Puffy skin disease (PSD) in rainbow trout, Oncorhynchus mykiss (Walbaum): a case definition

Puffy skin disease (PSD) is a disease that causes skin pathology in rainbow trout, Oncorhynchus mykiss (Walbaum). Incidence of PSD in UK fish farms and fisheries has increased sharply in the last decade, with growing concern from both industry sectors. This paper provides the first comprehensive case definition of PSD, combining clinical and pathological observations of diseased rainbow trout from both fish farms and fisheries. The defining features of PSD, as summarized in the case definition, were focal lateral flank skin lesions that appeared as cutaneous swelling with pigment loss and petechiae. These were associated with lethargy, poor body condition, inappetance and low level mortality. Epidermal hyperplasia and spongiosis, oedema of the dermis stratum spongiosum and a mild diffuse inflammatory cellularity were typical in histopathology of skin. A specific pathogen or aetiology was not identified. Prevalence and severity of skin lesions was greatest during late summer and autumn, with the highest prevalence being 95%. Atypical lesions seen in winter and spring were suggestive of clinical resolution. PSD holds important implications for both trout aquaculture and still water trout fisheries. This case definition will aid future diagnosis, help avoid confusion with other skin conditions and promote prompt and consistent reporting.

Relationship between European eel Anguilla anguilla infection with non-native parasites and swimming behaviour on encountering accelerating flow

The effect of Anguillicola crassus, Pseudodactylogyrus bini and Pseudodactylogyrus anguillae infection on the behaviour of downstream migrating adult European eels Anguilla anguilla as they encountered accelerating water velocity, common at engineered structures where flow is constricted (e.g. weirs and bypass systems), was evaluated in an experimental flume. The probability of reacting to, and rejecting, the velocity gradient was positively related to A. crassus larval, adult and total abundance. High abundance of Pseudodactylogyrus spp. reduced this effect, but A. crassus was the strongest parasitic factor associated with fish behaviour, and abundance was positively related to delay in downstream passage. Delayed downstream migration at hydraulic gradients associated with riverine anthropogenic structures could result in additional energetic expenditure for migrating A. anguilla already challenged by A. crassus infection.

Comparison of equilibrium and non-equilibrium distribution coefficients for the human drug carbamazepine in soil

The distribution coefficient (KD) for the human drug carbamazepine was measured using a non-equilibrium technique. Repacked soil columns were prepared using an Airport silt loam (Typic Natrustalf) with an average organic matter content of 2.45%. Carbamazepine solutions were then leached through the columns at 0.5, 1.0 and 1.5 mL min(-1) representing average linear velocities of 1.8, 3.5 and 5.3 cm h(-1) respectively. Each flow rate was replicated three times and three carbamazepine pulses were applied to each column resulting in a total of 9 columns with 27 total carbamazepine pulses. Breakthrough curves were used to determine KD using the parameter fitting software CXTFIT. Results indicate that as flow rate decreased from 5.3 to 1.8 cm h(-1), KD increased an average of 21%. Additionally, KD determined by column leaching (14.7-22.7 L kg(-1)) was greater than KD determined by a 2h batch equilibrium adsorption (12.6 L kg(-1)). Based on these KD's carbamazepine would be generally characterized as non-mobile in the soil investigated. However, repeated carbamazepine applications resulted in an average 22% decrease in KD between the first and third applications. Decreasing KD is attributed to differences in sorption site kinetics and carbamazepine residence time in contact with the soil. This would indicate that the repeated use of reclaimed wastewater at high application rates for long-term irrigation or groundwater recharge has the potential to lead to greater transport of carbamazepine than KD determined by batch equilibrium would predict.

Serum estrogenicity and biological responses in African catfish raised in wastewater ponds in Ghana

Reuse of wastewater for aquaculture improves the efficient use of water and promotes sustainability but the potential effects of endocrine disrupting compounds including estrogens in wastewater are an emerging challenge that needs to be addressed. We examined the biological effects of wastewater-borne estrogens on African catfish (Clarias gariepinus) raised in a wastewater stabilization pond (WSP) of a functioning municipal wastewater treatment plant, a wastewater polishing pond (WWP) of a dysfunctional treatment plant, and a reference pond (RP) unimpacted by wastewater, located in Ghana. Measurements of estrogen concentrations in pond water by liquid chromatography/tandem mass spectrometry showed that mean 17 β-estradiol concentrations were higher in the wastewater ponds (WWP, 6.6 ng/L±2.7 ng/L; WSP, 4.9 ng/L±1.0) than the reference (RP, 3.4±1.1 ng/L). Estrone concentrations were found to be highest in the WSP (7.8 ng/L±1.7) and lowest in the WWP (2.2 ng/L±2.4) with the RP intermediate (4.7±5.0). Fish serum estrogenicity assayed by E-SCREEN was significantly higher in female vs. male catfish in the RP and WSP but not in the WWP (p≤0.05). Histological examination of liver and gonad tissue showed no apparent signs of intersex or pathology in any ponds. The similarities in various measures of body indices between fish of this study and African catfish from freshwater systems suggest that aquaculture may be a suitable reuse option for treated municipal wastewater.

Non-invasive investigation of Spironucleus vortens transmission in freshwater angelfish Pterophyllum scalare

Spironucleus vortens is a protozoan fish parasite of veterinary and economic importance in the ornamental aquaculture industry. Despite this, key aspects of the life cycle of this organism, including its mode of transmission, have not been fully elucidated. We developed a non-invasive method for quantifying S. vortens in freshwater angelfish, which was then used to investigate parasite transmission and aggregation within host populations. As previously observed for S. meleagridis and S. salmonis, motile S. vortens trophozoites were detected in host faeces using light microscopy. Species-level identification of these flagellates was confirmed using 16S rDNA PCR. Faecal trophozoite counts were significantly correlated with trophozoite counts from the posterior intestine, the primary habitat of the parasite. This novel finding allowed effective prediction of intestinal parasite load from faecal counts. Overall, faecal count data revealed that 20% of hosts harbour 83% of parasites, conforming to the Pareto Principle (80/20 rule) of parasite aggregation with implications for parasite transmission. Trophozoites survived for ≥36 d outside the host within faeces and remained motile at low pH (comparable with that of angelfish stomach). No putative S. vortens cysts were observed in cultures or faecal samples. This calls into question the commonly accepted hypothesis that a protective cyst is required in the life cycle of S. vortens to facilitate transmission to a new host.

Sorption/Desorption of lincomycin from three arid-region soils

The antibiotic lincomycin is commonly found in treated municipal waste water and in waste from swine and poultry production. Environmental disposal of these wastes has the potential to introduce a significant mass of lincomycin into the ecosystem. In the present study, a series of sorption and desorption experiments were conducted to determine the potential mobility of lincomycin in soils from arid environments. Sorption and desorption isotherms were obtained for lincomycin using three different soils. Isotherms were fit to the Freundlich equation. Adsorption of lincomycin was found to have a of 11.98 for a biosolid-treated soil (1.58% OC) and a of 210.15 for a similar unamended soil (1.42% OC). It was also found that for a low-organic-content soil the was 5.09. The differences in adsorption can be related to the soil pH and the pKa of lincomycin (7.5-7.8). When the soil solution pH is below the pKa, the cationic species of lincomycin dominates, resulting in increased water solubility. Interaction with the cation exchange complex is minimal due to a high solution cation concentration (Ca and Na). Desorption isotherms also indicate that when the solution pH is lower than the pKa, retention of lincomycin is reduced. Our results indicate that the mobility of lincomycin in these arid region soils is dependent on soil pH.

Soil persistence and fate of carbamazepine, lincomycin, caffeine, and ibuprofen from wastewater reuse

The reuse of treated wastewater for groundwater recharge is an effective way to provide advanced treatment and water storage. Contaminants such as human drugs have been identified as a potential problem for use of this water. Gilbert, Arizona maintains a 28.3-ha facility designed to recharge 15,150 m d through recharge basins constructed on native soil. The facility averages an infiltration rate of >5 cm d, resulting in the potential of pharmaceutical compounds leaching to groundwater. One 4-ha basin was selected for spatial sampling of four pharmaceutically active compounds (PhACs). The compounds were carbamazepine, lincomycin, ibuprofen, and caffeine. Soils were extracted and analyzed using pressurized liquid extraction and liquid chromatography-mass spectrometry-mass spectrometry. The concentration of ibuprofen was below detection limits in all samples. Lincomycin exhibited no net accumulation from year to year but had significantly higher concentrations from depths of 0 to 5 cm than from depths >10 cm. Carbamazepine had the lowest concentration at 0 to 5 cm (0.18 ng g soil), providing evidence that there is potential degradation of carbamazepine in surface soils. Carbamazepine also exhibited significant accumulation from year to year. Caffeine exhibited net accumulation and had higher concentrations in surface samples. The accumulation of PhACs in the soil beneath recharge basins indicates that PhACs are being removed from the infiltrating water and that, regarding ibuprofen and lincomycin, the treatment is sustainable due to the lack of accumulation. Regarding carbamazepine and caffeine, further investigations are needed to determine possible management and environmental conditions that could prevent accumulation.

Histopathological and ultrastructural studies of the tapeworm Monobothrium wageneri (Caryophyllidea) in the intestinal tract of tench Tinca tinca

Monobothrium wageneri is a monozoic caryophyllidean tapeworm of tench Tinca tinca. The pathological changes caused by this parasite within the intestinal tract of wild tench are described for the first time. Parasites were found attached to the anterior third of the intestine in tight clusters comprising up to 109 tapeworms. Infection was associated with the formation of raised inflammatory swellings surrounding the parasites. This host response, combined with the deep penetration of the scolex into the gut wall, formed a very firm seat of parasite attachment. Histopathological changes were characterised by a pronounced fibrogranulomatous lesion that extended through all layers of the intestine. This was accompanied by haemorrhage, oedema, necrosis and degeneration of the muscularis. A marked eosinophilic interface layer between the scolex of the tapeworm and gut wall indicated intimate host-parasite contact. Ultrastructural examinations revealed coniform spinitriches covering the neck and lateral sides of the scolex and capilliform filitriches present on the apical end of the scolex. Numerous glandular cytons (tegumental glands) were recorded throughout the scolex tegument. Large numbers of secretory granules discharged from the glands through a network of processes onto the scolex surface were consistent with distancing the cellular responses of the host. Observations of severe inflammatory lesions, partial intestinal occlusion and the potential for intestinal perforation represent important pathological changes that are consistent with loss of normal gut function. The lesions associated with the attachment of M. wageneri are more severe than those recorded for any other tapeworm of British freshwater fish.

Parasite fauna of introduced pumpkinseed fish Lepomis gibbosus: first British record of Onchocleidus dispar (Monogenea)

A survey of pumpkinseed Lepomis gibbosus from a stillwater fishery in southern England revealed infections by the ancyrocephalid monogenean Onchocleidus dispar at 100% prevalence. Host specificity of O. dispar to North American centrarchid fish suggests that it is a non-native parasite, introduced to Britain with L. gibbosus. Mean intensity of O. dispar was significantly higher in male (25.5 parasites) compared to female (15) and immature (7) hosts, but was not influenced by host standard length or sampling time. This sex-biased parasitism is likely to be related to both ecological and physiological factors, such as differential exposure to infective stages during nest building, or higher susceptibility to infection due to enhanced host stress levels. O. dispar significantly dominated the external surfaces and the outer gill arches. Analysis of the spatial distribution of the parasite between the 9 regions of gill surface determined that as density increased, higher numbers of parasites were found on the anterior and central gill regions compared to posterior (distal) regions. Apparent microhabitat selection is discussed in terms O. dispar life cycle, maximising oxygen availability, avoiding unstable areas and increasing intraspecific contact. The absence of O. dispar in the gills of roach, rudd and gudgeon sampled from the same fishery supports the assumption that this parasite is currently of little threat to native fish populations.

Effect of primer selection on estimates of GB virus C (GBV-C) prevalence and response to antiretroviral therapy for optimal testing for GBV-C viremia

GB virus C (GBV-C; also called hepatitis G virus) is a common cause of infection associated with prolonged survival among HIV-infected individuals. The prevalences of GBV-C viremia vary widely in different studies, and there has been poor agreement among different laboratories performing GBV-C RNA detection in quality control studies. To determine the optimal method of measuring GBV-C RNA in clinical samples, samples obtained from 939 HIV-infected subjects were studied using reverse transcription (RT)-PCR methods amplifying four separate regions of the GBV-C genome. Primers amplifying the E2 coding region were 100% specific; however, their sensitivity was only 76.6%. In contrast, primers amplifying three additional conserved regions of the GBV-C genome (the 5' nontranslated region and the nonstructural protein-coding regions 3 and 5A) were more sensitive but produced higher rates of false-positive results. Using low-specificity primer sets influenced the significance of association between GBV-C viremia and response to antiretroviral therapy. Using a quantitative GBV-C RNA method, the GBV-C RNA concentration did not correlate with baseline or set point HIV RNA levels; however, a correlation between negative, low, and high GBV-C RNA levels and increasing reduction in HIV RNA following antiretroviral therapy was observed. Subjects with both GBV-C E2 antibody and viremia had significantly lower GBV-C RNA levels than did viremic subjects without E2 antibody. These studies demonstrate that accurate detection of GBV-C RNA by nested RT-PCR requires the use of primers representing multiple genome regions. Analyses based on testing with single primers do not lead to reliable conclusions about the association between GBV-C infection and clinical outcomes.

Effect of early and late GB virus C viraemia on survival of HIV-infected individuals: a meta-analysis

OBJECTIVES

To conduct a meta-analysis to synthesize the evidence regarding the effect of co-infection with GB virus C (GBV-C) on survival of HIV-infected individuals, and to estimate the effect.

METHODS

A Bayesian meta-analysis was conducted to synthesize evidence from eligible studies. Prospective survival studies of HIV-1-infected individuals, with outcome defined as time from baseline to all-cause death, were included and classified by whether GBV-C status was determined in early or late HIV disease. The primary measure was the hazard ratio (HR) of death for HIV-infected individuals with GBV-C infection versus those without GBV-C infection.

RESULTS

Eleven studies from eight publications met the inclusion criteria. For studies with GBV-C status measured 2 years or less after HIV seroconversion (912 subjects), the combined HR was 0.88 [95% credible interval (CI) 0.30, 1.50]. For studies with GBV-C status measured more than 2 years after HIV seroconversion (1294 subjects), the combined HR was 0.41 (95% CI 0.23, 0.69).

CONCLUSIONS

No conclusive evidence was found of an association between survival and GBV-C infection early in HIV disease. However, when GBV-C infection was present later in HIV disease, a significant reduction in the hazard for mortality was observed for those with co-infection. Potential explanations for this difference include a non-proportional benefit of GBV-C over time, possibly related to clearance of GBV-C infection early in HIV disease. The timing of GBV-C infection appears to account for the contradictory results of studies on the effect of GBV-C coinfection on survival of HIV-infected people.

Sorption-desorption of carbamazepine from irrigated soils

Th anti-seizure medication carbamazepine is often found in treated sewage effluent and environmental samples. Carbamazepine has been shown to be very persistent in sewage treatment, as well as ground water. Due to environmental persistence, irrigation with sewage effluent could result in carbamazepine contamination of surface and ground water. To determine the potential for leaching of carbamazepine, a series of adsorption and desorption batch equilibrium experiments were conducted on irrigated soils. It was found that carbamazepine adsorption to biosolid-amended (T) soils had a KD of 19.8 vs. 12.6 for unamended soil. Based on adsorption, carbamazepine leaching potential would be categorized as low. During desorption significant hysteresis was observed and KD increased for both soils. Desorption isotherms also indicate a potential for irreversibly bound carbamazepine in the T soil. Results indicate that initial removal of carbamazepine via adsorption from irrigation water is significant and that desorption characteristics would further limit the mobility of carbamazepine through the soil profile indicating that carbamazepine found in sewage effluent used for irrigation has a low leaching potential.

Excretion of bluetongue virus in cattle semen: a feature of laboratory-adapted virus

A series of experiments was conducted over a period of four years and involved both young (2-4 years) and old bulls (5-15 years) that were both naturally and experimentally infected with bluetongue virus (BTV). Several different virus serotypes were studied. In the Northern Territory, young bulls were exposed to natural infection with BTV over three wet seasons. During this time, bulls were infected with BTV-1, BTV-3, BTV-16 and BTV-20. In New South Wales, semen samples were examined from a large group of bulls of mixed ages that were naturally infected with BTV-1. Experimental infections in both young and old bulls (5-8 animals per group) employed both 'wild-type' and laboratory-adapted viruses from serotypes 1 and 23. A total of 41 bulls were included in the studies of natural BTV infection and 52 bulls in experimental infections. There was no evidence of BTV in any of the semen samples collected from naturally infected bulls or experimentally infected young bulls. BTV was detected intermittently in semen from a number of old bulls infected with both laboratory-adapted BTV-1 and BTV-23. These detections occurred during or immediately after the period of detectable viraemia. Virus was also detected in a few semen samples from very old bulls infected with 'wild-type' BTV-23. These samples were collected during the period of viraemia and there was usually evidence of blood in the semen. Viraemia varied in duration between 17 and 38 days. Following immunosuppression, there was no evidence of resurgence of viraemia, or excretion of virus in semen, even in animals in which virus had been previously detected in semen. When the bulls were slaughtered, virus was not detected in any tissues.

Molecular weight of dissolved organic matter-napropamide complex transported through soil columns

Soil-derived dissolved organic matter (DOM) has been shown to form stable complexes with the herbicide napropamide [2-(alpha-naphthoxy-N,N-diethylpropionamide] capable of enhancing the transport of napropamide through soil columns. Two soils, one containing sewage sludge-derived organic matter (SS) and the other having only natural organic matter (NoSS) were treated with napropamide and allowed to dry to promote complex formation. Soil columns were prepared by packing a 10-cm layer of untreated, dry, sieved soil followed by an overlying 5-cm layer of napropamide-treated soil. Columns were irrigated and the effluent collected and placed in dialysis chambers. After equilibration napropamide concentrations were determined on both sides of the membrane and complex and quantified based on the amount of napropamide unable to cross the membrane. it was found that for the SS soil 7% and for the NoSS 2.4% of the applied napropamide underwent facilitated transport. In addition, most of the complex transported through the columns had a molecular weight between 500 and 1000 Daltons (Da). The solutions from the SS soil were also found to have formed at least two distinct complexes that were resolved after passing through the untreated soil layer. The results obtained were in agreement with other published results and the techniques used offer a way to separate and concentrate DOM complexes from column effluents for further characterization.

Pollination, breeding system, and genetic structure in two sympatric Delphinium (Ranunculaceae) species

Two sympatric Delphinium species, D. barbeyi and D. nuttallianum, are ecologically and morphologically similar. However, D. barbeyi has multiple, large inflorescences while D. nuttallianum has a single, small inflorescence. These differences in floral display should result in greater intraplant pollen transfer in D. barbeyi, leading to higher rates of self-pollination through geitonogamy. Reduced gene flow by pollen should in turn produce greater population differentiation among populations of D. barbeyi relative to D. nuttallianum. We tested these predictions by comparing pollinator behavior, breeding systems, outcrossing rates, and population genetic structure of sympatric populations of the two species in Colorado. Bumble bee and hummingbird pollinators visit more flowers and inflorescences per foraging bout in D. barbeyi than in D. nuttallianum. The species differed in breeding system; D. barbeyi produced more seeds by autogamy (9 vs. 2%) than D. nuttallianum and suffered no reduction in seed set in hand-self vs. outcross pollinations, in contrast to a 41% decline in D. nuttallianum. The outcrossing rate in one D. barbeyi population was 55%, but ranged from 87 to 97% in four D. nuttallianum populations. Genetic differentiation among population subdivisions estimated by hierarchical F statistics was >10 times greater in D. barbeyi ( = 0.055-0.126) than D. nuttallianum ( = 0.004-0.009) at spatial scales ranging from metres to 3.5 km. Spatial autocorrelation analysis also indicated more pronounced local genetic structure in D. barbeyi than D. nuttallianum populations. Fixation indices (F(IS)) of D. barbeyi adults were much lower than expected based on mating system equilibrium and suggest that differences in the degree of self-compatibility and/or the timing of postpollination selection/inbreeding depression between the two species further contribute to the genetic differences between them.

Floral dimorphism, pollination, and self-fertilization in gynodioecious GERANIUM RICHARDSONII (Geraniaceae)

The selective maintenance of gynodioecy depends on the relative fitness of the male-sterile (female) and hermaphroditic morphs. Females may compensate for their loss of male fitness by reallocating resources from male function (pollen production and pollinator attraction) to female function (seeds and fruits), thus increasing seed production. Females may also benefit from their inability to self-fertilize if selfing and inbreeding depression reduce seed quality in hermaphrodites. We investigated how differences in floral resource allocation (flower size) between female and hermaphroditic plants affect two measures of female reproductive success, pollinator visitation and pollen receipt, in gynodioecious populations of Geranium richardsonii in Colorado. Using emasculation treatments in natural populations, we further examined whether selfing by autogamy and geitonogamy comprises a significant proportion of pollen receipt by hermaphrodites. Flowers of female plants are significantly smaller than those of hermaphrodites. The reduction in allocation to pollinator-attracting structures (petals) is correlated with a significant reduction in pollinator visitation to female flowers in artificial arrays. The reduction in attractiveness is further manifested in significantly less pollen being deposited on the stigmas of female flowers in natural populations. Autogamy is rare in these protandrous flowers, and geitonogamy accounts for most of the difference in pollen receipt between hermaphrodites and females. Female success at receiving pollen was negatively frequency dependent on the relative frequency of females in populations. Thus, two of the prerequisites for the maintenance of females in gynodioecious populations, differences in resource allocation between floral morphs and high selfing rates in hermaphrodites, occur in G. richardsonii.

Genome-wide analysis of DNA copy-number changes using cDNA microarrays

Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CGH, however, has a limited ( approximately 20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)-mapped human genes provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours. Using this assay, we were able to identify gene amplifications and deletions genome-wide and with high resolution, and compare alterations in DNA copy number and gene expression.

Genome-wide analysis of DNA copy-number changes using cDNA microarrays

Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CGH, however, has a limited ( approximately 20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)-mapped human genes provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours. Using this assay, we were able to identify gene amplifications and deletions genome-wide and with high resolution, and compare alterations in DNA copy number and gene expression.

Distinctive gene expression patterns in human mammary epithelial cells and breast cancers

cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of coexpressed genes identified through manipulations of mammary epithelial cells in vitro also showed consistent patterns of variation in expression among breast tumor samples. By using immunohistochemistry with antibodies against proteins encoded by a particular gene in a cluster, the identity of the cell type within the tumor specimen that contributed the observed gene expression pattern could be determined. Clusters of genes with coherent expression patterns in cultured cells and in the breast tumors samples could be related to specific features of biological variation among the samples. Two such clusters were found to have patterns that correlated with variation in cell proliferation rates and with activation of the IFN-regulated signal transduction pathway, respectively. Clusters of genes expressed by stromal cells and lymphocytes in the breast tumors also were identified in this analysis. These results support the feasibility and usefulness of this systematic approach to studying variation in gene expression patterns in human cancers as a means to dissect and classify solid tumors.

A novel fast split-echo multi-shot diffusion-weighted MRI method using navigator echoes

Difficulties in obtaining diffusion-weighted images of acceptable quality using conventional hardware and in a reasonable time have hindered the clinical application of diffusion-weighted magnetic resonance imaging (DWI). Diffusion-weighted fast spin-echo (FSE) sequences offer the possibility of fast DWI on standard hardware without the susceptibility problems associated with echoplanar imaging. However, motion in the presence of diffusion-sensitizing gradients can prevent fulfilment of the Meiboom Gill phase condition, leading to destructive interference between echo components and consequent signal losses. A recently proposed single-shot FSE sequence employed split-echo acquisition to address this problem. However, in a segmented FSE sequence, phase errors differ between successive echo trains, causing "ghosting" in the diffusion-weighted images that are not eliminated by split-echo acquistion alone. A DWI technique is presented that combines split-echo acquisition with navigator echo phase correction in a segmented FSE sequence. It is shown to be suitable for diffusion measurements in vivo using standard hardware.

Sources of artifact and systematic error in quantitative snapshot of FLASH imaging and methods for their elimination

Snapshot FLASH preceded by a preparation sequence is used to measure NMR parameters. Some preparation information is lost during snapshot FLASH acquisition as the magnetization evolves towards the steady state. This problem is often addressed by assuming that image intensity is proportional to the central k-space line, which may be sampled immediately after preparation using a centric-reordered scheme. Although some limitations of this assumption have been discussed, they are often ignored in parameter measurement. In this study, magnetization evolution effects in snapshot FLASH were investigated by computer simulation and phantom experiments in the context of T2 measurement. It was found that the standard analysis may lead to significant error in parameter measurement. Some improvement may be obtained using a more sophisticated analysis to take account of magnetization evolution. However, at the expense of a 50% reduction in signal intensity, accurate values may be obtained by a novel method that uses crusher gradients to eliminate evolved magnetization.

The complete sequence of four major structural proteins of African horse sickness virus serotype 6: evolutionary relationships within and between the orbiviruses

The amino acid sequences of four major capsid proteins of African horse sickness virus (serotype 6, AHSV-6) have been determined from analyses of cDNA clones representing the L2, L3, M6 and S7 RNA segments. The AHSV-6 L3 RNA segment has an open reading frame of 2715 base pairs and encodes the inner capsid protein VP3 which comprises 905 amino acids. The VP3 layer forms the subcore of the virion and is surrounded by the VP7 protein which is encoded by the S7 gene. The AHSV-6 S7 gene was found to be 1047 nucleotides in length with a coding capacity for the VP7 protein of 349 amino acids. These core proteins are encapsulated by the outer capsid proteins VP5 and VP2 which are encoded by the M6 and L2 genes respectively. The M6 gene of AHSV-6 was determined to be 1564 nucleotides in length and encoded a protein product of 504 amino acids while the L2 gene comprised 3203 nucleotides which encoded a predicted protein product of 1051 amino acids. Comparison of these four sequences with the core protein sequences of other serotypes of African horse sickness virus, Bluetongue virus which infects sheep, and Epizootic haemorrhagic disease virus of deer, demonstrated that despite the pathobiological properties and host range of these distinct orbiviruses, extreme conservation is evident within the capsid genes. Sequence analyses also suggested that the similarity levels between serogroups depict the structure and function of the individual capsid proteins. The data indicated that the evolution of the capsid genes of gnat transmitted orbiviruses is strongly influenced by functional and structural constraints.

The influence of stimulated echoes on contrast in fast spin-echo imaging

Tissue contrast obtained using fast spin-echo (FSE) and conventional spin-echo (SE) sequences is not identical and a number of mechanisms are thought to contribute to these contrast differences. The effect of stimulated echoes has previously been apparently ruled out as a contributing mechanism. Signal-to-noise ratios of single-slice matched FSE and conventional SE sequences were compared in aqueous solutions of CuSO4, Cr2(SO4)3 and MnSO4 with various T1 and T2 values. Enhancement of the FSE signal was observed in short T2 solutions and the effect was greater in samples where the T1 to T2 ratio was high. Reducing the refocusing pulse flip angle to increase the contribution from stimulated echoes also resulted in slightly increased enhancement. Experimental results were verified by computer simulations. Our results show that stimulated echoes do contribute to the contrast differences between FSE and conventional SE images and may be significant in the imaging of brain hemorrhage.

Essentiality of the lateral cervical spine radiograph

Proper interpretation of the lateral cervical spine (C-spine) film is a prime emergency medicine responsibility. Patients with potential neck injury must be identified rapidly and handled carefully; their C-spine films must be interpreted quickly and accurately. We stress the urgency in obtaining a good, readable lateral C-spine film and present a systemic "ABCs" approach to reading this film. This approach includes specific, sequential attention to Alignment, Bony integrity, Cartilaginous structures, and the surrounding Soft-tissue spaces. In the cases of 50 consecutive patients with C-spine injuries (49 adults, one child) seen recently in our emergency medicine program, we have correlated traumatic mechanisms with specific injury patterns. These analyses have been meshed with data from the patients' medical records and radiographs. In a significant number of instances (greater than 25% in this series), objective, careful radiographic interpretation is more important to the patient's objective, careful radiographic interpretation is more important to the patient's welfare than is any other diagnostic modality -- including history and physical examination.

Effects of irradiation on mixed müllerian tumors of the uterus

A retrospective study of 54 patients with histologically proven malignant mixed müllerian tumors of the uterus was undertaken with main emphasis on the evaluation of the effects of irradiation on pelvic tumor control. The tumors were staged according to the FIGO classification for endometrial carcinoma and 24 were classified as Stage I, 10 as Stage II, 13 as Stage III and seven as Stage IV. Patients with Stage I and II were treated with surgery alone (9 patients, three surviving) or preoperative intracavitary irradiation (13 patients, eight surviving) or preoperative combination of intracavitary and external irradiation (12 patients, six surviving). Five patients with Stage III and IV were treated with surgery alone, two were treated with a combination of irradiation and surgery and 11 with radiation alone. None of these patients survived. In seven patients showing no residual tumor in the uterine specimen after irradiation, no pelvic failures were noted, whereas seven of 17 (41.2%) with residual tumor developed pelvic recurrences. In patients with Stage I treated with surgery alone, three out of six recurred in the pelvis whereas only three of 17 (17%) receiving preoperative irradiation developed pelvic recurrences. However, in Stage II six of eight patients treated with preoperative irradiation failed in the pelvis. Correlation with the doses of irradiation given to the uterus or the pelvic lymph nodes indicate that with doses below 5000 rads a significantly higher number of pelvic recurrences take place, whereas these are uncommon with doses over 6000 rads. The difference in pelvic recurrences between dosage levels is not, however, statistically significant. It is suggested that patients with Stage I and II malignant mixed müllerian tumors of the uterus should be treated with preoperative radiation and total hysterectomy with bilateral salpingo-oophorectomy. Patients with more advanced disease have extremely poor prognosis and should be treated with radiation therapy alone. This tumor has a high propensity to spread through lymphatics and hematogenous metastases are seen in approximately 75% of the patients. Because of this dissemination, significant improvements in survival rate will not be seen until effective cytotoxic agents are available.

A SIMPLE DILATOMETER

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