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African cichlid fishes harbor an extraordinary diversity of sex-chromosome systems. Within just one lineage, the tribe Haplochromini, at least 6 unique sex-chromosome systems have been identified. Here we focus on characterizing sex chromosomes in cichlids from the Lake Victoria basin. In Haplochromis chilotes, we identified a new ZW system associated with the white blotch color pattern, which shows substantial sequence differentiation over most of LG16, and is likely to be present in related species. In Haplochromis sauvagei, we found a coding polymorphism in amh that may be responsible for an XY system on LG23. In Pundamilia nyererei, we identified a feminizing effect of B chromosomes together with XY- and ZW-patterned differentiation on LG23. In Haplochromis latifasciatus, we identified a duplication of amh that may be present in other species of the Lake Victoria superflock. We further characterized the LG5-14 XY system in Astatotilapia burtoni and identified the oldest stratum on LG14. This species also showed ZW differentiation on LG2. Finally, we characterized an XY system on LG7 in Astatoreochromis alluaudi. This report brings the number of distinct sex-chromosome systems in haplochromine cichlids to at least 13, and highlights the dynamic evolution of sex determination and sex chromosomes in this young lineage.

Crop production on the Llano Estacado of the Texas High Plains has used precipitation and supplemental irrigation with water pumped from the Ogallala aquifer at rates that have far exceeded recharge for many years. Over 20% of the U.S. cotton (Gossypium hirsutum L.) crop is produced currently in this once vast grassland. Most of this cotton is produced in monoculture systems that are economically risky and contribute to wind-induced erosion and depletion of ground water resources. Although large numbers of cattle are found in this region, little integration of livestock and crop production exists. Integrated crop–livestock systems could improve nutrient cycling, reduce soil erosion, improve water management, interrupt pest cycles, and spread economic risk through diversification. Two whole-farm scale systems compared (1) a cotton monoculture typical of the region; and (2) an alternative integrated system that included cotton, forage, and Angus-cross stocker beef steers (initial body weight 249 kg). Steers grazed the perennial warm-season grass ‘WW-B. Dahl’ old world bluestem [Bothriochloa bladhii (Retz) S.T. Blake] in sequence with rye (Secale cereale L.) and wheat (Triticum aestivum L.) from January to mid-July when they were sent to the feedyard for finishing. Grass seed were harvested from bluestem in October. Cotton in the alternative system was grown in a two-paddock rotation with the wheat and rye. Cotton was harvested from both systems in October. At the end of 5 years, the alternative system reduced needs for supplemental irrigation by 23% and for nitrogen fertilizer by 40% compared with the conventional cotton monoculture. Fewer chemical inputs including pesticides were required by the alternative system. Soil with perennial grass pasture was lower in predicted soil erosion and was higher in soil organic carbon, aggregate stability, and microbial biomass than soil where continuous cotton was grown. Profitability was greater for the alternative system until cotton lint yields reached about 1500 kg ha−1 for the continuous cotton system. Differences between the systems became larger as depth to ground water increased. Systems that are less dependent on supplemental irrigation and less consumptive of non-renewable resources and energy-dependent chemical inputs appear possible, but further improvements are required to ensure sustainability of agricultural systems for the future in the Texas High Plains.

Successful precision agriculture requires an understanding of spatial variability of soil properties, crop growth, and their interactions. The objectives of this study were 1) to examine the spatial variability of soil properties, cotton lint yield, and fiber quality and 2) to evaluate the spatial variability within mapping units at a production‐field scale. This research was conducted on an irrigated 49‐ha cotton field in Texas from 1998 through 2000. Samples were collected from regular 1‐ha grids, triangular, and random points. Results indicated that soil properties had stronger spatial dependence than did cotton lint yields and fiber quality. Soil properties, except nitrate (NO3 −) nitrogen (N) and Olsen phosphorus (P), were strongly spatially dependent, whereas lint yield was moderately to strongly spatially dependent. Fiber quality was moderately spatially dependent. Spatial appearance of higher yield in drier years was associated with the distribution of soil properties favoring cotton grow...

Background: enteral nutrition can be associated with gastrointestinal side effects and fibre supplementation has been proposed as a means to normalize bowel function. Aim: to evaluate systematically the effects of fibre supplementation of enteral feeds in healthy volunteers and patients both in the hospital and community settings. Methods: electronic and manual bibliographic searches were conducted. Controlled studies in adults or children, comparing fibre-supplemented vs. fibre-free formulae given as the sole source of nutrition for at least 3 days, were included. Results: fifty-one studies (including 43 randomized-controlled trials), enrolling 1762 subjects (1591 patients and 171 healthy volunteers) met the inclusion criteria. Fibre supplementation was generally well tolerated. In the hospital setting, the incidence of diarrhoea was reduced as a result of fibre administration (OR 0.68, 95% CI: 0.48–0.96; 13 randomized-controlled trials). Meta-regression showed a more pronounced effect when the baseline incidence of diarrhoea was high. In both patients and healthy subjects, fibre significantly reduced bowel frequency when baseline frequency was high and increased it when it was low, revealing a significant moderating effect of fibre. Conclusions: the review indicates that the fibre-supplemented enteral formulae have important physiological effects and clinical benefits. There is a need to use a consistent approach to undertake more studies on this issue in the community setting.

Summary The Foss-Let fat analyser–based on the density measurement of a fat/ tetrachloroethylene extract in a magnetic float cell–has been evaluated on a range of different foods, particularly meat and meat products. It is rapid (6–7 min per determination) and gives results that are reproducible and of acceptable accuracy for quality control work when compared with those obtained by standard methods.

Plants can play an important role in wastewater treatment and water reuse in terrestrial and space systems. Chive growth in biologically treated graywater, simulating the anticipated early planetary base graywater, was evaluated in this study for NASA. Phytotoxicity due to physiochemical parameters such as ammonium-nitrogen (NH4 +-N), nitrite-nitrogen (NO2 −-N), pH, and sodium (Na+) was assessed using a series of hydroponic experiments in an environmentally controlled growth chamber. Nitrification in wastewater was observed in all graywater treatments, which converted NO2 −-N (a toxic form of nitrogen) and NH4 +-N (toxic at high concentrations) to nitrate-nitrogen (NO3 −-N) (preferred N form for plant uptake). Irrespective of the increase in the NO3 –-N concentration due to nitrification, chives in the wastewater treatments typically had poor or no growth. The high levels of Na+ present in the graywater treatments affected potassium uptake and may have affected other nutrient uptake. The impact of nitrification on wastewater pH and NO2 −-N toxicity is believed to be the critical factor affecting chive growth and may hinder the use high nitrogen waste streams for plant growth unless NO2 −-N concentrations are controlled during biological treatment of graywater.

Bermudagrass (Cynodon dactylon (L.) Pers.) for- ages are potential alternatives to traditional row cropping in the Southern High Plains. Early per- sistence of certain bermudagrass selections and economic potential and nutritive value of known, improved cultivars in semiarid West Texas are uncertain. A 2-yr study was conducted to evalu- ate hay productivity and nutritive value of 10 cultivars and two selections of bermudagrass grown with subsurface drip irrigation. Grasses were irrigated with 312 mm of water from 1 May through 31 August in 2002 and 2003. Precipita- tion amounts during the growing season (May- September) were 195 and 184 mm for 2002 and 2003, respectively. 'Tifton 85' yielded the highest total annual biomass (20.4 Mg ha −1 ) and resulted in high irrigation water use effi ciency (IWUE; 65.2 kg ha −1 mm −1 ). 'World Feeder' and 'Macho' performed poorly with respect to yield when compared with the other 10 grasses. Although Tifton 85 exhibited high acid detergent fi ber (ADF; 349 g kg −1 ) and low total nonstruc- tural carbohydrates (TNC; 93 g kg −1 ), in vitro dry matter disappearance (IVDMD) was greatest (622 g kg −1 ) when contrasted with the mean of all other cultivars. Yields were similar for sprigged and seeded types. Results indicate that several bermudagrass cultivars maintained high yields and adequate nutrition 2 yr after establishment and, based on IWUE, may be an economically sound alternative to the existing cotton (Gossy- pium hirsutum L.) monoculture in the region.

The effects of hydroponic nutrient solution composition and pH on growth and mineral content of green onions was evaluated. Three onion varieties [Allium cepa L. (‘Deep Purple’ and ‘Purplette’) and A. fistulosum L. (‘Kinka’)] were propagated in three nutrient solutions (Peter's Hydro-Sol, modified Hoagland's, and half-strength modified Hoagland's) at two pH levels (5.8 and 6.5) in a three-by-two factorial design applied in a randomized block with three replications. Seeds were germinated in Cropking's Oasis Horticubes under greenhouse conditions and irrigated with tap water. Once the seedlings reached the flag stage, the plants were placed into hydroponic units within the greenhouse and grown under ambient conditions. Plants were harvested 30 d after transplanting to the hydroponic units. The results indicated nutrient solution, pH, and variety significantly affected several plant physiological variables. Total biomass and edible biomass production was as high for plants grown in half-strength Ho...

Two experiments were conducted as part of an effort to evaluate the suitability of onions as a candidate crop for testing in a closed, controlled environment, hydroponic-based plant facility designed for long-term manned space missions (NASA Engineering Development Unit). Composition and total flavonol content of the plants were determined as they matured in a hydroponic-versus a soil-based system. ‘Purplette’ onions (Allium cepa L.) were grown hydroponically in a greenhouse for as long as 77 days. Composition of the plant tissue was determined at weekly or biweekly intervals. Ca, Mg, K, and N (wet matter basis) all decreased as plants matured. Dry matter (DM) and S contents were constant regardless of age averaging 10.6% and 187 mg/100 g, respectively. Total flavonol (TF) content increased as plants matured (226–538 mg/100 g at 14 and 77 days, respectively). Onions grown in hydroponic units or in potting medium had similar composition for all constituents examined (10.38%, 0.550%, 4.15%, and 0.97% DM, N, C, and ash, respectively; and 126.0, 55.5, 270, 185 and 453 mg/100 g Ca, Mg, K, S and TF, respectively). Based on phenotypic characteristics and composition determined in this study, onions were well suited to hydroponic propagation.

Abbreviations – Amax, photosynthetic capacity at saturating light level (1500 mmol m 2 s 1 PPFD) and saturating atmospheric CO2 (Ca of 80 Pa CO2 )( mmol CO2 m 2 s 1 ); Asat, net photosynthesis at saturating irradiance (1500 mmol m 2 s 1 PPFD) and Ca of 37 Pa CO2 (mmol CO2 m 2 s 1 ); Ca, atmospheric CO2 partial pressure (Pa); Ci, intercellular CO2 partial pressure (Pa); Jmax, maximum rate of electron transport (mmol m 2 s 1 ); Ls, relative stomatal limitation to photosynthesis (%); Qcomp, photosynthetic light compensation point (mmol m 2 s 1 ); Qsat, photosynthetic light saturation point (mmol m 2 s 1 ); Vcmax, maximum rate of Rubisco carboxylation (mmol m 2 s 1 ).

Procedures to delineate management zones as a basis for making variable rate applications of fertilizers within a field have not been well defined.. The objective of this study was to evaluate a framework of procedures for delineating potential management zones. with data collected from 1-ha grids on an irrigated cotton (Gossypium hirsutum L.) field in Texas from 1998 through 2000. Selected measurements included lint yield, soil pH, exchangeable Ca 2 + and Mg 2 +, K saturation, sand and clay content, depth to free carbonate layer, depth to caliche, NO 3 -N, available P, elevation, and slope. Data were processed with k-means cluster analysis, multivariate analysis of variance (MANOVA), and discriminant analysis. Cluster analysis allowed grouping lint yield and soil properties into high and low yielding classes by their data structure. Using the most significant linear combination in terms of distinguishing 2+ 2+ two yield classes from MANOVA, soil pH, extractable Ca and Mg , K saturation, clay content, and soil N to P ratio were identified as variables that were most related to cotton yield classification and resulted in two potential management zones. The lowest misclassification rate (27%) appeared in the two classes developed from the six influential variables and misclassification mostly located near the pivot boundary and near high to low or low to high yield transition areas, possibly due to changes in soil properties coupled with differences in weather-year patterns in the3 years. Combined with other information, the delineated high and low yield . classes can serve as potential management zones for making detailed management prescriptions for irrigated cotton on these soils. (Soil Science 2005;170:371-385)

Agriculture in the Texas High Plains depends heavily on irrigation with water withdrawn from the Ogallala aquifer at nonsustainable rates. Our hypothesis was that integrating crop and livestock systems would reduce irrigation water use, maintain profitability, and diversify income compared with a cotton (Gossypium hirsutum L.) monoculture. Thus, from 1998 to 2002, two large-scale systems, with three replications in a randomized block design, compared water use, productivity, and economics of (i) a cotton (var 'Paymaster 2326RR') monoculture with terminated wheat (Triticum aestivum L.) and (ii) an integrated three-paddock system that included cotton in a two-paddock rotation with grazed wheat and rye (Secale cereale L.) and the perennial 'WW-B. Dahl' old world bluestem [Bothriochloa bladhii (Retz) S.T. Blake] for grazing and seed production. All paddocks were irrigated by subsurface drip. Angus crossbred beef steers (Bos taurus L.; initial body weight = 249 kg; standard deviation = 26 kg) grazed from January to mid-July. During the 4 yr of this experiment following the establishment year, cotton lint yield was 1036 and 1062 kg ha - 1 for the cotton monoculture and the integrated system, respectively. Bluestem seed yield averaged 24 kg pure live seed ha - 1 . Steers gained 153 kg on pasture and 0.82 kg d - 1 . Per hectare, the integrated system used 23% less (P < 0.001) irrigation water, 40% less N fertilizer, and fewer other chemical inputs than the cotton monoculture. Profitability was about 90% greater for the integrated system at described conditions. Integrated production systems that are less dependent on irrigation and chemical inputs appear possible while improving profitability.

Motivation: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. Results: CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches. Availability: Direct access: http://www.mgu.har.mrc.ac.uk/CRAVE/ Contact: g.gkoutos@har.mrc.ac.uk

Intercorrelation among soil properties can result in multicollinearity problems regarding relationships between soil properties and crop yield. The objective of this study was to compare statistical methods of examining relationships between cotton (Gossypium hirsutum L.) yield, quality, and soil properties. Soil and plant samples were collected from 1-ha grids on an irrigated production cotton field in Texas from 1998 through 2000. Ordinary least square regression (OLS), partial least square regression (PLS), and principal component regression (PCR) were compared as methods for quantifying relationships between cotton yield or quality and soil properties. The PLS method eliminated multicollinearity problems and resulted in the coefficient estimations with meaningful signs compared with their associations to cotton yield and fiber quality. Furthermore, loadings from linear combinations of variables in PLS allowed identifying soil properties that had the greatest influence on yield. While PCR identified the principal components that maximized the variance of independent variables, it did not improve the modeling of crop-soil relationships. Among the selected soil and landscape properties, sand and clay content, exchangeable Ca 2+ and Mg 2+ , NO - 3 , Olsen-P, pH, relative elevation, and slope were important factors affecting lint yield and fiber quality. Higher lint yields were usually accompanied by higher fiber quality. Magnitudes of influence of different soil properties on yield and quality, however, varied among the 3 yr, suggesting that long-term studies are needed to establish robust relationships for site-specific management.

The understanding of spatial dependence of yield and abiotic factors that influence yield plays a key role in successful application of precision agriculture. The objectives of this study were to (i) evaluate the application of both global and local autocorrelation statistics to explore the spatial dependence of cotton (Gossypium hirsutum) yield and yield pattern changes under two weather scenarios, and (ii) compare effects of weight selection on spatial autocorrelation statistics. Cotton yield was measured from 1 ha grids in a 49 ha production field from 1998 through 2000. Spatial dependence was described in terms of global Moran’s I and Geary’s C, local indicator of spatial association, and local Gi and G i ∗ statistics. While global spatial autocorrelation statistics could describe the overall spatial dependence of cotton yields over the entire field, local spatial autocorrelation statistics were useful in identifying the influences from individual positions compared to their neighbors. The application of Moran scatterplots could decompose the spatial dependence and identify influential positions. Spatial dependence of cotton yield was highly affected by weather conditions. The lint yields were significantly spatially autocorrelated in the drier years (1998 and 2000), but not in wetter year (1999) in this study. Furthermore, a trend existed with changing locations and the detrending decreased the spatial association. Additionally, spatial autocorrelation of lint yield in the drier years turned from positive into negative as contiguity order increased. Maximum spatial autocorrelation was obtained in inverse distance with power 1 and in k-nearest points with k as 4. In comparison, there were some similarities between spatial semivariogram, and global and local spatial association statistics but the latter can provide some useful spatial association to be used for management zone delineation. Based on global and local spatial statistics, three major and five minor management zones were identified, which could help decision making in site-specific management systems.

Elevated atmospheric CO 2 concentrations ([CO 2 ]) have been hypothesized to increase photosynthesis rates and volatile organic compound (VOC) emissions; however, field measurements from a select group of conifer and angiosperm trees have shown that VOC emissions are in fact not affected or reduced by elevated CO 2 levels. To broaden the understanding of how different plant species respond to elevated atmospheric [CO 2 ], air-flow-through, glass chambers were designed and utilized to measure photosynthesis and emissions from onion ( Allium cepa cv. ‘Purplette’) under controlled environmental conditions. Here we report on VOC release and root exudation while monitoring photosynthesis from whole plants grown under ambient (400 μmol mol −1 ) and elevated (1000 μmol mol −1 ) [CO 2 ]. A 22% increase in photosynthesis in the elevated CO 2 plants and a 17-fold and 38-fold increase in the VOC hydrocarbons 2-undecanone and 2-tridecanone, respectively, were observed in 30-day-old onion seedlings compared to plants grown under ambient CO 2 conditions. In contrast TOC from root exudates decreased significantly with elevated CO 2 conditions. Plants harvested at 30 days had on average over 40% greater biomass when grown at elevated CO 2 levels. The demonstration that VOC emissions increase in plants grown under elevated [CO 2 ] and higher photosynthesis rates points to a fundamental difference in how carbon partitioning alters in herbaceous species such as onion versus the previously studied tree species in response to elevated concentration of atmospheric CO 2 .

The narrow germplasm base of the upland cotton (Gossypium hirsutum L.), grown on the Texas high plains historically, has limited improvement of fiber quality. Chemical mutagenesis and subsequent selection have helped the development of lines with improved fiber quality in cultivars adapted to this region. This study was conducted to determine the inheritance of improvements in fiber quality. M3 lines with divergent fiber properties of micronaire, length, and strength were selected from a population of Paymaster HS 200 treated with 3% v/v ethyl methanesulfonate (EMS) for two hours. The 115 selected lines of M4 and M5 generation were evaluated for fiber quality and lint yield. Regression of the M4 and M5 on the M3 generation, as well as the M5 on the M4 was used to generate narrow sense heritability coefficients. Significant variations were observed between the mutant lines in all generations except for lint yield in the M5 (1997). The highest heritability estimates were found in fiber length (h2= 0.29** to 0.46**). Micronaire and strength showed intermediate heritability estimates of h2= 0.14 to 0.19, while lint yield had a very low heritability estimate of h2= 0.03. Fiber length and strength were correlated (r= 0.58** to 0.46**) in all the three generations. The mutants identified in these studies have the potential to improve fiber quality of upland cotton without introducing alien genes that may reduce adaptation to short growing season production regions.

Pre-plant soil NO⁻ ₃–N tests and petiole NO⁻ ₃–N analysis are bases for Upland cotton (Gossypium hirsutum L.) N management in the western USA. Alternative approaches include proximal multispectral reflectance sensing and chlorophyll meter readings. Our objective was to determine if spectral reflectance and chlorophyll meter measurements correlate with cotton leaf N and biomass. Urea ammonium nitrate was applied after emergence and with low energy precision (LEPA) center-pivot, surface or subsurface drip irrigation water up to peak bloom. Multispectral reflectance readings 0.5 m above the canopy, chlorophyll meter readings, and biomass samplings were taken at early squaring, early bloom, and peak bloom for 3 site-years in Lubbock, TX and Ropesville, TX. Green vegetative indices (GVI) and green normalized difference vegetative indices (GNDVI) calculated from reflectance data generally correlated better with leaf N and leaf N accumulation than did red vegetative indices (RVI) and red normalized difference vegetative indices (RNDVI). Biomass and lint yield correlated more often with red-based indices than green-based indices. Chlorophyll meter readings correlated with leaf N as often as GVI and GNDVI did. Biomass, however was poorly related to chlorophyll meter readings. These results demonstrate the effectiveness of GVI, GNDVI, and chlorophyll meter readings in assessing leaf N, and RVI and RNDVI in assessing cotton biomass. However, we recommend converting vegetative indices or chlorophyll meter readings to sufficiency indices, which are calculated from indices or readings relative to well-fertilized plots. Sufficiency indices were able to successfully predict little or no need for in-season N fertilizer in the low-yielding 2000 crops (sufficiency index > 0.95), and predicted greater need of N fertilizer in the high-yielding 2001 crop (sufficiency index < 0.95).

An important issue in population biology is the dynamic interaction between pathogens. Interest has focused mainly on the indirect interaction of pathogen strains, mediated by cross immunity1,2,3,4. However, a mechanism has recently been proposed for ‘ecological interference’ between pathogens through the removal of individuals from the susceptible pool after an acute infection. To explore this possibility, we have analysed and modelled historical measles and whooping cough records. Here we show that ecological interference is particularly strong when fatal infections permanently remove susceptibles. Disease interference has substantial dynamical consequences, making multi-annual outbreaks of different infections characteristically out of phase. So, when disease prevalence is high and is associated with significant mortality, it might be impossible to understand epidemic patterns by studying pathogens in isolation. This new ecological null model has important consequences for understanding the multi-strain dynamics of pathogens such as dengue and echoviruses.

Grasslands “Gala” (Bromus stamineus Desv.) bromegrass is generally regarded as high quality forage particularly adapted to grazing, but little is known about its growth response to N fertilization or potential to accumulate nitrate (NO3 −). Effects of N fertilization were investigated in two greenhouse experiments. Gala was grown in pots in a complete randomized design with four replications of the following N treatments: 0, 25, 50, 100, and 200 kg N ha−1 applied twice in Experiment 1, and 50, 100, 200, 300, and 400 kg N ha−1 applied five times in Experiment 2. Plants were harvested twice in Experiment 1, and five times in Experiment 2. Twenty-five kg N ha−1 per application did not sustain growth of Gala but little increase in growth occurred beyond 50 kg N ha−1 over five applications. About 90% of the 250 kg N ha−1 that was applied in 50 kg-increments was measured in the aerial plant biomass. Yield efficiency was also greatest at 50 kg N ha−1 per application and decreased with increasing N level...

Introduction Developmental dysplasia of the hip (DDH) is the most common congenital musculoskeletal abnormality. Recourse to definitive surgical treatment is not typically taken until over the age of 18–24 months. International consensus regarding age at surgery, degree of dysplasia requiring surgery and type of osteotomy is not available in the literature. Study aims To determine variation in timing and type of osteotomy for persistent DDH across the world. Methodology Senior authors of recent publications pertaining to hip dysplasia were sampled. Participants’ practice relating to age and radiological indications for surgery were determined. Results Thirty-two surgeons responded from five different geographical regions. No inter-regional consensus was established regarding investigations to determine the need for osteotomy, preferred osteotomy type or ideal age at which to perform an osteotomy. Conclusion International agreement regarding the surgical management of DDH does not exist. This common congenital condition warrants development of a treatment algorithm.

Precision agriculture technologies offer an opportunity to vary production inputs within a field. Variable rate application offers the potential to increase production efficiency and minimize potential adverse environmental effects of agricultural chemicals. As an initial step in the development of precision agriculture technologies for cotton, studies are needed to document variability of cotton. The primary objective of this study was to document variability of yield and quality of irrigated cotton within and across three growing seasons. This study was conducted on a 5.3 ha irrigated field located at the Erskine Research Farm at Texas Tech University, Lubbock, TX. The crop was grown under a conventional tillage system with a 1.0 m row spacing. With the exception of sample collection, the field was managed traditionally with respect to production inputs. A grid system (57 points) was established on 30.5 m (approximately 0.1 ha) intervals. Production of fruiting sites, fruit retention, lint yield, fiber ...

Previous studies of gastrocnemius muscle reinnervation showed specific normalization of the proportion and diameter of fast type 2b muscle fibres following NT-3 delivery to the proximal stump of the cut sciatic nerve. Here, we investigate if normalization was related to greater improvement of muscle reinnervation of fast (extensor digitorum longus; EDL) than slow (soleus) motor units. NT-3-impregnated (NT-3 group) or plain fibronectin (FN group) mats were inserted into a sciatic nerve gap. Neuromuscular junctions (NMJs) labelled with TRITC-alpha-bungarotoxin were colabelled with calcitonin gene-related peptide (CGRP) or 4E2 antisera and imaged using confocal microscopy. CGRP and 4E2 were used as markers for newly reinnervated and structurally mature NMJs, respectively. At 40 days postsurgery, denervated NMJs in EDL and soleus muscles of both groups presented a 50% decrease of surface area due to decreased width. At day 80 in EDL, more NMJs were reinnervated by CGRP-immunoreactive terminals in the NT-3 (7.1%) than in the FN group (4.2%); there was no difference between groups for soleus. At 120 days, 4E2-immunoreactive NMJs were more numerous in EDL of the NT-3 (40.0%) than in the FN group (7.3%), unlike in soleus (NT-3, 1.6%; FN, 1.8%), and presented a partial size recovery. These results indicate that NT-3 preferentially improves reinnervation of fast muscles over slow muscle, although the mechanism of this improvement is still unclear.

The presence of salts in soil or in irrigation water can adverselyaffectplantgrowthandsoilproperties.Salinityconcerns are more common in semiarid and arid regions than in more humid regions. Furthermore, salinity is often an important concern for irrigated agriculture. Therefore, it is critical to educate students in soils courses about the effects of salts on plants and soils. Many soils laboratory manuals focus on measurement of salts in soils, but few include demonstrations of how salt effects bothplantsandsoils.Demonstratingtheeffectsofsaltsonplants andsoilsshouldenhancelearningbyprovidingtangibleimages. Our purpose was to develop laboratory exercises that demonstrate these effects for use in soils and other science courses. To demonstrate differences in plant response to salinity, a hydroponic study utilizing a range in salinities and plants with differentsaltsensitivitieswasused.Todemonstratedifferencesinhow salteffectshydraulicconductivity,astudyutilizingthreesoilsand foursaltsolutionswasused.Theseprovidevisualrepresentations of the well-established effects of salts on plants and soils. Includingplantspecieswithdifferentsalttolerances,soilswithdifferent textures, and treatments such as elevated sodium and elevated total salt levels effectively demonstrate the relative importanceofsalts.Inclusionofthesevisualdemonstrationsofthe effects of salts on plants and soils should enhance student learning.

Soluble salts found in wastewater can be toxic when used for irrigation of forages. Thus, two greenhouse experiments were conducted to investigate effects of saline [CaCl2NaCl (3:1, w:w)] treatments on soil chemical properties and ‘Dekalb FS‐5’ forage sorghum [Sorghum bicolor(L.) Moench]. Treatments for the first experiment consisted of a nonsaline control or 500 mL of a solution with an electrical conductivity (EC) of 10 dS m−1 applied once. In the second experiment, treatments were salinity levels of 1.7,3.5,5.2,8.5, and 12.2 dS m−1, applied in non‐nitrogenous Hoagland's solution as the sole source of irrigation. Both experiments were replicated four times. For both experiments forage sorghum was seeded in pots containing 7 kg of air‐dried Amarillo fine sandy loam soil. Sorghum survivability and plant height were measured. In the second experiment, water use by sorghum was also measured. Plants were harvested 7 wk after seeding, weighed, dried at 55°C, weighed, and ground for subsequent mineral...

The purpose of this study was to evaluate the effect of neurotrophin 3 (NT-3) enhanced nerve regeneration on the reinnervation of a target muscle. Muscle fibers can be classified according to their mechanical properties and myosin heavy chain (MHC) isoform composition. MHC1 containing slow-type and MHC2a or 2b fast-type fibers are normally distributed in a mosaic pattern, their phenotype dictated by motor innervation. After denervation, all fibers switch to fast-type MHC2b expression and also undergo atrophy resulting in loss of muscle mass. After regeneration, discrimination between fast and slow fibers returns, but the distribution and fiber size change according to the level of reinnervation.In this study, rat gastrocnemius muscles (ipsilateral and contralateral to the side of nerve injury) were collected up to 8 mo after nerve repair, with or without local delivery of NT-3. The phenotype changes of MHC1, 2a, and 2b were analyzed by immunohistochemistry, and fiber type proportion, diameter, and grouping were assessed by computerized image analysis. At 8 mo, the local delivery of NT-3 resulted in significant improvement in gastrocnemius muscle weight compared with controls (NT-3 group 47%, controls 39% weight of contralateral normal muscle; P < 0.05). NT-3 delivery resulted in a significant increase in the proportion (NT-3 43.3%, controls 35.7%; P < 0.05) and diameter (NT-3 87.8 μm, controls 70.8 μm; P < 0.05) of fast type 2b fibers after reinnervation. This effect was specific to type 2b fibers; no normalization was seen in other fiber types.This study indicates that NT-3–enhanced axonal regeneration has a beneficial effect on the motor target organ. Also, NT-3 may be specifically affecting a subset of motoneurons that determine type 2b muscle fiber phenotype. As NT-3 was topically applied to cut nerves, our data suggest a discriminating effect of the neurotrophin on neuro–muscular interaction. These results would imply that muscle fibers may be differentially responsive to other neurotrophic factors and indicate the potential clinical role of NT-3 in the prevention of muscle atrophy after nerve injury.

Near–infrared spectroscopy has primarily been used in monitoring changes in cerebral haemoglobin oxygenatiuon and haemodynamics. However its use as a method for the assessment of tissue viability following transplantation has recently been explored experimentally in our laboratory. The ability to measure changes in oxygenation and perfusion during harvesting and following transplantation of organs or transfer of free and pedicled flaps is potentially important in reconstructive surgery. We have found that near–infrared spectroscopy is extremely useful in detecting vaso–occlusive events and can accurately and reliably distinguish between arterial, venous or total occlusions. Venous congestion indicated by raised levels of deoxygenated haemoglobin with a concomitant increase in blood volume and the presence and magnitude of reactive hyperaemia are both easily recognizable features by near–infrared spectroscopy. We have shown that near–infrared spectroscopy measurements of venous congestion in kidneys (and other tissues) following prolonged storage correlate with medullary vascular congestion confirmed by angiographical and histological analysis of intrarenal perfusion. Clinically we have shown that flap perfusion can be improved by altering fluid replacement regimes and the addition of ionotropes. Cerebral near–infrared spectroscopy measurements in a liver transplant model showed statistically significant differences within minutes after the anhepatic phase in cerebral perfusion and oxygenation, between animals transplanted with ischaemically damaged livers compared to those isografted with minimally stored livers. Similarly we have found that near–infrared spectroscopy can be used as a monitor to assess the adequacy of fluid or blood replacement in haemorrhagic and hypovolaemic models. We believe that near–infrared spectroscopy provides a sensitive and reliable postoperative method for the assessment of tissue viability following the transfer of free and pedicled flaps and organs.

This study introduces a new nerve conduit material consisting of orientated strands of the cell adhesive fibronectin. Axonal regeneration, Schwann cell behaviour and the degree of inflammation were quantified using immunohistochemical techniques and computerized image analysis. The results when fibronectin was used to bridge a 1 cm defect in rat sciatic nerve were compared to those with autologous nerve grafts and freeze-thawed muscle grafts used as controls. The nerve grafts supported the highest rate and amount of axonal regeneration in the first 10 days; however, the fibronectin supported a significantly faster rate of growth ( P=0.0008) and amount ( P=0.0001) of axons than the freeze-thawed muscle grafts. From day 15 onwards, the fibronectin and nerve grafts had comparable amounts of regenerating axons and Schwann cells. We conclude that the orientated form of fibronectin is a suitable material for successful nerve repair and has potential clinical use.

An interposed segment of nerve was used to enhance the distance over which freeze-thawed muscle autografts will support effective peripheral nerve regeneration. Gaps were created in the sciatic nerves of adult Lewis rats. Regeneration through 1 and 1.5 cm freeze-thawed muscle grafts was compared to regeneration through nerve-muscle sandwich grafts in which muscle grafts of equivalent length were divided and a 2 mm segment of the distal nerve sutured between the two halves of the muscle, providing an intermediate depot of Schwann cells. Electrophysiological and morphological evaluation was carried out 40 weeks after operation. Despite lengthening the graft, and having four anastomoses instead of two, this manoeuvre enhanced nerve regeneration over each gap studied and for the 1.5 cm gaps compared favourably with perfect match nerve autografts. In addition, a number of grafts were examined at 7 and 14 days by Sl00 immunohistochemistry. Schwann cell migration was seen to proceed both proximally and distally from the intermediate segment at a rate similar to that from the distal stump. It is concluded that sandwich grafts may prove to be effective alternatives to cutaneous nerve grafts for peripheral nerve reconstruction.

Rates of N fertilization required to attain maximum yields of corn (Zea mays L.) usually are less for corn grown after soybean [Glycine max (L.) Merr.] than for corn grown after corn, but the reason for the difference in N fertilizer requirement has not been clearly established. We studied immobilization and mineralization induced by various management histories and residue treatments to learn about the causes of differences in N fertilizer requirements. Soil samples were collected at five sites in the fall of 1990 from plots that had been planted to soybean and plots that had been planted to corn receiving various N rates. The soil samples were incubated for 42 wk after treatment with 15 N-labeled NO 3 - and with crop residues. All treatments showed a period of net immobilization followed by a period of net mineralization. Net amounts of N immobilization induced by soybean residue were approximately equal to those induced by corn residue from plots with the higher rates of fertilization. However, the soybean-induced immobilization was much more rapid. Rates of mineralization of nonlabeled N were not greater from soils having soybean residue than from soils having corn residue. Because soybean produces less residue under field conditions, the results suggest that differences in N fertilizer requirement are better explained by differences in amounts of N immobilized during residue decomposition than by mineralization of biologically fixed N associated with the soybean.

Additions of 15 N-labeled fertilizers to soils often induce mineralization of nonlabeled N, and such mineralization poses problems when interpreting the results of isotopic analyses. We studied the effects of added 15 NO 3 - on turnover of N during the decomposition of corn (Zea mays L.) residues in soils. Samples of a Galva silty clay loam (fine-silty, mixed, mesic Typic Hapludoll) were treated with various levels of corn stover and various levels of 15 N-labeled NO 3 - and were incubated for 90 d. Evolution of CO 2 and concentrations and isotopic composition of NO 3 - were monitored. Increases in rates of NO 3 - addition increased initial rates of immobilization of labeled N and subsequent rates of mineralization of nonlabeled N. The sequential immobilization of labeled N and mineralization of nonlabeled N resulted in substantial replacement of labeled NO 3 - by nonlabeled NO 3 - . Early added-N-induced immobilization of labeled N often was offset by subsequent added-N-induced mineralization of nonlabeled N before the end of the study. Sequential immobilization and mineralization should be recognized as a potential source of error in 15 N-tracer studies because sequential processes violate the commonly held assumptions that mineralization and immobilization occur simultaneously. This error could be avoided by recognizing that sequential immobilization and mineralization can occur and that the sequential processes result in a different distribution of isotopes than does simultaneous mineralization-immobilization turnover.

Nitrogen fertilization is widely recognized for its potential to help maintain soil organic matter (SOM) concentrations by increasing plant growth and amounts of plant material decomposed in soils. We studied possible mechanisms by which annual additions of more N than needed to maximize yields of corn (Zea mays L.) could cause losses of SOM. Various amounts of stover and NO − 3 were added to a Galva silty clay loam (fine-silty, mixed, mesic Typic Hapludoll), and NO − 3 concentrations and CO 2 evolution were monitored for periods up to 90 d at 24°C in the laboratory. The added NO − 3 suppressed mineralization of C from SOM and stimulated mineralization of C frome stover. Adjustment of rates of stover decomposition to temperature regimes normally encountered in Iowa fields after harvest showed that stover decomposition would not be complete within 1 yr and that increases in NO − 3 availability decreased the amount of stover C remaining in the soil. This effect of NO − 3 could explain how additions of unneeded N could decrease concentrations of SOM in long-term studies in which residues and NO − 3 are added in annual cycles. These observations suggest that practices that reduce unnecessary fertilization could help conserve SOM and reduce net amounts of CO 2 released to the atmosphere

Background Smoking has been linked to mucinous ovarian cancer, but its effects on other ovarian cancer subtypes and on overall ovarian cancer risk are unclear, and the findings from most studies with relevant data are unpublished. To assess these associations, we review the published and unpublished evidence. Methods Eligible epidemiological studies were identified by electronic searches, review articles, and discussions with colleagues. Individual participant data for 28 114 women with and 94 942 without ovarian cancer from 51 epidemiological studies were analysed centrally, yielding adjusted relative risks (RRs) of ovarian cancer in smokers compared with never smokers. Findings After exclusion of studies with hospital controls, in which smoking could have affected recruitment, overall ovarian cancer incidence was only slightly increased in current smokers compared with women who had never smoked (RR 1.06, 95% CI 1.01-1.11, p=0.01). Of 17 641 epithelial cancers with specified histology, 2314 (13%) were mucinous, 2360 (13%) endometrioid, 969 (5%) clear-cell, and 9086 (52%) serous. Smoking-related risks varied substantially across these subtypes (p(heterogeneity)

Background: Only about half the studies that have collected information on the relevance of women’s height and body mass index to their risk of developing ovarian cancer have published their results, and findings are inconsistent. Here, we bring together the worldwide evidence, published and unpublished, and describe these relationships. Methods and Findings: Individual data on 25,157 women with ovarian cancer and 81,311 women without ovarian cancer from 47 epidemiological studies were collected, checked, and analysed centrally. Adjusted relative risks of ovarian cancer were calculated, by height and by body mass index. Ovarian cancer risk increased significantly with height and with body mass index, except in studies using hospital controls. For other study designs, the relative risk of ovarian cancer per 5 cm increase in height was 1.07 (95% confidence interval [CI], 1.05-1.09; p

The effects of cold hypoxia were examined during a time-course at 2 degrees C on levels of glycolytic metabolites: glycogen, glucose, glucose-1-phosphate, glucose-6-phosphate, fructose-6-phosphate, fructose-1,6-bisphosphate, phosphoenolpyruvate, pyruvate, lactate and energetics (ATP, ADP, AMP) of livers from rats and columbian ground squirrels. Responses of adenylate pools reflected the energy imbalance created during cold hypoxia in both rat and ground squirrel liver within minutes of organ isolation. In rat, ATP levels and energy charge values for freshly isolated livers were 2.54 mumol.g-1 and 0.70, respectively. Within 5 min of cold hypoxia, ATP levels had dropped well below control values and by 8 h storage, ATP, AMP, and energy charge values were 0.21 mumol.g-1, 2.01 mumol.g-1, and 0.17, respectively. In columbian ground squirrels the patterns of rapid ATP depletion and AMP accumulation were similar to those found in rat. In rat liver, enzymatic regulatory control of glycolysis appeared to be extremely sensitive to the decline in cellular energy levels. After 8 h cold hypoxia levels of fructose-6-phosphate decreased and fructose-1,6-bisphosphate increased, thus reflecting an activation of glycolysis at the regulatory step catalysed by phosphofructokinase fructose-1,6-bisphosphatase. Despite an initial increase in flux through glycolysis over the first 2 min (lactate levels increased 3.7 mumol.g-1), further flux through the pathway was not permitted even though glycolysis was activated at the phosphofructokinase/fructose-1,6-bisphosphatase locus at 8 h, since supplies of phosphorylated substrate glucose-1-phosphate or glucose-6-phosphate remained low throughout the duration of the 24-h period.(ABSTRACT TRUNCATED AT 250 WORDS)

Hypoxic stress in tumor cells has been implicated in malignant progression and in the development of therapeutic resistance. We have investigated the effects of acute hypoxic exposure on regulation of the proto-oncogene c-jun in SiHa cells, a human squamous carcinoma cell line. Hypoxic exposure produced increased levels of c-jun mRNA resulting from both message stabilization and transcriptional activation. A superinduction of c-jun message resulted during simultaneous oxygen and glucose deprivation, with several characteristics of an induction mediated by oxidative-stress pathways. This superinduction was blocked by preincubation of cells with the glutathione precursor N-acetyl cysteine or with phorbol 12-myristate 13-acetate, which indicates redox control of c-jun expression and probable involvement of protein kinase C. By gel retardation assay, no increase in AP-1 DNA binding activity was found to be concomitant with the transcriptional activation of c-jun. A lack of increased DNA binding was observed for the consensus AP-1 sequence and for the two AP-1 sequence variants found within the c-Jun promoter. Additionally, hypoxic and low-glucose stress produced no activation of stably transfected AP-1 reporter sequences. Taken together, these results indicate that the transcriptional activation of c-jun during hypoxic and low-glucose stress involves redox control and is unlikely to be mediated by AP-1 recognition elements within the c-jun promoter.

Climate change models predict increasing frequency of extreme weather. One of the challenges hospitals face is how to make sure they have adequate staffing at various times of the year. The aim of this study was to examine the effect of this severe inclement weather on hospital admissions, operative workload and cost in the Irish setting. We hypothesised that there is a direct relationship between cold weather and workload in a regional orthopaedic trauma unit. Trauma orthopaedic workload in a regional trauma unit was examined over 2 months between December 2009 and January 2010. This corresponded with a period of severe inclement weather. We identified a direct correlation between the drop in temperature and increase in workload, with a corresponding increase in demand on resources. Significant cost savings could be made if these injuries were prevented. While the information contained in this study is important in the context of resource planning and staffing of hospital trauma units, it also highlights the vulnerability of the Irish population to wintery weather.

In the past, antioxidant and chelator studies have implicated a role for iron-dependent oxidative damage in tissues subjected to ischaemia followed by reperfusion. As ferritin is a major source of iron in non-muscular organs and therefore a potential source of the iron required for oxygen radical chemistry, we have determined conditions under which ferritin iron reduction leads to the formation of a pool of iron which is capable of catalysing lipid peroxidation. Under anaerobic conditions and in the presence of rat liver microsomes, flavin mononucleotide (FMN) catalysed the reduction of ferritin iron as shown by both continuous spectrophotometric measurements of tris ferrozine-Fe(II) complex formation and post-reaction Fe(II) determination. The presence of either ferrozine or citrate was not found to alter the time course or extent of ferritin reduction. In contrast, the addition of air to the reactants after a 20 min period of anaerobic reduction resulted in peroxidation of the microsome suspension (as determined with the 2-thiobarbituric acid test) only in the presence of a chelator such as citrate, ADP or nitrilotriacetic acid. These results support the concept that reduced ferritin iron can mediate oxidative damage during reperfusion of previously ischaemic tissues, provided that chelating agents such as citrate or ADP are present.

In this study we evaluated mitochondrial function after liver cold storage and normothermic reperfusion. The preservation solutions were: modified University of Wisconsin (mod UW) and sucrose-based solution (SBS). After cold preservation liver was re-perfused for 1 hour in vitro with Krebs-Ringer buffer at 37 degree C. Samples of tissue were taken for ATP determination. Mitochondrial respiratory parameters, succinate oxidase complex activity, mitochondrial H+- ATPase and intramitochondrial potassium concentration were assayed. It was shown, that brief (1 hour) cold storage and subsequent normothermic reperfusion revealed no difference in liver ATP content between mod UW and SBS groups but resulted in a gradual decrease of 50 percent after 24-hour storage and reperfusion. Mitochondrial potassium ion concentration increased by 40 percent after 1-hour cold storage in the mod UW as compared to control (P value less than 0.05) and SBS. After brief cold storage ADP and uncoupler-stimulated respiration increased by 120 percent in SBS group, unlike mod UW, when succinate was used as substrate, and was more pronounced after 24 hour. Succinate oxidase complex activity did not change over either cold storage or warm reperfusion. Mitochondrial H+-ATPase activities in SBS and mod UW did not differ and both were inhibited after 24-hour cold storage. Our data demonstrate that low ionic strength preservation solution can substantially modulate mitochondrial energy turnover due to substrate oxidation increase. Many of the changes in mitochondrial function follow brief exposure to low temperatures.

During the course of a study on preservation of small bowel transplants in rats, the hypothesis that histamine may play a role in graft damage has been investigated. Plasma and mucosal histamine levels have been measured after storage and reperfusion of Lewis rat small bowel transplants which have received an intravascular flush of saline or of one of the tissue preservation media, hypertonic citrate or University of Wisconsin solution. Plasma histamine concentration was unchanged from a control value of 23.2 +/- 2.6 ng/ml 15 min after reperfusion of grafts, whether fresh or stored for 24 h or for 48 h. Mucosal histamine levels in the grafts fell, however, from a control value of 371.0 +/- 22.9 ng/g tissue, first on storage then further after 15 min reperfusion. No differences were found in these parameters of histamine release between any of the preservation media. It is suggested that histamine may play a role in storage and reperfusion damage to small bowel transplants.

Background Oral contraceptives were introduced almost 50 years ago, and over 100 million women currently use them. Oral contraceptives can reduce the risk of ovarian cancer, but the eventual public-health effects of this reduction will depend on how long the protection lasts after use ceases. We aimed to assess these effects. Methods Individual data for 23 257 women with ovarian cancer (cases) and 87 303 without ovarian cancer (controls) from 45 epidemiological studies in 21 countries were checked and analysed centrally. The relative risk of ovarian cancer in relation to oral contraceptive use was estimated, stratifying by study, age, parity, and hysterectomy. Findings Overall 7308 (31%) cases and 32 717 (37%) controls had ever used oral contraceptives, for average durations among users of 4 . 4 and 5 . 0 years, respectively. The median year of cancer diagnosis was 1993, when cases were aged an average of 56 years. The longer that women had used oral contraceptives, the greater the reduction in ovarian cancer risk (p

Enteral nutrition can be associated with gastrointestinal side effects and fibre supplementation has been proposed as a means to normalize bowel function.To evaluate systematically the effects of fibre supplementation of enteral feeds in healthy volunteers and patients both in the hospital and community settings.Electronic and manual bibliographic searches were conducted. Controlled studies in adults or children, comparing fibre-supplemented vs. fibre-free formulae given as the sole source of nutrition for at least 3 days, were included.Fifty-one studies (including 43 randomized-controlled trials), enrolling 1762 subjects (1591 patients and 171 healthy volunteers) met the inclusion criteria. Fibre supplementation was generally well tolerated. In the hospital setting, the incidence of diarrhoea was reduced as a result of fibre administration (OR 0.68, 95% CI: 0.48-0.96; 13 randomized-controlled trials). Meta-regression showed a more pronounced effect when the baseline incidence of diarrhoea was high. In both patients and healthy subjects, fibre significantly reduced bowel frequency when baseline frequency was high and increased it when it was low, revealing a significant moderating effect of fibre.The review indicates that the fibre-supplemented enteral formulae have important physiological effects and clinical benefits. There is a need to use a consistent approach to undertake more studies on this issue in the community setting.

To evaluate placental morphology in pregnancies complicated by early- and late-onset pre-eclampsia (PET) with and without fetal growth restriction (FGR) using stereological techniques.A total of 69 pregnant women were studied. Twenty women had pregnancies complicated by PET, 17 by FGR and 16 by both PET and FUR; the remaining 16 were from gestational-age-matched controls. Each group was further classified into early onset (34 weeks) and late onsets (34 weeks) based on gestational ages.NPIMR at Northwick Park and St Marks Hospital.placentae from pregnant women.Formalin-fixed, wax-embedded sections stained with anti-CD34 antibodies and counterstained with haematoxylin.Volumes, surface areas, lengths, diameters and shape factors of the villous tissues and fetal vasculature in the intermediate and terminal villi of all the groups studied.Terminal villi volume and surface area were compromised in early-onset PET cases, late-onset PET had no impact on peripheral villi or vasculature features. The morphology of the vascular and villous subcomponents in the intermediate and terminal villi was significantly influenced by late-onset FGR, whereas early-onset FGR caused a reduction in placental weight. Length estimates were not influenced by PET, FGR or age of onset. Intermediate arteriole shape factor was significantly reduced in late-onset FGR.Isolated early-onset PET was associated with abnormal placental morphology, but placentas from late-onset PET were morphologically similar to placentas from gestational-age-matched controls, confirming the existence of two subsets of this condition and supporting the hypothesis that late-onset PET is a maternal disorder and not a placental disease.

Ontologies are becoming increasingly important for the efficient storage, retrieval and mining of biological data. The description of phenotypes using ontologies is a particularly complex problem. We outline a schema that can be used to describe phenotypes by combining orthologous axiomatic ontologies. We also describe tools for storing, browsing and searching such complex ontologies. Central to this approach is that assays (protocols for measuring phenotypic characters) describe what has been measured as well as how this was done, allowing assays to link individual organisms to ontologies describing phenotypes. We have evaluated this approach by automatically annotating data on 600 000 mutant mice phenotypes using the SHIRPA protocol. We believe this approach will enable the flexible, extensible and detailed description of phenotypes from any organism.

By combining ontologies from different sources the authors developed a novel approach to describing phenotypes of mutant mice in a standard, structured manner., The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sources. This produces a framework with greater flexibility, power and economy than previous approaches. We discuss some of the issues this approach raises.