Graph Theoretical Model of a Sensorimotor Connectome in Zebrafish

Mapping the detailed connectivity patterns (connectomes) of neural circuits is a central goal of neuroscience. The best quantitative approach to analyzing connectome data is still unclear but graph theory has been used with success. We present a graph theoretical model of the posterior lateral line sensorimotor pathway in zebrafish. The model includes 2,616 neurons and 167,114 synaptic connections. Model neurons represent known cell types in zebrafish larvae, and connections were set stochastically following rules based on biological literature. Thus, our model is a uniquely detailed computational representation of a vertebrate connectome. The connectome has low overall connection density, with 2.45% of all possible connections, a value within the physiological range. We used graph theoretical tools to compare the zebrafish connectome graph to small-world, random and structured random graphs of the same size. For each type of graph, 100 randomly generated instantiations were considered. Degree distribution (the number of connections per neuron) varied more in the zebrafish graph than in same size graphs with less biological detail. There was high local clustering and a short average path length between nodes, implying a small-world structure similar to other neural connectomes and complex networks. The graph was found not to be scale-free, in agreement with some other neural connectomes. An experimental lesion was performed that targeted three model brain neurons, including the Mauthner neuron, known to control fast escape turns. The lesion decreased the number of short paths between sensory and motor neurons analogous to the behavioral effects of the same lesion in zebrafish. This model is expandable and can be used to organize and interpret a growing database of information on the zebrafish connectome

A Second-Generation Device for Automated Training and Quantitative Behavior Analyses of Molecularly-Tractable Model Organisms

A deep understanding of cognitive processes requires functional, quantitative analyses of the steps leading from genetics and the development of nervous system structure to behavior. Molecularly-tractable model systems such as Xenopus laevis and planaria offer an unprecedented opportunity to dissect the mechanisms determining the complex structure of the brain and CNS. A standardized platform that facilitated quantitative analysis of behavior would make a significant impact on evolutionary ethology, neuropharmacology, and cognitive science. While some animal tracking systems exist, the available systems do not allow automated training (feedback to individual subjects in real time, which is necessary for operant conditioning assays). The lack of standardization in the field, and the numerous technical challenges that face the development of a versatile system with the necessary capabilities, comprise a significant barrier keeping molecular developmental biology labs from integrating behavior analysis endpoints into their pharmacological and genetic perturbations. Here we report the development of a second-generation system that is a highly flexible, powerful machine vision and environmental control platform. In order to enable multidisciplinary studies aimed at understanding the roles of genes in brain function and behavior, and aid other laboratories that do not have the facilities to undergo complex engineering development, we describe the device and the problems that it overcomes. We also present sample data using frog tadpoles and flatworms to illustrate its use. Having solved significant engineering challenges in its construction, the resulting design is a relatively inexpensive instrument of wide relevance for several fields, and will accelerate interdisciplinary discovery in pharmacology, neurobiology, regenerative medicine, and cognitive science

Runoff Loss of Pesticides and Soil: A Comparison between Vegetative Mulch and Plastic Mulch in Vegetable Production Systems

Current vegetable production systems use polyethylene (plastic) mulch and require multiple applications of agrochemicals. During rain events, runoff from vegetable production is enhanced because 50 to 75% of the field is covered with an impervious surface. This study was conducted to quantify off-site movement of soil and pesticides with runoff from tomato (Lycopersicon esculentum Mil.) plots containing polyethylene mulch and a vegetative mulch, hairy vetch (Vicia villosa Roth). Side-by-side field plots were instrumented with automated flow meters and samplers to measure and collect runoff, which was filtered, extracted, and analyzed to determine soil and pesticide loss. Seasonal losses of two to four times more water and at least three times as much sediment were observed from plots with polyethylene mulch (55.4 to 146 L m-2 and 247 to 535 g m-2, respectively) versus plots with hairy vetch residue (13.7 to 75.7 L m-2 and 32.8 to 118 g m-2, respectively). Geometric means (±standard deviation) of total pesticide loads for chlorothalonil (tetrachloroisophthalonitrile) and α- and β-endosulfan (6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3-benzodioxathiepin 3-oxide) for a runoff event were 19, 6, and 9 times greater from polyethylene (800 ± 4.6, 17.6 ± 3.9, and 39.1 ± 4.9 μg m-2, respectively) than from hairy vetch mulch plots (42 ± 6.0, 2.8 ± 5.0, and 4.3 ± 4.6 μg m-2, respectively) due to greater concentrations and larger runoff volumes. The increased runoff volume, soil loss, and off-site loading of pesticides measured in runoff from the polyethylene mulch suggests that this management practice is less sustainable and may have a harmful effect on the environment

Chronic in vivo imaging in the mouse spinal cord using an implanted chamber

Understanding and treatment of spinal cord pathology is limited in part by a lack of time-lapse in vivo imaging strategies at the cellular level. We developed a chronically implanted spinal chamber and surgical procedure suitable for time-lapse in vivo multiphoton microscopy of mouse spinal cord without the need for repeat surgical procedures. We routinely imaged mice repeatedly for more than 5 weeks postoperatively with up to ten separate imaging sessions and observed neither motor-function deficit nor neuropathology in the spinal cord as a result of chamber implantation. Using this chamber we quantified microglia and afferent axon dynamics after a laser-induced spinal cord lesion and observed massive microglia infiltration within 1 d along with a heterogeneous dieback of axon stumps. By enabling chronic imaging studies over timescales ranging from minutes to months, our method offers an ideal platform for understanding cellular dynamics in response to injury and therapeutic interventions. © 2012 Nature America, Inc. All rights reserved

A comparison of three cold-climate strawberry production systems: Environmental effects

The environmental effects of the three strawberry (Fragaria ×ananassa) cold-climate production systems were compared: the traditional method of conventional matted row (CMR) and the two more recently developed practices of advanced matted row (AMR) and cold-climate plasticulture (CCP). Side-by-side field plots were instrumented with automated flow meters and samplers to measure and collect runoff, which was filtered and analyzed to determine soil, pesticide, and nitrogen losses. Although annual mean runoff volumes were similar for all three production systems, the soil losses from CMR plots were two to three times greater than the CCP plots throughout the study and two to three times greater than the AMR plots only in the first year of the 3-year study. In general, decreases in erosion and runoff volumes were observed in plots that were disturbed less by machine operations and had less foot traffic as a result of decreased need for hand weeding and in the plots that used straw mulch in the furrows between the beds. Timing and intensity of precipitation events also influenced the amount of soil erosion. Pesticide residues and nitrogen losses were also greatest in the runoff from the CMR plots. The two systems that used drip fertigation, AMR and CCP, also had higher nitrogen uptake efficiencies. Overall, the CCP and AMR systems performed similarly for most criteria; however, considering the nonrenewable nature of the plastic mulch and the need to dispose of the plastic mulch in a landfill, the AMR system was more environmentally sustainable than the CCP system

A comparison of three cold-climate strawberry production systems: Environmental effects

The environmental effects of the three strawberry (Fragaria ×ananassa) cold-climate production systems were compared: the traditional method of conventional matted row (CMR) and the two more recently developed practices of advanced matted row (AMR) and cold-climate plasticulture (CCP). Side-by-side field plots were instrumented with automated flow meters and samplers to measure and collect runoff, which was filtered and analyzed to determine soil, pesticide, and nitrogen losses. Although annual mean runoff volumes were similar for all three production systems, the soil losses from CMR plots were two to three times greater than the CCP plots throughout the study and two to three times greater than the AMR plots only in the first year of the 3-year study. In general, decreases in erosion and runoff volumes were observed in plots that were disturbed less by machine operations and had less foot traffic as a result of decreased need for hand weeding and in the plots that used straw mulch in the furrows between the beds. Timing and intensity of precipitation events also influenced the amount of soil erosion. Pesticide residues and nitrogen losses were also greatest in the runoff from the CMR plots. The two systems that used drip fertigation, AMR and CCP, also had higher nitrogen uptake efficiencies. Overall, the CCP and AMR systems performed similarly for most criteria; however, considering the nonrenewable nature of the plastic mulch and the need to dispose of the plastic mulch in a landfill, the AMR system was more environmentally sustainable than the CCP system