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Sunday, March 21, 2021

Permaculture

From Wikipedia, the free encyclopedia
 

Permaculture is an approach to land management and philosophy that adopts arrangements observed in flourishing natural ecosystems. It includes a set of design principles derived using whole systems thinking. It uses these principles in fields such as regenerative agriculture, rewilding, and community resilience. Permaculture was originally a portmanteau of "permanent agriculture", but was later adjusted to "permanent culture", to incorporate necessary social aspects as inspired by Masanobu Fukuoka's natural farming. The term was coined by Bill Mollison and David Holmgren in 1978, who formulated the concept in opposition to Western industrialized methods and in congruence with Indigenous or traditional knowledge.

Permaculture has many branches including ecological design, ecological engineering, regenerative design, environmental design, and construction. It also includes integrated water resources management that develops sustainable architecture, and regenerative and self-maintained habitat and agricultural systems modeled from natural ecosystems. Permaculture has been implemented and gained widespread visibility throughout the world as an agricultural and architectural design system and as a guiding life principle or philosophy. Much of its success has been attributed to the role of Indigenous knowledge and traditions, which the practice itself is rooted in. In turn, the rise of permaculture has revalidated Indigenous knowledge in circles where it was previously devalued.

History

In 1929, Joseph Russell Smith added an antecedent term as the subtitle for Tree Crops: A Permanent Agriculture, which sums up his experience experimenting with fruits and nuts as human food and animal food crops. Smith saw the world as an inter-related whole and suggested mixed systems of trees with other crops underneath. This book inspired individuals such as Toyohiko Kagawa who pioneered forest farming in Japan in the 1930s.

In his 1964 book Water for Every Farm, Australian P. A. Yeomans advanced a definition of permanent agriculture as one that can be sustained indefinitely. Yeomans introduced both an observation-based approach to land use in Australia in the 1940s and the Keyline Design as a way of managing the supply and distribution of water in the 1950s. Other early influences include Stewart Brand's works, Ruth Stout and Esther Deans, who pioneered no-dig gardening, and Masanobu Fukuoka who, in the late 1930s in Japan, began advocating no-till orchards and gardens and natural farming.

Bill Mollison, who has been described as the "father of permaculture," cites Indigenous belief systems as an inspiration of the practice.

In the late 1960s, Bill Mollison, senior lecturer in Environmental Psychology at University of Tasmania, and David Holmgren, graduate student at the then Tasmanian College of Advanced Education started developing ideas about stable agricultural systems on the southern Australian island of Tasmania. Their recognition of the unsustainable nature of Western industrialized methods and their appreciation of Indigenous worldviews were critical to their formulation of permaculture. In their view, industrialized methods were highly dependent on non-renewable resources, and were additionally poisoning land and water, reducing biodiversity, and removing billions of tons of topsoil from previously fertile landscapes. They responded with permaculture. This term was first made public with their publication of their 1978 book Permaculture One.

Permaculture is a philosophy of working with, rather than against nature; of protracted and thoughtful observation rather than protracted and thoughtless labor; and of looking at plants and animals in all their functions, rather than treating any area as a single product system.

— Bill Mollison

Students of Mollison's Permaculture Design Course (PDC) included Lawton and Hemenway. Simon J. Fjell met Mollison and became a teacher of the first Permaculture Design Course in 1976. By the early 1980s, the concept had broadened from agricultural systems towards sustainable human habitats. After Permaculture One, Mollison further refined and developed the ideas while designing hundreds of permaculture sites and writing more detailed books, such as Permaculture: A Designers Manual. Mollison lectured in over 80 countries and taught his two-week PDC to hundreds of students. Mollison encouraged graduates to become teachers and set up their own institutes and demonstration sites. Critics suggest that this success weakened permaculture's social aspirations of moving away from industrial social forms. They argue that the self-help model (akin to franchising) has had the effect of creating market-focused social relationships that the originators initially opposed.

The permaculture movement spread throughout Asia and Central America. In Hong Kong the Asian Institute of Sustainable Architecture (AISA) was established. The Mesoamerican Permaculture Institute (IMAP) flourished in Guatemala. The Permaculture Institute of El Salvador is another example.

Foundational ethics

The ethics on which permaculture builds are:

  • Earth care: Provision for all life systems to continue and multiply.
  • People care: Provision for people to access those resources necessary for their existence.
  • Fair share: Setting limits to population and consumption so that people do not take more than what is needed. By governing our own needs, we can set resources aside to further the above principles. This principle is also described as share the surplus.

Permaculture emphasizes patterns of landscape, function, and species assemblies. It determines where these elements should be placed so they can provide maximum benefit to the local environment. Permaculture maximizes useful connections between components and synergy of the final design. The focus of permaculture, therefore, is not on individual elements, but rather on the relationships among them. Properly done, the whole becomes greater than the sum of its parts. Permaculture seeks to minimize waste, human labor, and energy input and maximize benefits through synergy.

Permaculture design is founded in replicating or imitating natural patterns found in ecosystems because these solutions have emerged through evolution over thousands of years and have proven to be effective. As a result, the implementation of permaculture design will vary widely depending on the region of the Earth it is located in. Design principles derive from the science of systems ecology and the study of pre-industrial examples of sustainable land use. Permaculture draws from disciplines including organic farming, agroforestry, integrated farming, sustainable development, physics, meteorology, sociology, anthropology, biochemistry, engineering, and applied ecology.

Theory

Design principles

The viewpoint of a chicken through the eyes of Permaculture design.

Holmgren articulated twelve permaculture design principles in his Permaculture: Principles and Pathways Beyond Sustainability:

  • Observe and interact: Take time to engage with nature to design solutions that suit a particular situation.
  • Catch and store energy: Develop systems that collect resources at peak abundance for use in times of need.
  • Obtain a yield: Emphasize projects that generate meaningful rewards.
  • Apply self-regulation and accept feedback: Discourage inappropriate activity to ensure that systems function well.
  • Use and value renewable resources and services: Make the best use of nature's abundance: reduce consumption and dependence on non-renewable resources.
  • Produce no waste: Value and employ all available resources: waste nothing.
  • Design from patterns to details: Observe patterns in nature and society and use them to inform designs, later adding details.
  • Integrate rather than segregate: Proper designs allow relationships to develop between design elements, allowing them to work together to support each other.
  • Use small and slow solutions: Small and slow systems are easier to maintain, make better use of local resources and produce more sustainable outcomes.
  • Use and value diversity: Diversity reduces system-level vulnerability to threats and fully exploits its environment.
  • Use edges and value the marginal: The border between things is where the most interesting events take place. These are often the system's most valuable, diverse and productive elements.
  • Creatively use and respond to change: A positive impact on inevitable change comes from careful observation, followed by well-timed intervention.

Layers

Suburban permaculture garden in Sheffield, UK with different layers of vegetation

Layers are a tool used to design sustainable ecosystems that directly benefit humans. A mature ecosystem has many relationships between its constituent parts such as trees, understory, ground cover, soil, fungi, insects, and animals. Because plants grow to different heights, a diverse community of organisms can occupy a relatively small space, each at a different layer. Forests offer seven basic layers, although there can be many more, such as fungi.

  • The canopy: the tallest trees. Large trees dominate, but typically do not saturate the area, i.e., some patches are devoid of trees.
  • Understory layer: trees that flourish under the canopy.
  • Shrub layer: woody perennials of limited height. Includes most berry bushes.
  • Herbaceous layer: Plants that die back to the ground every winter, if cold enough. No woody stems. Many beneficial plants such as culinary and medicinal herbs are in this layer. Annuals, biennials and perennials.
  • Soil surface/groundcover: Overlaps with the herbaceous layer and the groundcover layer; however plants in this layer grow much closer to the ground, densely fill bare patches, and typically can tolerate some foot traffic. Cover crops retain soil and lessen erosion, along with green manures that add nutrients and organic matter, especially nitrogen.
  • Rhizosphere: Root layers within the soil. The major components of this layer are the soil and the organisms that live within it such as plant roots and zomes (including root crops such as potatoes and other edible tubers), fungi, insects, nematodes, worms, etc.
  • Vertical layer: climbers or vines, such as runner beans and lima beans (vine varieties).

Guilds

Mycorrhizal fungi usually function in a mutualistic symbiotic relationship with plants.
 
Ladybugs are seen as beneficial insects in permaculture because of their help with aphid control

A guild is a mutually beneficial group of species that form a part of the larger ecosystem. Within a guild each species provides a unique set of diverse services that work in harmony. Guilds include compatible animals, insects, and plants that form symbiotic relationships which produce healthier plants and ecosystems as well as useful resources for humans. Plants may be grown for food production, drawing nutrients from deep in the soil through tap roots, balancing nitrogen levels in the soil (legumes), for attracting beneficial insects to the garden, and repelling undesirable insects or pests. There are several types of guilds, such as community function guilds, mutual support guilds, and resource partitioning guilds.

  • Community function guilds group species based on a specific function or niche that they fill in the garden. Examples of this type of guild include plants that attract a particular beneficial insect or plants that restore nitrogen to the soil. These types of guilds are aimed at solving specific problems which may arise in a garden, such as infestations of harmful insects and poor nutrition in the soil.
  • Mutual support guilds group species together that are complementary by working together and supporting each other. This guild may include a plant that fixes nitrogen, a plant that hosts insects that are predators to pests, and another plant that attract pollinators. An example of a mutual support guild is mycorrhizal fungi's symbiotic relationship with plants by providing minerals and nitrogen to plant roots and receiving sugars in return has been cited as an example of mutualistic guild. Permaculturalists take advantage of this beneficial relationship when designing their garden layouts.
  • Resource partitioning guilds group species based on their abilities to share essential resources with one another through a process of niche differentiation. A potential example of this type of guild includes placing a fibrous- or shallow-rooted plant next to a tap-rooted plant so that they draw from different levels of soil nutrients.
  • Establishment guilds are commonly used when working to establish target species (the primary vegetables, fruits, herbs, etc. you want established in your garden) with the support of pioneer species (plants that will help the target species succeed). For example, in temperate climates, plants such as comfrey (as a weed barrier and dynamic accumulator), lupine (as a nitrogen fixer), and daffodil (as a gopher deterrent) can together form a guild for a fruit tree. As the tree matures, the support plants will likely eventually be shaded out and can be used as compost.
  • Mature guilds form once your target species are established. For example, if the tree layer of your landscape closes its canopy, sun-loving support plants will be shaded out and die. Shade loving medicinal herbs such as ginseng, black cohosh, and goldenseal can be planted as an understory.

Edge effect

The edge effect in ecology is the effect of juxtaposing contrasting environments in an ecosystem. Permaculturists argue that where differing systems meet can become highly productive and offer useful connections. An example of this is a coast. Where land and sea meet is a rich area that meets a disproportionate percentage of human and animal needs. This idea is reflected in permacultural designs by using spirals in herb gardens, or creating ponds that have wavy undulating shorelines rather than a simple circle or oval (thereby increasing the amount of edge for a given area).

Zones

Permaculture zones 0-5

Zones intelligently organize design elements in a human environment based on the frequency of human use and plant or animal needs. Frequently manipulated or harvested elements of the design are located close to the house in zones 1 and 2. Manipulated elements located further away are used less frequently. Zones are numbered from 0 to 5 based on positioning.

Zone 0
The house, or home center. Here permaculture principles aim to reduce energy and water needs, harnessing natural resources such as sunlight, to create a harmonious, sustainable environment in which to live and work. Zone 0 is an informal designation, which is not specifically defined in Mollison's book.
Zone 1
The zone nearest to the house, the location for those elements in the system that require frequent attention, or that need to be visited often, such as salad crops, herb plants, soft fruit like strawberries or raspberries, greenhouse and cold frames, propagation area, worm compost bin for kitchen waste, etc. Raised beds are often used in Zone 1 in urban areas.
Zone 2
This area is used for siting perennial plants that require less frequent maintenance, such as occasional weed control or pruning, including currant bushes and orchards, pumpkins, sweet potato, etc. Also a good place for beehives, larger scale composting bins, etc.
Zone 3
The area where main-crops are grown, both for domestic use and for trade purposes. After establishment, care and maintenance required are fairly minimal (provided mulches and similar things are used), such as watering or weed control maybe once a week.
Zone 4
A semi-wild area, mainly used for forage and collecting wild plants as well as production of timber for construction or firewood.
Zone 5
A wilderness area. Humans do not intervene in zone 5 apart from observing natural ecosystems and cycles. This zone hosts a natural reserve of bacteria, moulds and insects that can aid the zones above it.

People care

Photos of the Village Building Convergence event (2020)

Permaculture emphasizes a "sharing and caring" approach built on respect and reciprocity in human relationships rather than a competitive approach. The people care ethic needs attention firstly because of the importance of interpersonal dynamics in permaculture and secondly because the principles of permaculture can be used to effectively create vibrant, healthy, and productive communities through reconnecting humans to nature in regenerative ways. Bill Mollison describes how reconnecting with the Earth is necessary for many people because of ancestral separation:

Tribal peoples are very much aware of, and tied to, their soil and landscapes, so that their mental and physical health depend on these ties being maintained. The rest of us have suffered forcible, historic dislocations from home sites, and many no longer know where their home is, although there are new and conscious moves to reinhabit the earth and to identify with a bioregion as "home."

Implementing permaculture principles may create possibilities for self-healing as well as family and community healing. Permaculture teaches practitioners the lessons of interconnectedness and sustainability. Learning these lessons may increase one's mindfulness; a realization that nothing exists or functions in isolation. Permaculture has been described as a peacebuilding tool for communities that are steeped in conflict.

Discussions of Indigenous ethics in regard to permaculture have concluded that the people care ethic of permaculture is "often missing in Eurocolonialist capitalist societies." A permaculture program in Pembroke, Illinois devised an Indigenous permaculture curriculum to address people care, integrating the Mayan concept of in lak'ech ("I am because you are"), the Lakota concept of mitakuye oyasin ("all my relations"), and the Nguni Bantu concept of ubuntu ("I am because we all are") in their classes.

Cultural change

Permaculture Action Day in Denver (2016)

More than an approach to land management, permaculture is also a worldview or philosophy that emphasizes holistic approaches to life and works to create a wider culture based on these values. The ethics of earth care, people care, and fair share are applied to all facets of life, including areas such as education and administration. David Holmgren writes that permaculture is inherently based in the acknowledgement that an environmental crisis threatening humanity and life as we know it is on the horizon and that, as a result, a cultural change is needed to address this crisis: "the process of providing for people’s needs within ecological limits requires a cultural revolution." Permaculture aims to make people and local communities self-reliant from the industrialized political economy that is responsible for much of the ecological damage on Earth. Holmgren writes:

The fact is that our own comfort is based on the rape of planetary wealth, depriving other people (and future generations) of their own local resources. Our own ‘‘hard work’’ and the so-called ‘‘creativity’’ of our economy and ‘‘fairness’’ of our system of government are all secondary factors in creating our privilege. Once we understand the massive structural inequities between rich and poor nations, urban and rural communities and human resources and natural resources, the emphasis on providing for one’s own needs is seen in a different light. As we reduce our dependence on the global economy and replace it with household and local economies, we reduce the demand that drives current inequities. Thus ‘‘look after yourself first’’ is not an invitation to greed but a challenge to grow up through self-reliance and personal responsibility.

Permaculture involves taking action locally while being conscious of larger global issues. As described by Craig Gibsone and Jan Martin Bang, "we may rail at distant miscarriages of justice, but if we can't do very much about them, we may well be better off doing something about our local situation. That old worn-out phrase, 'think globally, act locally' sits very well with permaculture." Research has found that subsistence farmers practicing permaculture methods are more autonomous than those who rely on the global economy for their essential needs and are therefore less apt to view economic collapse as 'the end of the world'. June Brawner writes, "those who practice subsistence—though often associated with rurality, poverty, and backwardness—are more immune to these threats." The self-reliance of subsistence farmers in the face of economic downturn illustrates that what is commonly interpreted as 'wealthy' is socially constructed. While money is often interpreted as wealth in 'modern' society, this can shift suddenly in times of economic collapse.

Individuals who attempt to adhere to permaculture philosophy may confront obstacles because of modern structural barriers, such as landlessness and private property, as well as ideological barriers, such as the prevalence of opposing worldviews that directly conflict with permaculture principles. For example, permaculture research in San Lucas Tolimán, Guatemala suggested that the land deprivation of local Kaqchikel residents coupled with the indoctrination of evangelicalism obstructed the embrace of permaculture philosophy. In Indigenous or traditional communities, what is referred to as permaculture may already be culturally familiar. For example, a researcher found that in the Bulgarian town of Shipka, permaculture principles were widely viewed as "nothing new." This was because "their ancestors had practiced similar agricultural methods long before the term ‘permaculture’ was invented." Protecting Indigenous traditions from marginalization and destruction is important to permaculture.

Common practices

Agroforestry

Agroforestry in Burkina Faso, with maize under trees

Agroforestry uses the interactive benefits from combining trees and shrubs with crops or livestock. It combines agricultural and forestry technologies to create more diverse, productive, profitable, healthy and sustainable land-use systems. Trees or shrubs are intentionally used within agricultural systems, or non-timber forest products are cultured in forest settings.

Forest gardening/food forests involve systems designed to mimic natural forests. Forest gardens, like other permaculture designs, incorporate processes and relationships that the designers understand to be valuable in natural ecosystems. The Charter of the Forest makes extended use of permaculture ideals and techniques such as forest gardening as they are related to the philosophy of anarchism. It also employs permaculture issues as metaphorical commentary on real-life events, such as referencing the 2020 COVID-19 pandemic timeline in the scene "Pale Rust and An Albino Hawk".

Proponents of forest gardens include Graham Bell, Patrick Whitefield, Dave Jacke, Eric Toensmeier and Geoff Lawton. Bell started building his forest garden in 1991 and wrote The Permaculture Garden in 1995, Whitefield wrote the book How to Make a Forest Garden in 2002, Jacke and Toensmeier co-authored the two volume book set Edible Forest Gardening in 2005, and Lawton presented the film Establishing a Food Forest in 2008.

Tree Gardens, such as Kandyan tree gardens, in South and Southeast Asia, are often hundreds of years old. It is not evident whether they came from agroforestry, or permaculture. Many studies of these systems, especially those that predate the term permaculture, consider these systems to be forms of agroforestry.

Suburban and urban permaculture

South Central Farm was one of the largest urban gardens in the United States before its demolition in 2006.

The fundamental element of suburban and urban permaculture is the efficient utilization of space. Maximizing the space for food production and minimizing wasted space is important. Wildfire journal suggests using methods such as the keyhole garden to address this issue of space. Neighbors can also collaborate with each other to increase the scale of transformation. Sites such as recreation centers, neighborhood associations, city program, faith groups, and schools can become part of a larger social and economic movement. Columbia, an ecovillage in Portland, Oregon consisting of 37 apartment condominiums, influenced surrounding neighbors to implement similar green-minded principals or permaculture, including front-yard gardens. Suburban permaculture sites such as one in Eugene, Oregon include rainwater catchment, edible landscaping, removing paved driveways, turning a garage into living space, changing a south side patio into passive solar, aesthetic features, detached structures.

Transforming vacant lots in suburban and urban settings is a common practice of creating community-managed agriculture or farm sites. However, some of these farm sites are perceived by those in power as temporary or informal solutions to the vacant lot rather than as permanent fixtures of the city. This threatens the fundamental principal of permaculture: permanence. For example, Los Angeles' South Central Farm (1994-2006), which was one of the largest urban gardens in the United States, was bulldozed with approval from property owner Ralph Horowitz, despite large-scale protest from the majority Latino community who had developed deep bonds with the site. Over 40 farmers were arrested and evicted. The land sat empty for over a decade until, in 2019, the city council approved the lot for offices and warehouses.

The possibilities and challenges for developing suburban or urban permaculture differ greatly as a result of how the built environment is designed and property is treated in particular areas of the world. For example, a study comparing the built environment in Jaisalmer, India and Los Angeles, United States concluded that the American planned city is ecologically disastrous:

the application of universal rules regarding set-backs from roads and property lines systematically creates unused and purposeless space as an integral part of the built landscape, well beyond the classic image of the vacant lot. [...] Because these spaces are created in accordance with a general pattern, rather than responding to any local need or desire, many if not most are underutilized, unproductive, and generally maintained as ecologically disastrous lawns by unenthusiastic owners. In this broadest understanding of wasted land, the concept is opened to reveal how our system of urban design gives rise to a ubiquitous pattern of land that, while not usually conceived as vacant, is in fact largely without ecological or social value.

Hügelkultur

Sketch of a Hügelkultur bed.

Hügelkultur is the practice of burying wood to increase soil water retention. The porous structure of wood acts as a sponge when decomposing underground. During the rainy season, sufficient buried wood can absorb enough water to sustain crops through the dry season. This technique is a traditional practice that has been developed over centuries in Europe and has been recently adopted by permaculturalists. The Hügelkultur technique can be implemented through building mounds on the ground as well as in raised garden beds. In raised beds, the practice "imitates natural nutrient cycling found in wood decomposition and the high water holding capacities of organic detritus, while also improving bed structure and drainage properties." This is done by placing wood material (e.g. logs and sticks) in the bottom of the bed before piling organic soil and compost on top. A study comparing the water retention capacities of Hügel raised beds to non-Hügel beds determined that Hügel beds are both lower maintenance and more efficient in the long term by requiring less irrigation.

Vermicomposting

Healthy population of red wigglers in a vermicomposting bin.

Vermicomposting is a common practice in permaculture. The practice involves using earthworms, such as red wigglers, to break down green and brown waste. The worms produce worm castings, which can be used to organically fertilize the garden. Worm castings have been noted to increase plant growth and decrease heavy-metals in the soil. Worms are also introduced to garden beds, helping to aerate the soil and improve water retention. Worms may multiply quickly if provided conditions which are ideal. For example, a permaculture farm in Cuba began with 9 tiger worms in 2001 and 15 years later had a population of over 500,000. The worm castings are particularly useful as part of a seed starting mix and regular fertilizer. Worm castings are reportedly more successful than conventional compost for seed starting.

Natural building

Small cob building with a living roof.

Natural building involves using a range of building systems and materials that apply permaculture principals. The focus is on durability and the use of minimally processed, plentiful or renewable resources, as well as those that, while recycled or salvaged, produce healthy living environments and maintain indoor air quality. For example, cement, a common building material, emits carbon dioxide and is harmful to the environment while natural building works with the environment, using materials that are biodegradable, such as cob, adobe, rammed earth (unburnt clay), and straw bale (which insulates as well as modern synthetic materials).

Natural building attempts to lessen environmental impacts of buildings without sacrificing comfort, health, or aesthetics. Natural building employs abundantly available natural materials (e.g., clay, rock, sand, straw, wood, reeds), and draws heavily on traditional architectural strategies found in various climates. Building compactly and minimizing the ecological footprint is common, as are on-site handling of energy acquisition, on-site water capture, alternate sewage treatment, and water reuse. Most materials are sourced regionally, locally, or even on-site. Roofing coverings often include sod or 'living roofs', thatch, and wooden shakes or shingles. Rubble trench foundations are popular, as they do not require concrete. Likewise, dry-stacked or lime mortared stem walls are common. Natural builders also regularly combine wall systems in a single building, making best use of for example each material's thermal or water resistant properties.

Rainwater harvesting

Rainwater collection is a common practice of permaculture.

Rainwater harvesting is the accumulation and storage of rainwater for reuse before it runs off or reaches the aquifer. It has been used to provide drinking water, water for livestock, and water for irrigation, as well as other typical uses. Rainwater collected from the roofs of houses and local institutions can make an important contribution to the availability of drinking water. It can supplement the water table and increase urban greenery. Water collected from the ground, sometimes from areas which are especially prepared for this purpose, is called stormwater harvesting.

Greywater is wastewater generated from domestic activities such as laundry, dishwashing, and bathing, which can be recycled for uses such as landscape irrigation and constructed wetlands. Greywater is largely sterile, but not potable (drinkable). Greywater differs from water from sewage or blackwater that contains human or animal waste. A permaculture approach to blackwater is composting through a process known as humanure; a portmanteau of human and manure. The methane in humanure can be collected and used similar to natural gas as a fuel, such as for heating or cooking, and is commonly referred to as biogas. Biogas can be harvested from human waste and the remainder used as humanure. The simplest forms of humanure include a composting toilet or an outhouse or dry bog surrounded by trees that are heavy feeders that can be coppiced for wood fuel. This process eliminates the use of a plumbed toilet.

Domesticated animals

A backyard chicken coop.
 
Chicken roaming in an herb garden.

Domesticated animals are often incorporated into site design. Animals are a critical component of any sustainable ecosystem. Research indicates that without animals' contribution, ecological integrity is diminished or lost. Activities that contribute to the system include: foraging to cycle nutrients, clearing fallen fruit, weed maintenance, spreading seeds, and pest maintenance. Nutrients are cycled by animals, transformed from their less digestible form (such as grass or twigs) into more nutrient-dense manure.

Multiple animals can contribute, including cows, goats, chickens, geese, turkey, rabbits, and worms. An example is chickens who can be used to scratch over the soil, thus breaking down the topsoil and using fecal matter as manure. Factors such as timing and habits are critical. For example, animals require much more daily attention than plants.

Vegan permaculture

Vegan permaculture (also known as veganic permaculture, veganiculture, or vegaculture) avoids the use of domesticated animals. It is essentially the same as permaculture except for the addition of a fourth core value; "Animal Care." Zalan Glen, a raw vegan, proposes that vegaculture emerge from permaculture in the same way veganism split from vegetarianism in the 1940s. Vegan permaculture recognizes the importance of free-living animals, rather than domesticated animals, to create a balanced ecosystem. Soil fertility is maintained by the use of green manures, cover crops, green wastes, composted vegetable matter in place of manure.

Sheet mulching

Mulch is a protective cover placed over soil. Mulch material includes stones, leaves, cardboard, wood chips and gravel, although in permaculture mulches of organic material are preferred because they perform more functions. These include absorbing rainfall, reducing evaporation, providing nutrients, increasing soil organic matter, creating habitat for soil organisms, suppressing weed growth and seed germination, moderating diurnal temperature swings, protecting against frost, and reducing erosion. Sheet mulching is a gardening technique that attempts to mimic natural forest processes. Sheet mulching mimics the leaf cover that is found on forest floors. When deployed properly and in combination with other permaculture principles, it can generate healthy, productive and low maintenance ecosystems.

Sheet mulch serves as a "nutrient bank," storing nutrients contained in organic matter and slowly making these nutrients available to plants as the organic matter slowly and naturally breaks down. It also improves the soil by attracting and feeding earthworms, slaters and many other soil micro-organisms, as well as adding humus. Earthworms "till" the soil, and their worm castings are among the best fertilizers and soil conditioners. Sheet mulching can be used to reduce or eliminate non-desired plants by starving them of light, and can surpass herbicide or other methods of control.

Grazing

Grazing is blamed for much destruction. However, when grazing is modeled after nature, it can have the opposite effect. Cell grazing is a system of grazing in which herds or flocks are regularly and systematically moved to fresh range with the intent to maximize forage quality and quantity. Sepp Holzer and Joel Salatin have shown how grazing can start ecological succession or prepare ground for planting. Allan Savory's holistic management technique has been likened to "a permaculture approach to rangeland management". One variation is conservation grazing, were the primary purpose of the animals is to benefit the environment and the animals are not necessarily used for meat, milk or fiber. Sheep can replace lawn mowers. Goats and sheep can eat invasive plants.

Keyline design

Keyline design is a technique for maximizing the beneficial use of water resources. It was developed in Australia by farmer and engineer P. A. Yeomans. Keyline refers to a contour line extending in both directions from a keypoint. Plowing above and below the keyline provides a watercourse that directs water away from a purely downhill course to reduce erosion and encourage infiltration. It is used in designing drainage systems.

Fruit tree management

Some proponents of permaculture advocate heavily restricted pruning. Holzer used the method in connection with Hügelkultur berms. He has grew fruiting trees at altitudes (approximately 9,000 feet (2,700 m)) far above their normal altitude, temperature, and snow load ranges. The Hügelkultur berms kept or generated enough heat to allow the roots to survive during alpine winter conditions. The point of having unpruned branches, he notes, was that the longer (more naturally formed) branches bend over under the snow load until they touched the ground, thus forming a natural arch against snow loads that would break a shorter, pruned, branch.

Masanobu Fukuoka, as part of early experiments on his family farm in Japan, experimented with no-pruning methods, noting that he ended up killing many fruit trees by simply letting them go, which made them become convoluted and tangled, and thus unhealthy. He learned that this is the difference between natural-form trees and previously-pruned fruit trees. He concluded that trees should be raised entirely without pruning, allowing them to form healthy and efficient natural branch patterns. This reflects the Tao-philosophy of Wú wéi translated in part as no-action (against nature). He interpreted this as no unnecessary pruning, nature farming or "do-nothing" farming, of fruit trees, distinct from non-intervention or literal no-pruning. He ultimately achieved yields comparable to or exceeding standard/intensive practices of using pruning and chemical fertilisation.

Marine systems

Harvesting of seaweed in Jambiani, Tanzania.

Permaculture derives its origin from agriculture, although the same principles, especially its foundational ethics, can also be applied to mariculture, particularly seaweed farming. An example is marine permaculture wherein artificial upwelling of cold, deep ocean water is induced. When attachment substrate is provided in association with such an upwelling, and kelp sporophytes are present, a kelp forest ecosystem can be established (kelp needs the cool temperatures and abundant dissolved macronutrients present in such an environment). Microalgae proliferate as well. Marine forest habitat is beneficial for many fish species, and the kelp is a renewable resource for food, animal feed, medicines and various other commercial products. It is also a powerful tool for carbon fixation.

The upwelling can be powered by renewable energy on location. Vertical mixing has been reduced due to ocean stratification effects associated with climate change. The Permian Mass Extinction was thought to have been brought on by such ocean warming, stratification, deoxygenation, wikt:anoxia, and subsequent extinction of 96% of all marine species. Reduced vertical mixing and marine heatwaves have decimated seaweed ecosystems in many areas. Marine permaculture mitigates this by restoring some vertical mixing and preserves these important ecosystems. By preserving and regenerating habitat offshore on a platform, marine permaculture employs natural processes to regenerate marine life.

Intellectual property

Trademark and copyright disputes surround the word permaculture. Mollison's books claimed on the copyright page, "The contents of this book and the word PERMACULTURE are copyright." Eventually Mollison acknowledged that he was mistaken and that no copyright protection existed.

In 2000, Mollison's U.S.-based Permaculture Institute sought a service mark (a form of trademark) for the word permaculture when used in educational services such as conducting classes, seminars, or workshops. The service mark would have allowed Mollison and his two institutes to set enforceable guidelines regarding how permaculture could be taught and who could teach it, particularly with relation to the PDC, despite the fact that he had been certifying teachers since 1993. This attempt failed and was abandoned in 2001. Mollison's application for trademarks in Australia for the terms "Permaculture Design Course" and "Permaculture Design" were withdrawn in 2003. In 2009 he sought a trademark for "Permaculture: A Designers' Manual" and "Introduction to Permaculture", the names of two of his books. These applications were withdrawn in 2011. Australia has never authorized a trademark for the word permaculture.

Criticism

Critics Peter Harper and Rob Scott pushed for less reliance on anecdote and extrapolation from ecological first principles, in favor of peer-reviewed research to substantiate productivity claims and to clarify methodology.

Defenders respond out that permaculture is not yet a mainstream scientific tradition and lacks the resources of traditional agriculture. Ferguson and Lovell point out that permaculturalists rarely engage with mainstream research in agroecology, agroforestry, or ecological engineering, and claim that mainstream science has an elitist or pro-corporate bias.

While there are long-term benefits from permaculture, the short-term decline in agricultural output compared to conventional farming may need to be combined with family planning or a two-child policy in most countries, so that no new farmland is needed for any given population.

Aquaculture

In his books Sustainable Freshwater Aquaculture and Farming in Ponds and Dams, Nick Romanowski expresses the view that the presentation of aquaculture in Bill Mollison's books is unrealistic and misleading.

Agroforestry

Greg Williams argues that forests cannot be more productive than farmland because the net productivity of forests declines as they mature due to ecological succession. Permaculture proponents respond that this is true only when comparing data between woodland forest and climax vegetation, but not when comparing farmland vegetation against woodland forest. For example, ecological succession generally results in rising productivity until it reaches the woodland state (67% tree cover), before declining until full maturity.

Regulation of gene expression

From Wikipedia, the free encyclopedia

Regulation of gene expression by a hormone receptor
 
Diagram showing at which stages in the DNA-mRNA-protein pathway expression can be controlled

Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network.

Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Although as early as 1951, Barbara McClintock showed interaction between two genetic loci, Activator (Ac) and Dissociator (Ds), in the color formation of maize seeds, the first discovery of a gene regulation system is widely considered to be the identification in 1961 of the lac operon, discovered by François Jacob and Jacques Monod, in which some enzymes involved in lactose metabolism are expressed by E. coli only in the presence of lactose and absence of glucose.

In multicellular organisms, gene regulation drives cellular differentiation and morphogenesis in the embryo, leading to the creation of different cell types that possess different gene expression profiles from the same genome sequence. Although this does not explain how gene regulation originated, evolutionary biologists include it as a partial explanation of how evolution works at a molecular level, and it is central to the science of evolutionary developmental biology ("evo-devo").

Regulated stages of gene expression

Any step of gene expression may be modulated, from the DNA-RNA transcription step to post-translational modification of a protein. The following is a list of stages where gene expression is regulated, the most extensively utilised point is Transcription Initiation:

Modification of DNA

Histone tails and their function in chromatin formation

In eukaryotes, the accessibility of large regions of DNA can depend on its chromatin structure, which can be altered as a result of histone modifications directed by DNA methylation, ncRNA, or DNA-binding protein. Hence these modifications may up or down regulate the expression of a gene. Some of these modifications that regulate gene expression are inheritable and are referred to as epigenetic regulation.

Structural

Transcription of DNA is dictated by its structure. In general, the density of its packing is indicative of the frequency of transcription. Octameric protein complexes called histones together with a segment of DNA wound around the eight histone proteins (together referred to as a nucleosome) are responsible for the amount of supercoiling of DNA, and these complexes can be temporarily modified by processes such as phosphorylation or more permanently modified by processes such as methylation. Such modifications are considered to be responsible for more or less permanent changes in gene expression levels.

Chemical

Methylation of DNA is a common method of gene silencing. DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called "CpG islands" when densely clustered). Analysis of the pattern of methylation in a given region of DNA (which can be a promoter) can be achieved through a method called bisulfite mapping. Methylated cytosine residues are unchanged by the treatment, whereas unmethylated ones are changed to uracil. The differences are analyzed by DNA sequencing or by methods developed to quantify SNPs, such as Pyrosequencing (Biotage) or MassArray (Sequenom), measuring the relative amounts of C/T at the CG dinucleotide. Abnormal methylation patterns are thought to be involved in oncogenesis.

Histone acetylation is also an important process in transcription. Histone acetyltransferase enzymes (HATs) such as CREB-binding protein also dissociate the DNA from the histone complex, allowing transcription to proceed. Often, DNA methylation and histone deacetylation work together in gene silencing. The combination of the two seems to be a signal for DNA to be packed more densely, lowering gene expression.

Regulation of transcription

1: RNA Polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA. Top: The gene is essentially turned off. There is no lactose to inhibit the repressor, so the repressor binds to the operator, which obstructs the RNA polymerase from binding to the promoter and making lactase. Bottom: The gene is turned on. Lactose is inhibiting the repressor, allowing the RNA polymerase to bind with the promoter, and express the genes, which synthesize lactase. Eventually, the lactase will digest all of the lactose, until there is none to bind to the repressor. The repressor will then bind to the operator, stopping the manufacture of lactase.

Regulation of transcription thus controls when transcription occurs and how much RNA is created. Transcription of a gene by RNA polymerase can be regulated by several mechanisms. Specificity factors alter the specificity of RNA polymerase for a given promoter or set of promoters, making it more or less likely to bind to them (i.e., sigma factors used in prokaryotic transcription). Repressors bind to the Operator, coding sequences on the DNA strand that are close to or overlapping the promoter region, impeding RNA polymerase's progress along the strand, thus impeding the expression of the gene. The image to the right demonstrates regulation by a repressor in the lac operon. General transcription factors position RNA polymerase at the start of a protein-coding sequence and then release the polymerase to transcribe the mRNA. Activators enhance the interaction between RNA polymerase and a particular promoter, encouraging the expression of the gene. Activators do this by increasing the attraction of RNA polymerase for the promoter, through interactions with subunits of the RNA polymerase or indirectly by changing the structure of the DNA. Enhancers are sites on the DNA helix that are bound by activators in order to loop the DNA bringing a specific promoter to the initiation complex. Enhancers are much more common in eukaryotes than prokaryotes, where only a few examples exist (to date). Silencers are regions of DNA sequences that, when bound by particular transcription factors, can silence expression of the gene.

Regulation of transcription in cancer

In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites. When many of a gene's promoter CpG sites are methylated the gene becomes silenced. Colorectal cancers typically have 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. However, transcriptional silencing may be of more importance than mutation in causing progression to cancer. For example, in colorectal cancers about 600 to 800 genes are transcriptionally silenced by CpG island methylation. Transcriptional repression in cancer can also occur by other epigenetic mechanisms, such as altered expression of microRNAs. In breast cancer, transcriptional repression of BRCA1 may occur more frequently by over-expressed microRNA-182 than by hypermethylation of the BRCA1 promoter.

Regulation of transcription in addiction

One of the cardinal features of addiction is its persistence. The persistent behavioral changes appear to be due to long-lasting changes, resulting from epigenetic alterations affecting gene expression, within particular regions of the brain. Drugs of abuse cause three types of epigenetic alteration in the brain. These are (1) histone acetylations and histone methylations, (2) DNA methylation at CpG sites, and (3) epigenetic downregulation or upregulation of microRNAs.

Chronic nicotine intake in mice alters brain cell epigenetic control of gene expression through acetylation of histones. This increases expression in the brain of the protein FosB, important in addiction. Cigarette addiction was also studied in about 16,000 humans, including never smokers, current smokers, and those who had quit smoking for up to 30 years. In blood cells, more than 18,000 CpG sites (of the roughly 450,000 analyzed CpG sites in the genome) had frequently altered methylation among current smokers. These CpG sites occurred in over 7,000 genes, or roughly a third of known human genes. The majority of the differentially methylated CpG sites returned to the level of never-smokers within five years of smoking cessation. However, 2,568 CpGs among 942 genes remained differentially methylated in former versus never smokers. Such remaining epigenetic changes can be viewed as “molecular scars” that may affect gene expression.

In rodent models, drugs of abuse, including cocaine, methampheamine, alcohol and tobacco smoke products, all cause DNA damage in the brain. During repair of DNA damages some individual repair events can alter the methylation of DNA and/or the acetylations or methylations of histones at the sites of damage, and thus can contribute to leaving an epigenetic scar on chromatin.

Such epigenetic scars likely contribute to the persistent epigenetic changes found in addiction.

Regulation of transcription in learning and memory

DNA methylation is the addition of a methyl group to the DNA that happens at cytosine. The image shows a cytosine single ring base and a methyl group added on to the 5 carbon. In mammals, DNA methylation occurs almost exclusively at a cytosine that is followed by a guanine.

In mammals, methylation of cytosine (see Figure) in DNA is a major regulatory mediator. Methylated cytosines primarily occur in dinucleotide sequences where cytosine is followed by a guanine, a CpG site. The total number of CpG sites in the human genome is approximately 28 million. and generally about 70% of all CpG sites have a methylated cytosine.

The identified areas of the human brain are involved in memory formation.

In a rat, a painful learning experience, contextual fear conditioning, can result in a life-long fearful memory after a single training event. Cytosine methylation is altered in the promoter regions of about 9.17% of all genes in the hippocampus neuron DNA of a rat that has been subjected to a brief fear conditioning experience. The hippocampus is where new memories are initially stored.

Methylation of CpGs in a promoter region of a gene represses transcription while methylation of CpGs in the body of a gene increases expression. TET enzymes play a central role in demethylation of methylated cytosines. Demethylation of CpGs in a gene promoter by TET enzyme activity increases transcription of the gene.

When contextual fear conditioning is applied to a rat, more than 5,000 differentially methylated regions (DMRs) (of 500 nucleotides each) occur in the rat hippocampus neural genome both one hour and 24 hours after the conditioning in the hippocampus. This causes about 500 genes to be up-regulated (often due to demethylation of CpG sites in a promoter region) and about 1,000 genes to be down-regulated (often due to newly formed 5-methylcytosine at CpG sites in a promoter region). The pattern of induced and repressed genes within neurons appears to provide a molecular basis for forming the first transient memory of this training event in the hippocampus of the rat brain.

Post-transcriptional regulation

After the DNA is transcribed and mRNA is formed, there must be some sort of regulation on how much the mRNA is translated into proteins. Cells do this by modulating the capping, splicing, addition of a Poly(A) Tail, the sequence-specific nuclear export rates, and, in several contexts, sequestration of the RNA transcript. These processes occur in eukaryotes but not in prokaryotes. This modulation is a result of a protein or transcript that, in turn, is regulated and may have an affinity for certain sequences.

Three prime untranslated regions and microRNAs

Three prime untranslated regions (3'-UTRs) of messenger RNAs (mRNAs) often contain regulatory sequences that post-transcriptionally influence gene expression. Such 3'-UTRs often contain both binding sites for microRNAs (miRNAs) as well as for regulatory proteins. By binding to specific sites within the 3'-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting translation or directly causing degradation of the transcript. The 3'-UTR also may have silencer regions that bind repressor proteins that inhibit the expression of a mRNA.

The 3'-UTR often contains miRNA response elements (MREs). MREs are sequences to which miRNAs bind. These are prevalent motifs within 3'-UTRs. Among all regulatory motifs within the 3'-UTRs (e.g. including silencer regions), MREs make up about half of the motifs.

As of 2014, the miRBase web site, an archive of miRNA sequences and annotations, listed 28,645 entries in 233 biologic species. Of these, 1,881 miRNAs were in annotated human miRNA loci. miRNAs were predicted to have an average of about four hundred target mRNAs (affecting expression of several hundred genes). Freidman et al. estimate that >45,000 miRNA target sites within human mRNA 3'-UTRs are conserved above background levels, and >60% of human protein-coding genes have been under selective pressure to maintain pairing to miRNAs.

Direct experiments show that a single miRNA can reduce the stability of hundreds of unique mRNAs. Other experiments show that a single miRNA may repress the production of hundreds of proteins, but that this repression often is relatively mild (less than 2-fold).

The effects of miRNA dysregulation of gene expression seem to be important in cancer. For instance, in gastrointestinal cancers, a 2015 paper identified nine miRNAs as epigenetically altered and effective in down-regulating DNA repair enzymes.

The effects of miRNA dysregulation of gene expression also seem to be important in neuropsychiatric disorders, such as schizophrenia, bipolar disorder, major depressive disorder, Parkinson's disease, Alzheimer's disease and autism spectrum disorders.

Regulation of translation

The translation of mRNA can also be controlled by a number of mechanisms, mostly at the level of initiation. Recruitment of the small ribosomal subunit can indeed be modulated by mRNA secondary structure, antisense RNA binding, or protein binding. In both prokaryotes and eukaryotes, a large number of RNA binding proteins exist, which often are directed to their target sequence by the secondary structure of the transcript, which may change depending on certain conditions, such as temperature or presence of a ligand (aptamer). Some transcripts act as ribozymes and self-regulate their expression.

Examples of gene regulation

  • Enzyme induction is a process in which a molecule (e.g., a drug) induces (i.e., initiates or enhances) the expression of an enzyme.
  • The induction of heat shock proteins in the fruit fly Drosophila melanogaster.
  • The Lac operon is an interesting example of how gene expression can be regulated.
  • Viruses, despite having only a few genes, possess mechanisms to regulate their gene expression, typically into an early and late phase, using collinear systems regulated by anti-terminators (lambda phage) or splicing modulators (HIV).
  • Gal4 is a transcriptional activator that controls the expression of GAL1, GAL7, and GAL10 (all of which code for the metabolic of galactose in yeast). The GAL4/UAS system has been used in a variety of organisms across various phyla to study gene expression.

Developmental biology

A large number of studied regulatory systems come from developmental biology. Examples include:

  • The colinearity of the Hox gene cluster with their nested antero-posterior patterning
  • Pattern generation of the hand (digits - interdigits): the gradient of sonic hedgehog (secreted inducing factor) from the zone of polarizing activity in the limb, which creates a gradient of active Gli3, which activates Gremlin, which inhibits BMPs also secreted in the limb, results in the formation of an alternating pattern of activity as a result of this reaction-diffusion system.
  • Somitogenesis is the creation of segments (somites) from a uniform tissue (Pre-somitic Mesoderm). They are formed sequentially from anterior to posterior. This is achieved in amniotes possibly by means of two opposing gradients, Retinoic acid in the anterior (wavefront) and Wnt and Fgf in the posterior, coupled to an oscillating pattern (segmentation clock) composed of FGF + Notch and Wnt in antiphase.
  • Sex determination in the soma of a Drosophila requires the sensing of the ratio of autosomal genes to sex chromosome-encoded genes, which results in the production of sexless splicing factor in females, resulting in the female isoform of doublesex.

Circuitry

Up-regulation and down-regulation

Up-regulation is a process that occurs within a cell triggered by a signal (originating internal or external to the cell), which results in increased expression of one or more genes and as a result the protein(s) encoded by those genes. Conversely, down-regulation is a process resulting in decreased gene and corresponding protein expression.

  • Up-regulation occurs, for example, when a cell is deficient in some kind of receptor. In this case, more receptor protein is synthesized and transported to the membrane of the cell and, thus, the sensitivity of the cell is brought back to normal, reestablishing homeostasis.
  • Down-regulation occurs, for example, when a cell is overstimulated by a neurotransmitter, hormone, or drug for a prolonged period of time, and the expression of the receptor protein is decreased in order to protect the cell.

Inducible vs. repressible systems

Gene Regulation can be summarized by the response of the respective system:

  • Inducible systems - An inducible system is off unless there is the presence of some molecule (called an inducer) that allows for gene expression. The molecule is said to "induce expression". The manner by which this happens is dependent on the control mechanisms as well as differences between prokaryotic and eukaryotic cells.
  • Repressible systems - A repressible system is on except in the presence of some molecule (called a corepressor) that suppresses gene expression. The molecule is said to "repress expression". The manner by which this happens is dependent on the control mechanisms as well as differences between prokaryotic and eukaryotic cells.

The GAL4/UAS system is an example of both an inducible and repressible system. Gal4 binds an upstream activation sequence (UAS) to activate the transcription of the GAL1/GAL7/GAL10 cassette. On the other hand, a MIG1 response to the presence of glucose can inhibit GAL4 and therefore stop the expression of the GAL1/GAL7/GAL10 cassette.

Theoretical circuits

  • Repressor/Inducer: an activation of a sensor results in the change of expression of a gene
  • negative feedback: the gene product downregulates its own production directly or indirectly, which can result in
    • keeping transcript levels constant/proportional to a factor
    • inhibition of run-away reactions when coupled with a positive feedback loop
    • creating an oscillator by taking advantage in the time delay of transcription and translation, given that the mRNA and protein half-life is shorter
  • positive feedback: the gene product upregulates its own production directly or indirectly, which can result in
    • signal amplification
    • bistable switches when two genes inhibit each other and both have positive feedback
    • pattern generation

Study methods

In general, most experiments investigating differential expression used whole cell extracts of RNA, called steady-state levels, to determine which genes changed and by how much. These are, however, not informative of where the regulation has occurred and may mask conflicting regulatory processes, but it is still the most commonly analysed (quantitative PCR and DNA microarray).

When studying gene expression, there are several methods to look at the various stages. In eukaryotes these include:

  • The local chromatin environment of the region can be determined by ChIP-chip analysis by pulling down RNA Polymerase II, Histone 3 modifications, Trithorax-group protein, Polycomb-group protein, or any other DNA-binding element to which a good antibody is available.
  • Epistatic interactions can be investigated by synthetic genetic array analysis
  • Due to post-transcriptional regulation, transcription rates and total RNA levels differ significantly. To measure the transcription rates nuclear run-on assays can be done and newer high-throughput methods are being developed, using thiol labelling instead of radioactivity.
  • Only 5% of the RNA polymerised in the nucleus exits, and not only introns, abortive products, and non-sense transcripts are degradated. Therefore, the differences in nuclear and cytoplasmic levels can be see by separating the two fractions by gentle lysis.
  • Alternative splicing can be analysed with a splicing array or with a tiling array.
  • All in vivo RNA is complexed as RNPs. The quantity of transcripts bound to specific protein can be also analysed by RIP-Chip. For example, DCP2 will give an indication of sequestered protein; ribosome-bound gives and indication of transcripts active in transcription (although a more dated method, called polysome fractionation, is still popular in some labs)
  • Protein levels can be analysed by Mass spectrometry, which can be compared only to quantitative PCR data, as microarray data is relative and not absolute.
  • RNA and protein degradation rates are measured by means of transcription inhibitors (actinomycin D or α-amanitin) or translation inhibitors (Cycloheximide), respectively.

Inequality (mathematics)

From Wikipedia, the free encyclopedia https://en.wikipedia.org/wiki/Inequality...