Functional connectivity and dendritic integration of feedback in visual cortex

A fundamental question in neuroscience is how different brain regions communicate with each other. Sensory processing engages distributed circuits across many brain areas and involves information flow in the feedforward and feedback direction. While feedforward processing is conceptually well understood, feedback processing has remained mysterious. Cortico-cortical feedback axons are enriched in layer 1, where they form synapses with the apical dendrites of pyramidal neurons. The organization and dendritic integration of information conveyed by these axons, however, are unknown. This thesis describes my efforts to link the circuit-level and dendritic-level organization of cortico-cortical feedback in the mouse visual system. First, using cellular resolution all-optical interrogation across cortical areas, I characterized the functional connectivity between the lateromedial higher visual area (LM) and primary visual cortex (V1). Feedback influence had both facilitating and suppressive effects on visually-evoked activity in V1 neurons, and was spatially organized: retinotopically aligned feedback was relatively more suppressive, while retinotopically offset feedback was relatively more facilitating. Second, to examine how feedback inputs are integrated in apical dendrites, I optogenetically stimulated presynaptic neurons in LM while using 2-photon calcium imaging to map feedback-recipient spines in the apical tufts of layer 5 neurons in V1. Activation of a single feedback-providing input was sufficient to boost calcium signals and recruit branch-specific local events in the recipient dendrite, suggesting that feedback can engage dendritic nonlinearities directly. Finally, I measured the recruitment of apical dendrites during visual stimulus processing. Surround visual stimuli, which should recruit relatively more facilitating feedback, drove local calcium events in apical tuft branches. Moreover, global dendritic event size was not purely determined by somatic activity but modulated by visual stimuli and behavioural state, in a manner consistent with the spatial organization of feedback. In summary, these results point toward a possible involvement of active dendritic processing in the integration of feedback signals. Active dendrites could thus provide a biophysical substrate for the integration of essential top-down information streams, including contextual or predictive processing

How Environmental Justice Patterns are Shaped by Place: Terrain and Tree Canopy in Cincinnati, Ohio, USA

Understanding the spatial distribution of environmental amenities requires consideration of social and biogeophysical factors, and how they interact to produce patterns of environmental justice or injustice. In this study, we explicitly account for terrain, a key local environmental factor, while assessing whether tree canopy is distributed equally in Cincinnati, Ohio, USA. We conducted separate analyses for all land and for residential land only. For all land, terrain alone accounted for 59% of the variation in tree canopy cover. In our spatial autoregressive model, socioeconomic variables describing race, wealth, and education did not explain significant variation in canopy cover. In other words, terrain is the primary factor related to tree canopy in Cincinnati. In our analysis of residential land only, terrain was again the dominant predictor of tree canopy cover, and percent black population and median home value were also positive, significant explanatory variables. Tree canopy was abundant in two hilly areas with dissimilar socioeconomic characteristics, with proportionally larger black populations in the western hills and higher home values in the eastern hills. In summary, the overwhelming importance of terrain may obscure subtler patterns between tree canopy and socioeconomic variables. Although general social processes may drive environmental injustice across disparate cities, our study highlights the need to account for local biogeophysical context

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

Cortico-cortical feedback engages active dendrites in visual cortex

Sensory processing in the neocortex requires both feedforward and feedback information flow between cortical areas 1. In feedback processing, higher-level representations provide contextual information to lower levels, and facilitate perceptual functions such as contour integration and figure–ground segmentation 2,3. 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

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

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

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

The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion

DNA double-stranded breaks (DSBs) are among the most severe forms of DNA damage and responsible for chromosomal translocations that may lead to gene fusions. The RAD51 family plays an integral role in preserving genome stability by homology directed repair of DSBs. From a proteomics screen, we recently identified SFPQ/PSF as an interacting partner with the RAD51 paralogs, RAD51D, RAD51C and XRCC2. Initially discovered as a potential RNA splicing factor, SFPQ was later shown to have homologous recombination and non-homologous end joining related activities and also to bind and modulate the function of RAD51. Here, we demonstrate that SFPQ interacts directly with RAD51D and that deficiency of both proteins confers a severe loss of cell viability, indicating a synthetic lethal relationship. Surprisingly, deficiency of SFPQ alone also leads to sister chromatid cohesion defects and chromosome instability. In addition, SFPQ was demonstrated to mediate homology directed DNA repair and DNA damage response resulting from DNA crosslinking agents, alkylating agents and camptothecin. Taken together, these data indicate that SFPQ association with the RAD51 protein complex is essential for homologous recombination repair of DNA damage and maintaining genome integrity

Expression of Mo3e antigen by cultured human umbilical vein endothelial cells (HUVEC) stimulated by phorbol myristate acetate (PMA) and related pharmacological inducers of protein kinase C

Mo3e is a protease-sensitive membrane antigen (p75,50) selectively expressed by human monocytic cells (monocytes and U-937 cells) stimulated in vitro by exposure to a variety of activating factors, including phorbol diester compounds, bacterial lipopolysaccharide (LPS), and muramyl dipeptide (MDP) (R. F. Todd et al., J. Immunol. 135, 3869, 1985). Here we report that primary and multiply-passaged cultures of HUVEC also express the Mo3e determinant after stimulation by phorbol myristate acetate (PMA) and related inducers of protein kinase C. As measured in a radioimmunoassay of anti-Mo3e antibody binding to monolayer cultures of HUVEC, unstimulated cells bore little if any Mo3e. After culture for 4-120 hr in medium containing PMA, 4[beta]-phorbol dibutyrate, 4[beta]-phorbol didecanoate, or mezerein (each at a conentration of 81 nM), or 1-oleoyl-2-acetoyl-sn-3-glycerol (1 mM), HUVEC were found to selectively express the Mo3e determinant. The magnitude of expression was dependent upon the concentration of the stimulus, maximal by 24 hr, and inhibited by cycloheximide. The combination of PMA and the calcium ionophore, ionomycin, had an additive or synergistic effect on HUVEC Mo3e expression. The biologically inactive phorbol compounds 4[beta]-phorbol and 4[alpha]-phorbol didecanoate failed to stimulate Mo3e expression. Also inactive as inducers of HUVEC Mo3e expression were crude lymphokine and monokine supernatants, recombinant human lymphokines (interferon-[gamma] and interleukin-2), recombinant human monokines (interleukin-1 and tumor necrosis factor), bacterial cell wall products including LPS and MDP, pharmacologic agents that increase intracellular cyclic adenosine monophosphate (prostaglandin E2, cholera toxin, theophylline, isoproterenol and isobutylmethylxanthine), lectins (Con A and PHA), and heparin. These results indicate that Mo3e is an inducible plasma membrane antigen of not only mononuclear phagocytes but also cultured HUVEC.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27376/1/0000404.pd

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data