Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina.

High-acuity vision in primates, including humans, is mediated by a small central retinal region called the fovea. As more accessible organisms lack a fovea, its specialized function and its dysfunction in ocular diseases remain poorly understood. We used 165,000 single-cell RNA-seq profiles to generate comprehensive cellular taxonomies of macaque fovea and peripheral retina. More than 80% of >60 cell types match between the two regions but exhibit substantial differences in proportions and gene expression, some of which we relate to functional differences. Comparison of macaque retinal types with those of mice reveals that interneuron types are tightly conserved. In contrast, projection neuron types and programs diverge, despite exhibiting conserved transcription factor codes. Key macaque types are conserved in humans, allowing mapping of cell-type and region-specific expression of >190 genes associated with 7 human retinal diseases. Our work provides a framework for comparative single-cell analysis across tissue regions and species.

Cortico-cortical feedback engages active dendrites in visual cortex.

Sensory processing in the neocortex requires both feedforward and feedback information flow between cortical areas1. In feedback processing, higher-level representations provide contextual information to lower levels, and facilitate perceptual functions such as contour integration and figure-ground segmentation2,3. However, we have limited understanding of the circuit and cellular mechanisms that mediate feedback influence. Here we use long-range all-optical connectivity mapping in mice to show that feedback influence from the lateromedial higher visual area (LM) to the primary visual cortex (V1) is spatially organized. When the source and target of feedback represent the same area of visual space, feedback is relatively suppressive. By contrast, when the source is offset from the target in visual space, feedback is relatively facilitating. Two-photon calcium imaging data show that this facilitating feedback is nonlinearly integrated in the apical tuft dendrites of V1 pyramidal neurons: retinotopically offset (surround) visual stimuli drive local dendritic calcium signals indicative of regenerative events, and two-photon optogenetic activation of LM neurons projecting to identified feedback-recipient spines in V1 can drive similar branch-specific local calcium signals. Our results show how neocortical feedback connectivity and nonlinear dendritic integration can together form a substrate to support both predictive and cooperative contextual interactions.

Iterative scenarios for social-ecological systems.

Managing social-ecological systems toward desirable regimes requires learning about the system being managed while preparing for many possible futures. Adaptive management (AM) and scenario planning (SP) are two systems management approaches that separately use learning to reduce uncertainties and employ planning to manage irreducible uncertainties, respectively. However, each of these approaches have limitations that confound management of social-ecological systems. Here, we introduce iterative scenarios (IS), a systems management approach that is a hybrid of the scopes and relationships to uncertainty and controllability of AM and SP that combines the "iterativeness" of AM and futures planning of SP. Iterative scenarios is appropriate for situations with high uncertainty about whether a management action will lead to intended outcomes, the desired benefits are numerous and cross-scale, and it is difficult to account for the social implications around the natural resource management options. The value of iterative scenarios is demonstrated by applying the approach to green infrastructure futures for a neighborhood in the city of Cleveland, Ohio, U.S., that had experienced long-term, systemic disinvestment. The Cleveland green infrastructure project was particularly well suited to the IS approach given that learning about environmental factors was necessary and achievable, but what would be socially desirable and possible was unknown. However, iterative scenarios is appropriate for many social-ecological systems where uncertainty is high as IS accommodates real-world complexity faced by management.

Widespread loss of intermediate soil horizons in urban landscapes.

Soils support terrestrial ecosystem function and therefore are critical urban infrastructure for generating ecosystem services. Urbanization processes modify ecosystem function by changing the layers of soils identified as soil horizons. Soil horizons are integrative proxies for suites of soil properties and as such can be used as an observable unit to track modifications within soil profiles. Here, in an analysis of 11 cities representing 10 of the 12 soil orders, we show that urban soils have ∼50% fewer soil horizons than preurban soils. Specifically, B horizons were much less common in urban soils and were replaced by a deepening of A horizons and a shallowing of C horizons. This shift is likely due to two processes: (i) local management, i.e., soil removal, mixing, and fill additions, and (ii) soil development timelines, i.e., urbanized soils are young and have had short time periods for soil horizon development since urbanization (decades to centuries) relative to soil formation before urbanization (centuries to millennia). Urban soils also deviated from the standard A-B-C horizon ordering at a much greater frequency than preurban soils. Overall, our finding of common shifts in urban soil profiles across soil orders and cities suggests that urban soils may function differently from their preurban antecedents. This work introduces a basis for improving our understanding of soil modifications by urbanization and its potential effects on ecosystem functioning and thereby has implications for ecosystem services derived from urban landscapes.

K in an Urban World: New Contexts for Hydraulic Conductivity.

Hydraulic conductivity (K) is a key hydrologic parameter widely recognized to be difficult to estimate and constrain, with little consistent assessment in disturbed, urbanized soils. To estimate K, it is either measured, or simulated by pedotransfer functions, which relate K to easily measured soil properties. We measured K in urbanized soils by double-ring infiltrometer (K dring), near-saturated tension infiltrometry (K minidisk), and constant head borehole permeametry (K borehole), along with other soil properties across the major soil orders in 12 United States cities. We compared measured K with that predicted from the pedotransfer function, ROSETTA. We found that regardless of soil texture, K dring was consistently larger than K minidisk; with the latter having slightly less sample variance. K borehole was dependent upon specific subsurface conditions, and contrary to common expectations, did not always decrease with depth. Based on either soil textural class, or percent textural separates (sand, silt clay), ROSETTA did not accurately predict measured K for surface nor subsurface soils. We go on to discuss how K varies in urban landscapes, the role of measurement methods and artifacts in the perception of this metric, and implications for hydrologic modeling. Overall, we aim to inspire consistency and coherence when addressing K-related challenges in sustainable urban water management.

C9orf72-associated neurodegeneration in ALS-FTD: breaking new ground in ribosomal RNA and nucleolar dysfunction.

Amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD) are neurodegenerative diseases with distinct clinical appearance. However, both share as major genetic risk factor a C9orf72 locus intronic hexanucleotide expansion. The pathogenic pathways associated with the expansion-dependent neuronal toxicity are still poorly understood. Recent efforts to identify common threads of neuronal dysfunction have pointed towards deficits of ribosomal RNA (rRNA) biogenesis and loss of nucleolar integrity, a condition known as nucleolar stress that is an emerging shared feature among neurodegenerative diseases. Intriguingly, the C9orf72 mutation in ALS-FTD interferes with the function of the nucleolus by transcripts and dipeptide repeats (DPRs) produced by the hexanucleotide expansion. Experimental discrepancies have given rise to different hypotheses with regard to the connection of C9orf72 and nucleolar activity. In this review, we present and discuss emerging concepts concerning the impact of C9orf72 expansion on nucleolar biology. Moreover, we discuss the "nucleolar stress hypothesis," according to which nucleolar malfunction accompanies, exacerbates, or potentially triggers a degenerative phenotype. Upcoming awareness of the involvement of nucleolar stress in C9orf72 ALS-FTD could shed light into its pathogenesis, enabling potential treatment options aimed at shielding an "Achilles' heel" of neurons.

The role of trees in urban stormwater management.

Urban impervious surfaces convert precipitation to stormwater runoff, which causes water quality and quantity problems. While traditional stormwater management has relied on gray infrastructure such as piped conveyances to collect and convey stormwater to wastewater treatment facilities or into surface waters, cities are exploring green infrastructure to manage stormwater at its source. Decentralized green infrastructure leverages the capabilities of soil and vegetation to infiltrate, redistribute, and otherwise store stormwater volume, with the potential to realize ancillary environmental, social, and economic benefits. To date, green infrastructure science and practice have largely focused on infiltration-based technologies that include rain gardens, bioswales, and permeable pavements. However, a narrow focus on infiltration overlooks other losses from the hydrologic cycle, and we propose that arboriculture - the cultivation of trees and other woody plants - deserves additional consideration as a stormwater control measure. Trees interact with the urban hydrologic cycle by intercepting incoming precipitation, removing water from the soil via transpiration, enhancing infiltration, and bolstering the performance of other green infrastructure technologies. However, many of these interactions are inadequately understood, particularly at spatial and temporal scales relevant to stormwater management. As such, the reliable use of trees for stormwater control depends on improved understanding of how and to what extent trees interact with stormwater, and the context-specific consideration of optimal arboricultural practices and institutional frameworks to maximize the stormwater benefits trees can provide.

Protein kinase CK2 interacts at the neuromuscular synapse with Rapsyn, Rac1, 14-3-3γ, and Dok-7 proteins and phosphorylates the latter two.

Previously, we demonstrated that the protein kinase CK2 associates with and phosphorylates the receptor tyrosine kinase MuSK (muscle specific receptor tyrosine kinase) at the neuromuscular junction (NMJ), thereby preventing fragmentation of the NMJs (Cheusova, T., Khan, M. A., Schubert, S. W., Gavin, A. C., Buchou, T., Jacob, G., Sticht, H., Allende, J., Boldyreff, B., Brenner, H. R., and Hashemolhosseini, S. (2006) Genes Dev. 20, 1800-1816). Here, we asked whether CK2 interacts with other proteins involved in processes at the NMJ, which would be consistent with the previous observation that CK2 appears enriched at the NMJ. We identified the following proteins to interact with protein kinase CK2: (a) the α and ß subunits of the nicotinic acetylcholine receptors with weak interaction, (b) dishevelled (Dsh), and (c) another four proteins, Rapsyn, Rac1, 14-3-3γ, and Dok-7, with strong interaction. CK2 phosphorylated 14-3-3γ at serine residue 235 and Dok-7 at several serine residues but does not phosphorylate Rapsyn or Rac1. Furthermore, phosphomimetic Dok-7 mutants aggregated nicotinic acetylcholine receptors in C2C12 myotubes with significantly higher frequency than wild type Dok-7. Additionally, we mapped the interacting epitopes of all four binding partners to CK2 and thereby gained insights into the potential role of the CK2/Rapsyn interaction.

Ecology for the Shrinking City.

This article brings together the concepts of shrinking cities-the hundreds of cities worldwide experiencing long-term population loss-and ecology for the city. Ecology for the city is the application of a social-ecological understanding to shaping urban form and function along sustainable trajectories. Ecology for the shrinking city therefore acknowledges that urban transformations to sustainable trajectories may be quite different in shrinking cities as compared with growing cities. Shrinking cities are well poised for transformations, because shrinking is perceived as a crisis and can mobilize the social capacity to change. Ecology is particularly well suited to contribute solutions because of the extent of vacant land in shrinking cities that can be leveraged for ecosystem-services provisioning. A crucial role of an ecology for the shrinking city is identifying innovative pathways that create locally desired amenities that provide ecosystem services and contribute to urban sustainability at multiple scales.

Biological invasions, ecological resilience and adaptive governance.

In a world of increasing interconnections in global trade as well as rapid change in climate and land cover, the accelerating introduction and spread of invasive species is a critical concern due to associated negative social and ecological impacts, both real and perceived. Much of the societal response to invasive species to date has been associated with negative economic consequences of invasions. This response has shaped a war-like approach to addressing invasions, one with an agenda of eradications and intense ecological restoration efforts towards prior or more desirable ecological regimes. This trajectory often ignores the concept of ecological resilience and associated approaches of resilience-based governance. We argue that the relationship between ecological resilience and invasive species has been understudied to the detriment of attempts to govern invasions, and that most management actions fail, primarily because they do not incorporate adaptive, learning-based approaches. Invasive species can decrease resilience by reducing the biodiversity that underpins ecological functions and processes, making ecosystems more prone to regime shifts. However, invasions do not always result in a shift to an alternative regime; invasions can also increase resilience by introducing novelty, replacing lost ecological functions or adding redundancy that strengthens already existing structures and processes in an ecosystem. This paper examines the potential impacts of species invasions on the resilience of ecosystems and suggests that resilience-based approaches can inform policy by linking the governance of biological invasions to the negotiation of tradeoffs between ecosystem services.

All-optical interrogation of neural circuits in behaving mice.

Recent advances combining two-photon calcium imaging and two-photon optogenetics with computer-generated holography now allow us to read and write the activity of large populations of neurons in vivo at cellular resolution and with high temporal resolution. Such 'all-optical' techniques enable experimenters to probe the effects of functionally defined neurons on neural circuit function and behavioral output with new levels of precision. This greatly increases flexibility, resolution, targeting specificity and throughput compared with alternative approaches based on electrophysiology and/or one-photon optogenetics and can interrogate larger and more densely labeled populations of neurons than current voltage imaging-based implementations. This protocol describes the experimental workflow for all-optical interrogation experiments in awake, behaving head-fixed mice. We describe modular procedures for the setup and calibration of an all-optical system (~3 h), the preparation of an indicator and opsin-expressing and task-performing animal (~3-6 weeks), the characterization of functional and photostimulation responses (~2 h per field of view) and the design and implementation of an all-optical experiment (achievable within the timescale of a normal behavioral experiment; ~3-5 h per field of view). We discuss optimizations for efficiently selecting and targeting neuronal ensembles for photostimulation sequences, as well as generating photostimulation response maps from the imaging data that can be used to examine the impact of photostimulation on the local circuit. We demonstrate the utility of this strategy in three brain areas by using different experimental setups. This approach can in principle be adapted to any brain area to probe functional connectivity in neural circuits and investigate the relationship between neural circuit activity and behavior.

Urbanization drives convergence in soil profile texture and carbon content.

Urban development has driven extensive modification of the global landscape. This shift in land use and land cover alters ecological functioning, and thereby affects sustainable management agendas. Urbanization fundamentally reshapes the soils that underlay landscapes, and throughout the soil profile, extends impacts of urbanization far below the landscape surface. The impacts of urbanization on deeper soils that are beyond the reach of regular land management are largely unknown, and validation of general theories of convergent ecosystem properties are thwarted by a dearth of both level of measurement effort and the substantial heterogeneity in soils and urban landscapes. Here, we examined two soil properties with strong links to ecological functioning-carbon and mineral-fraction particle size-measured in urban soils, and compared them to their pre-urbanization conditions across a continental gradient encompassing global soil diversity. We hypothesized that urbanization drove convergence of soils properties from heterogeneous pre-urban conditions towards homogeneous urban conditions. Based on our observations, we confirm the hypothesis. Both soil carbon and particle size converged toward an intermediate value in the full data distribution, from pre-urban to urban conditions. These outcomes in urban soils were observed to uniformly be fine textured soils with overall lower carbon content. Although these properties are desirable for supporting urban infrastructure (e.g. buildings, pipes), they constrain the potential to render ecosystem services. Since soil profile texture and carbon content were convergent and observed across 11 cities, we suggest that these property profiles can be used as a universal urban soil profile to: 1) provide a clear prediction for how urbanization will shift soil properties from pre-urban conditions, 2) facilitate the adoption of commonly-accepted soil profiles for process models, and 3) offer a reference point to test against urban management strategies and how they impact soil resources.

An analytical approach to ascertain saturation-excess versus infiltration-excess overland flow in urban and reference landscapes.

Uncontrolled overland flow drives flooding, erosion, and contaminant transport, with the severity of these outcomes often amplified in urban areas. In pervious media such as urban soils, overland flow is initiated via either infiltration-excess (where precipitation rate exceeds infiltration capacity) or saturation-excess (when precipitation volume exceeds soil profile storage) mechanisms. These processes call for different management strategies, making it important for municipalities to discern between them. In this study, we derived a generalized one-dimensional model that distinguishes between infiltration-excess overland flow (IEOF) and saturation-excess overland flow (SEOF) using Green-Ampt infiltration concepts. Next, we applied this model to estimate overland flow generation from pervious areas in 11 U.S. cities. We used rainfall forcing that represented low- and high-intensity events and compared responses among measured urban versus predevelopment reference soil hydraulic properties. The derivation showed that the propensity for IEOF versus SEOF is related to the equivalence between two nondimensional ratios: (a) precipitation rate to depth-weighted hydraulic conductivity and (b) depth of soil profile restrictive layer to soil capillary potential. Across all cities, reference soil profiles were associated with greater IEOF for the high-intensity set of storms, and urbanized soil profiles tended towards production of SEOF during the lower intensity set of storms. Urban soils produced more cumulative overland flow as a fraction of cumulative precipitation than did reference soils, particularly under conditions associated with SEOF. These results will assist cities in identifying the type and extent of interventions needed to manage storm water produced from pervious areas.

The Provision of Urban Ecosystem Services Throughout the Private-Social-Public Domain: A Conceptual Framework.

As cities are largely private systems, recent investigations have assessed the provision of ecosystem services from the private realm. However, these assessments are largely based on the concept of ownership and fail to capture the complexity of service provision mediated by interactions between people and ecological structures. In fact, people interact with ecological structures in their role of land tenants and stewards, further modulating the provision of ecosystem services. We devise a theoretical framework based on the concepts of ownership, tenancy, and stewardship, in which people, as mediators of ecosystem services, regulate the provision of services throughout the private-social-public domain. We survey relevant literature describing these dimensions and propose a comprehensive framework focused on the private-social-public domain. Our framework can advance ecosystem service research and enhance the provision of ecosystems services. The inclusion of people's individual, social and public roles in the mediation of ecosystem services could improve how benefits are planned for, prioritized, and optimized across cities.

Agroecology for the Shrinking City.

Many cities are experiencing long-term declines in population and economic activity. As a result, frameworks for urban sustainability need to address the unique challenges and opportunities of such shrinking cities. Shrinking, particularly in the U.S., has led to extensive vacant land. The abundance of vacant land reflects a loss of traditional urban amenities, economic opportunity, neighbors, businesses, and even basic city services and often occurs in neighborhoods with socially and economically vulnerable or underserved populations. However, vacant land also provides opportunities, including the space to invest in green infrastructure that can provide ecosystem services and support urban sustainability. Achieving desirable amenities that provide ecosystem services from vacant land is the central tenet of a recent urban sustainability framework termed ecology for the shrinking city. An agroecological approach could operationalize ecology for the shrinking city to both manage vacancy and address ecosystem service goals. Developing an agroecology in shrinking cities not only secures provisioning services that use an active and participatory approach of vacant land management but also transforms and enhances regulating and supporting services. The human and cultural dimensions of agroecology create the potential for social-ecological innovations that can support sustainable transformations in shrinking cities. Overall, the strength of agroecological principles guiding a green infrastructure strategy stems from its explicit focus on how individuals and communities can shape their environment at multiple scales to produce outcomes that reflect their social and cultural context. Specifically, the shaping of the environment provides a pathway for communities to build agency and manage for resilience in urban social-ecological systems. Agroecology for the shrinking city can support desirable transformations, but to be meaningful, we recognize that it must be part of a greater strategy that addresses larger systemic issues facing shrinking cities and their residents.

Factors Contributing to the Hydrologic Effectiveness of a Rain Garden Network (Cincinnati OH USA).

Infiltrative rain gardens can add retention capacity to sewersheds, yet factors contributing to their capacity for detention and redistribution of stormwater runoff are dynamic and often unverified. Over a four-year period, we tracked whole-system water fluxes in a two-tier rain garden network and assessed near-surface hydrology and soil development across construction and operational phases. The monitoring data provided a quantitative basis for determining effectiveness of this stormwater control measure. Based on 233 monitored warm-season rainfall events, nearly half of total inflow volume was detained, with 90 percent of all events producing no flow to the combined sewer. For the events that did result in flow to the combined sewer system, the rain garden delayed flows for an average of 5.5 h. Multivariate analysis of hydrologic fluxes indicated that total event rainfall depth was a predominant hydrologic driver for network outflow during both phases, with average event intensity and daily evapotranspiration as additional, independent factors in regulating retention in the operational phase. Despite sediment loads that can clog the rooting zone, and overall lower-than-design infiltration rates, tradeoffs among soil profile development and hydrology apparently maintained relatively high overall retention effectiveness. Overall, our study identified factors relevant to regulation of retention capacity of a rain garden network. These factors may be generalizable, and guide improvement of new or existing rain garden designs.