Distance maps to estimate cell volume from two-dimensional plankton images

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography: Methods 10 (2012): 278-288, doi:10.4319/lom.2012.10.278.We describe and evaluate an algorithm that uses a distance map to automatically calculate the biovolume of a planktonic organism from its two-dimensional boundary. Compared with existing approaches, this algorithm dramatically increases the speed and accuracy of biomass estimates from plankton images, and is thus especially suited for use with automated cell imaging technologies that produce large quantities of data. The algorithm operates on a two-dimensional image processed to identify organism boundaries. First, the distance of each interior pixel to the nearest boundary is calculated; next these same distances are assumed to apply for projection in the third dimension; and finally the resulting volume is adjusted by a multiplicative factor assuming locally circular cross-sections in the third dimension. Other cross-sectional shape factors can be applied as needed. In this way, the simple, computationally efficient, volume calculation can be refined to include taxon-specific shape information if available. We show that compared to traditional manual microscopic analysis, the distance map algorithm is unbiased and accurate (mean difference = -0.25%, standard deviation = 17%) for a range of cell morphologies, including those with concave boundaries that deviate from simple geometric shapes and whose volumes are not well represented by a solid of revolution around a single axis. Automated calculation of cell volumes can now be implemented with a combination of this new distance map algorithm for complex shapes and the solid of revolution approach for simple shapes, with an automated decision criterion to choose the appropriate approach for each image.This research was supported by grants (to HMS) from the Gordon and Betty Moore Foundation and NASA’s Ocean Biology and Biogeochemistry program, and a Woods Hole Oceanographic Institution Summer Student Fellow award (to EAM)

Evolutionary Trends in the Physciaceae

The current delimitation of the family Physciaceae has been generally accepted since detailed descriptions of ascus characters allowed for a more natural circumscription of lichenized ascomycetes. The generic relations within the family are, however, still controversial and depend on the importance different authors attribute to specific morphological or chemical characteristics. The aim of this paper is to describe ascospore ontogeny and to test the present taxonomic structure of the family against a parsimony-based cladistic analysis, which includes three different scenarios of a priori character weighting. A study of ascospore ontogeny revealed two distinct developmental lines. One line revealed a delayed septum formation, which clearly showed transitions from spores with apical and median thickenings to spores without apical, but still well developed median thickenings, and to spores without any thickenings. In the second developmental line with an early septum formation again taxa with no thickenings, median thickenings, and both median and apical thickenings were found. Although these characters were constant at a species level, median wall thickenings especially varied among otherwise closely related taxa. In the cladistic analyses the current taxonomic structure of the Physciaceae was only obtained after the five character groups, namely morphology and anatomy of the vegetative thallus, conidiomata and conidia, morphology and anatomy of the apothecia, ontogeny of the ascospores, and secondary metabolites of the thallus, were given equal importance, and after a subjective a priori weighting further increased the weight of the three characters ‘conidial shape', ‘presence of apical thickenings', and ‘spore septation delayed'. This structure was not supported by a cladistic analysis with equally weighted characters but reflected the biased character weighting of the present day Physdaceae taxonomy. The taxonomic importance of conidial characters and of anatomical and ontogenetical spore characteristics need, therefore, a careful reconsideration in futur

Bioeconomics and biodiversity in harvested metacommunities : a patch-occupancy approach

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecosphere 6, no. 11 (2015): 1-18, doi:10.1890/ES14-00503.1.We develop a coupled economic-metacommunity model to investigate the trade-off between diversity and profit for multispecies systems. The model keeps track of the presence or absence of species in habitat patches. With this approach, it becomes (relatively) simple to include more species than can typically be included in models that track species population density. We use this patch-occupancy framework to understand how profit and biodiversity are impacted by (1) community assembly, (2) pricing structures that value species equally or unequally, and (3) the implementation of marine reserves. We find that when local communities assemble slowly as a result of facilitative colonization, there are lower profits and optimal harvest rates, but the trade-off with diversity may be either large or small. The trade-off is diminished if later colonizing species are more highly valued than early colonizers. When the cost of harvesting is low, maximizing profits tends to sharply reduce biodiversity and maximizing diversity entails a large harvesting opportunity cost. In the models we analyze, marine reserves are never economically optimal for a profit-maximizing owner. However, management using marine reserves may provide low-cost biodiversity protection if the community is over-harvested.This research was supported by The Seaver Institute and the National Science Foundation (OCE-1031256) through grants awarded to J. B. Kellner and M. G. Neubert. E. A. Moberg was funded by NSF GRFP number 1122374 and MIT's Ida Green Fellowship

From "good for people" to "good for people and planet"-Placing health and environment on equal footing when developing food-based dietary guidelines

Dietary guidelines are a primary tool for promoting healthier and more sustainable diets. Despite several ex-amples of dietary guidelines that consider -to various degrees -aspects of environmental sustainability, there is currently no framework that systematically incorporates environmental sustainability as a primary consider-ation. We present a five-step framework for developing environmentally sustainable dietary guidelines that would simultaneously meet nutritional requirements while staying within environmental boundaries. The steps comprise: 1) determining an average healthy diet for different population groups and criteria for healthy diets; 2) identifying relevant environmental aspects and establishing corresponding boundaries; 3) identifying systemic effects and crucial sustainability aspects; 4) altering the average diet to meet environmental goals and resolve trade-offs between environmental and nutritional goals; and 5) formulating sustainable food-based dietary guidelines. To exemplify the framework, we pilot it in the Swedish context, but it could be utilised for any other country

Notiser ur sällskapets pro Fauna & Flora Fennica förhandlingar

Bihang till Acta Societatis scientiarum Fennicae

New kid on the ID block: Neural functions of the Nab2/ZC3H14 class of Cys3His tandem zinc-finger polyadenosine RNA binding proteins

Polyadenosine RNA binding proteins (Pabs) play critical roles in regulating the polyadenylation, nuclear export, stability, and translation of cellular RNAs. Although most Pabs are ubiquitously expressed and are thought to play general roles in post-transcriptional regulation, mutations in genes encoding these factors have been linked to tissue-specific diseases including muscular dystrophy and now intellectual disability (ID). Our recent work defined this connection to ID, as we showed that mutations in the gene encoding the ubiquitously expressed Cys3His tandem zinc-finger (ZnF) Pab, ZC3H14 (Zinc finger protein, CCCH-type, number 14) are associated with non-syndromic autosomal recessive intellectual disability (NS-ARID). This study provided a first link between defects in Pab function and a brain disorder, suggesting that ZC3H14 plays a required role in regulating RNAs in nervous system cells. Here we highlight key questions raised by our study of ZC3H14 and its ortholog in the fruit fly Drosophila melanogaster, dNab2, and comment on future approaches that could provide insights into the cellular and molecular roles of this class of zinc finger-containing Pabs. We propose a summary model depicting how ZC3H14-type Pabs might play particularly important roles in neuronal RNA metabolism

Ariel - Volume 8 Number 3

Executive Editor James W. Lockard, Jr. Business Manager Neeraj K. Kanwal University News Richard J . Perry World News Doug Hiller Opinions Elizabeth A. McGuire Features Patrick P. Sokas Sports Desk Shahab S. Minassian Managing Editor Edward H. Jasper Managing Associate Brenda Peterson Photography Editor Robert D. Lehman. Jr. Graphics Christine M. Kuhnl