Expansion of the half retinal projection to the tectum in goldfish: An electrophysiological and Anatomical study

The topographical retino-tectal projection of goldfish was electrophysiologically mapped at various intervals after surgical removal of the nasal half of the retina and pigment epithelium. The remaining projection was initially restricted to the appropriate rostral half of the tectum, even if the nerve was crushed and allowed to regenerate. But later, after 137 days or more, it showed a progressive expansion onto the foreign caudal half of the tectum. The magnification factor, the number of micrometers of tectum per degree in the visual field, doubled in the rostro-caudal but not in the medio-lateral direction. Analysis of the sequence of the expansion showed that a few fibers originally projecting nearest the denervated area were the first to spread over it. Then, progressively more fibers moved caudally until a nearly uniform representation of the half retina was established on the tectum. Radioautography also demonstrated that retinal fiber terminals had invaded the caudal tectum. The retinae of these fish were also examined histologically. The density of ganglion cells had not increased, but they consistently showed the axonal reaction. This was not found to be associated with any initial surgical trauma, but rather with the movement of their fiber terminals within the tectum. Frozen sections, through half retinal and normal eyes, were cut and photographed for comparison of ocular geometry. Operated eyes were normal except for a slight but consistent loss of ocular volume. Analysis of the optical geometry showed that recording with fish in air produced two effects: Myopia (10° blur circle, or less) and enlargement of the visual field by 15% to 20%.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/50003/1/901770206_ftp.pd

Modulation of cell proliferation in the embryonic retina of zebrafish ( Danio rerio )

We describe light-microscopically the development of the embryonic zebrafish eye with particular attention to cell number, cell proliferation, and cell death. The period from 16 to 36 hr post fertilization (hpf) comprises two phases; during the first (16–27 hpf) the optic vesicle becomes the eye cup, and during the second (27–36 hpf) the eye cup begins to differentiate into the neural retina and pigmented epithelium. All cells in the eye primordium are proliferative prior to 28 hpf, and the length of the cell cycle has been estimated to be 10 hr at 24–28 hpf (Nawrocki, 1985 ). Our cell counts are consistent with that estimate at that age, but not at earlier ages. A 10-hr cell cycle predicts that the cell number should increase by 7% per hr, but during 16–24 hpf the cell number increased by only 1.5% per hr. Despite the low rate of increase, all cells labeled with bromo-deoxyuridine, so all were proliferative. We considered three possible explanations for the nearly-constant cell number in the first phase: proliferation balanced by cell emigration from the eye, proliferation balanced by cell death, and low proliferation caused by a transient prolongation of the cell cycle. We excluded the first two, and found direct support for the third. Previous examinations of the cell cycle length in vertebrate central nervous system have concluded that it increases monotonically, in contrast to the modulation that we have shown. Modulation of the cell cycle length is well-known in flies, but it is generally effected by a prolonged arrest at one phase, in contrast to the general deceleration that we have shown. © 2000 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/35168/1/1063_ftp.pd

A Multi-Component Model of the Developing Retinocollicular Pathway Incorporating Axonal and Synaptic Growth

During development, neurons extend axons to different brain areas and produce stereotypical patterns of connections. The mechanisms underlying this process have been intensively studied in the visual system, where retinal neurons form retinotopic maps in the thalamus and superior colliculus. The mechanisms active in map formation include molecular guidance cues, trophic factor release, spontaneous neural activity, spike-timing dependent plasticity (STDP), synapse creation and retraction, and axon growth, branching and retraction. To investigate how these mechanisms interact, a multi-component model of the developing retinocollicular pathway was produced based on phenomenological approximations of each of these mechanisms. Core assumptions of the model were that the probabilities of axonal branching and synaptic growth are highest where the combined influences of chemoaffinity and trophic factor cues are highest, and that activity-dependent release of trophic factors acts to stabilize synapses. Based on these behaviors, model axons produced morphologically realistic growth patterns and projected to retinotopically correct locations in the colliculus. Findings of the model include that STDP, gradient detection by axonal growth cones and lateral connectivity among collicular neurons were not necessary for refinement, and that the instructive cues for axonal growth appear to be mediated first by molecular guidance and then by neural activity. Although complex, the model appears to be insensitive to variations in how the component developmental mechanisms are implemented. Activity, molecular guidance and the growth and retraction of axons and synapses are common features of neural development, and the findings of this study may have relevance beyond organization in the retinocollicular pathway

The DOE E3SM Coupled Model Version 1: Overview and Evaluation at Standard Resolution

This work documents the first version of the U.S. Department of Energy (DOE) new Energy Exascale Earth System Model (E3SMv1). We focus on the standard resolution of the fully coupled physical model designed to address DOE mission-relevant water cycle questions. Its components include atmosphere and land (110-km grid spacing), ocean and sea ice (60 km in the midlatitudes and 30 km at the equator and poles), and river transport (55 km) models. This base configuration will also serve as a foundation for additional configurations exploring higher horizontal resolution as well as augmented capabilities in the form of biogeochemistry and cryosphere configurations. The performance of E3SMv1 is evaluated by means of a standard set of Coupled Model Intercomparison Project Phase 6 (CMIP6) Diagnosis, Evaluation, and Characterization of Klima simulations consisting of a long preindustrial control, historical simulations (ensembles of fully coupled and prescribed SSTs) as well as idealized CO2 forcing simulations. The model performs well overall with biases typical of other CMIP-class models, although the simulated Atlantic Meridional Overturning Circulation is weaker than many CMIP-class models. While the E3SMv1 historical ensemble captures the bulk of the observed warming between preindustrial (1850) and present day, the trajectory of the warming diverges from observations in the second half of the twentieth century with a period of delayed warming followed by an excessive warming trend. Using a two-layer energy balance model, we attribute this divergence to the model’s strong aerosol-related effective radiative forcing (ERFari+aci = -1.65 W/m2) and high equilibrium climate sensitivity (ECS = 5.3 K).Plain Language SummaryThe U.S. Department of Energy funded the development of a new state-of-the-art Earth system model for research and applications relevant to its mission. The Energy Exascale Earth System Model version 1 (E3SMv1) consists of five interacting components for the global atmosphere, land surface, ocean, sea ice, and rivers. Three of these components (ocean, sea ice, and river) are new and have not been coupled into an Earth system model previously. The atmosphere and land surface components were created by extending existing components part of the Community Earth System Model, Version 1. E3SMv1’s capabilities are demonstrated by performing a set of standardized simulation experiments described by the Coupled Model Intercomparison Project Phase 6 (CMIP6) Diagnosis, Evaluation, and Characterization of Klima protocol at standard horizontal spatial resolution of approximately 1° latitude and longitude. The model reproduces global and regional climate features well compared to observations. Simulated warming between 1850 and 2015 matches observations, but the model is too cold by about 0.5 °C between 1960 and 1990 and later warms at a rate greater than observed. A thermodynamic analysis of the model’s response to greenhouse gas and aerosol radiative affects may explain the reasons for the discrepancy.Key PointsThis work documents E3SMv1, the first version of the U.S. DOE Energy Exascale Earth System ModelThe performance of E3SMv1 is documented with a set of standard CMIP6 DECK and historical simulations comprising nearly 3,000 yearsE3SMv1 has a high equilibrium climate sensitivity (5.3 K) and strong aerosol-related effective radiative forcing (-1.65 W/m2)Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151288/1/jame20860_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151288/2/jame20860.pd

Modeling atmospheric sulfur over the Northern Hemisphere during the Aerosol Characterization Experiment 2 experimental period

[1] A high-resolution (1 ° 1°, 27 vertical levels) Eulerian chemical transport and transformation model for sulfate, SO2, and related species driven by analyzed forecast meteorological data has been run for the Northern Hemisphere for June–July 1997 and extensively evaluated with observational data, mainly from air quality and precipitation chemistry networks. For 5000 evaluations, 50 % of the modeled sulfate 24-hour mixing ratios were within a factor of 1.85 of the observations; 50 % of 328 concurrent subgrid observations were within a factor of 1.33. Much greater subgrid variation for 24-hour SO2 mixing ratios (50 % of 3552 observations were within a factor of 2.32) reflects high variability of this primary species; for 12600 evaluations, 50 % of modeled mixing ratios were within a factor of 2.54 of the observations. These results indicate that a substantial fraction of the modeled and observed differences is due to subgrid variation and/or measurement error. Sulfate mixing ratios are identified by source type (biogenic, volcanic, and anthropogenic) and production mechanism (primary and by gas-phase and aqueous-phase oxidation). Examination of key diagnostics showed substantial variation for the different types of sulfur, e.g., SO2 aqueous-phase oxidatio

Methods for the quantification of GHG emissions at the landscape level for developing countries in smallholder contexts

Landscape scale quantification enables farmers to pool resources and expertise. However, the problem remains of how to quantify these gains. This article considers current greenhouse gas (GHG) quantification methods that can be used in a landscape scale analysis in terms of relevance to areas dominated by smallholders in developing countries. In landscape scale carbon accounting frameworks, measurements are an essential element. Sampling strategies need careful design to account for all pools/fluxes and to ensure judicious use of resources. Models can be used to scale-up measurements and fill data gaps. In recent years a number of accessible models and calculators have been developed which can be used at the landscape scale in developing country areas. Some are based on the Intergovernmental Panel on Climate Change (IPCC) method and others on dynamic ecosystem models. They have been developed for a range of different purposes and therefore vary in terms of accuracy and usability. Landscape scale assessments of GHGs require a combination of ground sampling, use of data from census, remote sensing (RS) or other sources and modelling. Fitting of all of these aspects together needs to be performed carefully to minimize uncertainties and maximize the use of scarce resources. This is especially true in heterogeneous landscapes dominated by smallholders in developing countries