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Selected AbstractsLineage-independent mosaic expression and regulation of the Ciona multidom gene in the ancestral notochordDEVELOPMENTAL DYNAMICS, Issue 7 2007Izumi Oda-Ishii Abstract The transcription factor Ciona Brachyury (Ci-Bra) plays an essential role in notochord development in the ascidian Ciona intestinalis. We characterized a putative Ci-Bra target gene, which we named Ci - multidom, and analyzed in detail its expression pattern in normal embryos and in embryos where Ci - Bra was misexpressed. Ci - multidom encodes a novel protein, which contains eight CCP domains and a partial VWFA domain. We show that an EGFP-multidom fusion protein localizes preferentially to the endoplasmic reticulum (ER), and is excluded from the nucleus. In situ hybridization experiments demonstrate that Ci - multidom is expressed in the notochord and in the anterior neural boundary (ANB). We found that the expression in the ANB is fully recapitulated by an enhancer element located upstream of Ci - multidom. By means of misexpression experiments, we provide evidence that Ci-Bra controls transcription of Ci - multidom in the notochord; however, while Ci-Bra is homogeneously expressed throughout this structure, Ci - multidom is transcribed at detectable levels only in a random subset of notochord cells. The number of notochord cells expressing Ci - multidom varies among different embryos and is independent of developmental stage, lineage, and position along the anterior,posterior axis. These results suggest that despite its morphological simplicity and invariant cell-lineage, the ancestral notochord is a mosaic of cells in which the gene cascade downstream of Brachyury is differentially modulated. Developmental Dynamics 236:1806,1819, 2007. © 2007 Wiley-Liss, Inc. [source] The effect of fixed-count subsampling on macroinvertebrate biomonitoring in small streamsFRESHWATER BIOLOGY, Issue 2 2000Craig P. Doberstein Summary 1When rigorous standards of collecting and analysing data are maintained, biological monitoring adds valuable information to water resource assessments. Decisions, from study design and field methods to laboratory procedures and data analysis, affect assessment quality. Subsampling - a laboratory procedure in which researchers count and identify a random subset of field samples - is widespread yet controversial. What are the consequences of subsampling? 2To explore this question, random subsamples were computer generated for subsample sizes ranging from 100 to 1000 individuals as compared with the results of counting whole samples. The study was done on benthic invertebrate samples collected from five Puget Sound lowland streams near Seattle, WA, USA. For each replicate subsample, values for 10 biological attributes (e.g. total number of taxa) and for the 10-metric benthic index of biological integrity (B-IBI) were computed. 3Variance of each metric and B-IBI for each subsample size was compared with variance associated with fully counted samples generated using the bootstrap algorithm. From the measures of variance, we computed the maximum number of distinguishable classes of stream condition as a function of sample size for each metric and for B-IBI. 4Subsampling significantly decreased the maximum number of distinguishable stream classes for B-IBI, from 8.2 for fully counted samples to 2.8 classes for 100-organism subsamples. For subsamples containing 100,300 individuals, discriminatory power was low enough to mislead water resource decision makers. [source] Spatially autocorrelated sampling falsely inflates measures of accuracy for presence-only niche modelsJOURNAL OF BIOGEOGRAPHY, Issue 12 2009Samuel D. Veloz Abstract Aim, Environmental niche models that utilize presence-only data have been increasingly employed to model species distributions and test ecological and evolutionary predictions. The ideal method for evaluating the accuracy of a niche model is to train a model with one dataset and then test model predictions against an independent dataset. However, a truly independent dataset is often not available, and instead random subsets of the total data are used for ,training' and ,testing' purposes. The goal of this study was to determine how spatially autocorrelated sampling affects measures of niche model accuracy when using subsets of a larger dataset for accuracy evaluation. Location, The distribution of Centaurea maculosa (spotted knapweed; Asteraceae) was modelled in six states in the western United States: California, Oregon, Washington, Idaho, Wyoming and Montana. Methods, Two types of niche modelling algorithms , the genetic algorithm for rule-set prediction (GARP) and maximum entropy modelling (as implemented with Maxent) , were used to model the potential distribution of C. maculosa across the region. The effect of spatially autocorrelated sampling was examined by applying a spatial filter to the presence-only data (to reduce autocorrelation) and then comparing predictions made using the spatial filter with those using a random subset of the data, equal in sample size to the filtered data. Results, The accuracy of predictions from both algorithms was sensitive to the spatial autocorrelation of sampling effort in the occurrence data. Spatial filtering led to lower values of the area under the receiver operating characteristic curve plot but higher similarity statistic (I) values when compared with predictions from models built with random subsets of the total data, meaning that spatial autocorrelation of sampling effort between training and test data led to inflated measures of accuracy. Main conclusions, The findings indicate that care should be taken when interpreting the results from presence-only niche models when training and test data have been randomly partitioned but occurrence data were non-randomly sampled (in a spatially autocorrelated manner). The higher accuracies obtained without the spatial filter are a result of spatial autocorrelation of sampling effort between training and test data inflating measures of prediction accuracy. If independently surveyed data for testing predictions are unavailable, then it may be necessary to explicitly account for the spatial autocorrelation of sampling effort between randomly partitioned training and test subsets when evaluating niche model predictions. [source] Nest Selection by Cavity-nesting Birds in Subtropical Montane Forests of the Andes: Implications for Sustainable Forest ManagementBIOTROPICA, Issue 3 2009Natalia Politi ABSTRACT Development of sustainable forestry has been hampered in tropical countries by a scarcity of research on the ecological effects of logging. We focused on cavity-nesting birds, a group known to be sensitive to logging. Cavities used for nesting were not a random subset of all available suitable cavities. Birds selected cavities that were relatively high above the ground, had smaller entrances, and were excavated by woodpeckers. The use of tree species was also not random: Calycophyllum multiflorum, Blepharocalyx gigantea, and Podocarpus parlatorei were disproportionately important. Cavity nests were also more likely to be found in areas with trees with high mean diameter at breast height. This study emphasizes the need to maintain some unlogged forest patches within logging areas and retain certain species of trees. This study has implications for forest management in Argentina, where a new law mandates the sustainable use of forest resources and where many landowners are interested in forest certification. RESUMEN En los países tropicales la implementación del manejo forestal sostenible se ha visto limitado debido a la escasez de estudios sobre los efectos ecológicos de la explotación forestal. Nos focalizamos en aves que nidifican en huecos de árboles porque este es un grupo sensible a las prácticas de manejo forestal. Los huecos en árboles utilizados para nidificar no fueron un conjunto al azar de todos los huecos adecuados disponibles. Las aves seleccionaron huecos en árboles que estaban a una altura elevada desde el suelo, con entradas chicas y excavadas por carpinteros. El uso de las especies de árboles tampoco fue al azar: Calycophyllum multiflorum, Blepharocalyx gigantea y Podocarpus parlatorei fueron desproporcionadamente importantes. Fue más probable encontrar nidos en parches de árboles que tuvieron un promedio de diámetro a la altura del pecho más alto. Este estudio resalta la necesidad de retener algunos parches del bosque sin intervención dentro del área de manejo y retener ciertas especies arbóreas. Este estudio tiene implicancias en el manejo forestal en Argentina, donde una nueva ley plantea un uso sostenible de los recursos forestales y donde muchos propietarios están interesados en obtener una certificación forestal. [source] Breeding bird species diversity in the Negev: effects of scrub fragmentation by planted forestsJOURNAL OF APPLIED ECOLOGY, Issue 5 2001Eyal Shochat Summary 1Afforestation of the Northern Negev, Israel, from 1956 resulted in patches of primarily coniferous trees that fragmented large scrubland areas. This alteration in landscape pattern was followed by immigration of mediterranean bird species to the Negev. 2We counted breeding birds, and measured various environmental variables in scrubland and planted forest patches, to test whether bird assemblages were random subsets of the regional species pool, and whether area or habitat structure was the major correlate with species abundance and distribution. 3Of 22 bird species recorded, only three appeared in both scrub and forest, showing that these two habitats were occupied by different species assemblages. In both habitats, species richness increased with area at a rate greater than that expected by random sampling. In the scrub this increase was related to area per se, while in the forest it was related to habitat diversity in terms of stand age and tree type. 4The density of forest species was unaffected by area, but specialist scrubland species declined as area decreased. We suggest that edge effects might reduce species abundance in small scrubland patches. 5Nested subset analysis indicated that, at the community level, species composition was not random. However, at the species level, the distribution of three forest-dwelling species appeared as random, as it was associated with habitat rather than with patch size. 6Our results indicate that increased diversity of breeding birds in the Northern Negev will require scrub patches larger than 50 ha among the increasingly forested landscape. In contrast, increasing forest area would hardly increase species diversity in the whole landscape. Future forest management regimes should also aim to increase habitat diversity by adding foliage layers, especially in the understorey. Exotic coniferous forests support fewer species than deciduous forests in mediterranean zones around the world. The suggested management regime may improve such forests as habitat for species-rich bird communities. [source] Spatially autocorrelated sampling falsely inflates measures of accuracy for presence-only niche modelsJOURNAL OF BIOGEOGRAPHY, Issue 12 2009Samuel D. Veloz Abstract Aim, Environmental niche models that utilize presence-only data have been increasingly employed to model species distributions and test ecological and evolutionary predictions. The ideal method for evaluating the accuracy of a niche model is to train a model with one dataset and then test model predictions against an independent dataset. However, a truly independent dataset is often not available, and instead random subsets of the total data are used for ,training' and ,testing' purposes. The goal of this study was to determine how spatially autocorrelated sampling affects measures of niche model accuracy when using subsets of a larger dataset for accuracy evaluation. Location, The distribution of Centaurea maculosa (spotted knapweed; Asteraceae) was modelled in six states in the western United States: California, Oregon, Washington, Idaho, Wyoming and Montana. Methods, Two types of niche modelling algorithms , the genetic algorithm for rule-set prediction (GARP) and maximum entropy modelling (as implemented with Maxent) , were used to model the potential distribution of C. maculosa across the region. The effect of spatially autocorrelated sampling was examined by applying a spatial filter to the presence-only data (to reduce autocorrelation) and then comparing predictions made using the spatial filter with those using a random subset of the data, equal in sample size to the filtered data. Results, The accuracy of predictions from both algorithms was sensitive to the spatial autocorrelation of sampling effort in the occurrence data. Spatial filtering led to lower values of the area under the receiver operating characteristic curve plot but higher similarity statistic (I) values when compared with predictions from models built with random subsets of the total data, meaning that spatial autocorrelation of sampling effort between training and test data led to inflated measures of accuracy. Main conclusions, The findings indicate that care should be taken when interpreting the results from presence-only niche models when training and test data have been randomly partitioned but occurrence data were non-randomly sampled (in a spatially autocorrelated manner). The higher accuracies obtained without the spatial filter are a result of spatial autocorrelation of sampling effort between training and test data inflating measures of prediction accuracy. If independently surveyed data for testing predictions are unavailable, then it may be necessary to explicitly account for the spatial autocorrelation of sampling effort between randomly partitioned training and test subsets when evaluating niche model predictions. [source] Validation of Computed Tomography Image Integration into the EnSite NavX Mapping System to Perform Catheter Ablation of Atrial FibrillationJOURNAL OF CARDIOVASCULAR ELECTROPHYSIOLOGY, Issue 8 2008LAURA RICHMOND R.N., M.Sc. Introduction: The complex anatomy of the left atrium (LA) makes location of ablation catheters difficult using fluoroscopy alone, and therefore 3D mapping systems are now routinely used. We describe the integration of a CT image into the EnSite NavX System with Fusion and its validation in patients undergoing atrial fibrillation (AF) or left atrial tachycardia (AT) catheter ablation. Methods and Results: Twenty-three patients (61 ± 9.2 years, 16 male) with paroxysmal (14) and persistent (8) AF and persistent (1) AT underwent ablation using CT image integration into the EnSite NavX mapping system with the EnSite Fusion Dynamic Registration software module. In all cases, segmentation of the CT data was accomplished using the EnSite Verismo segmentation tool, although repeat segmentation attempts were required in seven cases. The CT was registered with the NavX-created geometry using an average of 24 user-defined fiducial pairs (range 9 to 48). The average distance from NavX-measured lesion positions to the CT surface was 3.2 ± 0.9 mm (median 2.4 mm). A large, automated, retrospective test using registrations with random subsets of each patient's fiducial pairs showed this average distance decreasing as the number of fiducial pairs increased, although the improvement ceased to be significant beyond 15 pairs. In confirmation, those studies which had used 16 or more pairs had a smaller average lesion-to-surface distance (2.9 ± 0.7 mm) than those using 15 or fewer (4.3 ± 0.8 mm, P < 0.02). Finally, for the 13 patients who underwent left atrial circumferential ablation (LACA), there was no significant difference between the circumference computed using NavX-measured positions and CT surface positions for either the left pulmonary veins (178 ± 64 vs. 177 ± 60 mm; P = 0.81) or the right pulmonary veins (218 ± 86 vs. 207 ± 81 mm; P = 0.08). Conclusion: CT image integration into the EnSite NavX Fusion system was successful in all patients undergoing catheter ablation. A learning curve exists for the Verismo segmentation tool; but once the 3D model was created, the registration process was easily accomplished, with a registration error that is comparable with registration errors using other mapping systems with CT image integration. All patients went on to have subsequent successful ablation procedures. Where LACA was performed (13 patients), only four patients required segmental ostial lesions to achieve electrical isolation. [source] DATE analysis: A general theory of biological change applied to microarray dataBIOTECHNOLOGY PROGRESS, Issue 5 2009David Rasnick Abstract In contrast to conventional data mining, which searches for specific subsets of genes (extensive variables) to correlate with specific phenotypes, DATE analysis correlates intensive state variables calculated from the same datasets. At the heart of DATE analysis are two biological equations of state not dependent on genetic pathways. This result distinguishes DATE analysis from other bioinformatics approaches. The dimensionless state variable F quantifies the relative overall cellular activity of test cells compared to well-chosen reference cells. The variable ,i is the fold-change in the expression of the ith gene of test cells relative to reference. It is the fraction , of the genome undergoing differential expression,not the magnitude ,,that controls biological change. The state variable , is equivalent to the control strength of metabolic control analysis. For tractability, DATE analysis assumes a linear system of enzyme-connected networks and exploits the small average contribution of each cellular component. This approach was validated by reproducible values of the state variables F, RNA index, and , calculated from random subsets of transcript microarray data. Using published microarray data, F, RNA index, and , were correlated with: (1) the blood-feeding cycle of the malaria parasite, (2) embryonic development of the fruit fly, (3) temperature adaptation of Killifish, (4) exponential growth of cultured S. pneumoniae, and (5) human cancers. DATE analysis was applied to aCGH data from the great apes. A good example of the power of DATE analysis is its application to genomically unstable cancers, which have been refractory to data mining strategies. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] | ||||||||||