Synaptic Cleft Segmentation in Non-Isotropic Volume Electron Microscopy of the Complete Drosophila Brain

Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been demonstrated to provide the necessary resolution to segment or trace all neurites and to annotate all synaptic connections. Automatic annotation of synaptic connections has been done successfully in near isotropic electron microscopy of vertebrate model organisms. Results on non-isotropic data in insect models, however, are not yet on par with human annotation. We designed a new 3D-U-Net architecture to optimally represent isotropic fields of view in non-isotropic data. We used regression on a signed distance transform of manually annotated synaptic clefts of the CREMI challenge dataset to train this model and observed significant improvement over the state of the art. We developed open source software for optimized parallel prediction on very large volumetric datasets and applied our model to predict synaptic clefts in a 50 tera-voxels dataset of the complete Drosophila brain. Our model generalizes well to areas far away from where training data was available

Pattern Formation of Glioma Cells: Effects of Adhesion

We investigate clustering of malignant glioma cells. \emph{In vitro} experiments in collagen gels identified a cell line that formed clusters in a region of low cell density, whereas a very similar cell line (which lacks an important mutation) did not cluster significantly. We hypothesize that the mutation affects the strength of cell-cell adhesion. We investigate this effect in a new experiment, which follows the clustering dynamics of glioma cells on a surface. We interpret our results in terms of a stochastic model and identify two mechanisms of clustering. First, there is a critical value of the strength of adhesion; above the threshold, large clusters grow from a homogeneous suspension of cells; below it, the system remains homogeneous, similarly to the ordinary phase separation. Second, when cells form a cluster, we have evidence that they increase their proliferation rate. We have successfully reproduced the experimental findings and found that both mechanisms are crucial for cluster formation and growth.Comment: 6 pages, 6 figure

Synaptic transmission parallels neuromodulation in a central food-intake circuit

NeuromedinU is a potent regulator of food intake and activity in mammals. In Drosophila, neurons producing the homologous neuropeptide hugin regulate feeding and locomotion in a similar manner. Here, we use EM-based reconstruction to generate the entire connectome of hugin-producing neurons in the Drosophila larval CNS. We demonstrate that hugin neurons use synaptic transmission in addition to peptidergic neuromodulation and identify acetylcholine as a key transmitter. Hugin neuropeptide and acetylcholine are both necessary for the regulatory effect on feeding. We further show that subtypes of hugin neurons connect chemosensory to endocrine system by combinations of synaptic and peptide-receptor connections. Targets include endocrine neurons producing DH44, a CRH-like peptide, and insulin-like peptides. Homologs of these peptides are likewise downstream of neuromedinU, revealing striking parallels in flies and mammals. We propose that hugin neurons are part of an ancient physiological control system that has been conserved at functional and molecular level.SFB 645 and 704, DFG Cluster of Excellence ImmunoSensation, DFG grant PA 787, HHMI Janeli

Channel Transmission Loss Studies During Ephemeral Flow Events: ER-5-3 Channel and Cambric Ditch, Nevada Test Site, Nye County, Nevada

Transmission losses along ephemeral channels are an important, yet poorly understood, aspect of rainfall-runoff prediction. Losses occur as flow infiltrates channel bed, banks, and floodplains. Estimating transmission losses in arid environments is difficult because of the variability of surficial geomorphic characteristics and infiltration capacities of soils and near-surface low-permeability geologic layers (e.g., calcrete). Transmission losses in ephemeral channels are nonlinear functions of discharge and time (Lane, 1972), and vary spatially along the channel reach and with soil antecedent moisture conditions (Sharma and Murthy, 1994). Rainfall-runoff models used to estimate peak discharge and runoff volume for flood hazard assessment are not designed specifically for ephemeral channels, where transmission loss can be significant because of the available storage volume in channel soils. Accuracy of the flow routing and rainfall-runoff models is dependent on the transmission loss estimate. Transmission loss rate is the most uncertain parameter in flow routing through ephemeral channels. This research, sponsored by the U.S. Department of Energy, National Nuclear Security Administration (DOE/NNSA) and conducted at the Nevada Test Site (NTS), is designed to improve understanding of the impact of transmission loss on ephemeral flood modeling and compare various methodologies for predicting runoff from rainfall events. Various applications of this research to DOE projects include more site-specific accuracy in runoff prediction; possible reduction in size of flood mitigation structures at the NTS; and a better understanding of expected infiltration from runoff losses into landfill covers. Two channel transmission loss field experiments were performed on the NTS between 2001 and 2003: the first was conducted in the ER-5-3 channel (Miller et al., 2003), between March and June 2001, and the second was conducted in the Cambric Ditch (Mizell et al., 2005), between April and July 2003. Both studies used water discharged from unrelated drilling activities during well development and aquifer pump tests. Discharge measurements at several flumes located along the channels were used to directly measure transmission losses. Flume locations were chosen in relation to geomorphic surface types and ages, vegetative cover and types, subsurface indurated layers (calcrete), channel slopes, etc. Transmission losses were quantified using three different analysis methods. Method 1 uses Lane's Method (Lane, 1983) for estimating flood magnitude in ephemeral channels. Method 2 uses heat as a subsurface tracer for infiltration. Numerical modeling, using HYDRUS-2D (Simunek et al., 1999), a finite-element-based flow and transport code, was applied to estimate infiltration from soil temperature data. Method 3 uses hydraulic gradient and water content in a Darcy's Law approach (Freeze and Cherry, 1979) to calculate one-dimensional flow rates. Heat dissipation and water content data were collected for this analysis

S06RS SGR No. 8 (System President)

A Resolution to urge the LSU Board of Supervisors to include student representation on the search committee for the LSU System President

Neuronal wiring diagram of an adult brain

Connections between neurons can be mapped by acquiring and analysing electron microscopic brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative1–6, but nevertheless inadequate for understanding brain function more globally. Here we present a neuronal wiring diagram of a whole brain containing 5 × 107 chemical synapses7 between 139,255 neurons reconstructed from an adult female Drosophila melanogaster8, 9. The resource also incorporates annotations of cell classes and types, nerves, hemilineages and predictions of neurotransmitter identities10–12. Data products are available for download, programmatic access and interactive browsing and have been made interoperable with other fly data resources. We derive a projectome—a map of projections between regions—from the connectome and report on tracing of synaptic pathways and the analysis of information flow from inputs (sensory and ascending neurons) to outputs (motor, endocrine and descending neurons) across both hemispheres and between the central brain and the optic lobes. Tracing from a subset of photoreceptors to descending motor pathways illustrates how structure can uncover putative circuit mechanisms underlying sensorimotor behaviours. The technologies and open ecosystem reported here set the stage for future large-scale connectome projects in other species

Heterogenous mean-field analysis of a generalized voter-like model on networks

We propose a generalized framework for the study of voter models in complex networks at the the heterogeneous mean-field (HMF) level that (i) yields a unified picture for existing copy/invasion processes and (ii) allows for the introduction of further heterogeneity through degree-selectivity rules. In the context of the HMF approximation, our model is capable of providing straightforward estimates for central quantities such as the exit probability and the consensus/fixation time, based on the statistical properties of the complex network alone. The HMF approach has the advantage of being readily applicable also in those cases in which exact solutions are difficult to work out. Finally, the unified formalism allows one to understand previously proposed voter-like processes as simple limits of the generalized model

Large-Scale Assessment of the Zebrafish Embryo as a Possible Predictive Model in Toxicity Testing

Background: In the drug discovery pipeline, safety pharmacology is a major issue. The zebrafish has been proposed as a model that can bridge the gap in this field between cell assays (which are cost-effective, but low in data content) and rodent assays (which are high in data content, but less cost-efficient). However, zebrafish assays are only likely to be useful if they can be shown to have high predictive power. We examined this issue by assaying 60 water-soluble compounds representing a range of chemical classes and toxicological mechanisms. Methodology/Principal Findings: Over 20,000 wild-type zebrafish embryos (including controls) were cultured individually in defined buffer in 96-well plates. Embryos were exposed for a 96 hour period starting at 24 hours post fertilization. A logarithmic concentration series was used for range-finding, followed by a narrower geometric series for LC 50 determination. Zebrafish embryo LC50 (log mmol/L), and published data on rodent LD50 (log mmol/kg), were found to be strongly correlated (using Kendall’s rank correlation tau and Pearson’s product-moment correlation). The slope of the regression line for the full set of compounds was 0.73403. However, we found that the slope was strongly influenced by compound class. Thus, while most compounds had a similar toxicity level in both species, some compounds were markedly more toxic in zebrafish than in rodents, or vice versa. Conclusions: For the substances examined here, in aggregate, the zebrafish embryo model has good predictivity for toxicit

Selectivity of Pesticides used in Integrated Apple Production to the Lacewing, Chrysoperla externa

This research aimed to assess the toxicity of the pesticides abamectin 18 CE (0.02 g a.i. L-1), carbaryl 480 SC (1.73 g a.i. L-1), sulfur 800 GrDA (4.8 g a.i. L-1), fenitrothion 500 CE (0.75 g a.i. L-1), methidathion 400 CE (0.4 g a.i. L-1), and trichlorfon 500 SC (1.5 g a.i. L-1) as applied in integrated apple production in Brazil on the survival, oviposition capacity, and egg viability of the lacewing, Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) from Bento Gonçalves and Vacaria, Rio Grande do Sul State, Brazil. An attempt was made to study morphological changes caused by some of these chemicals, by means of ultrastructural analysis, using a scanning electronic microscope. Carbaryl, fenitrothion, and methidathion caused 100% adult mortality for both populations, avoiding evaluation of pesticides' effects on predator reproductive parameters. Abamectin and sulfur also affected the survival of these individuals with mortality rates of 10% and 6.7%, respectively, for adults from Bento Gonçalves, and were harmless to those from Vacaria at the end of evaluation. Trichlorfon was also harmless to adults from both populations. No compound reduced oviposition capacity. C. externa from Vacaria presented higher reproductive potential than those from Bento Gonçalves. In relation to egg viability, sulfur was the most damaging compound to both populations of C. externa. Ultrastructural analyses showed morphological changes in the micropyle and the chorion of eggs laid by C. externa treated with either abamectin or sulfur. The treatment may have influenced the fertilization of C. externa eggs and embryonic development. Sulfur was responsible for malformations in the end region of the abdomen and genitals of treated females. When applied to adults, abamectin, sulfur, and trichlorfon were harmless, while carbaryl, fenitrothion, and methidathion were harmful, according to the IOBC classification