Mapping the brain, cell by cell

MIT researchers used their new tissue preservation technique to label and image neurons in a brain region called the globus pallidus externa. Neurons that express a protein called parvalbumin are labeled in red, and neurons labeled blue express a protein called GAD1. Image: Young-Gyun Park, Changho Sohn, Ritchie Chen, and Kwanghun Chung

Technique for preserving tissue allows researchers to create maps of neural circuits with single-cell resolution.

Anne Trafton | MIT News Office | December 17, 2018
Original link:  http://news.mit.edu/2018/cell-neural-circuit-brain-map-1217 

MIT chemical engineers and neuroscientists have devised a new way to preserve biological tissue, allowing them to visualize proteins, DNA, and other molecules within cells, and to map the connections between neurons.

The researchers showed that they could use this method, known as SHIELD, to trace the connections between neurons in a part of the brain that helps control movement and other neurons throughout the brain.

“Using our technique, for the first time, we were able to map the connectivity of these neurons at single-cell resolution,” says Kwanghun Chung, an assistant professor of chemical engineering and a member of MIT’s Institute for Medical Engineering and Science and Picower Institute for Learning and Memory. “We can get all this multiscale, multidimensional information from the same tissue in a fully integrated manner because with SHIELD we can protect all this information.”

Chung is the senior author of the paper, which appears in the Dec. 17 issue of Nature Biotechnology. The paper’s lead authors are MIT postdocs Young-Gyun Park, Chang Ho Sohn, and Ritchie Chen.

Chung is now leading a team of researchers from several institutions that recently received a National Institutes of Health grant to use this technique to produce three-dimensional maps of the entire human brain. “We will be working with the Matthew Frosch group at MGH, the Van Wedeen group at MGH, the Sebastian Seung group at Princeton, and the Laura Brattain group at MIT Lincoln Lab to generate the most comprehensive brain map yet,” he says.

Preserving information

Brain tissue is very delicate and cannot be easily studied unless steps are taken to preserve the tissue from damage. Chung and other researchers have previously developed techniques that allow them to preserve certain molecular components of brain tissue for research, including proteins or messenger RNA, which reveals which genes are turned on.

However, Chung says, “there is no good method that can preserve everything.”

Chung and his colleagues hypothesized that they might be able to better preserve tissue using molecules called polyepoxides — reactive organic molecules that are often used to produce glues. They tested several commercially available polyepoxides and discovered one that had distinctive structural traits that made it ideally suited for their purposes.

The epoxide they chose has a flexible backbone and five branches, each of which can bind to certain amino acids (the building blocks of proteins), as well as other molecules such as DNA and RNA. The flexible backbone allows the epoxides to bind to several spots along the target molecules, and to form cross-links with nearby biomolecules. This renders individual biomolecules and the entire tissue structure very stable and resistant to damage from heat, acid, or other harmful agents. SHIELD also protects key properties of biomolecules, such as protein fluorescence and antigenicity.

To protect large-scale brain tissues and clinical samples, the researchers combined SHIELD with SWITCH, another technique they developed to control chemical reaction speed. They first use the SWITCH-OFF buffer, which halts chemical reactions, to give the epoxides time to diffuse through the entire tissue. When the researchers move the sample to SWITCH-ON condition, the epoxides begin to bind to nearby molecules.

To speed up the clearing and labeling process of SHIELD-protected tissue, the researchers also applied a randomly changing electric field, which they have previously shown increases the transport rate of the molecules. In this paper, they showed that the entire process from preservation to labeling of biopsy tissue could be performed in just four hours.

“We found that this SHIELD coating keeps proteins stable against harsh stressors,” Chung says. “Because we can preserve all the information that we want, and we can extract it at multiple stages, we can better understand the functions of biological components, including neural circuits.”

Once the tissue is preserved, the researchers can label a variety of different targets, including proteins and mRNA produced by the cells. They can also apply techniques such as MAP, which Chung developed in 2016, to expand the tissue and image it at different size scales.

In this paper, the researchers worked with Byungkook Lim’s group at the University of California at San Diego to use SHIELD to map a brain circuit that begins in the globus pallidus externa (GPe), part of the brain’s basal ganglia. This region, which is involved in motor control and other behaviors, is one of the targets of deep brain stimulation — a type of electrical stimulation sometimes used to treat Parkinson’s disease. In the mouse brain, Chung and his colleagues were able to trace the connections between neurons in the GPe and in other parts of the brain, and to count the number of putative synaptic connections between these neurons.

Better biopsies

The speed of SHIELD tissue processing means that it also holds promise for performing rapid, more informative biopsies of patient tissue samples, Chung says. Current methods require embedding tissue samples with paraffin, slicing them, and then applying stains that can reveal cell and tissue abnormalities.

“The current way of doing tissue diagnosis hasn’t changed in many decades, and the process takes days or weeks,” Chung says. “Using our technique, we can rapidly process intact biopsy samples and immuno-label them with really specific, clinically relevant antibodies, and then image the whole thing at high resolution, in three dimensions. And everything can be done in four hours.”

In this paper, the researchers showed that they could label mouse kidney tumor with an antibody that targets proliferating cancer cells.

“The stabilization and preservation of biological information within tissue samples is essential in experiments for optical microscopy,” says Liqun Luo, a professor of biology at Stanford University, who was not involved in the research. “The achievement of SHIELD is not a large advance in just one category, but rather marked improvements across the board, in preserving proteins, transcripts, and tissue structure, as samples are processed through the harsh techniques prescribed by today's best labeling and imaging protocols.”

The MIT team hopes to make this technology widely available and has already distributed it to more than 50 labs around the world. The research was funded by the Burroughs Wellcome Fund Career Award at the Scientific Interface, the Searle Scholars Program, the Packard Award in Science and Engineering, the NARSAD Young Investigator Award, the McKnight Foundation Technology Award, the JPB Foundation, and NCSOFT Cultural Foundation, and the National Institutes of Health.

Thorium vs. Molten Salt Reactor

Market Intelligence | 12/18/2018 | By Canon Bryan

Original link:  http://4thgeneration.energy/thorium-vs-molten-salt-reactor/?fbclid=IwAR0OXSkaAGq2MuY3X-AiEdIFOT9p8qIGreEuslpwHqrF4t5XSa60IGwCB7k 

 

To a limited group of technophiles and nuclear technology enthusiasts, thorium has become a unicorn. But does thorium really represent nuclear innovation?

Back in the 1950s and 1960s, the scientists at Oak Ridge National Laboratory in the USA developed the Molten Salt Reactor design – a liquid salt fueled and cooled nuclear reactor system. They designed it, they prototyped it, and they operated it. The experiment was called the Molten Salt Reactor Experiment, or MSRE. The MSRE used a thorium fuel cycle.  It used a lithium beryllium fluoride coolant salt mixture, called FLiBe. It used a graphite moderator. It used a special material called Hastelloy N – a nickel alloy developed specifically to withstand the harsh environment.

The experiment was a great success. It proved that this liquid fuel system could facilitate nuclear fission, and that it was tremendously stable, and easy to operate. Dick Engel, the project manager, even called it “boring” because the engineers had virtually nothing to do while it operated.

At the rudiments of the technology lay the liquid fuel. Liquid nuclear fuel-coolant, the MSRE discovered, was a much more efficient mechanism for capturing the immense heat from fission than solid fuel/water coolant. Salt coolant was a much more versatile coolant, with a huge thermal range, compared to a water coolant, and capable of storing and easily conveying that immense heat from fission.

The thorium-232/uranium-233 fuel cycle that was used in the MSRE was a departure from the uranium-235/uranium-238/plutonium-239 fuel cycle that was being used in the Light Water Reactor design, also invented by the Americans. The LWR was being used in the US Navy submarine program, and by the mid-1950s, started to be used in commercial power plants. Thorium, it was projected, could have some advantages over uranium, particularly in a liquid fuel application.

In order to make thorium fuel, Th232 must either be blended with U235 or Pu239, or it must be bombarded with neutrons to make a supply of U233, which is also fissile. The Th232 and U233 is then blended to create a fuel that is capable of achieving criticality. Since the dawn of the atomic age, there have been a small handful of commercial applications of a thorium fuel cycle.

In order to make commercial nuclear fuel, U235, which is about 0.7% of naturally-occurring uranium, must be concentrated to between 3% and 5% of the uranium fuel element. This is not so easily achieved either, but there is a multi-decade legacy of uranium enrichment. The fuel cycle is well-understood by regulators, operators and the supply chain.

What are the advantages of thorium?

Thorium is abundant. That is certainly an advantage it has over uranium. It is abundant and broadly geographically dispersed and easy to extract from nature. Unlike uranium, thorium is found in great concentrations right on the surface of the earth, most commonly, in black sand beaches.

Thorium is not fissile, which means that thorium by itself could never possibly be weaponized. However, because it is not fissile, it means that thorium always requires fissile material to make fuel, and that creates new proliferation risks.

This is where the actual advantages of thorium end.  All the other advantages commonly attributed to thorium are actually advantages of a Molten Salt Reactor – not of thorium itself. These virtues became conflated with the Molten Salt Reactor design. Because of the fact that thorium fuel was used, enthusiasts rediscovering this technology 40 years later have misplaced the rudiments of the innovation.

Molten Salt Reactors have tremendous safety, waste and proliferation virtues, which translate into substantial commercial virtues.  The following is a non-exhaustive list:

• Fluoride salts have an approximately 1,000C range in which they stay liquid – neither freezing nor boiling;
• Fluoride salts operate naturally at high temperature, obviating the need for immense pressure in a reactor vessel;
• Fluoride salts are chemically very stable and inert, eliminating the risk of chemical explosions in a reactor system;
• A liquid fuel is inherently easier and cheaper to chemically process, thereby creating a pathway for total nuclear waste elimination.

There are many others. These advantages are specific to Molten Salt Reactors, and not to thorium fuel.

The thorium enthusiasts will certainly find this controversial. However, if the goal is eliminating energy poverty and pollution, one must accurately assess the source terms of nuclear innovation.  The mystical nature of thorium has served its purpose by attracting all walks of life to develop an interest in advanced nuclear technology – including myself.  Now the market must focus on the most pragmatic way of commercializing true nuclear innovation.

About the author

Canon Bryan

Mr. Bryan has served as officer and director for private and public companies in Canada and the USA. Mr. Bryan has considerable experience providing financial management services to clients in various industries. He has focused primarily on energy and natural resources industries. Mr. Bryan was a co-founder of: Terrestrial Energy, a developer of commercial advanced nuclear power plants; NioCorp (NB: TSXV), a company developing the largest niobium deposit in North America; Uranium Energy Corp (UEC: NYSE), a producer of ISR uranium in the USA. Mr. Bryan was senior financial analyst for Lasik Vision Corporation (LSK: CDNX), which was the world’s largest provider of laser refractive surgical services. Mr. Bryan completed his studies in accounting and finance at the University of British Columbia.

Urban ecology

From Wikipedia, the free encyclopedia

Central Park represents an ecosystem fragment within a larger urban environment.

Urban ecology is the scientific study of the relation of living organisms with each other and their surroundings in the context of an urban environment. The urban environment refers to environments dominated by high-density residential and commercial buildings, paved surfaces, and other urban-related factors that create a unique landscape dissimilar to most previously studied environments in the field of ecology.

Urban ecology is a recent field of study compared to ecology as a whole. The methods and studies of urban ecology are similar to and comprise a subset of ecology. The study of urban ecology carries increasing importance because more than 50% of the world's population today lives in urban areas. At the same time, it is estimated that within the next forty years, two-thirds of the world's population will be living in expanding urban centers. The ecological processes in the urban environment are comparable to those outside the urban context. However, the types of urban habitats and the species that inhabit them are poorly documented. Often, explanations for phenomena examined in the urban setting as well as predicting changes because of urbanization are the center for scientific research.

History

The creation of an important stream water garden in Metz's centre during the early 70s was one of the materializations of Jean-Marie Pelt's works on urban ecology.

Ecology has historically focused on "pristine" natural environments, but by the 1970s many ecologists began to turn their interest towards ecological interactions taking place in, and caused by urban environments. Jean-Marie Pelt's 1977 book The Re-Naturalized Human, Brian Davis' 1978 publication Urbanization and the diversity of insects, and Sukopp et al.'s 1979 article "The soil, flora and vegetation of Berlin's wastelands" are some of the first publications to recognize the importance of urban ecology as a separate and distinct form of ecology the same way one might see landscape ecology as different from population ecology. Forman and Godron's 1986 book Landscape Ecology first distinguished urban settings and landscapes from other landscapes by dividing all landscapes into five broad types. These types were divided by the intensity of human influence ranging from pristine natural environments to urban centers. 

Urban ecology is recognized as a diverse and complex concept which differs in application between North America and Europe. The European concept of urban ecology examines the biota of urban areas, while the North American concept has traditionally examined the social sciences of the urban landscape, as well as the ecosystem fluxes and processes.

Methods

Since urban ecology is a subfield of ecology, many of the techniques are similar to that of ecology. Ecological study techniques have been developed over centuries, but many of the techniques use for urban ecology are more recently developed. Methods used for studying urban ecology involve chemical and biochemical techniques, temperature recording, heat mapping remote sensing, and long-term ecological research sites.

Chemical and biochemical techniques

Chemical techniques may be used to determine pollutant concentrations and their effects. Tests can be as simple as dipping a manufactured test strip, as in the case of pH testing, or be more complex, as in the case of examining the spatial and temporal variation of heavy metal contamination due to industrial runoff. In that particular study, livers of birds from many regions of the North Sea were ground up and mercury was extracted. Additionally, mercury bound in feathers was extracted from both live birds and from museum specimens to test for mercury levels across many decades. Through these two different measurements, researchers were able to make a complex picture of the spread of mercury due to industrial runoff both spatially and temporally. 

Other chemical techniques include tests for nitrates, phosphates, sulfates, etc. which are commonly associated with urban pollutants such as fertilizer and industrial byproducts. These biochemical fluxes are studied in the atmosphere (e.g. greenhouse gasses), aquatic ecosystems and soil vegetation. Broad reaching effects of these biochemical fluxes can be seen in various aspects of both the urban and surrounding rural ecosystems.

Temperature data and heat mapping

Temperature data can be used for various kinds of studies. An important aspect of temperature data is the ability to correlate temperature with various factors that may be affecting or occurring in the environment. Oftentimes, temperature data is collected long-term by the Office of Oceanic and Atmospheric Research (OAR), and made available to the scientific community through the National Oceanic and Atmospheric Administration (NOAA). Data can be overlaid with maps of terrain, urban features, and other spatial areas to create heat maps. These heat maps can be used to view trends and distribution over time and space.

Remote sensing

Remote sensing allows collection of data using satellites. This map shows urban tree canopy in Boston.

Remote sensing is the technique in which data is collected from distant locations through the use of satellite imaging, radar, and aerial photographs. In urban ecology, remote sensing is used to collect data about terrain, weather patterns, light, and vegetation. One application of remote sensing for urban ecology is to detect the productivity of an area by measuring the photosynthetic wavelengths of emitted light. Satellite images can also be used to detect differences in temperature and landscape diversity to detect the effects of urbanization.

LTERs and long-term data sets

Long-term ecological research (LTER) sites are research sites funded by the government that have collected reliable long-term data over an extended period of time in order to identify long-term climatic or ecological trends. These sites provide long-term temporal and spatial data such as average temperature, rainfall and other ecological processes. The main purpose of LTERs for urban ecologists is the collection of vast amounts of data over long periods of time. These long-term data sets can then be analyzed to find trends relating to the effects of the urban environment on various ecological processes, such as species diversity and abundance over time. Another example is the examination of temperature trends that are accompanied with the growth of urban centers.

Urban effects on the environment

Humans are the driving force behind urban ecology and influence the environment in a variety of ways, such as modifying land surfaces and waterways, introducing foreign species, and altering biogeochemical cycles. Some of these effects are more apparent, such as the reversal of the Chicago River to accommodate the growing pollution levels and trade on the river. Other effects can be more gradual such as the change in global climate due to urbanization.

Modification of land and waterways

Deforestation in the Amazon rainforest. The "fishbone pattern" is a result of the roads in the forest created by loggers.

Humans place high demand on land not only to build urban centers, but also to build surrounding suburban areas for housing. Land is also allocated for agriculture to sustain the growing population of the city. Expanding cities and suburban areas necessitate corresponding deforestation to meet the land-use and resource requirements of urbanization. Key examples of this are Deforestation in the United States and Brazil.

Along with manipulation of land to suit human needs, natural water resources such as rivers and streams are also modified in urban establishments. Modification can come in the form of dams, artificial canals, and even the reversal of rivers. Reversing the flow of the Chicago River is a major example of urban environmental modification. Urban areas in natural desert settings often bring in water from far areas to maintain the human population and will likely have effects on the local desert climate. Modification of aquatic systems in urban areas also results in decreased stream diversity and increased pollution.

Trade, shipping, and spread of invasive species

A ship navigates through the Firth of Clyde in Scotland, potentially carrying invasive species.

 

Invasive kudzu vines growing on trees in Atlanta, Georgia, USA

Both local shipping and long-distance trade are required to meet the resource demands important in maintaining urban areas. Carbon dioxide emissions from the transport of goods also contribute to accumulating greenhouse gases and nutrient deposits in the soil and air of urban environments. In addition, shipping facilitates the unintentional spread of living organisms, and introduces them to environments that they would not naturally inhabit. Introduced or alien species are populations of organisms living in a range in which they did not naturally evolve due to intentional or inadvertent human activity. Increased transportation between urban centers furthers the incidental movement of animal and plant species. Alien species often have no natural predators and pose a substantial threat to the dynamics of existing ecological populations in the new environment where they are introduced. Such invasive species are numerous and include house sparrows, ring-necked pheasants, European starlings, brown rats, Asian carp, American bullfrogs, emerald ash borer, kudzu vines, and zebra mussels among numerous others, most notably domesticated animals. In Australia, it has been found that removing Lantana (L. camara, an alien species) from urban greenspaces can surprisingly have negative impacts on bird diversity locally, as it provides refugia for species like the superb fairy (Malurus cyaneus) and silvereye (Zosterops lateralis), in the absence of native plant equivalents . Although, there seems to be a density threshold in which too much Lantana (thus homogeneity in vegetation cover) can lead to a decrease in bird species richness or abundance .

Human effects on biogeochemical pathways

Urbanization results in a large demand for chemical use by industry, construction, agriculture, and energy providing services. Such demands have a substantial impact on biogeochemical cycles, resulting in phenomena such as acid rain, eutrophication, and global warming. Furthermore, natural biogeochemical cycles in the urban environment can be impeded due to impermeable surfaces that prevent nutrients from returning to the soil, water, and atmosphere.

Graphical representation of the carbon cycle.

Demand for fertilizers to meet agricultural needs exerted by expanding urban centers can alter chemical composition of soil. Such effects often result in abnormally high concentrations of compounds including sulfur, phosphorus, nitrogen, and heavy metals. In addition, nitrogen and phosphorus used in fertilizers have caused severe problems in the form of agricultural runoff, which alters the concentration of these compounds in local rivers and streams, often resulting in adverse effects on native species. A well-known effect of agricultural runoff is the phenomenon of eutrophication. When the fertilizer chemicals from agricultural runoff reach the ocean, an algal bloom results, then rapidly dies off. The dead algae biomass is decomposed by bacteria that also consume large quantities of oxygen, which they obtain from the water, creating a "dead zone" without oxygen for fish or other organisms. A classic example is the dead zone in the Gulf of Mexico due to agricultural runoff into the Mississippi River. 

Just as pollutants and alterations in the biogeochemical cycle alter river and ocean ecosystems, they exert likewise effects in the air. Smog stems from the accumulation of chemicals and pollution and often manifests in urban settings, which has a great impact on local plants and animals. Because urban centers are often considered point sources for pollution, unsurprisingly local plants have adapted to withstand such conditions.

Urban effects on climate

Urban environments and outlying areas have been found to exhibit unique local temperatures, precipitation, and other characteristic activity due to a variety of factors such as pollution and altered geochemical cycles. Some examples of the urban effects on climate are urban heat island, oasis effect, greenhouse gases, and acid rain. This further stirs the debate as to whether urban areas should be considered a unique biome. Despite common trends among all urban centers, the surrounding local environment heavily influences much of the climate. One such example of regional differences can be seen through the urban heat island and oasis effect.

Urban heat island effect

Graphical representation of the rising temperature in Kanto, Japan due to urban heat island.

The urban heat island is a phenomenon in which central regions of urban centers exhibit higher mean temperatures than surrounding urban areas. Much of this effect can be attributed to low city albedo, the reflecting power of a surface, and the increased surface area of buildings to absorb solar radiation. Concrete, cement, and metal surfaces in urban areas tend to absorb heat energy rather than reflect it, contributing to higher urban temperatures. Brazel et al. found that the urban heat island effect demonstrates a positive correlation with population density in the city of Baltimore. The heat island effect has corresponding ecological consequences on resident species. However, this effect has only been seen in temperate climates.

Greenhouse gases

Greenhouse gas emissions include those of carbon dioxide and methane from the combustion of fossil fuels to supply energy needed by vast urban metropolises. Other greenhouse gases include water vapor, and nitrous oxide. Increases in greenhouse gases due to urban transport, construction, industry and other demands have been correlated strongly with increase in temperature. Sources of methane are agricultural dairy cows and landfills.

Acid rain and pollution

Smokestacks from a wartime production plant releasing pollutants into the atmosphere.

Processes related to urban areas result in the emission of numerous pollutants, which change corresponding nutrient cycles of carbon, sulfur, nitrogen, and other elements. Ecosystems in and around the urban center are especially influenced by these point sources of pollution. High sulfur dioxide concentrations resulting from the industrial demands of urbanization cause rainwater to become more acidic. Such an effect has been found to have a significant influence on locally affected populations, especially in aquatic environments. Wastes from urban centers, especially large urban centers in developed nations, can drive biogeochemical cycles on a global scale.

Urban environment as an anthropogenic biome

The urban environment has been classified as an anthropogenic biome, which is characterized by the predominance of certain species and climate trends such as urban heat island across many urban areas. Examples of species characteristic of many urban environments include, cats, dogs, mosquitoes, rats, flies, and pigeons, which are all generalists. Many of these are dependent on human activity and have adapted accordingly to the niche created by urban centers.

Biodiversity and urbanization

Research thus far indicates that, on a small scale, urbanization often increases the biodiversity of non-native species while reducing that of native species. This normally results in an overall reduction in species richness and increase in total biomass and species abundance. Urbanization also reduces diversity on a large scale.

Urban stream syndrome is a consistently observed trait of urbanization characterized by high nutrient and contaminant concentration, altered stream morphology, increased dominance of dominant species, and decreased biodiversity The two primary causes of urban stream syndrome are storm water runoff and wastewater treatment plant effluent.

Changes in diversity

Diversity is normally reduced at intermediate-low levels of urbanization but is always reduced at high levels of urbanization. These effects have been observed in vertebrates and invertebrates while plant species tend to increase with intermediate-low levels of urbanization but these general trends do not apply to all organisms within those groups. For example, McKinney’s (2006) review did not include the effects of urbanization on fishes and of the 58 studies on invertebrates, 52 included insects while only 10 included spiders. There is also a geographical bias as most of the studies either took place in North America or Europe. 

The effects of urbanization also depend on the type and range of resources used by the organism. Generalist species, those that use a wide range of resources and can thrive under a large range of living conditions, are likely survive in uniform environments. Specialist species, those that use a narrow range of resources and can only cope with a narrow range of living conditions, are unlikely to cope with uniform environments. There will likely be a variable effect on these two groups of organisms as urbanization alters habitat uniformity.

Cause of diversity change

The urban environment can decrease diversity through habitat removal and species homogenization - the increasing similarity between two previously distinct biological communities. Habitat degradation and habitat fragmentation reduces the amount of suitable habitat by urban development and separates suitable patches by inhospitable terrain such as roads, neighborhoods, and open parks. Although this replacement of suitable habitat with unsuitable habitat will result in extinctions of native species, some shelter may be artificially created and promote the survival of non-native species (e.g. house sparrow and house mice nests). Urbanization promotes species homogenization through the extinction of native endemic species and the introduction of non-native species that already have a widespread abundance. Changes to the habitat may promote both the extinction of native endemic species and the introduction of non-native species. The effects of habitat change will likely be similar in all urban environments as urban environments are all built to cater to the needs of humans.

The urban environment can also increase diversity in a number of ways. Many foreign organisms are introduced and dispersed naturally or artificially in urban areas. Artificial introductions may be intentional, where organisms have some form of human use, or accidental, where organisms attach themselves to transportation vehicles. Humans provide food sources (e.g. birdfeeder seeds, trash, garden compost) and reduce the numbers of large natural predators in urban environments, allowing large populations to be supported where food and predation would normally limit the population size. There are a variety of different habitats available within the urban environment as a result of differences in land use allowing for more species to be supported than by more uniform habitats.

Civil engineering and sustainability

Cities should be planned and constructed in such a way that minimizes the urban effects on the surrounding environment (urban heat island, precipitation, etc.) as well as optimizing ecological activity. For example, increasing the albedo, or reflective power, of surfaces in urban areas, can minimize urban heat island, resulting in a lower magnitude of the urban heat island effect in urban areas. By minimizing these abnormal temperature trends and others, ecological activity would likely be improved in the urban setting.

Need for remediation

Urbanization has indeed had a profound effect on the environment, on both local and global scales. Difficulties in actively constructing habitat corridor and returning biogeochemical cycles to normal raise the question as to whether such goals are feasible. However, some groups are working to return areas of land affected by the urban landscape to a more natural state. This includes using landscape architecture to model natural systems and restore rivers to pre-urban states.

Sustainability

Pipes carrying biogas produced by anaerobic digestion or fermentation of biodegradable materials as a form of carbon sequestration.

With the ever-increasing demands for resources necessitated by urbanization, recent campaigns to move toward sustainable energy and resource consumption, such as LEED certification of buildings, Energy Star certified appliances, and zero emission vehicles, have gained momentum. Sustainability reflects techniques and consumption ensuring reasonably low resource use as a component of urban ecology. Techniques such as carbon recapture may also be used to sequester carbon compounds produced in urban centers rather continually emitting more of the greenhouse gas.

Summary

Urbanization results in a series of both local and far-reaching effects on biodiversity, biogeochemical cycles, hydrology, and climate, among many other stresses. Many of these effects are not fully understood, as urban ecology has only recently emerged as a scientific discipline and much more research remains to be done. Research on cities outside the US and Europe remains limited. Observations on the impact of urbanization on biodiversity and species interactions are consistent across many studies but definitive mechanisms have yet to be established. Urban ecology constitutes an important and highly relevant subfield of ecology, and further study must be pursued to more fully understand the effects of human urban areas on the environment.

Vertical farming (updated)

From Wikipedia, the free encyclopedia

Lettuce grown in indoor vertical farming system

Vertical farming is the practice of producing food and medicine in vertically stacked layers, vertically inclined surfaces and/or integrated in other structures (such as in a skyscraper, used warehouse, or shipping container). The modern ideas of vertical farming use indoor farming techniques and controlled-environment agriculture (CEA) technology, where all environmental factors can be controlled. These facilities utilize artificial control of light, environmental control (humidity, temperature, gases...) and fertigation. Some vertical farms use techniques similar to greenhouses, where natural sunlight can be augmented with artificial lighting and metal reflectors.

Hydroponic systems can be lit by LEDs that mimic sunlight. Software can ensure that all the plants get the same amount of light, water and nutrients. Proper managements means that no herbicides or pesticides are required.

Types

The term "vertical farming" was coined by Gilbert Ellis Bailey in 1915 in his book Vertical Farming. His use of the term differs from the current meaning—he wrote about farming with a special interest in soil origin, its nutrient content and the view of plant life as "vertical" life forms, specifically relating to their underground root structures. Modern usage of the term "vertical farming" usually refers to growing plants in layers, whether in a multistory skyscraper, used warehouse, or shipping container.

Mixed-use skyscrapers

Mixed-use skyscrapers were proposed and built by architect Ken Yeang. Yeang proposes that instead of hermetically sealed mass-produced agriculture, plant life should be cultivated within open air, mixed-use skyscrapers for climate control and consumption. This version of vertical farming is based upon personal or community use rather than the wholesale production and distribution that aspires to feed an entire city.

Despommier's skyscrapers

Ecologist Dickson Despommier argues that vertical farming is legitimate for environmental reasons. He claims that the cultivation of plant life within skyscrapers will require less embodied energy and produce less pollution than some methods of producing plant life on natural landscapes. He moreover claims that natural landscapes are too toxic for natural agricultural production, despite the ecological and environmental costs of extracting materials to build skyscrapers for the simple purpose of agricultural production.

Despommier's concept of the vertical farm emerged in 1999 at Columbia University. It promotes the mass cultivation of plant life for commercial purposes in skyscrapers.

Stackable shipping containers

Several companies have developed stacking recycled shipping containers in urban settings. Brighterside Consulting created a complete off-grid container system. Freight Farms produces a "leafy green machine" that is a complete farm-to-table system outfitted with vertical hydroponics, LED lighting and intuitive climate controls built within a 12 m × 2.4 m shipping container. Podponics built a vertical farm in Atlanta consisting of over 100 stacked "growpods". A similar farm is under construction in Oman. TerraFarms offer a proprietary system of 40 foot shipping containers, which include computer vision integrated with an artificial neural network to monitor the plants; and are remotely monitored from California. It is claimed that the TerraFarm system "has achieved cost parity with traditional, outdoor farming" with each unit producing the equivalent of "three to five acres of farmland", using 97% less water through water recapture and harvesting the evaporated water through the air conditioning. As of December 2017 the TerraFarm system was in commercial operation. Plants can exploit light that varies in intensity through the day. Controlling light governs the growth cycle of the plant. E.g., infrared LEDs can mimic 5 minutes of sunset, stimulating some plants to begin flowering.

In abandoned mine shafts

Vertical farming in abandoned mine shafts is termed "deep farming," and is proposed to take advantage of consistent underground temperatures and locations near or in urban areas.

Technology

Lighting can be natural or via LEDs. As of 2018 commercial LEDs were about 28 per cent efficient, which keeps the cost of produce high and prevents vertical farms from competing in regions where cheap vegetables are abundant. However, lighting engineers at Philips have demonstrated LEDs with 68 per cent efficiency. Energy costs can be reduced because full-spectrum white light is not required. Instead, red and blue or purple light can be generated with less electricity.

History

One of the earliest drawings of a tall building that cultivates food was published in Life Magazine in 1909. The reproduced drawings feature vertically stacked homesteads set amidst a farming landscape. This proposal can be seen in Rem Koolhaas's Delirious New York. Koolhaas wrote that this 1909 theorem is 'The Skyscraper as Utopian device for the production of unlimited numbers of virgin sites on a metropolitan location'.

Hydroponicum

Early architectural proposals that contributge to VF include Le Corbusier's Immeubles-Villas (1922) and SITE's Highrise of Homes (1972). SITE's Highrise of Homes is a near revival of the 1909 Life Magazine Theorem. Built examples of tower hydroponicums are documented in The Glass House by John Hix. Images of the vertical farms at the School of Gardeners in Langenlois, Austria, and the glass tower at the Vienna International Horticulture Exhibition (1964) show that vertical farms existed. The technological precedents that make vertical farming possible can be traced back to horticultural history through the development of greenhouse and hydroponic technology. Early hydroponicums integrated hydroponic technology into building systems. These horticultural building systems evolved from greenhouse technology. The British Interplanetary Society developed a hydroponicum for lunar conditions, while other building prototypes were developed during the early days of space exploration. The first Tower Hydroponic Units were developed in Armenia.

The Armenian tower hydroponicums are the first built examples of a vertical farm, and are documented in Sholto Douglas' Hydroponics: The Bengal System, first published in 1951 with data from the then-East Pakistan, today's Bangladesh, and the Indian state of West Bengal.

Later precursors that have been published, or built, are Ken Yeang's Bioclimatic Skyscraper (Menara Mesiniaga, built 1992); MVRDV's PigCity, 2000; MVRDV's Meta City/ Datatown (1998–2000); Pich-Aguilera's Garden Towers (2001).

Ken Yeang is perhaps the most widely known architect who has promoted the idea of the 'mixed-use' Bioclimatic Skyscraper which combines living units and food production.

Vertical farm

Dickson Despommier is a professor of environmental health sciences and microbiology. He reopened the topic of VF in 1999 with graduate students in a medical ecology class. He speculated that a 30-floor farm on one city block could provide food for 50,000 people including vegetables, fruit, eggs and meat, explaining that hydroponic crops could be grown on upper floors; while the lower floors would be suited for chickens and fish that eat plant waste.

Although many of Despommier's suggestions have been challenged from an environmental science and engineering point of view, Despommier successfully popularized his assertion that food production can be transformed. Critics claimed that the additional energy needed for artificial lighting, heating and other operations would outweigh the benefit of the building's close proximity to the areas of consumption.

Despommier originally challenged his class to feed the entire population of Manhattan (about 2,000,000 people) using only 5 hectares (13 acres) of rooftop gardens. The class calculated that rooftop gardening methods could feed only two percent of the population. Unsatisfied with the results, Despommier made an off-the-cuff suggestion of growing plants indoors, vertically. By 2001 the first outline of a vertical farm was introduced. In an interview Despommier described how vertical farms would function:

Each floor will have its own watering and nutrient monitoring systems. There will be sensors for every single plant that tracks how much and what kinds of nutrients the plant has absorbed. You'll even have systems to monitor plant diseases by employing DNA chip technologies that detect the presence of plant pathogens by simply sampling the air and using snippets from various viral and bacterial infections. It's very easy to do.

Moreover, a gas chromatograph will tell us when to pick the plant by analyzing which flavenoids the produce contains. These flavonoids are what gives the food the flavors you're so fond of, particularly for more aromatic produce like tomatoes and peppers. These are all right-off-the-shelf technologies. The ability to construct a vertical farm exists now. We don't have to make anything new.

Architectural designs were independently produced by designers Chris Jacobs, Andrew Kranis and Gordon Graff.

Mass media attention began with an article written in New York magazine,^{[citation needed]} followed by others, as well as radio and television features.

In 2011 the Plant in Chicago was building an anaerobic digester into the building. This will allow the farm to operate off the energy grid. Moreover, the anaerobic digester will be recycling waste from nearby businesses that would otherwise go into landfills.

In 2013 the Association for Vertical Farming was founded in Munich, Germany. 

As of 2014, Vertical Fresh Farms was operating in Buffalo, New York, specializing in salad greens, herbs and sprouts. In March the world’s then largest vertical farm opened in Scranton, Pennsylvania, built by Green Spirit Farms (GSF). The firm is housed in a single story building covering 3.25 hectares, with racks stacked six high to house 17 million plants. The farm was to grow 14 lettuce crops per year, as well as spinach, kale, tomatoes, peppers, basil and strawberries. Water is scavenged from the farm's atmosphere with a dehumidifier.

A 2015 study utilized inexpensive metal reflectors to supply sunlight to the plants, reducing energy costs.

Kyoto-based Nuvege (pronounced “new veggie”) operates a windowless farm. Its LED lighting is tuned to service two types of chlorophyll, one preferring red light and the other blue. Nuvege produces 6 million lettuce heads a year.

The US Defense Advanced Research Projects Agency operates an 18-story project that produces genetically modified plants that make proteins useful in vaccines.

Problems

Economics

Opponents question the potential profitability of vertical farming. Its economic and environmental benefits rest partly on the concept of minimizing food miles, the distance that food travels from farm to consumer. However, a recent analysis suggests that transportation is only a minor contributor to the economic and environmental costs of supplying food to urban populations. The analysis concluded that "food miles are, at best, a marketing fad." Thus the facility would have to lower costs or charge higher prices to justify remaining in a city. 

Similarly, if power needs are met by fossil fuels, the environmental effect may be a net loss; even building low-carbon capacity to power the farms may not make as much sense as simply leaving traditional farms in place, while burning less coal. 

The initial building costs would exceed $100 million, for a 60 hectare vertical farm. Office occupancy costs can be high in major cities, with office space in cities such as Tokyo, Moscow, Mumbai, Dubai, Milan, Zurich, and Sao Paulo ranging from $1850 to $880 per square meter.

The developers of the TerraFarm system produced from second hand, 40 foot shipping containers claimed that their system "has achieved cost parity with traditional, outdoor farming".

Energy use

During the growing season, the sun shines on a vertical surface at an extreme angle such that much less light is available to crops than when they are planted on flat land. Therefore, supplemental light would be required. Bruce Bugbee claimed that the power demands of vertical farming would be uncompetitive with traditional farms using only natural light. Environmental writer George Monbiot calculated that the cost of providing enough supplementary light to grow the grain for a single loaf would be about $15. An article in the Economist argued that "even though crops growing in a glass skyscraper will get some natural sunlight during the day, it won't be enough" and "the cost of powering artificial lights will make indoor farming prohibitively expensive".

As "The Vertical Farm" proposes a controlled environment, heating and cooling costs will resemble those of any other tower. Plumbing and elevator systems are necessary to distribute nutrients and water. In the northern continental United States, fossil fuel heating cost can be over $200,000 per hectare.

Pollution

Depending on the method of electricity generation used, greenhouse produce can create more greenhouse gases than field produce, largely due to higher energy use per kilogram. Vertical farms require much greater energy per kilogram versus regular greenhouses, mainly through increased lighting. The amount of pollution produced is dependent on how the energy is generated. 

Greenhouses commonly supplement CO₂ levels to 3–4 times the atmospheric rate. This increase in CO₂ increases photosynthesis rates by 50%, contributing to higher yields. Some greenhouses burn fossil fuels purely for this purpose, as other CO₂ sources, such as those from furnaces, contain pollutants such as sulphur dioxide and ethylene which significantly damage plants. This means a vertical farm requires a CO₂ source, most likely from combustion. Also, necessary ventilation may allow CO₂ to leak into the atmosphere. 

Greenhouse growers commonly exploit photoperiodism in plants to control whether the plants are in a vegetative or reproductive stage. As part of this control, the lights stay on past sunset and before sunrise or periodically throughout the night. Single story greenhouses have attracted criticism over light pollution.

Hydroponic greenhouses regularly change the water, producing water containing fertilizers and pesticides that must be disposed of. The most common method of spreading the effluent over neighbouring farmland or wetlands would be more difficult for an urban vertical farm.

As of 2012, Vertical Harvest was raising funds for an urban, small-scale vertical farm in Jackson Hole, Wyoming.

Advantages

Many of VF's potential benefits are obtained from scaling up hydroponic or aeroponic growing methods.

A 2018 study estimated that the value of four ecosystem services provided by existing vegetation in urban areas was on the order of $33 billion annually. The study's quantitative framework projected annual food production of 100–180 million tonnes, energy savings ranging from 14 to 15 billion kilowatt hours, nitrogen sequestration between 100,000 and 170,000 tonnes and stormwater runoff reductions between 45 and 57 billion cubic meters annually. Food production, nitrogen fixation, energy savings, pollination, climate regulation, soil formation and biological pest control could be worth as much as $80–160 billion annually.

Preparation for the future

It is estimated that by the year 2050, the world's population will increase by 3 billion people and close to 80% will live in urban areas. Vertical farms have the potential to reduce or eliminate the need to create additional farmland.

Increased crop production

Unlike traditional farming in non-tropical areas, indoor farming can produce crops year-round. All-season farming multiplies the productivity of the farmed surface by a factor of 4 to 6 depending on the crop. With crops such as strawberries, the factor may be as high as 30.

Furthermore, as the crops would be consumed where they are grown, long-distance transport with its accompanying time delays, should reduce spoilage, infestation and energy needs. Globally some 30% of harvested crops are wasted due to spoilage and infestation, though this number is much lower in developed nations.

Despommier suggests that once dwarf versions of crops (e.g. dwarf wheat which is smaller in size but richer in nutrients), year-round crops and "stacker" plant holders are accounted for, a 30-story building with a base of a building block (2 hectares (5 acres)) would yield a yearly crop analogous to that of 1,000 hectares (2,400 acres) of traditional farming.

Weather disruption

Crops grown in traditional outdoor farming depend on supportive weather, and suffer from undesirable temperatures rain, monsoon, hailstorm, tornadoe, flooding, wildfires and drought. "Three recent floods (in 1993, 2007 and 2008) cost the United States billions of dollars in lost crops, with even more devastating losses in topsoil. Changes in rain patterns and temperature could diminish India's agricultural output by 30 percent by the end of the century."

VF productivity is mostly independent of weather, although earthquakes and tornadoes still pose threats.

Conservation

Up to 20 units of outdoor farmland per unit of VF could return to its natural state, due to VR's increased productivity. 

Vertical farming would thus reduce the amount of farmland, thus saving many natural resources. Deforestation and desertification caused by agricultural encroachment on natural biomes could be avoided. Producing food indoors reduces or eliminates conventional plowing, planting, and harvesting by farm machinery, protecting soil and reducing emissions.

Resource scarcity

The scarcity of fertilizer components like phosphorus poses a threat to industrial agriculture. The closed-cycle design of vertical farm systems minimizes the loss of nutrients, while traditional field agriculture loses nutrients to runoff and leeching.

Mass extinction

Withdrawing human activity from large areas of the Earth's land surface may be necessary to address anthropogenic mass extinctions. 

Traditional agriculture disrupts wild populations and may be unethical given a viable alternative. One study showed that wood mouse populations dropped from 25 per hectare to 5 per hectare after harvest, estimating 10 animals killed per hectare each year with conventional farming. In comparison, vertical farming would cause nominal harm to wildlife.

Human health

Traditional farming is a hazardous occupation that often affects the health of farmers. Such risks include: exposure to infectious diseases such as malaria and schistosomes, exposure to toxic pesticides and fungicides, confrontations with wildlife such as venomous snakes, and injuries that can occur when using large industrial farming equipment. VF reduces some of these risks. The modern industrial food system makes unhealthy food cheap while fresh produce is more expensive, encouraging poor eating habits. These habits lead to health problems such as obesity, heart disease and diabetes.

Poverty and culture

Food security is one of the primary factors leading to absolute poverty. Constructing farms will allow continued growth of culturally significant food items without sacrificing sustainability or basic needs, which can be significant to the recovery of a society from poverty.

Urban growth

Vertical farming, used in conjunction with other technologies and socioeconomic practices, could allow cities to expand while remaining substantially self-sufficient in food. This would allow large urban centers to grow without food constraints.

Energy sustainability

Vertical farms could exploit methane digesters to generate energy. Methane digesters could be built on site to transform the organic waste generated at the farm into biogas that is generally composed of 65% methane along with other gases. This biogas could then be burned to generate electricity for the greenhouse.

Technologies and devices

Vertical farming relies on the use of various physical methods to become effective. Combining these technologies and devices in an integrated whole is necessary to make Vertical Farming a reality. Various methods are proposed and under research. The most common technologies suggested are:

• Greenhouses
• The Folkewall and other vertical growing architectures
• Aeroponics
• Agricultural robot
• Aquaponics
• Composting
• Controlled-environment agriculture
• Flower pots
• Grow lights
• Hydroponics
• Phytoremediation
• Precision agriculture
• Skyscrapers
• TerraFarm

Plans

Developers and local governments in multiple cities have expressed interest in establishing a vertical farm: Incheon (South Korea), Abu Dhabi (United Arab Emirates), Dongtan (China), New York City, Portland, Oregon, Los Angeles, Las Vegas,^[69] Seattle, Surrey, B.C., Toronto, Paris, Bangalore, Dubai, Shanghai and Beijing.

In 2009, the world's first pilot production system was installed at Paignton Zoo Environmental Park in the United Kingdom. The project showcased vertical farming and provided a physical base to conduct research into sustainable urban food production. The produce is used to feed the zoo's animals while the project enables evaluation of the systems and provides an educational resource to advocate for change in unsustainable land use practices that impact upon global biodiversity and ecosystem services.

In 2010 the Green Zionist Alliance proposed a resolution at the 36th World Zionist Congress calling on Keren Kayemet L'Yisrael (Jewish National Fund in Israel) to develop vertical farms in Israel.

In 2012 the world's first commercial vertical farm was opened in Singapore, developed by Sky Greens Farms, and is three stories high. They currently have over 100 nine meter-tall towers.

In 2013 the Association for Vertical Farming (AVF) was founded in Munich (Germany). By May 2015 the AVF had expanded with regional chapters all over Europe, Asia, USA, Canada and the United Kingdom. This organization unites growers and inventors to improve food security and sustainable development. AVF focuses on advancing vertical farming technologies, designs and businesses by hosting international info-days, workshops and summits.