An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

A First Clinical Trial on Botulinum Toxin-A for Chronic Muscle-Related Pain in Cerebral Palsy

Objective: To test if botulinum toxin-A (BoNT-A) is effective in reducing chronic muscle-related pain in adults with spastic cerebral palsy (CP), as compared to placebo.

Design: A single-center, double-blind, parallel, randomized placebo-controlled trial. The design included an interim analysis to allow for confirmatory analysis, as well as pilot study outcomes.

Setting: Tertiary university hospital.

Participants: Adults with spastic CP and chronic pain associated with spastic muscle(s).

Intervention: Treatment was one session of electromyographically guided intramuscular injections of either BoNT-A or placebo normosaline.

Main Study Outcomes: The primary outcome was the proportion who achieved a reduction of pain intensity of two or more steps on the Numerical Rating Scale 6 weeks after treatment.

Results: Fifty individuals were screened for eligibility, of whom 16 were included (10 female, 6 male, mean age = 32 years, SD = 13.3 years). The randomization yielded eight participants per treatment arm, and all completed the study as randomized. The study was stopped at the interim analysis due to a low probability, under a preset threshold, of a positive primary outcome. Four individuals were treatment responders in the BoNT-A group for the primary outcome compared to five responders in the placebo group (p = 1.000). Adverse events were mild to moderate. In exploratory analysis, the BoNT-A group had a trend of continuing reduction of pain at the last follow-up, after the primary endpoint.

Conclusions: This study did not find evidence that BoNT-A was superior to placebo at the desired effect size (number needed to treat of 2.5) at 6 weeks after treatment.

Trial registration:ClinicalTrials.gov: NCT02434549

Differences in resource use lead to coexistence of seed-transmitted microbial populations

Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of two phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed microbiome, to find seed microbial residents capable of outcompeting this pathogen. According to taxonomic and functional inference performed on metagenomics reads, no shift in structure and function of the seed microbiome was observed following Abra43 and Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional resources between Xcc8004 and the major bacterial populations of radish seeds. However, two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore limit its transmission. The strategy we used may serve as a foundation for the selection of seed indigenous bacterial strains that could limit seed transmission of pathogens.

Isolation and Whole-Genome Sequencing of Environmental Campylobacter

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter has a significant impact on human health. In the developed world, most campylobacteriosis cases are attributed to the consumption of undercooked, contaminated poultry; however, it has been shown that Campylobacter can be transmitted to humans through contaminated water and other types of food, including beef and milk. As such, high-resolution microbial source-tracking is essential for health department officials to determine the source(s) of Campylobacter outbreaks. For these reasons, this protocol provides the techniques needed for isolation of Campylobacter from agricultural and environmental sources, as well as human clinical specimens. Additionally, we describe a simple method for preparing high-quality genomic DNA that can be used for whole-genome sequencing and downstream bioinformatics analyses of Campylobacter genotypes. © 2018 by John Wiley & Sons, Inc.

Improvement in lipids after switch to boosted atazanavir or darunavir in children/adolescents with perinatally acquired HIV on older protease inhibitors: results from the Pediatric HIV/AIDS Cohort Study

OBJECTIVES

Dyslipidaemia is common in perinatally HIV-infected (PHIV) youth receiving protease inhibitors (PIs). Few studies have evaluated longitudinal lipid changes in PHIV youth after switch to newer PIs.

METHODS

We compared longitudinal changes in fasting lipids [total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and TC:HDL-C ratio] in PHIV youth enrolled in the Pediatric HIV/AIDS Cohort Study (PHACS) Adolescent Master Protocol (AMP) study who switched to atazanavir/ritonavir (ATV/r)- or darunavir/ritonavir (DRV/r)-based antiretroviral therapy (ART) from an older PI-based ART and those remaining on an older PI. Generalized estimating equation models were fitted to assess the association of a switch to ATV/r- or DRV/r-based ART with the rate of change in lipids, adjusted for potential confounders.

RESULTS

From 2007 to 2014, 47 PHIV children/adolescents switched to ATV/r or DRV/r, while 120 remained on an older PI [primarily lopinavir/r (72%) and nelfinavir (24%)]. Baseline age ranged from 7 to 21 years. After adjustment for age, Tanner stage, race/ethnicity, and HIV RNA level, a switch to ATV/r or DRV/r was associated with a more rapid annual rate of decline in the ratio of TC:HDL-C. (β = -0.12; P = 0.039) than remaining on an older PI. On average, TC declined by 4.57 mg/dL/year (P = 0.057) more in the switch group. A switch to ATV/r or DRV/r was not associated with the rate of HDL-C, LDL-C, or TG change.

CONCLUSIONS

A switch to ATV/r or DRV/r may result in more rapid reduction in TC and the TC:HDL-C ratio in PHIV youth, potentially impacting long-term cardiovascular disease risk.

Chemiomics: network reconstruction and kinetics of port wine aging

Network reconstruction (NR) has proven to be useful in the detection and visualization of relationships among the compounds present in a Port wine aging data set. This view of the data provides a considerable amount of information with which to understand the kinetic contexts of the molecules represented by peaks in each chromatogram. The aim of this study was to use NR together with the determination of kinetic parameters to extract more information about the mechanisms involved in Port wine aging. The volatile compounds present in samples of Port wines spanning 128 years in age were measured with the use of GC-MS. After chromatogram alignment, a peak matrix was created, and all peak vectors were compared to one another to determine their Pearson correlations over time. A correlation network was created and filtered on the basis of the resulting correlation values. Some nodes in the network were further studied in experiments on Port wines stored under different conditions of oxygen and temperature in order to determine their kinetic parameters. The resulting network can be divided into three main branches. The first branch is related to compounds that do not directly correlate to age, the second branch contains compounds affected by temperature, and the third branch contains compounds associated with oxygen. Compounds clustered in the same branch of the network have similar expression patterns over time as well as the same kinetic order, thus are likely to be dependent on the same technological parameters. Network construction and visualization provides more information with which to understand the probable kinetic contexts of the molecules represented by peaks in each chromatogram. The approach described here is a powerful tool for the study of mechanisms and kinetics in complex systems and should aid in the understanding and monitoring of wine quality.

Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach

BACKGROUND

Induced resistance (IR) can be part of a sustainable plant protection strategy against important plant diseases. β-aminobutyric acid (BABA) can induce resistance in a wide range of plants against several types of pathogens, including potato infected with Phytophthora infestans. However, the molecular mechanisms behind this are unclear and seem to be dependent on the system studied. To elucidate the defence responses activated by BABA in potato, a genome-wide transcript microarray analysis in combination with label-free quantitative proteomics analysis of the apoplast secretome were performed two days after treatment of the leaf canopy with BABA at two concentrations, 1 and 10 mM.

RESULTS

Over 5000 transcripts were differentially expressed and over 90 secretome proteins changed in abundance indicating a massive activation of defence mechanisms with 10 mM BABA, the concentration effective against late blight disease. To aid analysis, we present a more comprehensive functional annotation of the microarray probes and gene models by retrieving information from orthologous gene families across 26 sequenced plant genomes. The new annotation provided GO terms to 8616 previously un-annotated probes.

CONCLUSIONS

BABA at 10 mM affected several processes related to plant hormones and amino acid metabolism. A major accumulation of PR proteins was also evident, and in the mevalonate pathway, genes involved in sterol biosynthesis were down-regulated, whereas several enzymes involved in the sesquiterpene phytoalexin biosynthesis were up-regulated. Interestingly, abscisic acid (ABA) responsive genes were not as clearly regulated by BABA in potato as previously reported in Arabidopsis. Together these findings provide candidates and markers for improved resistance in potato, one of the most important crops in the world.

Field-omics-understanding large-scale molecular data from field crops

The recent advances in gene expression analysis as well as protein and metabolite quantification enable genome-scale capturing of complex biological processes at the molecular level in crop field trials. This opens up new possibilities for understanding the molecular and environmental complexity of field-based systems and thus shedding light on the black box between genotype and environment, which in agriculture always is influenced by a multi-stress environment and includes management interventions. Nevertheless, combining different types of data obtained from the field and making biological sense out of large datasets remain challenging. Here we highlight the need to create a cross-disciplinary platform for innovative experimental design, sampling and subsequent analysis of large-scale molecular data obtained in field trials. For these reasons we put forward the term field-omics: "Field-omics strives to couple information from genomes, transcriptomes, proteomes, metabolomes and metagenomes to the long-established practice in crop science of conducting field trials as well as to adapt current strategies for recording and analysing field data to facilitate integration with '-omics' data."

Untangling the chemistry of port wine aging with the use of GC-FID, multivariate statistics, and network reconstruction

Chromatography separates the different components of complex mixtures and generates a fingerprint representing the chemical composition of the sample. The resulting data structure depends on the characteristics of the detector used, univariate for devices such as a flame ionization detector (FID) or multivariate for mass spectroscopy (MS). This study addresses the potential use of a univariate signal for a nontargeted approach to (i) classify samples according to a given process or perturbation, (ii) evaluate the feasibility of developing a screening procedure to select candidates related to the process, and (iii) provide insight into the chemical mechanisms that are affected by the perturbation. To achieve this, it was necessary to use and develop methods for data preprocessing and visualization tools to assist an analytical chemist to view and interpret complex multidimensional data sets. Dichloromethane Port wine extracts were collected using GC-FID; the chromatograms were then aligned with correlation optimized warping (COW) and subsequently analyzed with multivariate statistics (MVA) by principal component analysis (PCA) and partial least-squares regression (PLS-R). Furthermore, wavelets were used for peak calling and alignment refinement, and the resulting matrix was used to perform kinetic network reconstruction via correlation networks and maximum spanning trees. Network-target correlation projections were used to screen for potential chromatographic regions/peaks related to aging mechanisms. Results from PLS between aligned chromatograms and target molecules showed high X to Y correlations of 0.91, 092, and 0.89 with 5-hydroxymethylfurfural (HMF) (Maillard), acetaldehyde (oxidation), and 4,5-dimethyl-(5H)-3-hydroxy-2-furanone, respectively. The context of the correlation (and therefore likely kinetic) relationships among compounds detected by GC-FID and the relationships between target compounds within different regions of the network can be clearly seen.

Genetic analysis of the metabolic pathways responsible for aroma metabolite production by Saccharomyces cerevisiae

During alcoholic fermentation, higher alcohols, esters, and acids are formed from amino acids via the Ehrlich pathway by yeast, but many of the genes encoding the enzymes have not yet been identified. When the BAT1/2 genes, encoding transaminases that deaminate amino acids in the first step of the Ehrlich pathway are deleted, higher metabolite formation is significantly decreased. Screening yeast strains with deletions of genes encoding decarboxylases, dehydrogenases, and reductases revealed nine genes whose absence had the most significant impact on higher alcohol production. The seven most promising genes (AAD6, BAT2, HOM2, PAD1, PRO2, SPE1, and THI3) were further investigated by constructing double- and triple-deletion mutants. All double-deletion strains showed a greater decrease in isobutanol, isoamyl alcohol, isobutyric, and isovaleric acid production than the corresponding single deletion strains with the double-deletion strains in combination with ∆bat2 and the ∆hom2-∆aad6 strain revealing the greatest impact. BAT2 is the dominant gene in these deletion strains and this suggests the initial transaminase step of the Ehrlich pathway is rate-limiting. The triple-deletion strains in combination with BAT2 (∆bat2-∆thi3-∆aad6 and ∆bat2-∆thi3-∆hom2) had the greatest impact on the end metabolite production with the exception of isoamyl alcohol and isovaleric acid. The strain deleted for two dehydrogenases and a reductase (∆hom2-∆pro2-∆aad6) had a greater effect on the levels of these two compounds. This study contributes to the elucidation of the Ehrlich pathway and its significance for aroma production by fermenting yeast cells.

GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network

BACKGROUND

Gene Set Analysis (GSA) has proven to be a useful approach to microarray analysis. However, most of the method development for GSA has focused on the statistical tests to be used rather than on the generation of sets that will be tested. Existing methods of set generation are often overly simplistic. The creation of sets from individual pathways (in isolation) is a poor reflection of the complexity of the underlying metabolic network. We have developed a novel approach to set generation via the use of Principal Component Analysis of the Laplacian matrix of a metabolic network. We have analysed a relatively simple data set to show the difference in results between our method and the current state-of-the-art pathway-based sets.

RESULTS

The sets generated with this method are semi-exhaustive and capture much of the topological complexity of the metabolic network. The semi-exhaustive nature of this method has also allowed us to design a hypergeometric enrichment test to determine which genes are likely responsible for set significance. We show that our method finds significant aspects of biology that would be missed (i.e. false negatives) and addresses the false positive rates found with the use of simple pathway-based sets.

CONCLUSIONS

The set generation step for GSA is often neglected but is a crucial part of the analysis as it defines the full context for the analysis. As such, set generation methods should be robust and yield as complete a representation of the extant biological knowledge as possible. The method reported here achieves this goal and is demonstrably superior to previous set analysis methods.

The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L

BACKGROUND

Carotenoids are a heterogeneous group of plant isoprenoids primarily involved in photosynthesis. In plants the cleavage of carotenoids leads to the formation of the phytohormones abscisic acid and strigolactone, and C13-norisoprenoids involved in the characteristic flavour and aroma compounds in flowers and fruits and are of specific importance in the varietal character of grapes and wine. This work extends the previous reports of carotenoid gene expression and photosynthetic pigment analysis by providing an up-to-date pathway analysis and an important framework for the analysis of carotenoid metabolic pathways in grapevine.

RESULTS

Comparative genomics was used to identify 42 genes putatively involved in carotenoid biosynthesis/catabolism in grapevine. The genes are distributed on 16 of the 19 chromosomes and have been localised to the physical map of the heterozygous ENTAV115 grapevine sequence. Nine of the genes occur as single copies whereas the rest of the carotenoid metabolic genes have more than one paralogue. The cDNA copies of eleven corresponding genes from Vitis vinifera L. cv. Pinotage were characterised, and four where shown to be functional. Microarrays provided expression profiles of 39 accessions in the metabolic pathway during three berry developmental stages in Sauvignon blanc, whereas an optimised HPLC analysis provided the concentrations of individual carotenoids. This provides evidence of the functioning of the lutein epoxide cycle and the respective genes in grapevine. Similarly, orthologues of genes leading to the formation of strigolactone involved in shoot branching inhibition were identified: CCD7, CCD8 and MAX1. Moreover, the isoforms typically have different expression patterns, confirming the complex regulation of the pathway. Of particular interest is the expression pattern of the three VvNCEDs: Our results support previous findings that VvNCED3 is likely the isoform linked to ABA content in berries.

CONCLUSIONS

The carotenoid metabolic pathway is well characterised, and the genes and enzymes have been studied in a number of plants. The study of the 42 carotenoid pathway genes of grapevine showed that they share a high degree of similarity with other eudicots. Expression and pigment profiling of developing berries provided insights into the most complete grapevine carotenoid pathway representation. This study represents an important reference study for further characterisation of carotenoid biosynthesis and catabolism in grapevine.

Constitutive expression of a grapevine polygalacturonase-inhibiting protein affects gene expression and cell wall properties in uninfected tobacco

Background

Polygalacturonase-inhibiting proteins (PGIPs) directly limit the effective ingress of fungal pathogens by inhibiting cell wall-degrading endopolygalacturonases (ePGs). Transgenic tobacco plants over-expressing grapevine (Vitis vinifera) Vvpgip1 have previously been shown to be resistant to Botrytis infection. In this study we characterized two of these PGIP over-expressing lines with known resistance phenotypes by gene expression and hormone profiling in the absence of pathogen infection.

Results

Global gene expression was performed by a cross-species microarray approach using a potato cDNA microarray. The degree of potential cross-hybridization between probes was modeled by a novel computational workflow designed in-house. Probe annotations were updated by predicting probe-to-transcript hybridizations and combining information derived from other plant species. Comparing uninfected Vvpgip1-overexpressing lines to wild-type (WT), 318 probes showed significant change in expression. Functional groups of genes involved in metabolism and associated to the cell wall were identified and consequent cell wall analysis revealed increased lignin-levels in the transgenic lines, but no major differences in cell wall-derived polysaccharides. GO enrichment analysis also identified genes responsive to auxin, which was supported by elevated indole-acetic acid (IAA) levels in the transgenic lines. Finally, a down-regulation of xyloglucan endotransglycosylase/hydrolases (XTHs), which are important in cell wall remodeling, was linked to a decrease in total XTH activity.

Conclusions

This evaluation of PGIP over-expressing plants performed under pathogen-free conditions to exclude the classical PGIP-ePG inhibition interaction indicates additional roles for PGIPs beyond the inhibition of ePGs.

Thermal and Visual Observation of Water and Acetone Oscillating Heat Pipes

A visual and thermal experimental investigation of four oscillating heat pipes (OHPs) was conducted to observe fluid flow of liquid plugs and vapor bubbles in the OHP and its effect on the temperature distribution and heat transfer performance in an OHP. These four OHPs consist of an open loop water OHP, an open loop acetone OHP, a closed loop water OHP, and a closed loop acetone OHP. These copper OHPs were constructed identically with all six turns in the same plane. They were constructed out of 1.65 mm inner diameter copper tubing and copper heat spreading plates in the evaporator and condenser regions. The heat pipes were charged at a filling ratio of about 50%. The results show that the acetone OHP at low power performs better than the water OHP, while at high power the water OHP exceeds the acetone OHP. The experimental results show that both the acetone and water closed loop OHPs had reduced movement in the connecting turn between the two sides. However, in the water closed loop OHP, this prevented circulation altogether. Comparing the water closed loop OHP to the water open loop OHP, their flow patterns were similar. Therefore, improving the flow in this turn should increase the closed loop OHP's performance.

A systematic review of primary healthcare provider education and training using the Chronic Care Model for childhood obesity

The purpose of this systematic review was to examine 15 studies which evaluated interventions aimed at improving primary care providers' identification, assessment, prevention and/or management of obesity in children and adolescents. Interventions were evaluated in terms of length, components addressing nutrition, physical activity and behavioural counselling consistent with expert recommendations, and inclusion of components of the Chronic Care Model. Overall, training interventions were delivered face to face or in a combination of lecture, assigned readings, preceptorship with experienced providers, and critiqued evaluations of interactions of the provider with the patient and family. Many studies incorporated training of providers as an initial step prior to delivering an obesity intervention for children and adolescents measuring weight loss and behaviour change as outcomes. Each study was evaluated for components of the Chronic Care Model. The interventions most frequently utilized the elements of self-management support (69%), decision support (100%), delivery system support (77%) and clinical information systems (23%). Although science in this area is emerging, results suggest that intervention programmes that included more components of the Chronic Care Model were more effective.

Proteomic analysis of grape berry cell cultures reveals that developmentally regulated ripening related processes can be studied using cultured cells

BACKGROUND

This work describes a proteomics profiling method, optimized and applied to berry cell suspensions to evaluate organ-specific cultures as a platform to study grape berry ripening. Variations in berry ripening within a cluster(s) on a vine and in a vineyard are a major impediment towards complete understanding of the functional processes that control ripening, specifically when a characterized and homogenous sample is required. Berry cell suspensions could overcome some of these problems, but their suitability as a model system for berry development and ripening needs to be established first.

METHODOLOGY/PRINCIPAL FINDINGS

In this study we report on the proteomic evaluation of the cytosolic proteins obtained from synchronized cell suspension cultures that were established from callus lines originating from green, véraison and ripe Vitis vinifera berry explants. The proteins were separated using liquid phase IEF in a Microrotofor cell and SDS PAGE. This method proved superior to gel-based 2DE. Principal component analysis confirmed that biological and technical repeats grouped tightly and importantly, showed that the proteomes of berry cultures originating from the different growth/ripening stages were distinct. A total of twenty six common bands were selected after band matching between different growth stages and twenty two of these bands were positively identified. Thirty two % of the identified proteins are currently annotated as hypothetical. The differential expression profile of the identified proteins, when compared with published literature on grape berry ripening, suggested common trends in terms of relative abundance in the different developmental stages between real berries and cell suspensions.

CONCLUSIONS

The advantages of having suspension cultures that accurately mimic specific developmental stages are profound and could significantly contribute to the study of the intricate regulatory and signaling networks responsible for berry development and ripening.

Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses

Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs. This study employed amplified fragment length polymorphism (AFLP) to investigate the genetic variation in local banana cultivars from the southern region of Oman. Using 12 primer combinations, a total of 1094 bands were scored, of which 1012 were polymorphic. Eighty-two unique markers were identified, which revealed the distinct separation of the seven cultivars. The results obtained show that AFLP can be used to differentiate the banana cultivars. Further classification by phylogenetic, hierarchical clustering and principal component analyses showed significant differences between the clusters found with molecular markers and those clusters created by previous studies using morphological analysis. Based on the analytical results, a consensus dendrogram of the banana cultivars is presented.

Heat Transport Capability and Fluid Flow Neutron Radiography of Three-Dimensional Oscillating Heat Pipes

An experimental investigation into the parameters affecting heat transport in two three-dimensional oscillating heat pipes (OHPs) was implemented. A three-dimensional OHP is one in which the center axis of the circular channels containing the internal working fluid do not lie in the same plane. This novel design allows for more turns in a more compact size. The OHPs in the current investigation is made of copper tubings (3.175 mm outside diameter, 1.65 mm inside diameter) wrapped in a three-dimensional fashion around two copper spreaders that act as the evaporator and condenser. The two OHPs have 10 and 20 turns in both the evaporator and condenser. The 20-turn OHP was filled to 50% of the total volume with a high performance liquid chromatography grade water. Transient and steady state temperature data were recorded at different locations for various parameters. Parameters such as heat input, operating temperature, and filling ratio were varied to determine its effect on the overall heat transport. Neutron radiography was simultaneously implemented to create images of the internal working fluid flow at a rate of 30 frames per second. Results show the average temperature drop from the evaporator to condenser decreases at higher heat inputs due to an increase in temperature throughout the condenser region due to greater oscillations. These large oscillations were visually observed using neutron radiography. As the operating temperature is increased, the thermal resistance is reduced. A decrease in filling ratio tends to create more steady fluid motion; however, the heat transfer performance is reduced.

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

Background

Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.

Results

OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions.

Conclusion

OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at

Presence revisited: imagination, competence, and activity in text-based virtual worlds

Presence is the sense of being caught up in the representations of virtual worlds. Drawing on social and literary theories and on ethnographic fieldwork, this paper examines the ways in which imagination, competence, and activity promote or undermine a sense of presence in online text-based environments known as MOOs. These factors vary for newbies, socials, and techies, categories that reflect differences in length of experience in participating in these worlds, in comfort and/or competence in the use of commands for navigation and communication, and in the interests and/or degree of participation in socializing or programming.

Small-conductance calcium-activated potassium currents in mouse hyperexcitable denervated skeletal muscle

1. Hyperexcitability in denervated skeletal muscle is associated with the expression of SK3, a small-conductance Ca2+-activated K+ channel (SK channel). SK currents were examined in dissociated fibres from flexor digitorum brevis (FDB) muscle using the whole-cell patch clamp configuration. 2. Depolarization activated a K+-selective, apamin-sensitive and iberiotoxin-insensitive current, detected as a tail current upon repolarization, in fibres from denervated but not innervated muscle. Dialysis of the fibres with 20 mM EGTA in the patch pipette solution eliminated the tail current, consistent with this current reflecting Ca2+-activated SK channels expressed only in denervated muscle. 3. Activation of SK tail currents depended on the duration of the depolarizing pulse, consistent with a rise in intracellular Ca2+ due to release from the sarcoplasmic reticulum (SR) and influx through voltage-gated Ca2+ channels. 4. The envelope of SK tail currents was diminished by 10 microM ryanodine for all pulse durations, whereas 2 mM cobalt reduced the SK tail current for pulses greater than 80 ms, demonstrating that Ca2+ release from the SR during short pulses primarily activated SK channels. 5. In current clamp mode with the resting membrane potential set at -70 mV, denervation decreased the action potential threshold by approximately 8 mV. Application of apamin increased the action potential threshold in denervated fibres to that measured in innervated fibres, suggesting that SK channel activity modulates the apparent action potential threshold. 6. These results are consistent with a model in which SK channel activity in the T-tubules of denervated skeletal muscle causes a local increase in K+ concentration that results in hyperexcitability.

Effective strategies for managing pharmacy benefits

Prescription drug costs are among the fastest-growing healthcare costs. Effective plan design and benefit management strategies can help pharmacy benefit plans manage costs while maintaining quality and customer satisfaction. These strategies include using formulary management, intervention techniques, and cost sharing to encourage the use of generic drugs; employing a mail-service pharmacy benefit for maintenance medications; and implementing concurrent and retrospective review programs to ensure eligibility and plan compliance, identify practice patterns, and encourage appropriate drug selection.

Patient-reported nonadherence to HAART is related to protease inhibitor levels

OBJECTIVE

To compare self-reported nonadherence with antiretroviral therapy (ART) with predose plasma levels of protease inhibitor (PI).

DESIGN

A cross-sectional study of consecutive patients from a university-based HIV clinic in Rome, Italy, was conducted. One hundred and forty HIV-infected patients were prescribed regimens containing ritonavir or indinavir. A patient questionnaire assessing knowledge of treatment regimen, adherence behavior, reasons for taking and missing therapy, factors influencing adherence, and health behaviors was administered. A predose PI plasma level was measured concurrently.

RESULTS

By patient report, 12% missed at least one dose "yesterday," and 24% missed doses in the last 3 days; 14% had a predose plasma concentration below the assay limit of quantitation (2 ritonavir and 18 indinavir samples). Confusion, poor psychological well-being, long office wait, running out of drugs between visits, having relatives to remind the patient to take medication, children, and alteration of sense of taste were related to unquantifiable predose levels of PI. In multivariable analysis, reported nonadherence (odds ratio [OR], 15.8; 95% confidence interval [CI], 4.0-63.3) and confusion (OR, 9.9; 95% CI, 1.4-69.6) were related to unquantifiable predose levels of PI.

CONCLUSION

Self-report of missing a dose of antiretroviral medication "yesterday" was related to an unmeasurable plasma PI level.

Carbon dioxide and ER:YAG laser resurfacing. Results

Laser resurfacing is exciting "futuristic" surgery. The CO2 laser resurfaces using different parameters from the Er:YAG laser. When the surgeon understands these parameters, each laser can be used as a powerful tool for specific clinical applications. The Er:YAG laser was initially thought to be for the patient who has minimal skin laxity, but who desires skin resurfacing and needs a speedy return to social life. The CO2 laser has typically been thought to work best for skin laxity as well as rhytids, at the price of a longer recovery period. As the hardware and techniques continue to evolve, the differences between the clinical scope addressed by each laser diminishes. Both lasers deserve a place in the plastic surgeon's armamentarium. This new combination CO2/Er:YAG technique is intriguing and deserves further in-depth investigation. Laser resurfacing is not a cureall, but, when applied appropriately, it is an excellent tool that the plastic surgeon can use for skin rejuvenation.

Testicular Pathologic Changes and the Pituitary-Testicular Axis During Human Immunodeficiency Virus Infection

OBJECTIVE

To chronicle pituitary-testicular axis dysfunction and its clinicopathologic features in homosexual men.

METHODS

Between 1984 and 1992, 84 homosexual men underwent longitudinal follow-up for 4 years. At entry into the study, 28 were seronegative and 56 were seropositive for human immunodeficiency virus (HIV). Although 40 subjects remained asymptomatic (nonprogressors), 16 had progression to acquired immunodeficiency syndrome (AIDS). Of those 16 patients with progression, 8 had AIDS within 2 years (early progressors) and 8 demonstrated AIDS within 4 years after enrollment (late progressors), and all died. The testes of five patients were examined at autopsy. The control group had similar follow-up. Luteinizing hormone (LH), follicle-stimulating hormone (FSH), testosterone, and bioavailable testosterone (bio-T) were measured in stored sera collected at 2-year intervals. The last hormonal measurement was between 3 and 24 months before autopsy. Comparison was made between autopsied and nonautopsied patients with AIDS as well as between HIV nonprogressors and control seronegative men. The correlation between pathologic findings and hormonal status was examined by regression analysis.

RESULTS

At baseline, testosterone, bio-T, LH, and FSH were not significantly different among all patients and subjects. During the study period, testosterone, bio-T, and serum gonadotropin levels remained unchanged in the seronegative homosexual men. In nonprogressors, serum FSH and LH concentrations remained unchanged, whereas testosterone and bio-T levels decreased significantly during this 4-year period. After progression to AIDS (in both groups of progressors), the serum FSH and LH levels were higher and the serum testosterone and bio-T were lower in comparison with values in the seronegative men. In late progressors to AIDS, FSH and LH increased, whereas serum testosterone and bio-T decreased significantly from baseline. All five patients with AIDS on whom autopsy was done had boundary wall thickening of the seminiferous tubules and decreased spermatogenesis. No significant differences were found in serum testosterone, bio-T, and LH between those in whom autopsy was or was not done; however, FSH was significantly higher in the autopsied cases. The serum testosterone and bio-T levels were negatively correlated with the interstitial inflammation. A significant correlation was also observed between change of bio-T and weight loss.

CONCLUSION

We conclude that dysfunction of the pituitary-gonadal axis is common in HIV-infected men. All patients in whom autopsy was done because of AIDS-related diseases had been hypogonadal 3 to 24 months before death. Decreased spermatogenesis, subacute interstitial inflammation, or both were seen at autopsy of patients with AIDS. Pathologic damage to the testes during AIDS was associated with decreased testosterone and bio-T as well as increased serum gonadotropin levels. In a substantial proportion of men with progression to AIDS, compensated hypogonadism (normal serum testosterone and increased serum LH levels) preceded the development of low serum testosterone level.

Camalexin accumulation in Arabis lyrata

Inoculation of leaves of Arabis lyrata with either a bacterial pathogen Pseudomonas syringae pv. maculicola strain ES4326 or Cochliobolus carbonum, a fungal nonpathogen of A. lyrata, resulted in the accumulation of a compound with similar chromatographic and fluorescent properties to that of camalexin (I), a phytoalexin produced by Arabidopsis thaliana. A. lyrata is closely related to A. thaliana. High resolution electron impact mass spectroscopic and proton NMR analysis confirmed that the compound produced by A. lyrata is camalexin.

Reference ranges for serum prostate-specific antigen in black and white men without cancer

OBJECTIVES

To determine the age- and race-specific prostate-specific antigen (PSA) distributions in healthy men in central South Carolina and to compare these to data from other studies.

METHODS

Two thousand ninety-two black men aged 40 to 69 years and white men aged 50 to 69 years from the general population in 11 counties of central South Carolina participated in a prostate cancer educational program. Seventy-two percent of the participants were black-about double the proportion in the general population-and 63% of the men (1319 of 2092) subsequently obtained a PSA determination from their own physician. The distribution of serum PSA was compared with distributions from the Olmsted County study and from the Walter Reed Army Medical Center/Center for Prostate Disease Research study.

RESULTS

Older men without cancer had higher PSA levels. Regression analyses yielded an associated increase of about 3.3% per year. Reference ranges for normal PSA in men without cancer (based on their sample 95th percentiles) were zero to 1.9, 3.8, and 5.7 ng/mL in black men aged 40 to 49, 50 to 59, and 60 to 69 years, and zero to 2.7 and 4.9 mg/mL in white men aged 50 to 59 and 60 to 69 years, respectively.

CONCLUSIONS

Reference ranges for normal serum PSA levels should take into account the population from which they are derived and to which they will be applied. Reference ranges that are useful in the general population can differ from those that are appropriate in a hospital setting. For the general population in central South Carolina, reference ranges for serum PSA levels are lower than previously published reference ranges, particularly among black men.

Duplication of ATR inhibits MyoD, induces aneuploidy and eliminates radiation-induced G1 arrest

Chromosome 3q alterations occur frequently in many types of tumours. In a genetic screen for loci present in rhabdomyosarcomas, we identified an isochromosome 3q [i(3q)], which inhibits muscle differentiation when transferred into myoblasts. The i(3q) inhibits MyoD function, resulting in a non-differentiating phenotype. Furthermore, the i(3q) induces a 'cut' phenotype, abnormal centrosome amplification, aneuploidy and loss of G1 arrest following gamma-irradiation. Testing candidate genes within this region reveals that forced expression of ataxia-telangiectasia and rad3-related (ATR) results in a phenocopy of the i(3q). Thus, genetic alteration of ATR leads to loss of differentiation as well as cell-cycle abnormalities.

Evidence for reliability, validity and usefulness of the Medical Outcomes Study HIV Health Survey (MOS-HIV)

The Medical Outcomes Study HIV Health Survey (MOS-HIV) is a brief, comprehensive measure of health-related quality of life (HRQoL) used extensively in human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS). The 35-item questionnaire includes ten dimensions (health perceptions, pain, physical, role, social and cognitive functioning, mental health, energy, health distress and quality of life (QoL) and takes approximately 5 minutes to complete. Subscales are scored on a 0-100 scale (a higher score indicates better health) and physical and mental health summary scores can be generated. The MOS-HIV has been shown to be internally consistent, correlate with concurrent measures of health, discriminate between distinct groups, predict future outcomes and be responsive to changes over time. Limited experience suggests acceptable reliability and validity in women, injecting drug users and African-American and lower socioeconomic status patients. The MOS-HIV is available in 14 languages and has been included as a secondary outcome measure in numerous clinical trials for all stages of disease. In several studies it has detected significant differences between treatments; in some cases concordant with conventional endpoints and, in others, discordant. The interpretation of scores is facilitated by an explanation in terms meaningful to the intended audience. Research is needed to compare the MOS-HIV to other strategies for HRQoL assessment in early HIV disease.

Comparison of commonly used clinical indicators of hypovolaemia with gastrointestinal tonometry

OBJECTIVE

The gastrointestinal tonometer, which allows measurement of gastrointestinal mucosal CO2 and subsequent derivation of gut intramucosal pH (pHi), has been demonstrated to be a sensitive predictor of outcome following major surgery. Current theory suggests that the origin of the low pH may be hypovolaemia. This study was designed to compare the temporal sequence of changes in tonometric readings with invasive blood pressure, stroke volume, heart rate, lactate and arterial blood gas measurements during progressive haemorrhage.

DESIGN

Observational healthy volunteer study.

SETTING

Intensive care unit at University College London Hospitals.

SUBJECTS

Six healthy, medically qualified volunteers.

INTERVENTIONS

After obtaining baseline measurements, the subjects were progressively bled 25% (range = 21-31%) of their blood volume over a period of 1 h in two approximately equal aliquots. Equilibration was allowed for 30 min following the bleed, after which further measurements were made and the blood was then retransfused over 30 min.

MEASUREMENTS AND MAIN RESULTS

There was no consistent change in any of the haemodynamic variables other than gastric intramucosal CO2:arterial CO2 gap (PiCO2-PaCO2) after removal of the first aliquot of blood, although five of the six subjects also demonstrated a fall in pHi. After removal of the second aliquot of blood, PiCO2-PaCO2 gap and pHi continued to indicate a worsening gastric intramucosal acidosis; stroke volume, as measured by suprasternal Doppler, demonstrated a marked fall, while all other variables measured had not altered consistently or to such a degree as to elicit a clinical response or cause suspicion of a hypovolaemic state. On retransfusion, all variables returned towards baseline.

CONCLUSIONS

This study demonstrates the value of tonometry as an early monitor of hypovolaemia and highlights the shortcomings of other more commonly measured clinical variables.

Cardiorespiratory and tissue oxygen dose response to rat endotoxemia

The dose response to endotoxin (Escherichia coli serotype 127:B8) was assessed in a spontaneously breathing, halothane-anesthetized, Sprague-Dawley rat model monitoring blood pressure, aortic and renal blood flows, blood gases, and bladder epithelial PO2, a marker of organ perfusion. The animals received either saline or endotoxin at doses of 1, 10 and 100 mg/kg body wt. Blood pressure changed significantly in all three endotoxin groups, though only the 100 mg/kg group showed significant changes in arterial PCO2, arterial PO2, and body temperature compared with controls. Whereas aortic and renal blood flow rose significantly in the two lower-dose groups, an approximate one-third fall occurred in the 100 mg/kg group (P < 0.001). Notwithstanding these macrocirculatory hemodynamic changes, both bladder epithelial PO2 and arterial base deficit rose significantly in all groups, though only the base deficit showed a progressive dose response. This model illustrates that responses to endotoxin are dose dependent but with changing patterns for different variables. The consistent finding of an elevated tissue PO2 in endotoxemia, regardless of dose, is suggestive of defective cellular oxygen metabolism.