, 47.0% achieved a major cytogenetic response, and 32.4% achieved a complete cytogenetic response. The proportion of patients with hematologic relapse was 10.9% at 12 months and 14.6% at 18 months. In a univariate Cox regression analysis, the only pretreatment characteristics that correlated with an increased risk of hematologic relapse were hemoglobin level less than 120 g/L (12 g/dL) (P = .02), increased bands in the peripheral blood (P = .01), and clonal evolution (P < .0001). In a multivariate analysis, an elevated platelet count (P = .03) and clonal evolution (P < .0001) were the only significant factors for hematologic relapse. During treatment, the absence of a major cytogenetic response within the first 6 months also significantly correlated with relapse (P = .03). Notably, patients failing to achieve a major cytogenetic response by 6 months had a significantly higher rate of hematologic relapse (27%) compared with those who achieved a major cytogenetic response by 6 months (3%), and patients with clonal evolution had a significantly higher risk of hematologic relapse (50%) than those without clonal evolution (9%).
Hematopoietic NF-κB1 deficiency results in small atherosclerotic lesions with an inflammatory phenotype
Authors: Kanters Edwin , Gijbels Marion J.J. , van der Made Ingeborg , Vergouwe Monique N. , Heeringa Peter , Kraal Georg , Hofker Marten H. , de Winther Menno P. J.
Published: September 2003

Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipid-laden macrophages in the vessel wall. One of the major transcription factors in inflammation is nuclear factor κB (NF-κB), and we have studied its role in the development of atherosclerosis. Bone marrow from mice targeted in the NF-κB1 gene encoding for the p50 subunit was used to reconstitute irradiated LDLR-/- mice as a model for atherosclerosis. After feeding the mice a high-fat diet, those deficient in NF-κB1 had a 41% lower rate of atherosclerosis than control mice, as judged by the sizes of the lesions. Furthermore, in the absence of NF-κB1, the lesions were characterized by an inflammatory phenotype, contained increased numbers of small cells, and were almost devoid of normal foam cells. In vitro studies using bone marrow (BM)-derived macrophages showed that macrophages lacking p50 had a prolonged production of tumor necrosis factor (TNF) in response to lipopolysaccharide (LPS), and other cytokines were also affected. Interestingly, the uptake of oxidized low-density lipoprotein (LDL) was greatly reduced in activated p50-deficient macrophages, probably because of a reduction in the expression of scavenger receptor class A. The effects on atherosclerosis might have resulted from the changes in cytokine production and the uptake of modified lipoproteins, making p50 a pivotal regulator of atherogenesis. (Blood. 2004;103:934-940)
Highly efficient lentiviral-mediated human cytokine transgenesis on the NOD/scid background
Authors: Punzon Isabel , Criado Luis M. , Serrano Alfredo , Serrano Fernando , Bernad Antonio
Published: September 2003

Human neo-organ formation from stem cells can only be assayed by in vivo xenotransplantation. The human nonobese diabetic–severe combined immunodeficient (HuNOD/scid) CD34+ cell transplantation is a model that allows examination of hematopoietic tissue formation, although human hematopoietic cell maturation is abortive. Conventional humanization of the cytokine microenvironment has depended on generation of human cytokine-transgenic mice in strains appropriate for conventional plasmid microinjection, followed by backcrossing, a costly and time-consuming approach. Lentiviral vector infection of single-cell embryos was recently reported to produce transgenic animals. Using this approach, we have generated direct human granulocyte-macrophage colony-stimulating factor (hGM-CSF) transgenic mice from lentivirus-microinjected NOD/scid embryos, with 68% efficiency and 100% penetrance; this allowed us to obtain NOD/scid transgenic mice with considerable savings of resources. This powerful technique should assist in producing novel mouse models for the study of human blood cell lineage development and other human neo-organs from stem cell xenotransplantation for which a similar “humanization” rationale may be required.
Induction of cytotoxic T-lymphocyte responses to enhanced green and yellow fluorescent proteins after myeloablative conditioning
Authors: Morris Julia C. , Conerly Melissa , Thomasson Bobbie , Storek Jan , Riddell Stanley R. , Kiem Hans-Peter
Published: September 2003

Lentiviral vectors are increasingly being used for transferring genes into hematopoietic stem cells (HSCs) due to their ability to transduce nondividing cells. Whereas results in in vitro studies and the nonobese diabetic/severe combined immunodeficiency (NOD/SCID) model have been highly encourgaging, studies in large animals have not confirmed the superior transduction of HSCs using lentiviral vectors versus oncoretroviral vectors. In contrast to the stable gene marking we have consistently achieved with oncoretroviral vectors in animals that received myeloablative conditioning, we observed the complete disappearance of genetically modified enhanced green or yellow fluorescent protein–expressing cells in 5 baboons that received transplants of HSCs transduced with lentiviral vectors alone or in combination with oncoretroviral vectors. Immune responses to transgene products have been found to be involved in the disappearance of gene-modified cells after nonmyeloablative conditioning. Thus, we examined whether the disappearance of genemodified cells after ablative conditioning may be due to an immune response. In 4 of 5 animals, cytotoxic T lymphocytes specific for the transgene protein were readily detected, demonstrating that immune reactions were responsible for the disappearance of the gene-marked cells in the animals. In summary, we report the induction of transgene-specific immune responses after transplantation of lentivirally transduced repopulating cells in a myeloablative setting.
VWF73, a region from D1596 to R1668 of von Willebrand factor, provides a minimal substrate for ADAMTS-13
Authors: Kokame Koichi , Matsumoto Masanori , Fujimura Yoshihiro , Miyata Toshiyuki
Published: September 2003

ADAMTS-13 was recently identified as a new hemostatic factor, von Willebrand factor (VWF)–cleaving protease. Either congenital or acquired defects of the enzymatic activity lead to thrombotic thrombocytopenic purpura (TTP). ADAMTS-13 specifically cleaves a peptidyl bond between Y1605 and M1606 in the A2 domain of VWF. Here, we determined the minimal region recognized as a specific substrate by ADAMTS-13. A series of partial deletions in the A2 domain flanked with N- and C-terminal tags were expressed in Escherichia coli and affinity-purified. These purified proteins were incubated with human plasma, subjected to sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE), and analyzed by Western blot. Judging from mobility shifts, all constructs except one were cleaved at the expected site. Data suggested that a minimal region as a functional substrate consisted of 73 amino acid residues from D1596 to R1668 of VWF, designated VWF73, and that further deletion of the E1660-R1668 region led to the loss of cleavage by ADAMTS-13. VWF73 was not cleaved by plasma from patients with congenital or acquired TTP, but cleaved by plasma from patients with hemolytic uremic syndrome, suggesting that VWF73 is a specific substrate forADAMTS-13. Thus, VWF73 will be a useful seed to develop a new rapid assay to determine ADAMTS-13 activity.
A Convenient Method for the Preparation of Symmetrical or Unsymmetrical Ethers by The Coupling of Two Alcohols via A New Type of Oxidation–reduction Condensation Using Tetrafluoro-1,4-benzoquinone
Authors: Shintou Taichi , Mukaiyama Teruaki
Published: September 2003

A new type of oxidation–reduction condensation by using tetrafluoro-1,4-benzoquinone (fluoranil), alcohols and alkoxydiphenylphosphines, in situ formed from nBuLi-treated alcohols and chlorodiphenylphosphine, proceeded smoothly to afford the corresponding symmetrical or unsymmetrical ethers in good to high yields.
Temperature-dependent Regulation of Antisense Activity Using a DNA/poly(N-isopropylacrylamide) Conjugate
Authors: Murata Masaharu , Kaku Wataru , Anada Takahisa , Sato Yoshikuni , Maeda Mizuo , Katayama Yoshiki
Published: September 2003

We prepared a novel antisense reagent comprising of oligodeoxynucleotides (ODNs) and a thermo-responsive polymer, poly(N-isopropylacrylamide) (PNIPAAm). The conjugate demonstrated stimuli-responsive regulation of gene expression via conformational change of the polymer chain.
Aza-Michael Reactions in Ionic Liquids. A Facile Synthesis of β-Amino Compounds
Authors: Yadav J S , Reddy B V S , Basak A K , Narsaiah A V
Published: September 2003

Electron-deficient olefins undergo smoothly aza-Michael reactions with a wide range of amines in ionic liquids in the absence of any acid catalyst to produce the corresponding β-amino compounds in excellent yields with high 1,4-selectivity. The recovered ionic liquids can be reused in subsequent reactions without loss of activity. Owing to the high polarity of ionic liquids, the enones show enhanced reactivity thereby reducing reaction times and improving the yields significantly.
Male management: coping with aggression problems in male laboratory mice
Authors: Van Loo P. L. P. , Van Zutphen L. F. M. , Baumans V.
Published: September 2003

In a laboratory environment, aggressive interactions between male mice may exceed normal levels leading to negative effects both on the well-being of the animals and on the validity of experimental results. In this paper we review results from the literature and our own research with regard to coping with excessive aggressive behaviour in male laboratory mice. Based on this review practical recommendations concerning the housing and care of male laboratory mice are formulated. In short, it is recommended to avoid individual housing, to transfer odour cues from the nesting area during cage cleaning and to apply nesting material as environmental enrichment. Furthermore, group size should be optimized to three animals per cage. Further research, in particular into the effects of frequency, duration, type and severity of disturbances during an experiment on the degree of aggression, is recommended.
Are the effects of different enrichment designs on the physiology and behaviour of DBA/2 mice consistent?
Authors: Tsai P. P. , Stelzer H. D. , Hedrich H. J. , Hackbarth H.
Published: September 2003

Environmental enrichment is intended to improve the well-being of laboratory animals. Although many researchers have indicated that environmental enrichment may enhance animal well-being, there is some evidence that enrichment differs in its effects on physiology and behaviour between species and strains. The present study focuses on the effects of different enrichment designs on the physiology and behaviour of male and female DBA/2 mice. A total of 48 DBA/2J mice, 24 males and 24 females were used for this experiment. Upon arrival at about 3 weeks of age, the animals were randomly allotted to three experimental groups: NE, non-enrichment; E1, enriched with nest box, wooden climbing bar and nest material according to Scharmann (1993); E2, enriched with horizontal and vertical dividers, modified from Haemisch and Gärtner (1994). Same-sex groups of four mice were housed for 12 weeks in type III Makrolon cages with (E1 or E2) or without (NE) enrichment objects. Behavioural performance (Open Field, Food Drive and Elevated Plus Maze tests) and physiological traits (haematological variables, body weight and organ weights, corticosterone and thyroxine levels) were measured. This study observed that enrichment had significant effects on the mean values of body weight (females), Open Field and Food Drive tests. The most significant housing differences were found between the E2 and NE/E1 groups. Furthermore, sex differences in the NE, E1 and E2 groups were not consistent for several variables (growth rate, relative weights of spleen, kidney and heart, Food Drive and Elevated Plus Maze behavioural performance). There was often a higher coefficient of variation (CV) in the E1 and E2 groups as compared to the NE group, chiefly in physiological traits and in the Open Field and Food Drive tests. The results of this study indicate, that the effects of enrichment designs used in the present study are not consistent, but vary according to sex and the variable studied.
Effect of enrichment on variation and results in the light/dark test
Authors: Augustsson Hanna , van de Weerd Heleen A. , Kruitwagen Cas L. J. J. , Baumans Vera
Published: September 2003

Several confounding factors may influence the outcome of an experiment and the extent of inter-individual variation. The aim of this study was to investigate if cage enrichment induces an effect on experimental mean values and on inter-individual variation in the light/dark paradigm using diazepam as the anxiolytic drug. The behaviour of 216 naive adult male mice of two different strains (BALB/c and C57BL/6) was studied. The animals were housed in groups of four in 'non-enriched', 'enriched' (nesting material) or 'super-enriched' (nest-box, nesting material, wooden gnawing stick and PVC tube) cages. After 5 weeks the animals were assigned to one of three treatments: control (no injection), sham (saline injection i.p.) or diazepam (1 mg/kg bw i.p.) and tested in the light/dark test for 5 min. Variation data were analysed using three different methods (mean absolute deviation, coefficient of variation and power analysis). The C57BL/6 mice scored higher than BALB/c mice in activity related measurements and showed a less 'emotional' behaviour profile in the pharmacological control situation of the light/dark test. In this study the anxiolytic effect of diazepam was clear in BALB/c mice but absent in C57BL/6 mice. Mice housed in enriched and super-enriched cages gained more weight than mice in non-enriched cages, although food intake was not affected. Generally, the strain of mouse had the greatest impact on both mean values and variation. However, there was no consistent increase for one particular strain. The choice of statistical method for analysing variation may influence the interpretation of within-group variability, but none of the methods showed any significant differences between standard and enriched conditions on variability in any of the parameters measured.
Quantitative analysis of peroxisome proliferator‐activated receptor gamma (PPARγ) expression in arteries and hearts of patients with ischaemic or dilated cardiomyopathy
Authors: Mehrabi Mohammad R. , Haslmayer Petra , Humpeler Susanne , Strauss‐Blasche Gerhard , Marktl Wolfgang , Tamaddon Forouzan , Serbecic Nermin , Wieselthaler Georg , Thalhammer Theresia , Glogar Helmut D. , Ekmekcioglu Cem
Published: October 2003

PPARγ, a nuclear transcription factor, is expressed in various cells within the vasculature and in cardiomyocytes. It has been suggested that PPARγ is involved in atherogenesis and in cardiac hypertrophy. Therefore, we sought to quantify PPARγ mRNA in coronary arteries, the aorta and left ventricular specimens from patients with ischaemic (CHD) and dilated cardiomyopathy (CMP). Using real‐time PCR, we were able to demonstrate the expression of PPARγ in all of the human specimens. The lowest expression of PPARγ was detected in the aorta specimens of both groups (this was set to one). In comparison, the expression in coronary arteries was 2.32‐fold in CHD‐ and 3.78‐fold in CMP specimens and in the left ventricle specimens, 2.12‐fold in CHD‐ and 3.51‐fold in CMP. Samples from CHD patients showed a higher expression of PPARγ in all of the samples compared to those from CMP patients (aorta: 1.99‐fold; coronary arteries: 1.35; left ventricles: 1.23). PPARγ levels were not significantly correlated to CD 36 expression values in any group, suggesting that higher levels of PPARγ are not principally due to increased PPARγ expression in macrophages. This was confirmed by immunohistochemical analysis, which showed that PPARγ is also located in the smooth muscle layer and in cardiomyocytes. In conclusion, our observations of increased PPAR mRNA expression in the coronary arteries and left ventricles from CHD and CMP patients suggest an important function of this nuclear receptor in the pathogenesis of heart disease.
REVISION OF PLATHYMENIA (LEGUMINOSAE–MIMOSOIDEAE)
Authors: WARWICK M. C. , LEWIS G. P.
Published: October 2003

Plathymenia (Leguminosae–Mimosoideae) has been variously regarded as comprising one to three species and one variety. The genus is here considered to be monospecific, containing only Plathymenia reticulata. This is in agreement with the conclusion of Ducke in 1925. A full description is given of P. reticulata in its emended sense, with notes on ecology, uses, vernacular names and a list of herbarium specimens examined.
Computational detection of cis -regulatory modules
Authors: Aerts Stein , Van Loo Peter , Thijs Gert , Moreau Yves , De Moor Bart
Published: October 2003

Motivation: The transcriptional regulation of a metazoan gene depends on the cooperative action of multiple transcription factors that bind to cis-regulatory modules (CRMs) located in the neighborhood of the gene. By integrating multiple signals, CRMs confer an organism specific spatial and temporal rate of transcription.

Results: Based on the hypothesis that genes that are needed in exactly the same conditions might share similar regulatory switches, we have developed a novel methodology to find CRMs in a set of coexpressed or coregulated genes. The ModuleSearcher algorithm finds for a given gene set the best scoring combination of transcription factor binding sites within a sequence window using an A*procedure for tree searching. To keep the level of noise low, we use DNA sequences that are most likely to contain functional cis-regulatory information, namely conserved regions between human and mouse orthologous genes. The ModuleScanner performs genomic searches with a predicted CRM or with a user-defined CRM known from the literature to find possible target genes. The validity of a set of putative targets is checked using Gene Ontology annotations. We demonstrate the use and effectiveness of the ModuleSearcher and ModuleScanner algorithms and test their specificity and sensitivity on semi-artificial data. Next, we search for a module in a cluster of gene expression profiles of human cell cycle genes.

Availability: The ModuleSearcher is available as a web service within the TOUCAN workbench for regulatory sequence analysis, which can be downloaded from http://www.esat.kuleuven.ac.be/~dna/BioI.

Contact: stein.aerts@esat.kuleuven.ac.be

*To whom correspondence should be addressed.
Inferring strengths of protein-protein interactions from
experimental data using linear programming
Authors: Hayashida Morihiro , Ueda Nobuhisa , Akutsu Tatsuya
Published: October 2003

Motivation: Several computational methods have been proposed for inference of protein-protein interactions. Most of the existing methods assume that protein-protein interaction data are given as binary data (i.e. whether or not each protein pair interacts). However, multiple biological experiments are performed for the same protein pairs and thus the ratio (strength) of the number of observed interactions to the number of experiments is available for each protein pair.

Results: We propose a new method for inference of protein-protein interactions from such experimental data. This method tries to minimize the errors between the ratios of observed interactions and the predicted probabilities in training data, where this problem is formalized as a linear program based on a probabilistic model. We compared the proposed method with the association method, the EM method and the SVM-based method using real interaction data. It is shown that a variant of the method is comparable to existing methods for binary data. It is also shown that the method outperforms existing methods for numerical data.

Availability: Programs transforming input data into LP format files are available upon request.

Supplementary information: http://sunflower.kuicr.kyoto-u.ac.jp/~morihiro/protint/supplement.html

Contact: akutsu@kuicr.kyoto-u.ac.jp

*To whom correspondence should be addressed.
Gene networks inference using dynamic Bayesian networks
Authors: Perrin Bruno-Edouard , Ralaivola Liva , Mazurie Aurélien , Bottani Samuele , Mallet Jacques , d’Alché–Buc Florence
Published: October 2003

This article deals with the identification of gene regulatory networks from experimental data using a statistical machine learning approach. A stochastic model of gene interactions capable of handling missing variables is proposed. It can be described as a dynamic Bayesian network particularly well suited to tackle the stochastic nature of gene regulation and gene expression measurement. Parameters of the model are learned through a penalized likelihood maximization implemented through an extended version of EM algorithm. Our approach is tested against experimental data relative to the S.O.S. DNA Repair network of the Escherichia coli bacterium. It appears to be able to extract the main regulations between the genes involved in this network. An added missing variable is found to model the main protein of the network. Good prediction abilities on unlearned data are observed. These first results are very promising: they show the power of the learning algorithm and the ability of the model to capture gene interactions.

Keywords: gene regulatory networks, structure extraction, expression profiles, dynamic Bayesian networks, Kalman filter, penalized likelihood, EM algorithm.

Contact: perrin@poleia.lip6.fr

*To whom correspondence should be addressed.
An assessment of ADAMs in bone cells: absence of TACE activity prevents osteoclast recruitment and the formation of the marrow cavity in developing long bones
Authors: Boissy Patrice , Lenhard Thomas R , Kirkegaard Tove , Peschon Jacques J , Black Roy A , Delaissé Jean-Marie , del Carmen Ovejero Maria
Published: October 2003

ADAMs (A Disintegrin And Metalloprotease domain) are metalloprotease–disintegrin proteins that have been implicated in cell adhesion, protein ectodomain shedding, matrix protein degradation and cell fusion. Since such events are critical for bone resorption and osteoclast recruitment, we investigated whether they require ADAMs. We report here which ADAMs we have identified in bone cells, as well as our analysis of the generation, migration and resorptive activity of osteoclasts in developing metatarsals of mouse embryos lacking catalytically active ADAM 17 [TNFα converting enzyme (TACE)]. The absence of TACE activity still allowed the generation of cells showing an osteoclastic phenotype, but prevented their migration into the core of the diaphysis and the subsequent formation of marrow cavity. This suggests a role of TACE in the recruitment of osteoclasts to future resorption sites.
The positive charge at Lys‐288 of the glucagon‐like peptide‐1 (GLP‐1) receptor is important for binding the N‐terminus of peptide agonists
Authors: Al-Sabah Suleiman , Donnelly Dan
Published: October 2003

Lysine‐288 in the glucagon‐like peptide‐1 receptor was predicted to be ideally positioned to play a role in hormone binding. Subsequent mutation of Lys‐288 to Ala or Leu greatly reduced hormone affinity, while substitution with Arg had minimal effect. Compared to wild type, the Lys288‐Ala receptor had a reduced affinity for three peptide ligands with complete N‐terminal sequences but not for their N‐truncated analogues. Hence, the role of this positively charged residue, which is conserved at the equivalent position in all other Family B receptors, was determined to be important for receptor interaction with the N‐terminal eight residues of peptide agonists.
Breaking the Bonds of Precedent: The 1905–6 Government Reform Commission and the Remaking of the Qing Central State
Authors: Horowitz Richard S.
Published: October 2003

On January 29, 1901, in the grim aftermath of the Boxer Uprising and the humiliating foreign invasion of north China that followed, the Empress Dowager Cixi issued a famous edict that initiated the New Policy (xinzheng) reforms.

The weakness of China is caused by the strength of convention and the rigid network of regulations. We have many mediocre officials but few men of talent and courage. The regulations are used by mediocre men as the means of their self-protection, and taken advantage of by government clerks as sources of profit. The government officials exchange numerous documents but they never touch reality. The appointment of capable men is restricted by regulations so rigid that even men of exceptional talent are missed. What misleads the country can be expressed in one word, selfishness, and what suffocates all under heaven is precedent.
Abolishing ‘Cruel Punishments’: A Reappraisal of the Chinese Roots and Long-term Efficiency of the Xinzheng Legal Reforms
Authors: Bourgon Jérôme
Published: October 2003

The 24th of April 1905 is a date of no particular significance in the current historiography of China. However, the memorial submitted this day by the Imperial Commissioners in charge of legal reforms, Wu Tingfang and Shen Jiaben, entailed the immediate suppression of so-called ‘cruel punishments’ (kuxing), such as dismemberment (lingchi), exposure of the head (xiaoshou) and desecration of the corpse (lushi). Judicial torture and bamboo flogging were suppressed straight after. From then on, cruelties of the past were illegal, and prohibited in practice, even though a penal code conforming to modern standards was not completed before 1928. China thus entered into the age of uneven and uncertain eradication of illegal but recurrent practices of torture. Though spectacular outbursts of violence occurred in contemporary China, with the complicity or under instigation of the highest authorities, those were not openly authorized by law, and they were eventually denounced, and some of their authors prosecuted. The shift from cruelty openly legitimized and practiced by the state to its official prohibition and ashamed toleration is an epochal change, which stems from the April 24th 1905 memorials.
Whose Method? Culture, Commerce, and American Performer Training
Authors: Walden Keith
Published: October 2003

The rapid acceptance in America of Stanislavsky's approach to actor training is often presented as an unexpected and unaccountable imposition of foreign culture. But Keith Walden argues that, while the ‘method’ may have been an innovation in acting schools, its goals and techniques were already familiar in other spheres of American life – particularly in the voluminous advice literature directed at salespeople. The similarities are not surprising, since both attempts to shape performances were inspired by the erosion of older notions of coherent, stable selfhood. Though the cultural purposes of acting and selling remained sharply different, the transgressive potential of modern theatre was dependent on a widespread belief that the roles required in ordinary work should be competently enacted. Keith Walden is a member of the History Department at Trent University in Peterborough, Ontario. He is a former editor of the Canadian Historical Review and author of Becoming Modern in Toronto: the Industrial Exhibition and the Shaping of a Late-Victorian Culture.
A binding event converted into a folding event
Authors: Martı́n-Sierra F.M , Candel A.M , Casares S , Filimonov V.V , Martı́nez J.C , Conejero-Lara F
Published: October 2003

We have designed a chimeric protein by connecting a circular permutant of the α‐spectrin SH3 domain to the proline‐rich decapeptide APSYSPPPPP with a three‐residue link. Our aim was to obtain a single‐chain protein with a tertiary fold that would mimic the binding between SH3 domains and proline‐rich peptides. A comparison of the circular‐dichroism and fluorescence spectra of the purified chimera and the SH3 circular permutant showed that the proline‐rich sequence occupies the putative SH3 binding site in a similar conformation and with comparable interactions to those found in complexes between SH3 and proline‐rich peptides. Differential scanning calorimetry indicated that the interactions in the binding motif interface are highly cooperative with the rest of the structure and thus the protein unfolds in a two‐state process. The chimera is more stable than the circular permutant SH3 by 6–8 kJ mol−1 at 25°C and the difference in their unfolding enthalpy is approximately 32 kJ mol−1, which coincides with the values found for the binding of proline‐rich peptides to SH3 domains. This type of chimeric protein may be useful in designing SH3 peptide ligands with improved affinity and specificity.
Inhibition of influenza A virus sialidase activity by sulfatide
Authors: Suzuki Takashi , Takahashi Tadanobu , Nishinaka Daisuke , Murakami Masanori , Fujii Satoshi , Hidari Kazuya I.-P.Jwa , Miyamoto Daisei , Li Yu-Teh , Suzuki Yasuo
Published: October 2003

Sulfatide, which binds to influenza A viruses and prevents the viral infection, was found to inhibit the sialidase activities of influenza A viruses in a pH‐dependent manner. The kinetic parameters of the effect of sulfatide on the sialidase activities of human influenza A viruses using fluorometric assay indicated that sulfatide was a powerful and non‐competitive type inhibitor in low‐pH conditions.