In Vitro Assessment of Developmental Neurotoxicity: Use of Microelectrode Arrays to Measure Functional Changes in Neuronal Network Ontogeny1

Because the Developmental Neurotoxicity Testing Guidelines require large numbers of animals and is expensive, development of in vitro approaches to screen chemicals for potential developmental neurotoxicity is a high priority. Many proposed approaches for screening are biochemical or morphological, and do not assess function of neuronal networks. In this study, microelectrode arrays (MEAs) were used to determine if chemical-induced changes in function could be detected by assessing the development of spontaneous network activity. MEAs record individual action potential spikes as well as groups of spikes (bursts) in neuronal networks, and activity can be assessed repeatedly over days in vitro (DIV). Primary cultures of rat cortical neurons were prepared on MEAs and spontaneous activity was assessed on DIV 2, 6, 9, 13, and 20 to determine the in vitro developmental profile of spontaneous spiking and bursting in cortical networks. In addition, 5 μM of the protein kinase C inhibitor bisindolylmaleamide-1 (Bis-1) was added to MEAs (n = 9–18) on DIV 5 to determine if changes in spontaneous activity could be detected in response to inhibition of neurite outgrowth. A clear profile of in vitro activity development occurred in control MEAs, with the number of active channels increasing from 0/MEA on DIV 2 to 37 ± 5/MEA by DIV 13; the rate of increase was most rapid between DIV 6 and 9, and activity declined by DIV 20. A similar pattern was observed for the number of bursting channels, as well as the total number of bursts. Bis-1 decreased the number of active channels/MEA and the number of bursting channels/MEA. Burst characteristics, such as burst duration and the number of spikes in a burst, were unchanged by Bis-1. These results demonstrate that MEAs can be used to assess the development of functional neuronal networks in vitro, as well as chemical-induced dysfunction

Evaluating Aspen Responses to Changes in Elk Abundance, Distribution and Behavior Following Wolf Reestablishment in West-Central Yellowstone National Park

The reintroduction of wolves to Yellowstone National Park created a unique “natural experiment” to study trophic interactions in a large-scale terrestrial system among wolves, elk, and aspen. This study utilized data from a long-term elk demography study that was established prior to wolf reintroduction. Significant changes in the abundance and distribution of the Madison headwaters elk herd were observed following wolf reestablishment. The spatial arrangement of these changes made it possible to directly test for the occurrence of a density-mediated trophic cascade. The objectives of this study were to answer the following questions: 1) was there a marked decrease in browsing pressure on aspen where elk densities declined, and 2) was there a corresponding plant-growth response indicating that aspen were released from browsing pressure? Historical browsing conditions and aspen height were observed for 31 aspen stands to assess the occurrence of a density-mediated trophic cascade following wolf reintroduction. Browse conditions and aspen morphology in stands where elk densities declined dramatically following wolf reintroduction were compared to stands that experienced persistent heavy browsing throughout this period. A major decline in browsing pressure along with a modest increase in aspen height and leader longevity was detected, supporting the hypothesis of a density-mediated trophic cascade. However, the magnitude of the growth response was weak, suggesting that browsing was not the dominant limiting factor to aspen growth in the study area and that aspen may be more strongly limited by bottom-up regulation

Resolving IRAS 09111-1007 at 350 microns - a different path to ULIRG formation?

We have resolved the ultraluminous infrared galaxy (ULIRG), IRAS 09111-1007, with the new 350 micron-optimised Second Generation Submillimeter High Angular Resolution Camera (SHARC II) and present the first submillimetre fluxes and images for the system. IRAS 09111-1007 comprises two interacting luminous infrared galaxies (LIRGs) with a projected nuclear separation of 39 kpc. The Western galaxy is roughly four times more luminous in the submillimetre than its Eastern counterpart. It is an extremely bright LIRG with an AGN. The classification of the Eastern source is uncertain: it could be a Seyfert 2 galaxy or a LINER. We highlight IRAS 09111-1007 as a system that necessitates further study: a double AGN ULIRG whose molecular gas content differs from other widely separated pairs and whose ULIRG phase might not be explained by current multiple merger and/or final stage ULIRG scenarios.Comment: 6 pages, 4 figures. Accepted for publication in MNRAS Letter

Adaptive-optics Optical Coherence Tomography Processing Using a Graphics Processing Unit

Graphics processing units are increasingly being used for scientific computing for their powerful parallel processing abilities, and moderate price compared to super computers and computing grids. In this paper we have used a general purpose graphics processing unit to process adaptive-optics optical coherence tomography (AOOCT) images in real time. Increasing the processing speed of AOOCT is an essential step in moving the super high resolution technology closer to clinical viability

First Constraints on Source Counts at 350 Microns

We have imaged a $\sim$6 arcminute$^2$ region in the Bo\"otes Deep Field using the 350 $\mu$m-optimised second generation Submillimeter High Angular Resolution Camera (SHARC II), achieving a peak 1$\sigma$ sensitivity of $\sim$5 mJy. We detect three sources above 3$\sigma$, and determine a spurious source detection rate of 1.09 in our maps. In the absence of $5\sigma$ detections, we rely on deep 24 $\mu$m and 20 cm imaging to deduce which sources are most likely to be genuine, giving two real sources. From this we derive an integral source count of 0.84$^{+1.39}_{-0.61}$ sources arcmin$^{-2}$ at $S>13$ mJy, which is consistent with 350 $\mu$m source count models that have an IR-luminous galaxy population evolving with redshift. We use these constraints to consider the future for ground-based short-submillimetre surveys.Comment: accepted for publication in The Astrophysical Journa

Urban case studies : general discussion

Urban case studies: general discussio

Estimating HIV Incidence among Adults in Kenya and Uganda: A Systematic Comparison of Multiple Methods

CITATION: Kim, A. A. et al. 2011. Estimating HIV incidence among adults in Kenya and Uganda : a systematic comparison of multiple methods. PLos ONE, 6(3): e17535, doi:10.1371/journal.pone.0017535.The original publication is available at http://journals.plos.org/plosoneBackground: Several approaches have been used for measuring HIV incidence in large areas, yet each presents specific challenges in incidence estimation. Methodology/Principal Findings: We present a comparison of incidence estimates for Kenya and Uganda using multiple methods: 1) Epidemic Projections Package (EPP) and Spectrum models fitted to HIV prevalence from antenatal clinics (ANC) and national population-based surveys (NPS) in Kenya (2003, 2007) and Uganda (2004/2005); 2) a survey-derived model to infer age-specific incidence between two sequential NPS; 3) an assay-derived measurement in NPS using the BED IgG capture enzyme immunoassay, adjusted for misclassification using a locally derived false-recent rate (FRR) for the assay; (4) community cohorts in Uganda; (5) prevalence trends in young ANC attendees. EPP/Spectrum-derived and survey-derived modeled estimates were similar: 0.67 [uncertainty range: 0.60, 0.74] and 0.6 [confidence interval: (CI) 0.4, 0.9], respectively, for Uganda (2005) and 0.72 [uncertainty range: 0.70, 0.74] and 0.7 [CI 0.3, 1.1], respectively, for Kenya (2007). Using a local FRR, assay-derived incidence estimates were 0.3 [CI 0.0, 0.9] for Uganda (2004/2005) and 0.6 [CI 0, 1.3] for Kenya (2007). Incidence trends were similar for all methods for both Uganda and Kenya. Conclusions/Significance: Triangulation of methods is recommended to determine best-supported estimates of incidence to guide programs. Assay-derived incidence estimates are sensitive to the level of the assay's FRR, and uncertainty around high FRRs can significantly impact the validity of the estimate. Systematic evaluations of new and existing incidence assays are needed to the study the level, distribution, and determinants of the FRR to guide whether incidence assays can produce reliable estimates of national HIV incidence.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017535Publisher's versio

Moult cycle specific differential gene expression profiling of the crab Portunus pelagicus

Background: Crustacean moulting is a complex process involving many regulatory pathways. A holistic approach to examine differential gene expression profiles of transcripts relevant to the moulting process, across all moult cycle stages, was used in this study. Custom cDNA microarrays were constructed for Portunus pelagicus. The printed arrays contained 5000 transcripts derived from both the whole organism, and from individual organs such as the brain, eyestalk, mandibular organ and Y-organ from all moult cycle stages.Results: A total of 556 clones were sequenced from the cDNA libraries used to construct the arrays. These cDNAs represented 175 singletons and 62 contigs, resulting in 237 unique putative genes. The gene sequences were classified into the following biological functions: cuticular proteins associated with arthropod exoskeletons, farnesoic acid O-methyltransferase (FaMeT), proteins belonging to the hemocyanin gene family, lectins, proteins relevant to lipid metabolism, mitochondrial proteins, muscle related proteins, phenoloxidase activators and ribosomal proteins. Moult cycle-related differential expression patterns were observed for many transcripts. Of particular interest were those relating to the formation and hardening of the exoskeleton, and genes associated with cell respiration and energy metabolism.Conclusions: The expression data presented here provide a chronological depiction of the molecular events associated with the biological changes that occur during the crustacean moult cycle. Tracing the temporal expression patterns of a large variety of transcripts involved in the moult cycle of P. pelagicus can provide a greater understanding of gene function, interaction, and regulation of both known and new genes with respect to the moulting process

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives