Large-scale Manipulation Research Articles

Large scale manipulation of the dark spot by phase modulation of azimuthally polarized light

A new method is proposed to focus azimuthally polarized beam into an ultra-small or ultra-big dark spot under high numerical aperture lens system. Manipulated by proper designed binary 0-π phase plate, an ultra small dark spot regardless of side-lobe intensity is generated with main-lobe peak to peak distance shrunk to 0.24λ, which is 46% of the case without phase plate. For potential applications, shrinking the dark spot and suppressing the side-lobe intensity are analyzed, and several cases of squeezed dark spots with different levels of side-lobe intensities are presented. Additionally, using a two-zone phase plate to enlarge the dark spot is investigated in this paper, and an enlarged dark spot is readily acquired with the main-lobe peak to peak distance in a range of 100%–200%. The advantages of this method are its large scale manipulation of the dark spot size and its high performance in suppressing side-lobe intensity, which is of great worth in enhancing the performance of many systems such as optical tweezers and stimulated emission depletion (STED) microscope.

The Wickedness and Complexity of Decision Making in Geoengineering

Geoengineering, the deliberate large-scale manipulation of the planetary environment to counteract anthropogenic climate change, has been more widely considered as an accompanying strategy to conventional climate change mitigation measures to combat global warming. However, this approach is far from achieving agreements from different institutional domains. Geoengineering, intended to be deployed on a planetary scale, would cause fundamental interventions to the human-environment system and create new risks and problems with high uncertainty and uneven distribution around the globe. Apart from the physical effects, conflicting attitudes appear from social, economic, and environmental worldviews in the international community. The intertwined sociotechnical complexity and conflicting attitudes make geoengineering a wicked and complex issue. This article elaborates the wickedness and complexity from a system perspective, primarily for an interdisciplinary, policy-oriented audience.

Review of geoengineering approaches to mitigating climate change

Geoengineering, which is the intentional large-scale manipulation of the environment, has been suggested as an effective means of mitigating global warming from anthropogenic greenhouse gas emissions. In this paper, we will review and assess technical and theoretical aspects of land-based, atmosphere-based, ocean-based and space-based geoengineering schemes as well as their potential impacts on global climate and ecosystem. Most of the proposed geoengineering schemes carried out on land or in the ocean are to use physical, chemical or biological approaches to remove atmospheric CO2. These schemes are able to only sequester an amount of atmospheric CO2 that is small compared with cumulative anthropogenic emissions. Most of geoengineering schemes carried out in the atmosphere or space are based on increasing planetary albedo. These schemes have relatively low costs and short lead times for technical implementation, and can act rapidly to reduce temperature anomalies caused by greenhouse gas emissions. The costs and benefits of geoengineering are likely to vary spatially over the planet with some countries and regions gaining considerably while others may be faced with a worse set of circumstances than would be the case without geoengineering. Since current research on geoengineering is limited and various international treaties may limit some geoengineering experiments in the real world, the Geoengineering Model Intercomparison Project (GeoMIP) provides a framework of coordinated experiments for all earth system modeling groups to test geoengineering schemes. However, these experiments used on a global scale have difficulty with accurate resolution of regional and local impacts, so future research on geoengineering is expect to be done by combining earth system models with regional climate models.

The evolution of the hygiene hypothesis: the role of early-life exposures to viruses and microbes and their relationship to asthma and allergic diseases.

Understanding the mechanisms involved in the development of asthma and allergic diseases is expanding, due in part to sequencing advances that have led to the identification of new viral strains such as human rhinovirus strain C (HRV-C) and the human microbiome project. Recent studies have identified new ways in which viral and microbial exposures in early life interact with host genetic background/variants to modify the risk for developing asthma and allergic diseases. Recent research suggests that HRV-C is the main pathogenic agent associated with infant wheeze, hospitalizations and likely the subsequent development of asthma. Pulmonary He MRI suggests that HRV infection in early childhood and subsequent immune responses initiate airway remodeling. Numerous studies of the microbiome indicate that intestinal and airway microbiome diversity and composition contribute to the cause of asthma and allergic diseases. Susceptibility to asthma and allergic diseases is complex and involves genetic variants and environmental exposures (bacteria, viruses, smoking, and pet ownership), alteration of our microbiome and potentially large-scale manipulation of the environment over the past century.

An iterated randomized search algorithm for large-scale texture synthesis and manipulations

In this paper, we introduce a novel iterated random search method for large-scale texture synthesis and manipulations. Previous researches on texture synthesis and manipulation have reached a great achievement both on quality and performance. However, the cost of the popular exhaustive search-based methods is still high especially for large-scale and complex synthesis scenes. Our algorithm contributes great improvements on performances about 2---50 times over the typical patch-based synthesis methods. Texture patterns have been well-known formalized as a Markov Random Field (MRF) whose two hypotheses, stationarity and locality, drive our bold guess that a random sampling may just catch a good match and allows us to propagate the natural coherence in the neighborhood. Meanwhile, the iteration constantly updates the bad guesses to make our algorithm converge fast with the results in the state of the art. We also provide a simple theoretical analysis to compare our iterated randomized search model and the classical synthesis algorithms. Besides, this simple method turns out to work well in various applications as well, such as texture transfer, image completion and video synthesis.

On the Design of an International Governance Framework for Geoengineering

This paper explores the governance options surrounding geoengineering—the deliberate, large-scale manipulation of the Earth's climate system to counteract climate change. The authors focus solely on methods that affect the incoming solar radiation to the atmosphere, referred to as solar radiation management (SRM). They examine whether an international governance framework for SRM is needed, how it should be designed, and whether it is feasible. The authors propose a governance regime that initially has small membership and weak legalization, and is flexible in that future institutional reforms allow for broader membership and deeper commitments. The article provides supporting evidence for key aspects of the regime through past international treaties in arms control and environmental protection, including the Antarctica, Outer Space, and Montreal Protocol treaty regimes. For these cases, acting early and treating the respective problems as part of the “regulation of unexplored territory” produced more effective outcomes than the “national appropriation” approach that characterizes arms control.

An improved, low-cost, hydroponic system for growing Arabidopsis and other plant species under aseptic conditions

BackgroundHydroponics is a plant growth system that provides a more precise control of growth media composition. Several hydroponic systems have been reported for Arabidopsis and other model plants. The ease of system set up, cost of the growth system and flexibility to characterize and harvest plant material are features continually improved in new hydroponic system reported.ResultsWe developed a hydroponic culture system for Arabidopsis and other model plants. This low cost, proficient, and novel system is based on recyclable and sterilizable plastic containers, which are readily available from local suppliers. Our system allows a large-scale manipulation of seedlings. It adapts to different growing treatments and has an extended growth window until adult plants are established. The novel seed-holder also facilitates the transfer and harvest of seedlings. Here we report the use of our hydroponic system to analyze transcriptomic responses of Arabidopsis to nutriment availability and plant/pathogen interactions.ConclusionsThe efficiency and functionality of our proposed hydroponic system is demonstrated in nutrient deficiency and pathogenesis experiments. Hydroponically grown Arabidopsis seedlings under long-time inorganic phosphate (Pi) deficiency showed typical changes in root architecture and high expression of marker genes involved in signaling and Pi recycling. Genome-wide transcriptional analysis of gene expression of Arabidopsis roots depleted of Pi by short time periods indicates that genes related to general stress are up-regulated before those specific to Pi signaling and metabolism. Our hydroponic system also proved useful for conducting pathogenesis essays, revealing early transcriptional activation of pathogenesis-related genes.

An integrative approach to understanding host–parasitoid population dynamics in real landscapes

Many of our advances regarding the spatial ecology of predators and prey have been attributed to research with insect parasitoids and their hosts. Host–parasitoid systems are ideal for spatial-ecological studies because of the small size of the organisms, the often discrete distribution of their resources, and the relative ease with which host mortality from parasitoids can be determined. We outline an integrated approach to studying host–parasitoid interactions in heterogeneous natural landscapes. This approach involves conducting experiments to obtain critically important information on dispersal and boundary behavior of the host and parasitoid, large-scale manipulations of landscape structure to reveal the impacts of landscape change on host–parasitoid interactions and temporal population dynamics, and the development of spatially realistic, behavior-based landscape models. The dividends from such an integrative approach are far reaching, as is illustrated in our research on the prairie planthopper Prokelisia crocea and its egg parasitoid Anagrus columbi that occurs in the tall-grass prairies of North America. Here, we describe the population structure of this system which is based on a long-term survey of planthoppers and parasitoids among host–plant patches. We also outline novel approaches to experimentally quantify and model the movement and boundary behavior of animals in general. The value of this information is revealed in a landscape-level field experiment that was designed to test predictions about how landscape change affects the spatial and temporal population dynamics of the host and parasitoid. Finally, with these empirical data as the foundation, we describe novel simulation models that are spatially realistic and behavior based. Drawing from this integrated approach and case study, we identify key research questions for the future.

Climatic change special issue: geoengineering research and its limitations

Even under scenarios that assume that humanity will move aggressively away from fossil fuels as the predominant source of energy for the world economy, the equivalent carbon dioxide concentration in the atmosphere is expected to at least double its preindustrial value by the end of this century. If reductions are not aggressive, or if emissions continue their rapid upward trend, then a tripling is likely, and perhaps even a quadrupling by early in the 22 century. Under such emission scenarios, it is likely that the global average temperature will come to exceed levels that numerous experts say will greatly harm ecosystems and human health, security and welfare. Given continuing political inertia surrounding global emissions reductions, such an outcome is becoming more and more difficult to avoid; indeed, at this point, some believe it inevitable if climate policy confines itself to conventional methods, such as mitigation and adaptation. In this context, discussion of “geoengineering”—roughly the “deliberate large-scale manipulation of the planetary environment to counteract anthropogenic climate change” (Shepherd et al. 2009)—has become a hot topic. Proposed geoengineering approaches fall into two broad categories: those that attempt to limit solar radiation (termed solar radiation management, SRM) and those that attempt to remove carbon dioxide from the atmosphere (carbon drawdown and removal, CDR). A landmark study conducted by the United Kingdom’s Royal Society in 2009 concluded that “geoengineering is likely to be technically feasible, and could substantially reduce the costs and risks of climate change”. However, the report also maintained that not all proposed methods are likely to be equally effective, and that there is a need for further research to understand the feasibility, climate impacts and social dimensions (including ethics, law and governance) of proposed geoengineering schemes. One specific recommendation of the report was the need to “develop a code of practice for geoengineering research and provide recommendations to the international scientific community for a voluntary research governance Climatic Change (2013) 121:427–430 DOI 10.1007/s10584-013-1000-4

Large-Scale Referencing of the Telemetric Neurovent-P-tel Intracranial Pressure Sensor in a Porcine Model

The Neurovent-P-tel sensor is a promising device for telemetric intracranial pressure (ICP) measurements in cases of complex hydrocephalus. Data on its accuracy within a broad ICP range are missing. We applied a porcine model for large-scale manipulation of the ICP values. The telemetric ICP sensor was referenced against ICP values measured directly from a water column within a riser tube. A total of 34 comparative ICP measurements within an ICP range from 2 cm H₂O to 31 mm Hg were performed. The mean difference between both measurement techniques was 0.4 mm Hg. The limits of agreement, where 95% of differences between both methods are expected, were from -2.4 to 3.1 mm Hg. The telemetric Neurovent-P-tel sensor system provides good accuracy within a broad range exceeding normal ICP values and might be useful in clinical practice.

Earthmasters: the dawn of the age of climate engineering

This book goes to the heart of the unfolding reality of the twenty-first century: international efforts to reduce greenhouse gas emissions have all failed and before the end of the century Earth is projected to be warmer than it has been for 15 million years. The question, the crisis be avoided? has been superseded by a more frightening one, can be done to prevent the devastation of the living world?. And the disturbing answer, now under wide discussion both within and outside the scientific community, is to seize control of the very climate of the Earth itself. Clive Hamilton begins by exploring the range of technologies now being developed in the field of geoengineering - the intentional, enduring, large-scale manipulation of Earth's climate system. He lays out the arguments for and against climate engineering, and reveals the extent of vested interests linking researchers, venture capitalists and corporations. He then examines what it means for human beings to be making plans to control the planet's atmosphere, probes the uneasiness we feel with the notion of exercising technological mastery over nature, and challenges the ways we think about ourselves and our place in the natural world.

Recombineering Homologous Recombination Constructs in <em>Drosophila</em>

The continued development of techniques for fast, large-scale manipulation of endogenous gene loci will broaden the use of Drosophila melanogaster as a genetic model organism for human-disease related research. Recent years have seen technical advancements like homologous recombination and recombineering. However, generating unequivocal null mutations or tagging endogenous proteins remains a substantial effort for most genes. Here, we describe and demonstrate techniques for using recombineering-based cloning methods to generate vectors that can be used to target and manipulate endogenous loci in vivo. Specifically, we have established a combination of three technologies: (1) BAC transgenesis/recombineering, (2) ends-out homologous recombination and (3) Gateway technology to provide a robust, efficient and flexible method for manipulating endogenous genomic loci. In this protocol, we provide step-by-step details about how to (1) design individual vectors, (2) how to clone large fragments of genomic DNA into the homologous recombination vector using gap repair, and (3) how to replace or tag genes of interest within these vectors using a second round of recombineering. Finally, we will also provide a protocol for how to mobilize these cassettes in vivo to generate a knockout, or a tagged gene via knock-in. These methods can easily be adopted for multiple targets in parallel and provide a means for manipulating the Drosophila genome in a timely and efficient manner.

Messing with nature? Exploring public perceptions of geoengineering in the UK

Anthropogenic influence on the climate – and possible societal responses to it – offers a unique window through which to examine the way people think about and relate to the natural world. This paper reports data from four, one-day deliberative workshops conducted with members of the UK public during early 2012. The workshops focused on geoengineering – the deliberate, large-scale manipulation of the planetary environment – as one of three possible responses to climate change (alongside mitigation and adaptation). Here, we explore one of the most pervasive and wide-ranging themes to emerge from the workshops: whether geoengineering represented an unprecedented human intervention into ‘nature’, and what the moral consequences of this might be. Using the concept of ‘messing with nature’ as an analytical lens, we explore public perceptions of geoengineering. We also reflect on why ‘messing with nature’ was such a focal point for debate and disagreement, and whether the prospect of geoengineering may reveal new dimensions to the way that people think about the natural world, and their relationship to it.

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.

Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental dissection by directed regulatory motif disruption has remained unfeasible at the genome scale. Here, we use a massively parallel reporter assay (MPRA) to measure the transcriptional levels induced by 145-bp DNA segments centered on evolutionarily conserved regulatory motif instances within enhancer chromatin states. We select five predicted activators (HNF1, HNF4, FOXA, GATA, NFE2L2) and two predicted repressors (GFI1, ZFP161) and measure reporter expression in erythroleukemia (K562) and liver carcinoma (HepG2) cell lines. We test 2104 wild-type sequences and 3314 engineered enhancer variants containing targeted motif disruptions, each using 10 barcode tags and two replicates. The resulting data strongly confirm the enhancer activity and cell-type specificity of enhancer chromatin states, the ability of 145-bp segments to recapitulate both, the necessary role of regulatory motifs in enhancer function, and the complementary roles of activator and repressor motifs. We find statistically robust evidence that (1) disrupting the predicted activator motifs abolishes enhancer function, while silent or motif-improving changes maintain enhancer activity; (2) evolutionary conservation, nucleosome exclusion, binding of other factors, and strength of the motif match are predictive of enhancer activity; (3) scrambling repressor motifs leads to aberrant reporter expression in cell lines where the enhancers are usually inactive. Our results suggest a general strategy for deciphering cis-regulatory elements by systematic large-scale manipulation and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to develop predictive models of gene expression.

Indirect and mitigated effects of pulsed resources on the population dynamics of a northern rodent

Pulsed resources have significant effects on population and community dynamics in terrestrial ecosystems. Mast seeding is an important resource pulse in deciduous forests; these boom and bust cycles of seed production generate strong lagged population responses by post-dispersal seed predators such as rodents, which then cascade through multiple trophic levels and regulate population dynamics of their predators and prey. However, similar interactions in another major pulsed system, coniferous forests, are inconsistent, and the effects of interannual variation in conifer seed production on many consumer populations are largely unknown. We used large-scale manipulation and intensive monitoring to examine the population dynamics of deer mice (Peromyscus maniculatus) in relation to fall seed production by two northern conifers, white spruce (Picea glauca) and subalpine fir (Abies lasiocarpa). Previous studies have shown that spruce seeds are a preferred food source of mice, while fir seeds are generally avoided if other foods are available. Therefore, we expected that there would be a positive relationship between mouse demography and previous spruce seed production, but no effect of fir mast seeding. Supplementation of a mouse population using spruce seeds indicated that increased fall spruce seed availability can enhance overwinter survival and population densities in the following spring, summer, and fall. However, long-term population monitoring indicated that mouse demography was not positively affected by spruce mast seeding, likely due to strong interspecific competition with the North American red squirrel (Tamiasciurus hudoniscus), a dominant pre-dispersal spruce seed predator. Conversely, we observed an unexpected delayed effect of fir mast seeding, where increased fall fir seed production did not influence overwinter or spring mouse demography, but instead enhanced summer survival, body masses and pregnancy rates of overwintered adults. This led to increased summer population densities and may have been mediated by population responses of invertebrate post-dispersal seed predators to increased fir seed availability. Our results indicate that rodent responses to resource pulses in coniferous forests are more complex than in deciduous environments and reveal previously unobserved direct and indirect consumer-resource dynamics that require further examination. This system is ideal for the large-scale, integrative ecosystem studies that ecologists are encouraged to pursue.

Piecewise Disassembly of a Large-Herbivore Community across a Rainfall Gradient: The UHURU Experiment

Large mammalian herbivores (LMH) strongly influence plant communities, and these effects can propagate indirectly throughout food webs. Most existing large-scale manipulations of LMH presence/absence consist of a single exclusion treatment, and few are replicated across environmental gradients. Thus, important questions remain about the functional roles of different LMH, and how these roles depend on abiotic context. In September 2008, we constructed a series of 1-ha herbivore-exclusion plots across a 20-km rainfall gradient in central Kenya. Dubbed "UHURU" (Ungulate Herbivory Under Rainfall Uncertainty), this experiment aims to illuminate the ecological effects of three size classes of LMH, and how rainfall regimes shape the direction and magnitude of these effects. UHURU consists of four treatments: total-exclusion (all ungulate herbivores), mesoherbivore-exclusion (LMH >120-cm tall), megaherbivore-exclusion (elephants and giraffes), and unfenced open plots. Each treatment is replicated three times at three locations (“sites”) along the rainfall gradient: low (440 mm/year), intermediate (580 mm/year), and high (640 mm/year). There was limited variation across sites in soil attributes and LMH activity levels. Understory-plant cover was greater in plots without mesoherbivores, but did not respond strongly to the exclusion of megaherbivores, or to the additional exclusion of dik-dik and warthog. Eleven of the thirteen understory plant species that responded significantly to exclusion treatment were more common in exclusion plots than open ones. Significant interactions between site and treatment on plant communities, although uncommon, suggested that differences between treatments may be greater at sites with lower rainfall. Browsers reduced densities of several common overstory species, along with growth rates of the three dominant Acacia species. Small-mammal densities were 2–3 times greater in total-exclusion than in open plots at all sites. Although we expect patterns to become clearer with time, results from 2008–2012 show that the effects of excluding successively smaller-bodied subsets of the LMH community are generally non-additive for a given response variable, and inconsistent across response variables, indicating that the different LMH size classes are not functionally redundant. Several response variables showed significant treatment-by-site interactions, suggesting that the nature of plant-herbivore interactions can vary across restricted spatial scales.

Research on the key technology of automatic manipulation at micro/nano scale by optically-induced electrokinetics

The optically-induced dielectrophoresis method, as a novel micro-/nano-scaled technology, has been commonly explored and used in biomedical engineering and micro/nano material fields, due to the advantages of the scheme of the programmable, automatic, large scale and real time assembly and manipulation. In this paper, the generation function of the optically-induced nonuniform electric field is elucidated followed with a finite element simulation of the positive and negative dielectrophoresis force, respectively. The fabrication process of the optoelectronic tweezers is shown and the configuration of the experimental setup is described. Then, the polystyrene beads with three sizes of 500 nm, 1 μm and 10 μm are separated by utilizing different magnitude and direction of the optically-induced dielectrophoresis. Finally, the separation of cancer cells is also successfully achieved.

Situating and Abandoning Geoengineering: A Typology of Five Responses to Dangerous Climate Change

Geoengineering, the “deliberate, large-scale manipulation of the planetary environment in order to counteract anthropogenic climate change” (Shepherd et al. 2009, 1), is attracting increasing interest. As well as the Royal Society, various scientific and government organizations have produced reports on the potential and challenge of geoengineering as a potential strategy, alongside mitigation and adaptation, to avoid the vast human and environmental costs that climate change is thought to bring (Blackstock et al. 2009; GAO 2010; Long et al. 2011; Rickels et al. 2011). “Geoengineering” covers a diverse range of proposals conventionally divided into carbon dioxide removal (CDR) proposals and solar radiation management (SRM) proposals. This article argues that “geoengineering” should not be regarded as a third category of response to climate change, but should be disaggregated. Technically, CDR and SRM are quite different and discussing them together under the rubric of geoengineering can give the impression that all the technologies in the two categories of response always raise similar challenges and political issues when this is not necessarily the case. However, CDR and SRM should not be completely subsumed into the preexisting categories of mitigation and adaptation. Instead, they can be regarded as two parts of a five-part continuum of responses to climate change. To make this case, the first section of this article discusses whether geoengineering is distinctive, and the second situates CDR and SRM in relation to other responses to climate change.

Growth responses of mature loblolly pine to dead wood manipulations

Large-scale manipulations of dead wood in mature Pinus taeda L. stands in the southeastern United States included a major one-time input of logs (fivefold increase in log volume) created by felling trees onsite, annual removals of all dead wood above ⩾10cm in diameter and ⩾60cm in length, and a reference in which no manipulations took place. We returned over a decade later to determine how these treatments affected tree growth using increment cores. There were no significant differences in tree density, basal area or tree diameters among treatments at the time of sampling. Although tree growth was consistently higher in the log-input plots and lower in the removal plots, this was true even during the 5year period before the experiment began. When growth data from this initial period were included in the model as a covariate, no differences in post-treatment tree growth were detected. It is possible that treatment effects will become apparent after more time has passed, however.

Climate engineering: The way forward?

The deliberate large-scale manipulation of the climate is increasingly being discussed as a potential tool to ensure the basic condition for a sustainable future: a habitable climate. While far from the ideal solution, the rate of climate change continues to outpace our attempts at a response, prompting some scientists and politicians to call for the consideration of climate engineering or geoengineering to avoid catastrophic climate change, while political processes to reduce greenhouse gases catch up. A November 2010 expert meeting was held at UNESCO to raise awareness of geoengineering, its potential to counteract climate change and its risks, and to broaden the discussion within the international community. Potential geoengineering methods include solar radiation management and carbon dioxide removal techniques that are largely theoretical and remain untested, despite a long history. Responsible research can only proceed, and informed decisions be made, once governance structures have been developed beyond mere principles insufficient to guide researchers and policy makers. At the same time, realistic communication on these activities must increase and improve so that civil society can play a role in determining acceptable levels and types of human intervention. Appropriate geoengineering research should be considered for solar geoengineering methods that promise to quickly and affordably decrease global mean temperature, and for carbon geoengineering methods that target the core problem of climate change by directly removing carbon dioxide from the atmosphere. A small cadre of scientists and policy makers has advanced the discussion of geoengineering and its likely impacts, but the path to a sustainable future cannot be charted until the wider international community asks some fundamental questions about what kind of regulation is appropriate, how it should be implemented and by whom and at what cost. This task is urgent, and only by raising awareness of geoengineering can we secure the participation of the international community in developing governance structures and ensuring that responsible research on geoengineering proceeds in a timely and consensual manner.