Effects Of Experimental Treatments Research Articles

Advancing Synthetic Ecology: A Database System to Facilitate Complex Ecological Meta‐Analyses

Advancing Synthetic Ecology: A Database System to Facilitate Complex Ecological Meta-Analyses

A covariate‐adjustment regression model approach to noninferiority margin definition

To maintain the interpretability of the effect of experimental treatment (EXP) obtained from a noninferiority trial, current statistical approaches often require the constancy assumption. This assumption typically requires that the control treatment effect in the population of the active control trial is the same as its effect presented in the population of the historical trial. To prevent constancy assumption violation, clinical trial sponsors were recommended to make sure that the design of the active control trial is as close to the design of the historical trial as possible. However, these rigorous requirements are rarely fulfilled in practice. The inevitable discrepancies between the historical trial and the active control trial have led to debates on many controversial issues. Without support from a well-developed quantitative method to determine the impact of the discrepancies on the constancy assumption violation, a correct judgment seems difficult. In this paper, we present a covariate-adjustment generalized linear regression model approach to achieve two goals: (1) to quantify the impact of population difference between the historical trial and the active control trial on the degree of constancy assumption violation and (2) to redefine the active control treatment effect in the active control trial population if the quantification suggests an unacceptable violation. Through achieving goal (1), we examine whether or not a population difference leads to an unacceptable violation. Through achieving goal (2), we redefine the noninferiority margin if the violation is unacceptable. This approach allows us to correctly determine the effect of EXP in the noninferiority trial population when constancy assumption is violated due to the population difference. We illustrate the covariate-adjustment approach through a case study.

Effects of Socioeconomic and Racial Residential Segregation on Preterm Birth: A Cautionary Tale of Structural Confounding

Confounding associated with social stratification or other selection processes has been called structural confounding. In the presence of structural confounding, certain covariate strata will contain only subjects who could never be exposed, a violation of the positivity or experimental treatment effect assumption. Thus, structural confounding can prohibit the exchangeability necessary for meaningful causal contrasts across levels of exposure. The authors explored the presence and magnitude of structural confounding by estimating the independent effects of neighborhood deprivation and neighborhood racial composition (segregation) on rates of preterm birth in Wake and Durham counties, North Carolina (1999-2001). Tabular analyses and random-intercept fixed-slope multilevel logistic models portrayed different structural realities in these counties. The multilevel modeling results suggested some nonsignificant effect of residence in tracts with high levels of socioeconomic deprivation or racial residential segregation on adjusted odds of preterm birth for white and black women living in these counties, and the confidence limit ratios indicated fairly consistent levels of precision around the estimates. The results of the tabular analysis, however, suggested that many of these regression modeling findings were off-support and based on no actual data. The implications for statistical and public health inference, in the presence of no data, are considered.

Students as Experimental Participants: A Defense of the 'Narrow Data Base'

We investigate the extent to which using students as experimental participants creates problems for causal inference. First, we discuss the impact of student subjects on a study’s internal and external validity. In contrast to common claims, we argue that student subjects do not intrinsically pose a problem for a study’s external validity. Second, we use simulations to identify situations when student subjects are likely to constrain experimental inferences. We show that such situations are relatively limited; any convenience sample poses a problem only when the size of an experimental treatment effect depends upon a characteristic on which the convenience sample has virtually no variance. Third, we briefly survey empirical evidence that provides guidance on when researchers should be particularly attuned to taking steps to ensure appropriate generalizability from student subjects. We conclude with a discussion of the practical implications of our findings. In short, we argue that student subjects are not an inherent problem to experimental research; moreover, the burden of proof - of student subjects being a problem - should lie with critics rather than experimenters.

Who's assessing tobacco use in cancer clinical trials?

Clinical trials that do not collect data on tobacco use/exposure may not adequately assess the efficacy and effectiveness of experimental treatments. A cross-sectional study of interventional trials cited on ClinicalTrials.gov was undertaken that inquired of Local Project Directors from Connecticut guiding studies of breast, prostate, or colorectal cancer chemotherapy (N = 68) whether their protocols measured tobacco use by trial participants. Information pertaining to 46 trials (68%) is reported here. All but 1 were multicentered trials enrolling patients around the country. Only 3 trials (7%) reported routine collection of tobacco use information at baseline and no trial reported monitoring tobacco use during treatment follow-up. None of the 3 trials collecting tobacco data reported using exposure information in analysis of treatment effects. Survey respondents suggested that uncertainty about the relevance of tobacco exposure to therapeutic efficacy, ambivalence about how to incorporate such data into analyses, insufficient resources for collecting such information, and uncertainty about the validity of assessment methods might be reasons why tobacco use is not routinely assessed. Additional studies that address a fuller range of cancers, therapies, disease states, and clinical environments are needed to fully define the extent of this data lapse. Providing clinicians and trialists with appropriate tools for tobacco use assessment and encouraging them to collect such information about patients during treatment and follow-up may offer a simple cost-effective way to improve the quality and consequences of cancer care for every patient.

Spatial heterogeneity confounded ozone-exposure experiment in semi-natural grassland

Interpretation of observations from manipulative experiments is often complicated by a multitude of uncontrolled processes operating at various spatial and temporal scales. As such processes may differ among experimental plots there is a risk that effects of experimental treatments are confounded. Here we report on a free-air ozone-exposure experiment in permanent semi-natural grassland that suggested strong ozone effects on community productivity after 5 years. We tested ozone effects and investigated the potential of confounding due to changes in nutrient management. Repeated-measure ANOVA revealed mainly negative temporal trends for frequency of abundant productive plant species. Constrained ordination additionally showed converging trajectories of species compositions for ozone and control treatments with time. Yields sampled prior to the start of the experiment and soil nitrogen concentrations revealed that spatial heterogeneity in the soil nutrient status was not accounted for by the random allocation of treatments to plots with a bias towards less productive patches in the elevated-ozone plots. Re-analysis of yield data using repeated-measure ANOVA with a covariable to account for productivity prior to the start of fumigation revealed effects on the temporal changes in total yield and yield of legumes that cannot be separated between ozone and pre-treatment nutrient status. Changes in species composition favour an ecological interpretation with spatial heterogeneity as the major cause of different yield declines. Although elevated ozone may cause subtle physiological changes with longer term implications, our new results suggest that species-rich mature grassland such as the one studied at Le Mouret may be less sensitive to elevated ozone than previously assumed. In this experiment a confounded design was hidden at the start by transitory effects of a prior change in nutrient treatments.

Monitoring of acute axonal injury in the swine spinal cord with EAE by diffusion tensor imaging

To evaluate the ability of diffusion tensor imaging (DTI) to detect and monitor acute axonal injury in swine spinal cord with acute experimental allergic encephalomyelitis (EAE). Magnetic resonance imaging of the cervical spinal cord was performed in vivo at different time points through the onset and progression of EAE using a 3 Tesla clinical scanner. The DTI parameters were calculated in four separate regions of interest at the C2/C3 level. The quantitative DTI-pathology and DTI-clinical correlations were verified. In the monophasic acute course of EAE onset and progression, axial diffusivity (AD) decrease correlates with acute axonal injury (r = -0.84; P < 0.001). By contrast, radial diffusivity does not change and no demyelination in histopathology was detected. Moreover, a clear correlation between clinical disease and axial diffusivity was found in two swine EAE models (r = -0.86; P < 0.001 and r = -0.92; P < 0.001). AD corresponds with axonal injury in the absence of demyelination and may be a useful noninvasive tool to investigate the underlying pathogenic processes of multiple sclerosis and to monitor the effects of experimental treatments for axonal injury.

Effect of pH on Microstructure and Characteristics of Cream Cheese

This study evaluated the effect of pH on the microstructure of cream cheese and compared pH-induced changes in its microstructure with concomitant changes in cheese firmness and meltability. On 4 different days, experimental batches of cultured hot pack cream cheese were manufactured and analyzed for initial chemical composition. The cheeses were then sectioned into samples that were randomly assigned to 7 different treatment groups. Three groups were exposed to ammonia vapor for 1, 3, and 5 min to increase the pH; 3 groups were exposed to acetic acid vapor for 30, 60, and 90 min to decrease the pH; and 1 unexposed group served as the control. After equilibration at 4 degrees C, samples were analyzed for pH, firmness, meltability, and microstructure by scanning electron microscopy. The effects of experimental treatments on cheese pH, firmness, and meltability were analyzed by randomized complete block analysis of variance (ANOVA). Relationships between cheese pH and firmness and meltability were evaluated by regression. Experimental treatments significantly affected cheese pH, firmness, and meltability. Cheese firmness decreased and meltability increased with increasing pH from about pH 4.2 to 6.8. Cheese microstructure also changed dramatically over the same approximate pH range. Specifically, the volume of the protein network surrounding the fat droplets increased markedly with increasing pH, presumably due to casein swelling. These data support the hypothesis that protein-to-water interactions increased as the cheese pH increased, which gave rise to progressive swelling of the casein network, softer texture, and increased meltability.

Effect of experimental heat treatment on mechanical properties of resin composites

The aim of this study was to verify the influence of an experimental heat treatment (170 masculineC/10 min) using a casting furnace on the mechanical properties (hardness and flexural strength) of 2 commercial direct resin composites (TPH Spectrum and Filtek P60) compared to a commercial indirect resin system (BelleGlass). Heat treatment temperature was determined after thermal characterization by thermogravimetry (TG) and differential scanning calorimetry (DSC). Data was analyzed by ANOVA and Tukey's test at 5% significance level. There was statistical significance for the main factor heat treatment (p=0.03) and composite (p=0.02), for flexural strength. For Knoop hardness, only the main factor composite was statistically significant (p=0.00). P60 presented higher hardness than TPH. No statistically significant correlation between mechanical properties tested was detected. Based on these results, it was possible to conclude that heat treatment influenced flexural strength of direct composites, while it was not observed for hardness. The association of direct composites with a simple post-cure heat treatment may be an alternative for current indirect composite systems, although more studies are needed to verify other properties of the composites for this application.

Experimental Psychology: Continuity and Change

Like the volumes of previous years, Volume 56/2009 of Experimental Psychology is characterized by both continuity and change. One of the changes in 2009 refers to the team of editors. After serving as editors for several years, Ute J. Bayen, Anthony G. Greenwald, Glynn W. Humphreys, Dirk Kerzel, and Herbert Schriefers decided to step down upon completion of Volume 55. I would like to thank all of the outgoing editors for their excellent editorial work and their continuous support in the past years. Starting with Issue 1 of Volume 56, the outgoing editors will be replaced by seven new editors, namely, Arndt Broder (Rheinische Friedrich-Wilhelms University, Bonn, Germany), Roberto Dell’Acqua (University of Padova, Italy), Adele Diederich (Jacobs University, Bremen, Germany), Nachshon Meiran (Ben-Gurion University of the Negev, Beer-Sheva, Israel), Neil W. Mulligan (University of North Carolina, Chapel Hill, NC, USA), Manuel Perea (University of Valencia, Spain), and Melanie C. Steffens (FriedrichSchiller-University, Jena, Germany). I would like to thank these colleagues for their willingness to contribute to our common editorial work in the next years. In addition, I would also like to thank Iring Koch, Hartmut Leuthold, Thorsten Meiser, Jochen Musch, Klaus Rothermund, and Eva Walther for agreeing to stay in the team of editors. We are thus well prepared to manage the steadily increasing number of manuscript submissions to Experimental Psychology until the next major change in the team of editors in 2011. A second change concerns the editorial board. To cope with the wealth and the heterogeneity of topics addressed in research papers submitted to our journal, we decided to extend the editorial board of Experimental Psychology. I am grateful to Ute J. Bayen (Heinrich-Heine University, Dusseldorf, Germany), Hartmut Blank (University of Portsmouth, UK), Anthony G. Greenwald (University of Washington, Seattle, WA, USA), Ralph Hertwig (University of Basel, Switzerland), Dirk Kerzel (University of Geneva, Switzerland), Elizabeth F. Loftus (University of California, Irvine, CA, USA), Michel Regenwetter (University of Illinois at Urbana-Champaign, IL, USA), Jeffrey N. Rouder (University of Missouri-Columbia, Columbia, MO, USA), and Herbert Schriefers (Catholic University of Nijmegen, The Netherlands) for agreeing to supplement our editorial board in the next years. A third change concerns the book review section that will not be continued in 2009. Although Experimental Psychology switched from a quarterly to a bimonthly publication cycle in 2008, journal space continues to be scarce. To be able to publish accepted research articles as quickly as possible, we were forced to drop the book review section. This means that, beginning with the year 2009, new book review submissions will not be considered for publication anymore. Book reviews that have already been accepted will, of course, be published. The decision to drop the book review section was not easy. It has a long tradition both in Experimental Psychology and its predecessor journal, the Zeitschrift fur Experimentelle Psychologie. In recent years, Andreas Voss, our book review editor, did a great job in acquiring excellent book reviews addressing topics of high relevance for experimental psychologists. Nevertheless, given the current situation, we all agreed that the goal of reducing publication lag is more important than the continuation of the book review section. As with the other outgoing editors, I would also like to thank Andreas Voss for his excellent work as book review editor in the past years. Despite these major changes in the editorial team, the content and the scope of Experimental Psychology will not change. As Klauer (2002, p. 1) already stated in his first editorial of Experimental Psychology, ‘‘the scope of the journal is defined by the experimental method, and thus, papers based on experiments from all areas of psychology are welcome’’. We will stick to this strict definition in the future. By implication, papers comparing nonexperimental groups of participants (e.g., men and women, old and young people, amnesics and controls, participants with and without prosopagnosia, etc.) will not be considered for publication unless they report manipulations of at least one experimental independent variable (IV) in addition to the nonexperimental IV of interest. In other words, papers comparing experimental treatment effects between nonexperimental groups of participants would be appropriate in principle (e.g., experimental age group comparisons; cf. Carretti, Borella, & De Beni, 2007; Jansen-Osmann & Heil, 2007; Taconnat, Froger, Sacher, & Isingrini, 2008; Tsujimoto, Kuwajima, & Sawaguchi, 2007). We are also willing to consider correlational studies to some extent (see, e.g., Friese, Bluemke, & Wanke, 2007; Hilbig & Pohl, 2008; Nosek &

The Effect of Reminiscence Group Work on Life Satisfaction, Self‐Esteem and Mood of Ageing People with Intellectual Disabilities

Background This study evaluates the effects of reminiscence group work on the subjective well‐being of ageing people with intellectual disabilities.Methods The content of the successive group work sessions was manipulated as follows: a control‐phase with three ‘current topics’ sessions, an experimental phase with six ‘reminiscence’ sessions and finally three ‘current topics’ sessions. Life satisfaction, perceived self‐competence and mood were measured by questionnaires, filled in by the participants and direct support workers.Results A quasi‐experimental pre‐test–post‐test design (n = 41) did not detect any changes in life satisfaction and perceived self‐competence. For mood, a quasi‐experimental ABA‐design (n = 41) did not yield an experimental treatment effect, but a significant increase in scores was observed over time. Personality characteristics ‘extraversion’ and ‘emotional stability’, but not memory specificity were found to be significant covariates for the mood scores.Conclusion Although the study’s design did not allow us to confirm the effect of reminiscence group work, the analysis nonetheless revealed some useful indications for further research. Also, interviews conducted before and after the programme resulted in positive appraisals of the programme as a worthwhile and meaningful activity for ageing people with intellectual disability.

Focused Microarrays as a Method to Evaluate Subtle Changes in Gene Expression

Recent studies using microarray technologies for the chicken have reported information regarding the effects of specific experimental treatments on gene expression levels often resulting in large gene lists and limitations on the statistical significance levels detected. In most cases, with these limitations, along with thresholds of ±2-fold differences in expression levels, that are used to create these gene lists, much of the biological information may have been overlooked. In this study, a focused 70-mer oligonucleotide microarray was developed to address the apparent limits of detection and issues with multiple testing resulting from the use of microarrays that include only a single spot (probe) for each gene. Gene expression was assayed across the development of the chicken embryonic heart from d 7 to 20 of incubation. When using a mixed-model approach and ANOVA with Bonferroni correction for multiple testing, including replicates within the focused array significantly increased the sensitivity with which differences could be detected across sample groups, as compared with single-spot data. By incorporating replication into the focused array, 50 genes were detected as being differentially expressed in the embryonic heart across the time points sampled. This compares with only 7 genes detected as being differentially expressed when a more typical, less statistically stringent single-spot analysis is conducted. Based on our observations, the use of focused microarrays allows for the thorough investigation of gene expression patterns, with detection of significant changes in gene expression of ±7%. This limit of detection is far superior to that of real-time PCR, which is able to detect significant changes in expression from ±33 to 55%, depending on the specific application. The ability to detect small differences in expression will allow investigators to identify subtle effects that have perhaps been overlooked in many prior assays, including single-spot arrays. Subtle shifts in gene expression are exactly those that occur during embryonic development, nutritional manipulation, and the initial stages of disease before clinical signs appear.

The Causal Generalization Paradox: The Case of Treatment Outcome Research

Data from psychological experiments pose a causal generalization paradox. Unless the experimental results have some generality, they contribute little to scientific knowledge. Yet, because most experiments use convenience samples rather than probability-based samples, there is almost never a formal justification, or set of rigorous guidelines, for generalizing the study's findings to other populations. This article discusses the causal generalization paradox in the context of outcome findings from experimental evaluations of psychological treatment programs and services. In grappling with the generalization paradox, researchers often make misleading (or at least oversimplified) assumptions. The article analyzes 10 such assumptions, including the belief that a significant experimental treatment effect is likely to be causally generalizable and the belief that the magnitude of a significant experimental effect provides a sound effect size estimate for causal generalization. The article then outlines 10 constructive strategies for assessing and enhancing causal generality. They include strategies involving the scaling level of outcome measures, variable treatment dosages, effectiveness designs, multiple measures, corroboration from observational designs, and the synthesis of multiple studies. Finally, the article's discussion section reviews the conditions under which causal generalizations are justified.

Bayesian designs to account for patient heterogeneity in phase II clinical trials.

Between-patient heterogeneity is very common in clinical trials. This complicates treatment evaluation, due to known prognostic subgroup effects or potential treatment-subgroup interactions. We review two Bayesian phase II clinical trial designs that account explicitly for patient heterogeneity. The first design uses analysis of covariance to assess treatment effects in subgroups known to have different prognoses. The second design uses a hierarchical model for settings where, a priori, the experimental treatment effects in the subgroups are assumed to be exchangeable. Compared with simpler designs that ignore patient heterogeneity, each design provides substantial improvements by reducing both false positive and false negative rates and focusing resources on subgroups where an experimental treatment is more likely to provide an advance over standard therapy. In either case, accounting for potential treatment-subgroup interactions is extremely important. Due to the rapidly increasing number of potential new treatments to be evaluated clinically, increasing costs and limited resources, it is critically important to perform early phase clinical trials efficiently. The new Bayesian methods described here and other related methods provide efficient, broadly applicable tools to address these problems.

Neighborhood Effects on Economic Self‐Sufficiency: A Reconsideration of the Moving to Opportunity Experiment

This article revisits the Moving to Opportunity housing mobility experiment, which heretofore has not provided strong evidence to support the hypothesis of neighborhood effects on economic self‐sufficiency among adults. The authors undertake a conceptual and empirical analysis of the study’s design and implementation to gain a better understanding of the selection processes that occur within the study. The article shows that the study is potentially affected by selectivity at several junctures: in determining who complied with the program’s requirements, who entered integrated versus segregated neighborhoods, and who left neighborhoods after initial relocation. Furthermore, previous researchers have not found an experimental treatment effect on adult economic self‐sufficiency, relative to controls. The authors propose an alternative approach that involves measuring the cumulative amount of time spent in different neighborhood environments. With this method, they find evidence that neighborhood is associated with outcomes such as employment, earnings, TANF receipt, and use of food stamps.

In Vitro Antimyeloma Effects of Inhibitors of the Heat Shock Protein 70 (Hsp70) Molecular Chaperone.

Background: Multiple myeloma (MM) remains incurable, primarily due to drug resistance; recent research indicates that Hsp70 induction may accompany this process. Cytoplasmic Hsp70 is upregulated in MM, particularly after proteasome or Hsp90 inhibition. Hsp70 homolog in the ER helps fold immunoglobulins whose overexpression and misassembly trigger the unfolded protein response (UPR). We thus explored the antimyeloma effects of MAL3-101, a recently developed Hsp70 inhibitor on MM cell lines, primary MM cells, and endothelial progenitor cells (EPCs), a key MM microenvironment component; we also determined its synergy with proteasome and Hsp90 inhibition.Methods: MM cells (NCI-H929, RPMI-8266, and U266) were treated with MAL3–101, proteasome inhibitor MG-132, or Hsp90 inhibitor 17-AAG, alone and in combination. MTS assay and Annexin V-PI were used to detect survival and apoptosis, respectively. Primary MM cells and EPCs were outgrown from bone marrows of untreated patients. Synergistic effects were determined by Chou-Talalay combination index (CI).Results: Dose-effect and time course studies showed that MAL3–101 was most effective in NCI-H929 cells and induced maximum cytotoxicity at 40h (IC50 of 8.3μM). In contrast, MAL3–51, a less potent Hsp70 modulator, was less effective, suggesting that MAL3–101's effects are due to Hsp70 inhibition. Next, MAL3–101 or MG-132 were added alone or combined at 0.01–20μM. MG-132 decreased NCI-H929 cell survival (IC50 of 1.7μM); at 0.01–0.10 μM, both drugs were ineffective alone, whereas combined, a >60% decrease in survival resulted with CIs ≤0.01. Synergy was also observed in primary MM cells, reducing survival by 75±10%, and in EPCs by 60±16%. Induction of Hsp70 may provide a means of resisting apoptosis induced by Hsp90 inhibition. We thus exposed NCI-H929 cells to MAL3–101 with 17-AAG (0.025–10μM) for 40h. IC50 for 17-AAG decreased from 0.4μM to 0.3 and 0.03μM in the presence of either 5 or 10μM of MAL3–101, respectively, with CIs <1. We next examined the effect of MAL3–101 on UPR induction as indicated by XBP-1 splicing. None of the drugs, alone or in combination, resulted in XBP-1 splicing, while, as expected, tunicamycin induced XBP-1 splicing, in these cells. Levels of BiP, an ER lumenal chaperone whose synthesis is enhanced by UPR activation, also did not change. These data suggest that MAL3–101-mediated apoptosis may not occur via UPR activation. Whether ERAD might still be functional even though a significant proportion of the proteasome and/or Hsp70 is inhibited or whether certain MM cells might lack the ability to sufficiently induce the UPR are being studied.Conclusions: These results show for the first time that Hsp70 inhibition may provide a viable means of enhancing the antimyeloma effects of both established (i.e., proteasome inhibition) and experimental (i.e., Hsp90 inhibition) MM treatments. MAL3–101, a recently described Hsp70 modulator effective in killing breast cancer cells, sensitizes MM cells to proteasome and Hsp90 inhibition. These data also suggest that the previously reported upregulation of Hsp70 in MM cells is required to promote the growth and survival of MM tumors and its microvasculature. Finally, because Hsp upregulation may occur in response to the apoptotic effects of other MM-modulators, such as HDAC and tubulin inhibitors, we suggest that Hsp70 inhibition might provide a means to overcome drug resistance in MM.

Improvement in Survival Associated With Adult-to-Adult Living Donor Liver Transplantation

More than 2000 adult-to-adult living donor liver transplantations (LDLT) have been performed in the United States, yet the potential benefit to liver transplant candidates of undergoing LDLT compared with waiting for deceased donor liver transplantation (DDLT) is unknown. The aim of this study was to determine whether there is a survival benefit of adult LDLT. Adults with chronic liver disease who had a potential living donor evaluated from January 1998 to February 2003 at 9 university-based hospitals were analyzed. Starting at the time of a potential donor's evaluation, we compared mortality after LDLT to mortality among those who remained on the waiting list or received DDLT. Median follow-up was 4.4 years. Comparisons were made by hazard ratios (HR) adjusted for LDLT candidate characteristics at the time of donor evaluation. Among 807 potential living donor recipients, 389 underwent LDLT, 249 underwent DDLT, 99 died without transplantation, and 70 were awaiting transplantation at last follow-up. Receipt of LDLT was associated with an adjusted mortality HR of 0.56 (95% confidence interval [CI]: 0.42-0.74; P < .001) relative to candidates who did not undergo LDLT. As centers gained greater experience (>20 LDLT), LDLT benefit was magnified, with a mortality HR of 0.35 (95% CI: 0.23-0.53; P < .001). Adult LDLT was associated with lower mortality than the alternative of waiting for DDLT. This reduction in mortality was magnified as centers gained experience with LDLT. This reduction in transplant candidate mortality must be balanced against the risks undertaken by the living donors themselves.

Comparison of treatment effects between animal experiments and clinical trials: systematic review

Objective To examine concordance between treatment effects in animal experiments and clinical trials. Study design Systematic review. Data sources Medline, Embase, SIGLE, NTIS, Science Citation Index, CAB, BIOSIS. Study selection...

Multiple stressors on an Antarctic microplankton assemblage: water soluble crude oil and enhanced UVBR level at Ushuaia (Argentina)

Changes in phytoplankton pigment content, in vivo fluorescence as well as in abundance and cell characteristics of phyto- and bacterioplankton were investigated on a field-collected microplankton assemblage from Ushuaia Bay (Southern Argentina). Effects of different experimental treatments were examined: natural and enhanced ultraviolet-B radiation (UVBR: 280–320 nm) exposures, and water soluble fraction (WSF) of crude oil contamination under both UVBR exposures. After a 5-day exposure to experimental treatments in microcosms, significant UVBR-induced deleterious effects were observed with afternoon depression of the photochemical yield followed by night-time recovery. A significant increase in photoprotective pigments (PPCs) was also observed. Due to their smaller size, picophytoplankton cells appeared to be more impacted than nanophytoplankton cells as revealed by their increasing mean cell size and decreasing growth rate implying a perturbation of the cell cycle. On the other hand, the differential response between the two bacterial sub-populations identified (i.e., as sub-populations 1 and 2 according to their cellular characteristics) suggests a higher vulnerability for only one of these sub-populations to UVBR stress. WSF alone was also shown to induce deleterious effects on phytoplankton assemblage. Nevertheless, bacteria were positively affected, and particularly bacterial sub-population 2. The combination of WSF and enhanced UVBR exposure resulted in an exacerbation of these individual effects, demonstrating a synergistic effect of both stresses. Moreover, Cryptomonas sp. were observed to develop only under dual stresses in response to their capacity to switch between phototrophic and mixotrophic states following stressed conditions. In situ studies with natural communities provided a unique tool for determining the short-term biological response of microplankton assemblages exposed to multiple stressors.

Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species

BackgroundThe results of transcriptome microarray analysis are usually presented as a list of differentially expressed genes. As these lists can be long, it is hard to interpret the desired experimental treatment effect on the physiology of analysed tissue, e.g. via selected metabolic or other pathways. For some organisms, gene ontologies and data visualization software have been implemented to overcome this problem, whereas for others, software adaptation is yet to be done.ResultsWe present the classification of tentative potato contigs from the potato gene index (StGI) available from Dana-Farber Cancer Institute (DFCI) into the MapMan ontology to enable the application of the MapMan family of tools to potato microarrays. Special attention has been focused on mapping genes that could not be annotated based on similarity to Arabidopsis genes alone, thus possibly representing genes unique for potato. 97 such genes were classified into functional BINs (i.e. functional classes) after manual annotation. A new pathway, focusing on biotic stress responses, has been added and can be used for all other organisms for which mappings have been done. The BIN representation on the potato 10 k cDNA microarray, in comparison with all putative potato gene sequences, has been tested. The functionality of the prepared potato mapping was validated with experimental data on plant response to viral infection. In total 43,408 unigenes were mapped into 35 corresponding BINs.ConclusionThe potato mappings can be used to visualize up-to-date, publicly available, expressed sequence tags (ESTs) and other sequences from GenBank, in combination with metabolic pathways. Further expert work on potato annotations will be needed with the ongoing EST and genome sequencing of potato. The current MapMan application for potato is directly applicable for analysis of data obtained on potato 10 k cDNA microarray by TIGR (The Institute for Genomic Research) but can also be used by researchers working on other potato gene sets. The potato mapping file and the stress mapping diagram are available from the MapMan website [1].