bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of a neutralizing epitope in the βE–βF loop of VP1 of equine rhinitis A virus, defined by a neutralization-resistant variant
Authors: Stevenson Rachel A. , Huang Jin-an , Studdert Michael J. , Hartley Carol A.
Published: August 2004

Equine rhinitis A virus strain 393/76 (ERAV.393/76) was passaged in the presence of post-infection ERAV.393/76 equine polyclonal antiserum (EPA). Viruses with increased resistance to neutralization by EPA were obtained after 15 passages. Compared with the parent virus, five plaque-purified, neutralization-resistant mutant viruses, in addition to the non-plaque-purified viruses that were examined, had a Glu→Lys change at position 658, which is located in the predicted βE–βF (EF) loop of VP1. Rabbit antiserum was prepared against the isolated EF loop of ERAV.393/76 VP1 expressed as a fusion protein with glutathione S-transferase. This antiserum bound to purified ERAV.393/76 in Western blots, but not to the neutralization-resistant mutant virus or to ERAV.PERV/62, a naturally occurring ERAV strain that has a Lys residue at position 658. These results suggest that the EF loop of VP1 is involved in a neutralization epitope of ERAV.
Quantitative parameters determining whitefly (Bemisia tabaci) transmission of Lettuce infectious yellows virus and an engineered defective RNA
Authors: Ng James C. K. , Tian Tongyan , Falk Bryce W.
Published: August 2004

In this study, quantitative parameters affecting in vitro acquisition and whitefly (Bemisia tabaci) transmission of Lettuce infectious yellows virus (LIYV) were examined and B. tabaci transmission of an engineered defective RNA (D-RNA) was demonstrated. Virions purified from virus- and virion RNA-inoculated Chenopodium murale plants and protoplasts of Nicotiana tabacum, respectively, were consistently transmitted to plants by B. tabaci when virion concentrations were 0·1 ng μl−1 or greater. Transmission efficiency increased with increasing virion concentration and number of whiteflies used for inoculation. When in vitro-derived transcripts of the M5gfp D-RNA (engineered to express the green fluorescent protein, GFP) were co-inoculated to protoplasts with wild-type LIYV virion RNAs, the resulting virions were transmissible to plants. LIYV and the M5gfp D-RNA systemically invaded inoculated plants; however, GFP expression was not detected in these plants. Unlike LIYV, the M5gfp D-RNA was not subsequently transmitted by B. tabaci from the initially infected plants, but, when high concentrations of virions from plants infected by LIYV and the M5gfp D-RNA were used for in vitro acquisition by whiteflies, both were transmitted to plants. Quantitative and qualitative analyses showed that, although the M5gfp D-RNA replicated within and systemically invaded plants along with LIYV, compared with LIYV RNA 2 it was not as abundant in plants or in the resulting virions, and concentration of encapsidated RNAs is an important factor affecting transmission efficiency.
Hepatitis C virus NS5A: tales of a promiscuous protein
Authors: Macdonald Andrew , Harris Mark
Published: August 2004

The non-structural 5A (NS5A) protein of hepatitis C virus (HCV) has been the subject of intensive research over the last decade. It is generally accepted that NS5A is a pleiotropic protein with key roles in both viral RNA replication and modulation of the physiology of the host cell. Our understanding of the role of NS5A in the virus life cycle has been hampered by the lack of a robustin vitrosystem for the study of HCV replication, although the recent development of the subgenomic replicon has at least allowed us to begin to dissect the involvement of NS5A in the process of viral RNA replication. Early studies into the effects of NS5A on cell physiology relied on expression of NS5A either alone or in the context of other non-structural proteins; the advent of the replicon system has allowed the extrapolation of these studies to a more physiologically relevant cellular context. Despite recent progress, this field is controversial, and there is much work to be accomplished before we fully understand the many functions of this protein. In this article, the current state of our knowledge of NS5A, discussing in detail its direct involvement in virus replication, together with its role in modulating the cellular environment to favour virus replication and persistence, are reviewed. The effects of NS5A on interferon signalling, and the regulation of cell growth and apoptosis are highlighted, demonstrating that this protein is indeed of critical importance for HCV and is worthy of further investigation.
Sialic acid acts as a receptor for equine rhinitis A virus binding and infection
Authors: Stevenson Rachel A. , Huang Jin-an , Studdert Michael J. , Hartley Carol A.
Published: August 2004

Equine rhinitis A virus (ERAV) is a member of the genus Aphthovirus, family Picornaviridae, and causes respiratory disease in horses worldwide. To characterize the putative receptor molecule(s) of the ERAV isolate 393/76 (ERAV.393/76) on the surface of Vero and other cells, an assay was developed to measure the binding of purified biotinylated ERAV.393/76 virions to cells by flow cytometry. Using this assay, the level of binding to different cell types correlated with the relative infectivity of ERAV in each cell type. In particular, equine fetal kidney cells, mouse fibroblast cells, rabbit kidney-13 and Crandell feline kidney cells bound virus at high levels and produced high virus yields (⩾107 TCID50 ml−1). Madin–Darby bovine kidney and baby hamster kidney cells showed little or no binding of virus, producing yields of ⩽101·8 TCID50 ml−1. Treatment of Vero and other cells with sodium periodate and the metabolic inhibitors tunicamycin, benzyl N-acetyl-α-d-galactosamide, d,l-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol and proteases indicated that part of the receptor-binding and entry complex for ERAV.393/76 is on N-linked carbohydrates and that the carbohydrate is likely to be present on a protein rather than a lipid backbone. The effect of carbohydrate-specific lectins and neuraminidases on ERAV.393/76 binding and infection of Vero and other cell types implicated α2,3-linked sialic acid residues on the carbohydrate complex in the binding and infection of ERAV.
Two novel HLA‐DRB1 alleles identified using a sequence‐based typing: HLA‐DRB1*1443 and HLA‐DRB1*1351*
Authors: Chu C.C. , Lee H.L. , Hsieh N.K. , Trejaut J. , Lin M.
Published: August 2004

Abstract:  Two novel HLA‐DRB1 alleles, DRB1*1443 and DRB1*1351, were identified using a sequence‐based typing protocol. DRB1*1443 differed from DRB1*140501 by one single‐nucleotide substitution in exon‐2 (codon 77, ACC→GCC), which corresponded to an amino acid change of threonine to alanine. DRB1*1351 was identical to DRB1*1301 but differed by a single‐nucleotide substitution at codon 50 (GTG→TTG), resulting in an amino acid change of valine to leucine. Both new alleles present unique polymorphisms, which have not been seen among other DRB1 alleles and which have no known effect on peptide binding.
Identification of two new HLA‐DRB1 alleles: HLA‐DRB1*1350 and DRB1*140502
Authors: Chen Z.X. , Tsan S.G. , Dang C.W. , Chu C.C. , Lin M. , Lee Y.J.
Published: August 2004

Abstract:  Two new HLA‐DRB1 alleles have been found by using high‐resolution sequence‐based typing. The two sequences have been officially named DRB1*1350 (HWS10001327‐AY048687) and DRB1*140502 (HWS10001790‐AY129430). DRB1*1350 differs from DRB1*110101 by two amino acids at positions 37 (Y→N) and 58 (A→E). This allele may arise from gene conversion between DRB1*110101 and DRB1*130201 or DRB1*030101, which are commonly found in Taiwan populations. The other allele, DRB1*140502, obtained from a patient with rheumatoid arthritis, differs from DRB1*140501 at codon 58 (GCC→GCT). However, it causes no change in amino acid sequence and would therefore not have direct clinical implications.
The LILR family: modulators of innate and adaptive immune pathways in health and disease
Authors: Brown D. , Trowsdale J. , Allen R.
Published: August 2004

Abstract:  Leukocyte immunoglobulin (Ig)‐like receptors [LILRs, also known as Ig‐like transcripts (ILTs)] are a family of inhibitory and stimulatory receptors encoded within the leukocyte receptor complex and are expressed by immune cell types of both myeloid and lymphoid lineage. Several members of the LILR family recognize major histocompatibility complex class I. The immunomodulatory role of LILR receptors indicates that they may exert an influence on signaling pathways of both innate and adaptive immune systems. LILR activity can also influence the antigen‐presenting properties of macrophages and dendritic cells and may thus play a role in T‐cell tolerance. The wide‐ranging effects of LILR signaling on immune cell activity imply that these receptors are likely to play an important role in a range of clinical situations including pregnancy, transplantation, and arthritis (including the human leukocyte antigen B27‐associated spondyloarthropathies). In this review, we summarize current knowledge on the nature and function of LILRs, focusing on their regulation of immune cell activity and their potential role in disease.
Molecular typing of human leukocyte antigen and related polymorphisms following whole genome amplification
Authors: Shao W. , Tang J. , Dorak M. T. , Song W. , Lobashevsky E. , Cobbs C. S. , Wrensch M. R. , Kaslow R. A.
Published: August 2004

Abstract:  Reliable, high‐resolution genotyping of human leukocyte antigen (HLA) polymorphisms is often compromised by DNA samples of suboptimal quality or limited quantity. We tested the feasibility of molecular typing for variants at HLA and neighboring loci using whole genome amplification (WGA) strategy facilitated by the Φ29 DNA polymerase. With little (5–100 ng) starting genomic DNA of varying quality and source materials, WGA was deemed successful in 167 of 169 DNA from 47 cell lines, 100 European Americans, and 22 native Africans. The Φ29‐processed DNA provided adequate templates for polymerase chain reaction (PCR)‐based analyses of several HLA (A, B, C, DRB1, and DQB1) and related loci (HFE, MICA, and 10 microsatellites) in the 6p24.3–6p21.3 region, with PCR amplicons ranging from 92 to 2200 bp. Five different genotyping techniques resolved and confirmed 364 genotypes when both original and Φ29‐processed DNA worked in PCRs. General population genetic analyses provided additional evidence that WGA may represent a reliable and simple approach to securing ample genomic DNA for typing HLA, MICA, and related variants.
Testing Vocabulary Knowledge: Size, Strength, and Computer Adaptiveness
Authors: Laufer Batia , Goldstein Zahava
Published: August 2004

In this article, we describe the development and trial of a bilingual computerized test of vocabulary size, the number of words the learner knows, and strength, a combination of four aspects of knowledge of meaning that are assumed to constitute a hierarchy of difficulty: passive recognition (easiest), active recognition, passive recall, and active recall (hardest). The participants were 435 learners of English as a second language. We investigated whether the above hierarchy was valid and which strength modality correlated best with classroom language performance. Results showed that the hypothesized hierarchy was present at all word frequency levels, that passive recall was the best predictor of classroom language performance, and that growth in vocabulary knowledge was different for the different strength modalities.
The Relationship Between Text Comprehension and Second Language Incidental Vocabulary Acquisition: A Matter of Topic Familiarity?
Authors: Pulido Diana
Published: August 2004

The study examines the relationship between second language (L2) passage comprehension and intake (form recognition), gain (meaning recognition and production), and retention of new lexical items from the passages. The effect of topic familiarity on the above relationships is also examined. Participants were a cross‐sectional sample of L2 learners. All participants read more and less familiar script‐based narratives containing nonsense words. After reading they performed a free‐written recall in their first language. Two days after reading, an intake and 2 gain measures were administered. Twenty‐eight days after reading, the 2 gain measures were repeated. Analyses reveal a generally robust consistent role of passage comprehension in lexical gain and retention, but differential patterns of relationships in intake due to effects of topic familiarity.
A Multiple‐Data Analysis of the 3.5‐Year Development of EFL Student Writers
Authors: Sasaki Miyuki
Published: August 2004

The present study investigated the changes in Japanese students’ English writing behaviors over a 3.5‐year period using multiple data sources including written texts, videotaped writing behaviors, and stimulated‐recall protocols. Data from student interviews supplemented the analyses. Because 6 (henceforth, English as a second language [ESL] students) out of the 11 participants spent 2 to 8 months in English‐speaking environments, the study was also able to examine the effects of such overseas experiences. The results revealed that over the observation period (a) both the English as a foreign language (EFL, remaining in Japan) and the ESL students improved their English proficiency, English composition quality/fluency, and confidence in English writing; (b) the ESL students’ overseas experiences were helpful for improving their writing strategy use and motivation to write better compositions; and (c) neither group's abilities or skills became like those of the EFL experts studied in Sasaki (2002).
Seedling dynamics of shrubs in a fully closed temperate forest: greater than expected
Authors: Laskurain N. A. , Escudero A. , Olano J. M. , Loidi J.
Published: August 2004

Shrub seedling emergences were studied in a beech‐birch forest in the Basque Country (Spain). During four years (1998–2001) all emerging shrubs were tagged and regularly monitored in 198 1 m2 plots. Seedling emergence was intense during the entire study period and primarily occurred in early spring. Emerging seedlings mainly belonged to Hedera helix, Rubus gr. glandulosus and several heath species (including genera Erica, Calluna and Daboecia). In contrast, some dominant species components of the shrub layer (Vaccinium myrtillus and Lonicera periclymenum) showed no emergences. While small seeded species (heath species and Rubus) showed clear microsite preferences, avoiding litter for emergence, that was not the case of large seeded Hedera helix. Strict microsite requirements appear clearly associated with having seed bank, suggesting that this trait may allow these species to select favourable microenvironment prior to germination. Average life varied largely among the different taxa. It was very low for Rubus (7.4 months) and heath (4.9), and high for Hedera seedlings (23.1). Final survival was extremely low in the case of small‐seeded species. Survival of Hedera seedlings was high, although their growth was very low, suggesting the existence of a conspicuous seedling bank. Our results clearly show that several shrubs species have dramatic seedling dynamics in full closed forest stands. Small seeded species preferentially emerge on bare surfaces in early spring from the soil seed banks. On the other hand, Hedera seedlings are able to emerge on litter and maintain a conspicuous seedling bank based on an efficient dispersal capability.
Estimating species richness at large spatial scales using data from small discrete plots
Authors: Krishnamani R. , Kumar A. , Harte J.
Published: August 2004

Estimating species richness in large biomes is a central challenge in ecology and conservation biology. However, accurate census data is often available only from small discrete plots distributed within the biome. Using tree species richness data collected from 48 plots (0.25 ha each) widely distributed through 60 000 km2 in the rainforests of the Western Ghats of southern India, we test the application of a proposed method for estimating species richness at large scales from measured species commonalities between pairs of censused plots. We show that the method allows extrapolation of species richness from a scale of 0.25 ha plots to that of the entire biome, or 105 km2.
Predicting the geographical distribution of plant communities in complex terrain – a case study in Fushian Experimental Forest, northeastern Taiwan
Authors: Chang Chi‐Ru , Lee Pei‐Fen , Bai Mei‐Ling , Lin Tzer‐Tong
Published: August 2004

Ecosystem management and biodiversity conservation are usually implemented using information of several targeted species or cover‐types and usually do not include information about communities. This is not because community‐level information is unimportant for management purposes, but because the detailed fieldwork required for gathering community‐level information at the scale for ecosystem management is usually impractical. We propose two methods to estimate the geographical distribution of plant communities with the objectives of covering large areas with minimal field efforts. The first method estimates the geographical distribution of plant communities by combining clustering methods with vegetation modeling, and the second extrapolates the geographical distribution of gradients in plant communities by combining gradient analysis with vegetation modeling. Vegetation modeling with clustering methods can be used to allocate sites with potentially higher alpha diversity, with the benefit of having a list of species associated with the clustered type. Vegetation modeling with gradient analysis can be used to identify regions with potentially the highest beta diversity by means of selecting regions with the widest range or highest variability in major DCA axes scores, and thereby help to preserve the scope of environmental conditions that lead to diversity in species assemblages. This is especially important because biological entities such as species, communities, or even ecosystems may cease to exist in the long run, and the preservation of processes that lead to biodiversity will eventually become more meaningful. We conclude that new methods to study and manage the processes that contribute to biodiversity at all scales should be and can be developed.
Abundance – occupancy relationships in macrofauna on exposed sandy beaches: patterns and mechanisms
Authors: T. Frost Matthew , J. Attrill Martin , A. Rowden Ashley , Foggo Andrew
Published: August 2004

We studied the relationship between abundance and extent of occupancy of 158 species of macrofauna inhabiting 66 sandy beaches around the coast of Great Britain. We also used these data to test the predictions of two hypotheses proposed to explain positive abundance‐occupancy relationships. We found a strong positive relationship between abundance and extent of occupancy; this pattern was apparent in taxonomic subsets of organisms which have contrasting reproductive and dispersal traits such as planktotrophic/lecithotrophic development in the plankton vs brood development under parental care. Moreover, the abundance‐occupancy relationships in these taxonomic subsets had statistically indistinguishable slopes, and elevation. We propose that this lends support to the notion that differences in population structure such as the tendency to form metapopulations may not be primary determinants of the abundance‐occupancy pattern in these taxa as proposed by the rescue/metapopulation hypothesis. To test the predictions of the niche‐breadth hypothesis we derived values describing the range of sediment grain‐sizes exploited by members of two taxonomic subgroups: amphipods and bivalves. We found a weak, statistically non‐significant relationship between this niche‐breadth measure and occupancy in bivalves which have been shown to respond to grain‐size in previous studies, however this was negated after correction for possible artefacts of sampling effort. All other relationships between abundance or occupancy and grain‐size range were non‐significant. The consistency of the demonstrated abundance‐occupancy relationship with those demonstrated in other studies of primarily terrestrial fauna indicates some shared mechanistic explanation, but our data fail to provide support for the two mechanistic hypotheses investigated.
Determinants of mountain birch growth in situ: effects of temperature and herbivory
Authors: Karlsson P. S. , Tenow O. , Bylund H. , Hoogesteger J. , Weih M.
Published: August 2004

Variation in in situ growth performance of the mountain birch as indicated by the widths of annual rings was analysed and related mainly to temperature and herbivory using ring width series from five heath forest sites in the Lake Torneträsk area, northern Sweden. Climate explained 48–64% of the variation in age‐corrected mean ring width series. In general, the effect of current year July followed by June temperature was most important at all sites. A warm May resulted in wider rings due to an earlier budburst. Short‐term (inter‐annual) responses to increased temperature were in most cases not reflected into long‐term responses (decades). A large proportion of the variation in stem mean ring width was due to variation among stems within trees (81%) in these polycormic trees, while variation among sites was marginal (0.4%). Within trees, main stems grew faster and were more responsive to climate variation than subordinate stems. No effect of insect herbivory on ring width was found at low defoliation levels (≤12%). At a defoliation level of ca 84% a one‐year reduction in stem growth was observed while the growth reduction (ca 50% reduction in ring width) lasted for 4 yr after ca 93% defoliation. After outbreaks resulting in complete defoliation and some stem mortality, ring widths of surviving stems mainly responded with increased growth. Basal sprouts, emerging just after a severe insect outbreak with a high mortality of old stems, grew faster than sprouts occurring during other periods. It is concluded that the mountain birch is well adapted to recover from Epirrita outbreaks; the ability to produce basal sprouts, that can benefit from an existing root system for fast initial growth, is one important mechanism for this.
Ground beetle responses to patch retention harvesting in high elevation forests of British Columbia
Authors: Lemieux Jeffrey P. , Lindgren B. Staffan
Published: August 2004

The effect of a forest harvesting system whereby small (typically 0.1–2.0 ha) patches of standing timber are retained inside of harvests, was compared to conventional clearcutting for its effect on ground beetle assemblages. Two seasons of pitfall trapping entailed 46 451 trap days, and yielded 15 799 individuals of 28 species; abundance was dominated by four species comprising 92.4% of the catch. Most species were known to have wide geographic distributions in Canada and Alaska but many species seemed to respond to disturbance on a site‐specific basis. Contrary to findings of similar studies, no species could be characterized as “mature‐forest specialists”, or “forest generalists”. Forest patches and edge habitats immediately inside the forest canopy contained assemblages more closely related to mature forest than to cleared areas. Harvested areas with patches yielded catches distinct from typical clearcuts, based primarily on changes in abundance of one common species. Climatic regimes and landscape disturbance levels were the two important factors distinguishing our study from others, and we have suggested that these may influence the degree to which patches are an effective conservation tool.
Trends in diversity and abundance of obligate epiphytic bryophytes in a highly managed landscape
Authors: Vanderpoorten Alain , Engels Patrick , Sotiaux André
Published: August 2004

Although forest stands represent 47% of the total land area in Europe, alterations to the forest habitat through logging and plantation of exotic trees has led to significant changes in forest biocenoses. Due to their peculiar biology and life history, epiphytic bryophytes, which include a number of species of high conservation value, are especially concerned. Ordinal logit regression was used to test whether trends in diversity and abundance of obligate epiphytic bryophytes are explained by forest cover and spruce plantation and determine specific optima and degree of reliance to these factors at the landscape scale. Spruce plantations had a negative impact on both species diversity and abundance. Although large forest patches were important for a set of species exclusively or more frequently occurring under the forest cover, the abundance of a number of species previously identified as woodland bryophytes decreased or was uncorrelated with increasing forest cover. Furthermore, the species pool adapted to edge‐related abiotic conditions was important. The global epiphytic diversity did consequently not decrease with decreasing forest cover at the landscape scale. If large forest patches are important for the conservation of a set of species exclusively or more frequently occurring under the forest cover, the conservation of epiphytic bryophytes thus also involves the conservation of pioneer trees in open landscapes. A series of management measures, which may help maximize the species diversity and probability of occurrence of key‐species of high conservation interest, are proposed.
Landscape effects on butterfly assemblages in an agricultural region
Authors: Bergman Karl‐Olof , Askling John , Ekberg Oscar , Ignell Håkan , Wahlman Henrik , Milberg Per
Published: August 2004

We examined the butterfly fauna at 62 sites in southeastern Sweden within a region exhibiting high variation in the landscape surrounding the studied grasslands. The landscape varied from an intensively‐managed agricultural landscape with a large amount of open fields to a landscape with a high amount of deciduous forest/semi‐natural grassland. We made 12 179 observations of 57 species of butterflies. The amount of neighbouring deciduous forest/semi‐natural grassland, with >25% tree and bush cover, was the most important environmental factor explaining the variation in the butterfly assemblages. Landscape analyses at three different spatial scales showed that the variation in butterfly assemblages could be explained only at the largest scale (radius 5000 m) and not at the smaller ones (radii 500 and 2000 m).

Logistic regressions were used to predict presence/absence of butterfly species. Our study indicated that there may be critical thresholds for the amount of habitat at the landscape scale for several butterfly species as well as for species richness. ForMelitaea athalia, there was a sharp increase in occupancy probability between 3 and 10% deciduous forests/semi‐natural grasslands at the 5000‐m scale. For 12 other species, the value for 50% probability of occurrence varied between 2 and 12% deciduous forest/semi‐natural grassland. Species which had high occupancy probabilities in landscapes with a low amount of surrounding deciduous forests/semi‐natural grasslands were significantly more mobile than others.

Our study highlights the importance of applying a landscape perspective in conservation management, and that single‐patch management might fail in maintaining a diverse butterfly assemblage.
Age‐related environmental sensitivity and weather mediated nestling mortality in white storksCiconia ciconia
Authors: Jovani Roger , Tella José L.
Published: August 2004

We studied environmental sensitivity and mortality related to weather inclemency in white stork nestlingsCiconia ciconiain their southern European boundary (Doñana, SW Spain). The study of homeothermy acquisition and fault bars (i.e. a measure of stress on feathers) revealed that stork nestlings were specially sensitive to environmental conditions occurring before 20 d of age. Accordingly, most of nestling mortality concentrated during this sensitive period: 91% of deaths corresponded to nestlings younger than 20 d, 73% concentrating on nestlings up to 10 d‐old. Nestling mortality and total breeding failure were highly variable among years, being especially high when rainy periods coincided with the early live of nestlings (between 1 April and 15 May). Maximum temperatures had a positive correlation with breeding success and nestling survival but this effect disappeared when controlling for rainfall. Our results are in agreement with previous studies conducted in other white stork populations in other latitudes. We suggest that this could be the result of a low homeothermy capacity of young nestlings jointly with an early breeding phenology that expose white storks to rain, but not to high temperatures. In the context of global climate change we suggest that the current decrease on spring rainfall could increase nestling survival while punctual rainy springs could have a negative effect on the reproduction of white storks.
Can climate data from METEOSAT improve wildlife distribution models?
Authors: Suárez‐Seoane Susana , Osborne Patrick E. , Rosema Andries
Published: August 2004

Global climate change generated by human activities is likely to affect agroecosystems in several ways: reinforcing intensification in northern and western Europe, and extensification in the Mediterranean countries. If we are to predict the consequences of global warming for wildlife, distribution models have to include climate data. The METEOSAT temporal series from EWBMS offers an attractive alternative to using climatic surfaces derived from ground stations. The aim of this paper is to test whether this climatic satellite data can improve the distribution models obtained previously by Suárez‐Seoane et al. using habitat variables for three agro‐steppe bird species: great bustard, little bustard and calandra lark in Spain. Rainfall, radiation balance, evapotranspiration and soil moisture images were incorporated together with the other variables used as predictors in the published stepwise GAM models. Changes in the predicted distributions from the habitat only and climate‐habitats models were assessed by reference to the CORINE land cover categories. Inclusion of climatic variables from METEOSAT led to statistically superior models for all three species. There were large differences in the climatic variables selected and the original variables dropped among the species. Evapotranspiration variables were the most frequently selected. Maps of the differences between the habitat and climate‐habitat models showed very different patterns for the three species. Inclusion of climate variables led to a wider range of land cover types being deemed suitable. Despite the statistical superiority of models, care is needed in deciding whether to use climatic variables because they may emphasize the fundamental rather than the realized niche. Used together, however, habitat and climate models can provide new insights into factors limiting species distributions and how they may respond to climate change.
Associations of garden birds with gradients in garden habitat and local habitat
Authors: Chamberlain D. E. , Cannon A. R. , Toms M. P.
Published: August 2004

Habitat associations of 40 bird species were analysed using data from a survey of 12892 garden sites throughout the United Kingdom between 1995 and 2002. Gradients in 20 garden habitat variables and 25 variables describing the surrounding local habitat were derived from Detrended Correspondence Analysis. The main garden axis explained 13.3% of variation in the data and described a gradient from sites containing and bounded by high levels of vegetation cover to open sites bounded by walls and fences. The main local axis explained 29.9% of variation in the data and described a gradient from rural to urban habitats. Higher probability of occurrence was detected in larger sites in 25 species and in smaller sites in four (urban‐associated) species. Many species (22 out of 40) were significantly associated with the local gradient: seven species showed the highest probability of occurrence in sites within more urbanised habitats. Other species were most likely to occur in sites within rural or suburban habitats. Only five species showed a significant association with garden habitat gradient, four of these being most likely to occur in sites with highest vegetation cover. These associations were similar when controlling for garden size and for food provision in gardens. The results imply that the likelihood of many species occurring in gardens is dependent on the surrounding local habitat rather than the garden habitat. However, survey participants were likely to have “bird‐friendly” gardens which may have reduced the variation in garden habitat across the sample. An assessment of the representativeness of survey sites is needed to further understand habitat associations of garden birds.
500. Aconitum Hemsleyanum
Authors: Sinnott Mike
Published: August 2004

Summary.  The climbing Monkshood of gardens is investigated and one of the climbing species A. hemsleyanum Pritz. is described. Some suggestions on its cultivation are provided.
501. Rubus Calophyllus
Authors: Rix Martyn
Published: August 2004

Summary.  A rare bramble from the eastern Himalaya, Rubus calophyllus C.B. Clarke is illustrated. Its distribution and habitat are described and related species are discussed.
502. Sinningia Pusilla
Authors: Biggs Nicki
Published: August 2004

Summary.  A miniature gesneriad, Sinningia pusilla(C. Mart.) Baill. from Brazil is described and illustrated, and notes are given on the horticultural history of the genus Sinningia
503. Epigeneium Cacuminis
Authors: Wood Jeffrey
Published: August 2004

Summary.  Epigeneium cacuminis(Gagnep.) Summerh. from Vietnam is illustrated. Its taxonomy, relationships, distribution and cultivation are discussed and a full description provided. A brief taxonomic and nomenclatural history of the genus is also provided.
504. Agapanthus Africanus SUBSP. Walshii
Authors: Duncan Graham
Published: August 2004

Summary.  The history, taxonomy, distribution and cultivation requirements of the South African Agapanthus africanus(L.) Hoffmanns. subsp. walshii(L. Bolus) Zonn. & G.D. Duncan (Agapanthaceae) are discussed; a full botanical description and an illustration are provided.
Triglyceride accumulation and altered composition of triglyceride‐associated fatty acids in the skin of tenascin‐X‐deficient mice
Authors: Matsumoto Ken‐ichi , Sato Takashige , Oka Seiko , Orba Yasuko , Sawa Hirofumi , Kabayama Kazuya , Inokuchi Jin‐ichi , Ariga Hiroyoshi
Published: August 2004

Tenascin‐X (TNX) is a member of the tenascin family of glycoproteins of the extracellular matrix. Here, we observed abnormalities in the skin of TNX‐deficient mice in comparison with that of wild‐type mice. Histological analysis with Oil Red O staining demonstrated that there was considerable accumulation of lipid in the skin of TNX‐deficient (TNX−/−) mice. By thin‐layer chromatography of total lipids, it was found that the level of triglyceride was significantly increased in TNX−/− mice. The mRNA levels of most of the lipogenic enzyme genes examined were remarkably increased in TNX−/− mice. By gas chromatography‐mass spectrometry analysis of triglyceride‐associated fatty acids in the skin, saturated fatty acid palmitoic acid was decreased, whereas unsaturated fatty acids palmitoleic acid and oleic acid were increased in TNX−/− mice compared with those in wild‐type mice. Conversely, fibroblast cell lines transfected with TNX showed a significant decrease in the amount of triglyceride. An increase in the saturated fatty acid stearic acid and decreases in the unsaturated fatty acids palmitoleic acid, oleic acid and linoleic acid, compared to those in mock‐transfected cells were also caused by over‐expression of TNX. These results indicate that TNX is involved in the regulation of triglyceride synthesis and the regulation of composition of triglyceride‐associated fatty acids.
XSENP1, a novel sumo‐specific protease in Xenopus, inhibits normal head formation by down‐regulation of Wnt/β‐catenin signalling
Authors: Yukita Akira , Michiue Tatsuo , Fukui Akimasa , Sakurai Kenji , Yamamoto Hideki , Ihara Motomasa , Kikuchi Akira , Asashima Makoto
Published: August 2004

Small Ubiqutin‐related modifier (SUMO), which is responsible for the ubiquitination‐like post‐translational modification ‘sumoylation’, regulates a number of biological processes including, in particular, transcription. The rat protein Axam, which possesses SUMO‐specific protease activity, was shown to inhibit the Wnt signalling pathway. Several other components of the pathway are also sumoylated, so the mechanism of this modification has itself been linked to Wnt signalling. However, the functional interactions between SUMO and Wnt signalling are not well understood. This study identified a novel SUMO‐specific protease in Xenopus, which was denoted XSENP1. The C‐terminus of XSENP1 is highly conserved across the SUMO‐specific protease family, and in vitro XSENP1 possesses hydrolase and desumoylation activity. Over‐expression of XSENP1 in vivo inhibited dorso‐anterior development of Xenopus embryos and suppressed Wnt signalling target gene expression in a manner similar to Axam. Deletion analysis of XSENP1 showed that inhibition of the Wnt signalling pathway requires protease activity. Moreover, XSENP1 inhibits ectopic axis induction by Dvl, β‐catenin and the constitutively active form of β‐catenin, but not by siamois. These results indicate that the dorsal expression of XSENP1 obstructs head development in Xenopus laevis and that this effect may result from inhibition of the canonical Wnt pathway downstream of β‐catenin, but upstream of siamois.
Meiosis induced by inactivation of Pat1 kinase proceeds with aberrant nuclear positioning of centromeres in the fission yeast Schizosaccharomyces pombe
Authors: Chikashige Yuji , Kurokawa Rumi , Haraguchi Tokuko , Hiraoka Yasushi
Published: August 2004

Nuclear organization of chromosomes proceeds with significant changes during meiosis. In the fission yeast Schizosaccharomyces pombe, centromeres are clustered at the spindle‐pole body (SPB) during the mitotic cell cycle; however, during meiotic prophase telomeres become clustered to the SPB and centromeres dissociate from the SPB. We followed the movement of telomeres, centromeres and sister chromatids in living S. pombe cells that were induced to meiosis by inactivation of Pat1 kinase (a key negative regulator of meiosis). Time‐course observation in living cells determined the temporal order of DNA synthesis, telomere clustering, centromere separation and meiotic chromosome segregation. When meiosis was induced by Pat1 inactivation at the G1 phase of mitosis, telomeres clustered to the SPB as per normal meiosis, but in most cells the centromeres remained partially associated with the SPB. When meiosis was initiated at the G2 phase by Pat1 inactivation, both telomeres and centromeres retained their mitotic nuclear positions in the majority of cells. These results indicate that the progression of meiosis induced by Pat1 inactivation is aberrant from normal meiosis in some events. As Pat1 inactivation is often useful to induce S. pombe cells synchronously into meiosis, the temporal order of chromosomal events determined here will provide landmarks for the progression of meiosis downstream the Pat1 inactivation.
Screening of FGF target genes in Xenopus by microarray: temporal dissection of the signalling pathway using a chemical inhibitor
Authors: Chung Hyeyoung A. , Hyodo‐Miura Junko , Kitayama Atsushi , Terasaka Chie , Nagamune Teruyuki , Ueno Naoto
Published: August 2004

Microarray is a powerful tool for analysing gene expression patterns in genome‐wide view and has greatly contributed to our understanding of spatiotemporal embryonic development at the molecular level. Members of FGF (fibroblast growth factor) family play important roles in embryogenesis, e.g. in organogenesis, proliferation, differentiation, cell migration, angiogenesis, and wound healing. To dissect spatiotemporally the versatile roles of FGF during embryogenesis, we profiled gene expression in Xenopus embryo explants treated with SU5402, a chemical inhibitor specific to FGF receptor 1 (FGFR1), by microarray. We identified 38 genes that were down‐regulated and 5 that were up‐regulated in response to SU5402 treatment from stage 10.5–11.5 and confirmed their FGF‐dependent transcription with RT‐PCR analysis and whole‐mount in situ hybridization (WISH). Among the 43 genes, we identified 26 as encoding novel proteins and investigated their spatial expression pattern by WISH. Genes whose expression patterns were similar to FGFR1 were further analysed to test whether any of them represented functional FGF target molecules. Here, we report two interesting genes: one is a component of the canonical Ras‐MAPK pathway, similar to mammalian mig6 (mitogen‐inducible gene 6) acting in muscle differentiation; the other, similar to GPCR4 (G‐protein coupled receptor 4), is a promising candidate for a gastrulation movement regulator. These results demonstrate that our approach is a promising strategy for scanning the genes that are essential for the regulation of a diverse array of developmental processes.
In vivo synthesis of Taf1p lacking the TAF N‐terminal domain using alternative transcription or translation initiation sites
Authors: Kasahara Koji , Kawaichi Masashi , Kokubo Tetsuro
Published: August 2004

The TAF N‐terminal domain (TAND) of TAF1 includes two subdomains, TAND1 and TAND2, which bind to the concave and convex surfaces of TBP, respectively. Previous studies showed that the substitution of yeast TAND1 or TAND2 with the equivalent domain from a Drosophila homologue leads to accumulation of truncated Taf1p in yeast. This study demonstrates that these truncated Taf1p derivatives lack TAND. However, full‐length Taf1p and untruncated derivatives are produced in yeast when several Met‐to‐Ala mutations are introduced in the carboxy‐terminus of TAND. In contrast, mutations that reduce expression of full‐length TAF1 do not reduce the amount of truncated Taf1p derivatives that are produced. These data suggest that TAND‐deficient TAF1 derivatives are produced by initiating translation at alternative initiation sites. In addition, the TAF1 mRNA structure suggests that the TAND‐deficient TAF1 derivatives may also be formed in yeast by use of (cryptic) alternative transcription initiation sites. Importantly, TAND‐deficient truncated Taf1p appears to be produced at a low level in wild‐type yeast as well. Finally, this study also demonstrates that Drosophila TAND2 substitutes functionally for yeast TAND2, but Drosophila TAND1 does not substitute for yeast TAND1.
Serum adiponectin and metabolic parameters in HIV‐1‐infected patients after substitution of nevirapine for protease inhibitors
Authors: Petit J. M. , Duong M. , Masson D. , Buisson M. , Duvillard L. , Bour J. B. , Brindisi M. C. , Galland F. , Guiguet M. , Gambert P. , Portier H. , Vergès B.
Published: August 2004

Background  In the context of HIV infection and antiretroviral therapy, adiponectin concentrations have been shown to be related to lipodystrophy, metabolic alterations and HIV‐protease inhibitor (PI) use. The replacement of PI by nevirapine has improved the lipid profile of patients under antiretroviral therapy. The aim of the present study was to examine whether adiponectin concentration or insulin sensitivity level correlate with the modifications of lipid parameters after the switch of PI by nevirapine.

Material and methods  The evolution of metabolic parameters before and after 6 months of substitution of nevirapine for protease inhibitors was evaluated in a cohort of 55 HIV‐1 infected patients. Adiponectin concentration, insulin sensitivity, lipid profile, cholesterol ester transfer protein (CETP) mass concentration and triglyceride enrichment of HDL were determined before and after the replacement of PI by nevirapine. Insulin sensitivity was evaluated by the HOMA model assessment.

Results  Twenty‐four weeks of treatment with nevirapine improved significantly the lipid profile with a significant reduction of apoB (from 0·98 to 0·92 g L−1; P = 0·005) and triglyceride (from 2·02 to 1·66 mmol L−1; P = 0·02). HDL cholesterol and apoA1 increased significantly (from 0·99 to 1·19 mmol L−1; P = 0·001 and from 1·40 to 1·57 g L−1; P < 0·001, respectively). The triglyceride enrichment of HDL significantly decreased after the replacement of PI by nevirapine (from 0·248 ± 0·092 to 0·213 ± 0·093; P = 0·003). At baseline, and after 24 weeks of nevirapine treatment, we observed significant correlations between adiponectin level and lipid parameters [(HDL‐cholesterol (r = 0·66, P = 0·001 and r = 0·69, P = 0·001); triglycerides (r = −0·42, P = 0·002 and r  =−0·57, P = 0·001), and triglyceride enrichment of HDL (r = −0·43, P = 0·005 and r = −0·53, P = 0·005)]. Twenty‐four weeks of treatment with nevirapine did not significantly change adiponectin concentrations (from 984 to 1086 µg L−1, P = 0·22), CETP mass and insulin sensitivity.

Conclusion  This study shows that even though a strong correlation was found between adiponectin and some metabolic parameters at baseline and after 24 weeks of treatment by nevirapine, the improvement of lipid profile observed after the replacement of PI by nevirapine was not in relation to the change of plasma adiponectin concentration. The significant decrease of triglyceride enrichment of HDL after the replacement of PI by nevirapine probably leads to a decreased catabolism of HDL lipoprotein, and consequently explains the increase of plasma HDL concentration observed in this study.
Low‐dose growth hormone and human immunodeficiency virus‐associated lipodystrophy syndrome: a pilot study
Authors: Andersen O. , Haugaard S. B. , Flyvbjerg A. , Andersen U. B. , Ørskov H. , Madsbad S. , Nielsen J. O. , Iversen J.
Published: August 2004

Background  Treatment with high doses (2–6 mg day−1) of human growth hormone (hGH) in patients with human immunodeficiency virus (HIV)‐associated lipodystrophy syndrome (HALS) has been shown to increase concentrations of total insulin‐like growth‐factor‐I (IGF‐I) more than twofold greater than the normal upper range and is accompanied by adverse effects such as joint pain and glucose intolerance.

Materials and methods  We performed a 16‐week open‐labelled prospective pilot study in six male HALS patients using a s.c. low‐dose hGH, 0·7 mg day−1, aiming to examine the impact on total and free IGF‐I and fat distribution. Glucose metabolism was examined by oral glucose tolerance tests and hyperinsulinaemic euglycaemic clamps.

Results  Total IGF‐I increased twofold (P < 0·01) and free IGF‐I increased 2·5‐fold (P < 0·01) to the level of the normal upper range. HDL‐cholesterol increased (P = 0·01). Patients reported improvements of lipodystrophy, which was supported by a decreased waist‐to‐thigh ratio (P = 0·01), and waist‐to‐hip ratio (P = 0·06). Ratio of peripheral to trunk soft tissue mass increased (P = 0·01, measured by dual‐energy X‐ray absorptiometry scans) and a trend towards reduction in percentage of trunk fat was suggested (P = 0·12). Total fat mass, exercise capacity, glucose tolerance, glucose disposal rate and immune status, respectively, did not change (all P > 0·5). The patients did not complain of arthralgia or other known GH‐related side‐effects.

Conclusions  Sixteen weeks’ treatment of lipodystrophic HIV‐infected patients with hGH, 0·7 mg day−1, increased total and free IGF‐I twofold and appeared safe and tolerable. The potential of low‐dose hGH in the treatment of HIV‐lipodystrophy awaits examination by placebo‐controlled, randomized trials.