bluuebunny/crossref_metadata_2025 huggingface dataset:
DEPD: a novel database for differentially expressed proteins
Authors: He Quan-Yuan , Cao Jing , Liu Xiang-Hua , Li Miao-Xin , Liu Yi-Song , Xie Jin-Yun , Liang Song-Ping
Published: July 2005

Summary: The Differentially Expressed Protein Database was designed to store the output of comparative proteomics studies and provides a publicly available query and analysis platform for data mining. The database contains information about more than 3000 differentially expressed proteins (DEPs) manually extracted from the published literature, including relevant biological, experimental and methodological elements. Tools for visualization and functional analysis of DEPs are provided via a user-friendly webinterface.

Availability:  http://protchem.hunnu.edu.cn/depd/

Contact:  liangsp@hunnu.edu.cn
A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips
Authors: Liu Xuejun , Milo Marta , Lawrence Neil D. , Rattray Magnus
Published: July 2005

Motivation: Affymetrix GeneChip® arrays are currently the most widely used microarray technology. Many summarization methods have been developed to provide gene expression levels from Affymetrix probe-level data. Most of the currently popular methods do not provide a measure of uncertainty for the expression level of each gene. The use of probabilistic models can overcome this limitation. A full hierarchical Bayesian approach requires the use of computationally intensive MCMC methods that are impractical for large datasets. An alternative computationally efficient probabilistic model, mgMOS, uses Gamma distributions to model specific and non-specific binding with a latent variable to capture variations in probe affinity. Although promising, the main limitations of this model are that it does not use information from multiple chips and does not account for specific binding to the mismatch (MM) probes.

Results: We extend mgMOS to model the binding affinity of probe-pairs across multiple chips and to capture the effect of specific binding to MM probes. The new model, multi-mgMOS, provides improved accuracy, as demonstrated on some bench-mark datasets and a real time-course dataset, and is much more computationally efficient than a competing hierarchical Bayesian approach that requires MCMC sampling. We demonstrate how the probabilistic model can be used to estimate credibility intervals for expression levels and their log-ratios between conditions.

Availability: Both mgMOS and the new model multi-mgMOS have been implemented in an R package, which is available at http://www.bioinf.man.ac.uk/resources/puma

Contact:  magnus@cs.man.ac.uk
Genetic mapping of the compatibility between a lily isolate of Cucumber mosaic virus and a satellite RNA
Authors: Yamaguchi Naoya , Seshimo Yuko , Yoshimoto Eri , Ahn Hong Il , Ryu Ki Hyun , Choi Jang Kyung , Masuta Chikara
Published: July 2005

Five isolates of Cucumber mosaic virus (CMV) from Lilium sp. (lily), which were isolated from specimens in Japan, Korea and Taiwan, were unable to support satellite RNA (satRNA) accumulation. In order to map the CMV sequences that are involved in satRNA support, HL-CMV (Japanese lily isolate), Y-CMV (ordinary strain) and Y-satellite RNA (Y-sat) were used as the source material. The pseudorecombinants between Y-CMV and HL-CMV revealed that RNA1 was essential for satRNA replication in lily. The results of chimeric constructs and various mutations showed that two amino acid residues (at positions 876 and 891) in the 1a protein were the determinants for the inability of HL-CMV to support a satRNA. Specifically, Thr at position 876 had a more pronounced effect than Met at position 891. Specific changes in RNA sequence were also detected in the 3′ terminus of Y-sat and these particular alterations allowed it to be supported by HL-CMV. It is believed that, through evolution, the adaptation of CMV to lily resulted in the introduction of amino acid changes in the 1a protein, changes that coincidentally affected the ability of lily CMV to support satRNAs.
Low frequency of PrP genotype 225SF among free-ranging mule deer (Odocoileus hemionus) with chronic wasting disease
Authors: Jewell Jean E. , Conner Mary M. , Wolfe Lisa L. , Miller Michael W. , Williams Elizabeth S.
Published: July 2005

The prion protein (PrP) gene was characterized in 1482 free-ranging mule deer (Odocoileus hemionus) from Wyoming and Colorado. Using DNA sequences from 363 deer, dimorphisms at codons 20 (aspartate/glycine) and 225 [serine (S)/phenylalanine (F)] were found; silent changes occurred at codons 131 (tyrosine) and 247 (isoleucine). The remaining samples were surveyed for codon 225 genotype and all were characterized for chronic wasting disease (CWD) infection status. A total of 112 deer with the genotype 225SF or FF were found, of which one was CWD-positive; 1370 were 225SS, with 289 positive for CWD. Among CWD-negative deer, the frequency of 225SF/FF genotypes was 9·3 % but among CWD-positive deer it was only 0·3 %. For all samples combined, CWD status was not independent of codon 225 genotype (P<0·0001). The odds that a deer of the 225SS genotype was CWD-infected were 30 times greater (95 % confidence intervals=4–213) than for a 225SF deer. The proportion of 225SF animals in sampled subpopulations varied from 0 to 18 %; the CWD prevalence varied from 0 to 25 %. However, no relationship was observed between genotype frequency and CWD prevalence in different areas. The PrP sequences of experimentally infected mule deer were analysed from pre-existing projects and 10 animals were found with 225SF genotypes, all of which were positive for CWD. Data available from some of these animals suggest that the 225SF genotype could be associated with longer incubation periods in CWD infection compared with the 225SS genotype.
Geminin regulates neuronal differentiation by antagonizing Brg1 activity
Authors: Seo Seongjin , Herr Anabel , Lim Jong-Won , Richardson Genova A. , Richardson Helena , Kroll Kristen L.
Published: July 2005

Precise control of cell proliferation and differentiation is critical for organogenesis. Geminin (Gem) has been proposed to link cell cycle exit and differentiation as a prodifferentiation factor and plays a role in neural cell fate acquisition. Here, we identified the SWI/SNF chromatin-remodeling protein Brg1 as an interacting partner of Gem. Brg1 has been implicated in cell cycle withdrawal and cellular differentiation. Surprisingly, we discovered that Gem antagonizes Brg1 activity during neurogenesis to maintain the undifferentiated cell state. Down-regulation of Gem expression normally precedes neuronal differentiation, and gain- and loss-of-function experiments inXenopusembryos and mouse P19 cells demonstrated that Gem was essential to prevent premature neurogenesis. Misexpression of Gem also suppressed ectopic neurogenesis driven by Ngn and NeuroD. Gem's activity to block differentiation depended upon its ability to bind Brg1 and could be mediated by Gem's inhibition of proneural basic helix–loop–helix (bHLH)–Brg1 interactions required for bHLH target gene activation. Our data demonstrate a novel mechanism of Gem activity, through regulation of SWI/SNF chromatin-remodeling proteins, and indicate that Gem is an essential regulator of neurogenesis that can control the timing of neural progenitor differentiation and maintain the undifferentiated cell state.
RNA meets chromatin
Authors: Bernstein Emily , Allis C. David
Published: July 2005

In the universe of science, two worlds have recently collided—those of RNA and chromatin. The intersection of these two fields has been impending, but evidence for such a meaningful collision has only recently become apparent. In this review, we discuss the implications for noncoding RNAs and the formation of specialized chromatin domains in various epigenetic processes as diverse as dosage compensation, RNA interference-mediated heterochromatin assembly and gene silencing, and programmed DNA elimination. While mechanistic details as to how the RNA and chromatin worlds connect remain unclear, intriguing parallels exist in the overall design and machinery used in model organisms from all eukaryotic kingdoms. The role of potential RNA-binding chromatin-associated proteins will be discussed as one possible link between RNA and chromatin.
A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation
Authors: Horn Peter J. , Bastie Jean-Noël , Peterson Craig L.
Published: July 2005

Heterochromatin is critical for proper centromere and telomere function, and it plays a key role in the transcriptional silencing of specific genomic loci. In fission yeast, the Rik1 protein functions with the Clr4 histone methyltransferase at an early step in heterochromatin formation. Here, we use mass spectrometry and tandem affinity purification of a Rik1-TAP fusion protein to identify Rik1-associated proteins. These studies identify two novel proteins, Raf1 and Raf2, which we find are required for H3-K9 methylation and for transcriptional silencing within centromeric heterochromatin. We also find that subunits of a cullin-dependent E3 ubiquitin ligase are associated with Rik1 and Clr4, and Rik1-TAP preparations exhibit robust E3 ubiquitin ligase activity. Furthermore, expression of a dominant-negative allele of the Pcu4 cullin subunit disrupts regulation of K4 methylation within heterochromatin. These studies provide evidence for a novel Rik1-associated E3 ubiquitin ligase that is required for heterochromatin formation.
Invasive and native Rhododendron ponticum populations: is there evidence for genotypic differences in germination and growth?
Authors: Erfmeier Alexandra , Bruelheide Helge
Published: July 2005

Previous studies have shown that the invasive spread of Rhododendron ponticum in the British Isles is influenced by the more favourable environmental conditions in the new territory than in the species’ home range. In this study, we asked whether the species’ invasion success might also involve a genotypic background for higher growth and germination rates in invasive populations. We tested the hypotheses that invasive populations have higher absolute germination rates, germinate faster and exhibit higher growth rates. We present data from greenhouse and climate chamber experiments with seed material and Rhododendron cuttings from six populations each of native Georgian, native Spanish and invasive Irish populations subjected to different temperature environments.

There were no differences in the maximum germination rate and optimum germination temperature between native and invasive origins. We found significant differences in germination velocity with the Irish seeds responding most rapidly to all germination treatments. Accordingly, in the growth experiment the invasive Irish origins had the highest relative growth rates in all environments tested.

Our results provide evidence for a genetic shift in invasive populations towards an increased investment in growth and towards a faster germination rate. Both traits would contribute to explaining this species’ range expansion. The underlying evolutionary mechanisms for this shift are discussed, including the possibility of hybridisation or of an ecological release from hitherto experienced constraints in the native area.
Using high‐resolution multi‐spectral imagery to estimate habitat complexity in open‐canopy forests: can we predict ant community patterns?
Authors: Lassau Scott A. , Cassis Gerasimos , Flemons Paul K. J. , Wilkie Lance , Hochuli Dieter F.
Published: July 2005

The structure and composition of arthropod assemblages are strongly associated with habitat complexity. Accurate, time efficient estimates of habitat complexity may provide insights for biodiversity management in natural systems. We obtained high‐resolution (0.7 m pixel) multi‐spectral aerial imagery of National Parks 20 km north and 20 km south of Sydney, Australia. We explored both the Normalised Difference Vegetation Index (NDVI) and the standard deviation of reflectance in the near‐infrared spectrum (stdevRNIR) as indicators of low and high habitat complexity in sandstone forests north of Sydney. We then tested described predictions of ant community patterns (based on a previous study) using sites selected from high‐resolution multi‐spectral imagery in sandstone forests south of Sydney. Ground‐scored habitat complexity was positively correlated with NDVIs and, to a lesser extent, stdevRNIR values in sandstone forests north of Sydney. As predicted, ant species richness was negatively correlated with NDVIs in forests to the south of Sydney. Also, ant species composition was different in areas with contrasting NDVIs. The ant species driving composition differences responded to habitat complexity in a similar way in forests to the north, and south, of Sydney. The strong association we detected between NDVIs and habitat complexity, most likely reflects the relatively exposed nature of the vegetative layers in the forests we sampled. Remote sensing, integrated with quantitative research testing predictive faunal responses to vegetation structure and biomass at landscape scales, may provide efficient means of estimating biodiversity for management in particular habitats.
Abundance – distribution relationships in fish assembly of the Amazonas floodplain lakes
Authors: Granado‐Lorencio Carlos , Lima Carlos R. M. Araujo , Lobón‐Cerviá Javier
Published: July 2005

This study shows that patterns in some community assemblages are not mainly governed by local factors but also by regional ones. Using field data from 36 floodplain forest lakes in the Amazon basin, we present transect count data on the richness, abundance and distribution of floodplain lake fish species. A total of 194 fish species were collected, of which 43 were classified as short‐distance migrants. A positive relation was found for local migratory and sedentary species abundances with distribution at a regional scale. The study also suggests that the probability of the presence of a migratory species is more affected by aspects of river‐lake connectivity than sedentary species. Our results seem to indicate that migratory species play an important role in local dynamics of floodplain lakes.
Geographic variation in plant species richness patterns within temperate eucalypt woodlands of eastern Australia
Authors: T. Hunter John
Published: July 2005

Species density, pattern diversity and species pool are often studied in isolation and correlated individually to environmental gradients. However analysis of how these three measures interrelate can give insights into the interpretation of local and regional processes. In addition, an understanding of how these diversity measures change across the natural distribution of a community may help in decision making processes regarding reservation. Temperate eucalypt woodlands in eastern Australia are one of the most visible and ubiquitous communities in eastern Australia, but have undergone one of the most significant modification and fragmentation processes due to past and current pressure to clear for agriculture. Data from 176 vascular plant survey sites sampled across 14 woodland assemblages are used here to analyse geographic gradients in species density, pattern diversity and species pool size. It was discovered that species density was significantly correlated to pattern diversity and species pool size but that pattern diversity and species pool size were uncorrelated. There was a significant relationship whereby species density increased as pattern diversity decreased. These patterns may be explained by the maintenance of interconnectedness, dispersal and rescue effects at this scale of investigation but local interactions cannot be ruled out as important. Generally species density and species pool size increased from west to east in the study area and pattern diversity was strongly correlated to the coldest minimum winter temperatures. It is suggested that if local woodland richness is maintained by low pattern diversity and greater habitat connectedness then larger reserves are required in order to maintain the largest area of contiguous habitat. In such situations small isolated patches, which are increasingly fragmented by the pressure to clear for agriculture will accumulate larger extinction debts.
Nested pattern in flea assemblages across the host's geographic range
Authors: Krasnov Boris R. , Shenbrot Georgy I. , Khokhlova Irina S. , Poulin Robert
Published: July 2005

Understanding non‐random patterns in the taxonomic composition of communities occurring in insular or fragmented habitats remains a major goal of ecology. Nested subset patterns are one possible departure from random community assembly that has been reported for communities of both free‐living and parasitic animals. Here, we investigate the effects of extrinsic factors on the occurrence of nestedness among the assemblages of fleas found in different populations of the same host species, using data on 25 mammalian host species. The patterns of flea species composition among host populations spanned the entire spectrum from significantly nested to significantly anti‐nested. After controlling for host phylogeny, we found that across host species, the tendency for flea assemblages to approach nestedness increased with increasing host geographic range size and with decreasing latitude of the host's geographic range. This tendency also decreased with an increase in a composite variable combining data on mean January and July temperature. The number of closely‐related mammalian species living in sympatry with a given host species had no influence on whether or not the structure of flea assemblages among its populations departed from randomness. We propose explanations for these results that include: the possible gradual loss of flea species as a host expands its range from its initial area of origin, the lack of specific flea faunas in narrowly‐distributed host species, interspecific differences in the dispersal abilities of flea species becoming amplified in hosts with broad geographical ranges, and the effect of latitude, climate and environment on the probabilities of host‐switching and extinction in fleas. Overall, our results suggest that the structure of flea assemblages in mammalian hosts may be driven by features of host biology.
A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences
Authors: Bertelli Sara , Giannini Norberto P.
Published: July 2005

The phylogenetic relationships among the penguins have received little attention, despite their well‐known anatomy and the conspicuous nature of the group. Previous attempts have included datasets limited to few, mostly osteological characters, and one study was based on integumentary and breeding characters. We developed a morphological matrix comprising 159 morphological characters of osteology (70 characters), myology (15), digestive tract (1), integument (66), and breeding (7 characters), scored in 18 extant forms (all currently recognized species plus one distinct subspecies). A gaviiform was placed at the root, and 11 species of representative procellariiform groups completed the outgroup. A heuristic parsimony analysis under equal weights was performed. We also compiled DNA sequences available in GenBank for the mitochondrial genes 12S rDNA and cytochrome b. We included the two data partitions in a combined analysis under direct optimization. Both analyses recovered the monophyly of Sphenisciformes and all the traditional polytypic genera. Morphological characters performed optimally at the ordinal and generic nodes, also providing resolution and varying degrees of support at supra‐ and intrageneric nodes. The comparison of molecular and morphological results indicated that the most significant problem in the phylogeny of extant penguins is rooting the ingroup. The mutual interaction of molecular and morphological data decreases the ambiguity regarding the placement of the root, and provides a resolved, relatively well‐supported phylogeny of extant penguins. Biogeographical patterns based on breeding ranges and derived from the combined analysis show that the major intercontinental vicariance events detected are consistent with cold marine current patterns of the Southern Hemisphere.

© The Willi Hennig Society 2005.
Thyroid hormones as molecular determinants of thermogenesis
Authors: Silvestri E. , Schiavo L. , Lombardi A. , Goglia F.
Published: July 2005

Thyroid hormones (TH) are major modulators of energy metabolism and thermogenesis. It is generally believed that 3,5,3′‐triiodo‐l‐thyronine (T3) is the only active form of TH, and that most of its effects are mediated by nuclear T3 receptors, which chiefly affect the transcription of target genes. Some of these genes encode for the proteins involved in energy metabolism. However, a growing volume of evidence now indicates that other iodothyronines may be biologically active. Several mechanisms have been proposed to explain the calorigenic effect of TH, but none has received universal acceptance. Cold acclimation/exposure and altered nutritional status are physiological conditions in which a modulation of energy expenditure is particularly important. TH seem to be deeply involved in this modulation, and this article will review some aspects of their possible influence in these conditions.
NEAT – non‐exercise activity thermogenesis – egocentric & geocentric environmental factors vs. biological regulation
Authors: Levine J. A. , Kotz C. M.
Published: July 2005

Non‐exercise activity thermogenesis (NEAT) is the energy expenditure of all physical activities other than volitional sporting‐like exercise. NEAT includes all those activities that render us vibrant, unique and independent beings such as going to work, playing guitar, toe‐tapping and dancing. The factors that account for the 2000 kcal day−1 variability of NEAT can be categorized as environmental or biological. The environmental determinants of NEAT can be view using one of two models. In the egocentric model we consider a single person as the focus, e.g. ‘my job’. In the geocentric model we consider the ‘environment’ as the focus, e.g. well‐lit and safe walk ways. These models provide us with a theoretical framework to understand NEAT and how best to intervene to promote NEAT. As well as environmental effectors of NEAT, there are also biological regulatory mechanisms that enable us to account for three‐quarters of the biological variance in susceptibility and resistance to fat gain with human over‐feeding. NEAT is likely to be regulated through a central mechanism that integrates NEAT with energy intake and energy stores so that NEAT is activated with over‐feeding and suppressed with under‐feeding. In conclusion, NEAT is likely to serve as a crucial thermoregulatory switch between energy storage and dissipation that is biologically regulated and influenced, and perhaps over‐ridden, by environment. Deciphering the role of NEAT may lead to a better understanding of the pathogenesis, prevention and treatment of obesity.
A review of an anaesthetic led vascular access list
Authors: Galloway S. , Sharma A. , Ward J. , Bodenham A. R.
Published: July 2005

The demand for insertion of long‐term central venous (Hickman type) catheters is thought to be increasing. Organisation is required to meet this demand in a safe and efficient manner. This report reviews the results from a dedicated, anaesthetic led vascular access list over the initial 61‐month period. One thousand procedures were performed. Nine hundred and twenty catheters were inserted under local anaesthesia, with or without intravenous sedation and analgesia. Eighty catheters were removed. All procedures were performed during a dedicated once weekly, morning list. A total of 53% of all procedures were performed on a day‐case basis, 43% on in‐patients. Only 1.5% of patients required an unexpected overnight stay (usually medically unfit patients). There were 81 (9%) cancellations on the day of procedure due to neutropaenia, pneumonia or urinary tract infections. Ultrasound guidance was used initially selectively in 14%, latterly in 100% of procedures and fluoroscopy in all insertions to confirm or adjust catheter position. This service has been well received by patients and oncology services. In addition it provides an interesting area of practice for anaesthetists and an ideal environment for teaching more advanced aspects of central venous access. It may provide a template of service for other centres.
Hypoxaemia during open‐airway apnoea: a computational modelling analysis
Authors: McNamara M. J. , Hardman J. G.
Published: July 2005

Hypoxaemia during open‐airway apnoea, e.g. during brainstem death testing, may cause organ damage. The effect of ambient oxygen fraction on the extent of hypoxaemia has not been established. We validated the Nottingham Physiology Simulator in this context by reproducing the methodologies and results of four published clinical studies. We then used the simulator to examine the effects of different ambient oxygen fractions (0.21–1.0) and shunt fractions (1–30% of cardiac output) during apnoea. Increasing ambient oxygen fraction from 0.9 to 1.0 more than doubled the time to haemoglobin desaturation at all shunt fractions, and extended apnoea longer than when the ambient oxygen fraction was increased from 0.21 to 0.9. When ambient oxygen fraction and shunt fraction were large, arterial oxygen tension transiently increased during apnoea. A very high ambient oxygen fraction and a patent airway are likely to delay dangerous hypoxaemia during apnoea.
Radial to femoral arterial blood pressure differences during liver transplantation
Authors: Arnal D. , Garutti I. , Perez‐Peña J. , Olmedilla L. , Tzenkov I. G.
Published: July 2005

This observational study compared femoral and radial arterial blood pressure in 72 patients undergoing liver transplant surgery. Simultaneous femoral and radial arterial blood pressures, cardiac index, core temperature and vasoconstrictor therapy were recorded at seven time points during the operation. No significant differences between radial and femoral pressures were found at the start of surgery. Femoral and radial systolic arterial blood pressures were statistically significantly different during liver reperfusion (mean (SD) arterial pressure = 92 (22) mmHg vs. 76 (22) mmHg, p < 0.01). Mean arterial blood pressures showed no statistically significant differences throughout the study. Vasoconstrictor drug administration was associated with a larger systolic pressure difference between femoral and radial arteries (28 (24) mmHg in patients being given vasoconstrictor drugs vs. 9 (19) mmHg in patients not needing vasoconstrictors during reperfusion, p < 0.001). In conclusion, differences in systolic arterial blood pressure occur between femoral and radial arterial monitoring sites during liver reperfusion, and in particular in patients being given vasoconstrictor therapy. Thus, if femoral arterial monitoring is not available, clinicians should rely on mean rather than systolic arterial pressure measurements from a radial artery catheter during liver transplantation.
Genome screen for twinning rate QTL in four North American Holstein families
Authors: Cobanoglu O. , Berger P. J. , Kirkpatrick B. W.
Published: July 2005

The objective of this study was to identify twinning rate quantitative trait loci (QTL) by typing pooled samples in a preliminary screening followed by interval mapping to test QTL effects. Four elite North American Holstein half‐sib sire families with high twinning rate predicted transmitting abilities (PTA) were used in this study. Chromosomes 5, 7, 19 and 23 were not genotyped as these chromosomes were scanned for QTL in these families in a previous study. DNA was extracted from phenotypically extreme sons in each sire family. Two pools were prepared from sons of sires in each phenotypic tail, two each for high and low PTA levels for twinning rates. Each pool contained DNA from 4 to 15% of all sons of the sire depending on family. A total of 268 fluorescently labelled microsatellite markers were tested for heterozygosity in sires. About 135–170 informative markers per family were genotyped using pooled DNA samples. Based on the preliminary evidence for potential twinning rate QTL from pooled typing, interval mapping was performed subsequently on 12 chromosomal regions by family combinations. Evidence of QTL for twinning rate was found in one family on BTA21 and 29 at a chromosome‐wide P < 0.05 and on BTA8, 10 and 14 with a chromosome‐wide P < 0.01.
Characterization and comparison of microsatellites derived from repeat‐enriched libraries and expressed sequence tags
Authors: Coulibaly I. , Gharbi K. , Danzmann R. G. , Yao J. , Rexroad C. E.
Published: July 2005

The construction of high‐density linkage maps for use in identifying loci underlying important traits requires the development of large numbers of polymorphic genetic markers spanning the entire genome at regularly spaced intervals. As part of our efforts to develop markers for rainbow trout (Oncorhynchus mykiss), we performed a comparison of allelic variation between microsatellite markers developed from expressed sequence tag (EST) data and anonymous markers identified from repeat‐enriched libraries constructed from genomic DNA. A subset of 70 markers (37 from EST databases and 33 from repeat enriched libraries) was characterized with respect to polymorphism information content (PIC), number of alleles, repeat number, locus duplication within the genome and ability to amplify in other salmonid species. Higher PIC was detected in dinucleotide microsatellites derived from ESTs than anonymous markers (72.7% vs. 54.0%). In contrast, dinucleotide repeat numbers were higher for anonymous microsatellites than for EST derived microsatellites (27.4 vs. 18.1). A higher rate of cross‐species amplification was observed for EST microsatellites. Approximately half of each marker type was duplicated within the genome. Unlike single‐copy markers, amplification of duplicated microsatellites in other salmonids was not correlated to phylogenetic distance. Genomic microsatellites proved more useful than EST derived microsatellites in discriminating among the salmonids. In total, 428 microsatellite markers were developed in this study for mapping and population genetic studies in rainbow trout.
Muscarinic cholinergic receptors in the human melanoma cell line SK-Mel 28: modulation of chemotaxis
Authors: Boss A. , Oppitz M. , Drews U.
Published: July 2005

Primary and metastatic human melanomas express muscarinic receptors. In embryonic tissues, expression of muscarinic receptors is correlated with morphogenesis. The hypothesis has been put forward that muscarinic receptors are involved in morphogenetic movements in the embryo, and in cellular movements in melanoma cells during invasive growth. The purpose of the present study was to characterize the muscarinic receptors in the human melanoma cell line SK-Mel 28 and to test in a Boyden chamber assay whether the chemotactic activity towards fibronectin can be influenced by muscarinic stimulation. In Western blots with the monoclonal antibody M35, muscarinic receptors were localized in a strong band at 66 kDa, and in a weak band at 63 kDa. Western blot with M3 subtype specific antibodies reproduced the line at 66 kDa. RT-PCR revealed mRNA for subtypes M3 and M5. These findings suggest that SK-Mel 28 cells express a large number of subtype M3 and a small number of subtype M5 receptors. Microscopic observation of calcium mobilization after muscarinic stimulation indicated that all cells carried functional muscarinic receptors. A standardized chemotaxis assay was established in modified Boyden chambers using fibronectin as chemotactic agent. After addition of carbachol to the upper compartment, an increase of fibronectin induced chemotaxis of ∼30% was observed, an effect abrogated by atropine. These results demonstrate that muscarinic cholinergic treatment has a modulatory effect on fibronectin-induced chemotaxis in SK-Mel 28 melanoma cells, indicating that the muscarinic system is involved in regulation of cell movement.
Instrumentation and patient characteristics that influence postoperative haemorrhage rates following tonsil and adenoid surgery
Authors: Tomkinson A. , De Martin S. , Gilchrist C. R. , Temple M.
Published: July 2005

Objectives:  To investigate the effect of the type instrumentation used and the age and gender characteristics of patients on postoperative haemorrhage rates following tonsil and adenoid surgery.

Design:  A retrospective analysis of 13 593 procedures was performed from The Patient Episode Database for Wales between 1 January 1999 and 31 March 2004.

Setting:  National health policy changes created four periods of different instrument usage (reusable, single‐use with diathermy, single‐use alone, specified single‐use with diathermy). These and the age and gender distribution of the patients were examined against four categories of postoperative haemorrhage.

Main outcome measures:  Postoperative haemorrhage rates were expressed as the number of complications per operations performed. Primary postoperative haemorrhage that occurred during the initial admission either required a return to theatre [R1] or was managed conservatively [N1]; secondary postoperative haemorrhage that required a return to hospital either returned to theatre [R2] or was managed conservatively [N2], were compared.

Results:  Primary haemorrhage with return to theatre doubled, from the baseline rate with reusable instruments, from 0.6% (CI 0.5–0.8) to 1.2% (CI 0.7–1.9) when single‐use instruments were introduced and remained high at 1.4% (CI 0.9–2.1) after the withdrawal of single‐use diathermy. This haemorrhage rate returned to the baseline rate (0.6% CI 0.3–1.0) when specified single‐use instruments were introduced. None of the other haemorrhage rates changed significantly throughout the four observation periods. Adenotonsillectomy and tonsillectomy patients have different age and gender patterns. In a univariate analysis, males over the age of 12 years were twice as likely to have haemorrhage with return to theatre than girls of the same age, 3.8% (CI 3.0–4.7) versus 1.7% (CI 1.4–2.1).

Conclusions:  A significant rise in serious postoperative primary haemorrhage but not secondary haemorrhage was seen following the initial introduction of single‐use instruments that reverted to baseline with the introduction of specified single‐use instruments. Diathermy does not appear to have affected the haemorrhage rates. There is a distinct age and gender pattern for tonsil and adenoid surgery and risk of postoperative haemorrhage. The use of arbitrary divisions of age may be misleading in studies that examine post‐tonsillectomy haemorrhage.
Modelling denitrification including the dynamics of denitrifiers and their progressive ability to reduce nitrous oxide: comparison with batch experiments
Authors: Khalil K. , Renault P. , Guérin N. , Mary B.
Published: July 2005

Nitrous oxide contributes to the global greenhouse effect and affects the chemistry of O3 in the upper troposphere and lower stratosphere. To define a relevant model for microbial NO3– and N2O reductions in soil and estimate the parameters involved, we propose a method combining measurements of anaerobic soil slurry and simulations of NO3– and N2O reductions, including non‐enzymatic competition between NO3– and N2O as electron acceptors and the microbial dynamics of two denitrifier groups that are either able or unable to reduce N2O. Three models varying in the description of soil capability to reduce N2O through denitrification were assessed. The procedure was applied on an arable soil known for its small N2O emissions in situ during wet events. Experiments consisted of N2O measurements in anoxic conditions (i) with C2H2, (ii) without C2H2 or (iii) without C2H2 and N2O addition, at various NO3– concentrations. The first model that accounts for microbial growth and considers a constant specific N2O reductase activity could not reproduce experimental data. It was necessary to consider that some denitrifiers initially unable to reduce N2O into N2 became able to undertake this process. We evaluated two models taking into account the induction of N2O reductase, either with the progressive synthesis of this reductase simultaneously for all N2O reducers or with the sudden synthesis of this reductase distributed over a range of times for N2O reducers. Both models could approximately describe experimental kinetics, although some biases remained. The biomass of denitrifiers estimated by fitting simulated to experimental data was consistent with the biomass measured using chloroform fumigation–extraction and microbial enumeration.
Iron‐cyanide complexes in soil under varying redox conditions: speciation, solubility and modelling
Authors: Rennert T. , Mansfeldt T.
Published: July 2005

The distribution of iron‐cyanide complexes between ferrocyanide, [FeII(CN)6]4–, and ferricyanide, [FeIII(CN)6]3–, in soils on contaminated sites depends on the redox potential, EH. We carried out microcosm experiments in which ferrocyanide (20 mg l−1) was added to an uncontaminated moderately acidic subsoil (pH 5.2), and varied the EH of the soil suspension between 200 and 700 mV over up to 109 days. Ferrocyanide and ferricyanide were analysed by capillary isotachophoresis. At redox potentials ranging from 400 to 700 mV, small amounts of iron‐cyanide complexes were adsorbed, and ferrocyanide was almost completely oxidized to ferricyanide. Decreasing EH to 200 mV led to nearly complete removal of iron‐cyanide complexes from solution, and the complexes were not mobilized after subsequent aeration (EH > 350 mV). Under weakly to moderately reducing conditions (EH ≈ 200 mV), iron‐cyanide complexes were removed from solution by precipitation, which occurred, presumably in the form of e.g. Fe2[FeII(CN)6], Fe4[FeII(CN)6]3 or Mn2[FeII(CN)6], after reductive dissolution of Mn and Fe oxides. Four different sets of geochemical model calculations were carried out. The species distribution between ferrocyanide and ferricyanide in solution was predicted reliably under varying pH and redox conditions when iron‐cyanide complex concentrations and Fe concentrations, excluding Fe bound in iron‐cyanide complexes, were used in model calculations. In model calculations on the fate of iron‐cyanide complexes in soil, adsorption reactions must be considered, especially under oxidizing conditions. Otherwise, the calculated iron‐cyanide complex concentrations are larger than those actually measured.
Bacteria and algae in stream periphyton along a nutrient gradient
Authors: CARR GENEVIÈVE M. , MORIN ANTOINE , CHAMBERS PATRICIA A.
Published: July 2005

1. Stream riffles in southern Ontario and western Quèbec were sampled for biomass (58 stations from 51 streams) and production (22 stations from 21 streams) of algae and bacteria in periphyton to test the hypothesis that bacteria in benthic biofilms compete with algae for nutrients.

2. Algal and bacterial biomass were positively correlated, as were algal and bacterial production. Bacterial production was also positively correlated to algal and bacterial biomass, but the relationship was not significant. The ratio of algal to bacterial biomass did not vary with nutrients whereas algal production tended to increase with nutrients more rapidly than bacterial production.

3. Instream nitrogen concentrations explained 38–58% of the variability in algal biomass and production. Bacterial abundance explained an additional 9–29% of the residual variance in algal production and biomass. However, the relationship between bacterial abundance and algal production and biomass, once nutrients were taken into account, was positive, in contrast to the predicted effect of competition.

4. Hence, we reject our original hypothesis that bacteria in biofilms compete with algae for nutrients and instead suggest that bacteria and algae in biofilms coexist in an association that offers space and resources to sustain production of both groups of organisms.
Changes in biotic communities developing from freshwater wetland sediments under experimental salinity and water regimes
Authors: BROCK MARGARET A. , NIELSEN DARYL L. , CROSSLÉ KATHARINE
Published: July 2005

1. Reduction in diversity of both freshwater aquatic and terrestrial ecosystems has been attributed to salinity increase and such increases are a symptom of changes to land use. Hydrological alteration to ground and surface water are likely to be associated with salinity increase and its influence on biodiversity. However the combined effects of salinity and hydrology on aquatic biodiversity have not been elucidated fully in either field or experimental situations.

2. The effect of salinity and water regime on the biota in sediments from seven wetlands from inland south‐eastern Australia was tested experimentally using germination of aquatic plant seeds (five salinity and two water levels) and emergence of zooplankton eggs (five salinity levels). Salinity levels were <300, 1000, 2000, 3000, 5000 mg L−1 and water regimes were damp (waterlogged) and submerged.

3. Aquatic plant germination and zooplankton hatching was not consistent for all seven wetland sediments. Four of the wetland sediments, Narran Lakes, Gwydir Wetlands, Macquarie Marshes and Billybung Lagoon showed similar responses to salinity and water regime but the other three wetland sediments from Lake Cowal, Great Cumbung Swamp and Darling Anabranch did not.

4. As salinity increased above 1000 mg L−1 there was a decrease in the species richness and the abundance of biota germinating or hatching from sediment from four of the wetlands.

5. Salinity had a particularly strong effect in reducing germination from sediments in damp conditions when compared to the flooded conditions. In parallel, salts accumulated in the sediment in damp conditions but did not in flooded conditions.

6. There is potential for increasing salinity in freshwater rivers and wetlands to decrease the species richness of aquatic communities and thus of the wetland community as a whole, resulting in loss of wetland biodiversity. This reduction in diversity varies between wetlands and is at least partly related to hydrology. For aquatic plants the reduction in diversity will be more marked for plants germinating from seed banks at the edges of wetlands where plants are not completely submerged than for the same seed bank germinating in submerged conditions.
A seasonally breeding tropical bird lacks absolute photorefractoriness in the wild, despite high photoperiodic sensitivity
Authors: BEEBE K. , BENTLEY G. E. , HAU M.
Published: July 2005

Photoperiod is an important seasonal cue for temperate seasonal breeders. In birds, increasing photoperiod typically stimulates reproductive maturation, while also triggering gonad regression through photorefractoriness at a later date. Curiously, many tropical birds show photoperiodic reproductive responses, even though day‐length changes in their natural habitat are minimal.

Spotted Antbirds (Hylophylax n. naevioides) from a near‐equatorial rainforest in Panama are highly sensitive to small photoperiodic changes at the onset of reproduction. We therefore tested whether these tropical birds use photoperiod as the primary signal for seasonal processes, as do most temperate birds, and terminate reproduction through photorefractoriness.

Male and female Spotted Antbirds captured during postbreeding moult significantly increased gonad sizes when exposed to a photoperiod of 22 h. Furthermore, males exposed to a naturalistic 1‐h increase in photoperiod (to 13 h) also grew their gonads, suggesting that these birds retain photosensitivity at a time of year when most temperate birds are unable to grow their gonads. Hatch‐year birds in all groups showed reproductive development indicating their capability to breed. Unlike in many temperate‐zone birds, the moult of adult birds was not inhibited by gonad development.

The lack of photorefractoriness allows Spotted Antbirds to flexibly adjust the end of breeding to environmental conditions. Our findings support the view that photoperiodic mechanisms are evolutionary plastic and match the ecology of a particular species.
Alteration of TGA factor activity in rice results in enhanced tolerance to Xanthomonas oryzae pv. oryzae
Authors: Fitzgerald Heather A. , Canlas Patrick E. , Chern Maw‐Sheng , Ronald Pamela C.
Published: July 2005

In dicotyledonous plants broad‐spectrum resistance to pathogens is established after the induction of the systemic acquired resistance (SAR) response. In Arabidopsis the NPR1 protein can regulate SAR by interacting with members of the TGA class of basic, leucine‐zipper transcription factors to alter pathogenesis‐related (PR) gene expression. Overexpression of (At)NPR1 in Arabidopsis enhances resistance to multiple pathogens. Similarly, overexpression of (At)NPR1 in rice enhances resistance to the bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo). These results suggest that components of the (At)NPR1‐mediated SAR defense response may be conserved between monocots and dicots. To determine whether or not rice TGA factors are involved in disease resistance responses, the effect of altering the function of rice TGA2.1 was analyzed in transgenic plants. Transgenic rice overexpressing an rTGA2.1 mutant, that can no longer bind DNA, and transgenic rice that have the endogenous rTGA2.1 silenced by dsRNA‐mediated silencing were generated. Both types of transgenic rice displayed increased tolerance to Xoo, were dwarfed, and had altered accumulation of PR genes. The results presented in this study suggest that wild‐type rTGA2.1 has primarily a negative role in rice basal defense responses to bacterial pathogens.
Patterns of alcohol consumption in bipolar patients comorbid for alcohol abuse or dependence
Authors: McKowen James W , Frye Mark A , Altshuler Lori L , Gitlin Michael J
Published: July 2005

Objectives:  Despite a high prevalence rate, patients with bipolar disorder and active alcohol use are routinely excluded from controlled clinical trials leaving clinicians with little evidence‐based medicine to guide treatment. This report evaluates preliminary data of alcohol consumption patterns utilizing the Alcohol Timeline Followback (TLFB) method in actively drinking patients with bipolar disorder.

Methods:  A sample of 30 patients underwent a Structured Diagnostic Interview for DSM‐IV (SCID‐IV) as well as completing various measures of alcohol use and associated morbidity.

Results:  In the month prior to study entry, the TLFB reported 18.4/30 ± 9.12 drinking days, 9.9 ± 4.73 drinks per drinking day and 169.4 ± 101.71 total standard drinks for this study group. There was a significant difference in the number of drinks per drinking day between those diagnosed with rapid cycling than non‐rapid cycling bipolar disorder and those with a new diagnosis versus established diagnosis of bipolar disorder.

Discussion:  This study highlights heavy alcohol use in patients with bipolar disorder and alcohol comorbidity. The TLFB method provides ‘real world’ quantification of use. Further studies are encouraged to elucidate implications of heavy drinking patterns as found in our rapid cycling and newly diagnosed cohorts.