SUMMARY / RELATED TOPICS

Compost

Compost is organic matter, decomposed in a process called composting. This process recycles various organic materials otherwise regarded as waste products and produces a soil conditioner. Compost is rich in nutrients, it is used, for example, in gardens, horticulture, urban agriculture and organic farming. The compost itself is beneficial for the land in many ways, including as a soil conditioner, a fertilizer, addition of vital humus or humic acids, as a natural pesticide for soil. In ecosystems, compost is useful for erosion control and stream reclamation, wetland construction, as landfill cover. At the simplest level, the process of composting requires making a heap of wet organic matter, such as leaves and food scraps, waiting for the materials to break down into humus after a period of months. However, composting can take place as a multi-step monitored process with measured inputs of water and carbon- and nitrogen-rich materials; the decomposition process is aided by shredding the plant matter, adding water and ensuring proper aeration by turning the mixture when open piles or "windrows" are used.

Fungi and other detritivores further break up the material. Bacteria requiring oxygen to function and fungi manage the chemical process by converting the inputs into heat, carbon dioxide, ammonium. Composting is an aerobic method of decomposing organic solid wastes, it can therefore be used to recycle organic material. The process involves decomposition of organic material into a humus-like material, known as compost, a good fertilizer for plants. Composting requires the following three components: human management, aerobic conditions, development of internal biological heat. Composting organisms require four important ingredients to work effectively: Carbon — for energy. High carbon materials tend to be dry. Nitrogen — to grow and reproduce more organisms to oxidize the carbon. High nitrogen materials tend to be wet. Oxygen — for oxidizing the carbon, the decomposition process. Water — in the right amounts to maintain activity without causing anaerobic conditions. Certain ratios of these materials will provide microorganisms to work at a rate that will heat up the pile.

Active management of the pile is needed to maintain sufficient supply of oxygen and the right moisture level. The air/water balance is critical to maintaining high temperatures 130–160 °F until the materials are broken down; the most efficient composting occurs with an optimal carbon:nitrogen ratio of about 25:1. Hot container composting focuses on retaining the heat to increase decomposition rate and produce compost more quickly. Rapid composting is favored by having a C/N ratio of ~30 or less. Above 30 the substrate is nitrogen starved, below 15 it is to outgas a portion of nitrogen as ammonia. Nearly all plant and animal materials have both carbon and nitrogen, but amounts vary with characteristics noted above. Fresh grass clippings have an average ratio of about 15:1 and dry autumn leaves about 50:1 depending on species. Mixing equal parts by volume approximates the ideal C:N range. Few individual situations will provide the ideal mix of materials at any point. Observation of amounts, consideration of different materials as a pile is built over time, can achieve a workable technique for the individual situation.

With the proper mixture of water, oxygen and nitrogen, micro-organisms are able to break down organic matter to produce compost. The composting process is dependent on micro-organisms to break down organic matter into compost. There are many types of microorganisms found in active compost of which the most common are: Bacteria- The most numerous of all the microorganisms found in compost. Depending on the phase of composting, mesophilic or thermophilic bacteria may predominate. Actinobacteria- Necessary for breaking down paper products such as newspaper, etc. Fungi- molds and yeast help break down materials that bacteria cannot lignin in woody material. Protozoa- Help consume bacteria and micro organic particulates. Rotifers- Rotifers help control populations of bacteria and small protozoans. In addition, earthworms not only ingest composted material, but continually re-create aeration and drainage tunnels as they move through the compost. Under ideal conditions, composting proceeds through three major phases: Mesophilic phase: An initial, mesophilic phase, in which the decomposition is carried out under moderate temperatures by mesophilic microorganisms.

Thermophilic phase: As the temperature rises, a second, thermophilic phase starts, in which the decomposition is carried out by various thermophilic bacteria under high temperatures. Maturation phase: As the supply of high-energy compounds dwindles, the temperature starts to decrease, the mesophiles once again predominate in the maturation phase. There are many proponents of rapid composting that attempt to correct some of the perceived problems associated with traditional, slow composting. Many advocate. Many such short processes involve a few changes to traditional methods, including smaller, more homogenized pieces in the compost, controlling carbon-to-nitrogen ratio at 30 to 1 or less, monitoring the moisture level more carefully. However, none of these parameters differ from the early writings of compost researchers, suggesting that, in fact, modern composting has not made si

Artichoke (band)

Artichoke is an indie pop band in Los Angeles. Formed in 1999 by Timothy Sellers, the band is best known for their concept albums. In 2005, Artichoke’s “26 Scientists: Volume One Anning - Malthus” was featured in the science section of the “New York Times” in an article about the emerging songs-of-science micro-niche, as spearheaded by such artists as They Might Be Giants and Tom Lehrer. In 2010, Lisa Carver of the “LA Weekly” wrote about Artichoke’s family album “26 Animals” and described their sound as “music for kids and drunks.”In 2011 Sellers was the songwriter in residence for NIMBioS, National Institute for Mathematical and Biological Synthesis. In March of 2018, “Echoes”, an album including ten stylistically tweaked cover songs, reached #71 on north American college radio. Echoes Etchy Sketchy Skies Bees 26 Animals Historic Highland Park 26 Scientists, Volume Two: Newton - Zeno Nevermind the Bollocks here’s Artichoke 26 Scientists, Volume One: Anning - Malthus 20 Grit Evaporation Sing in Traffic Golden Eyelids Official website

Luciferase

Luciferase is a generic term for the class of oxidative enzymes that produce bioluminescence, is distinguished from a photoprotein. The name was first used by Raphaël Dubois who invented the words luciferin and luciferase, for the substrate and enzyme, respectively. Both words are derived from the Latin word lucifer – meaning lightbringer. Luciferases are used in biotechnology, for microscopy and as reporter genes, for many of the same applications as fluorescent proteins. However, unlike fluorescent proteins, luciferases do not require an external light source, but do require addition of luciferin, the consumable substrate. A variety of organisms regulate their light production using different luciferases in a variety of light-emitting reactions; the majority of studied luciferases have been found in animals, including fireflies, many marine animals such as copepods and the sea pansy. However, luciferases have been studied in luminous fungi, like the Jack-O-Lantern mushroom, as well as examples in other kingdoms including luminous bacteria, dinoflagellates.

The luciferases of fireflies – of which there are over 2000 species – and of the other Elateroidea are diverse enough to be useful in molecular phylogeny. In fireflies, the oxygen required is supplied through a tube in the abdomen called the abdominal trachea. One well-studied luciferase is that of the Photinini firefly Photinus pyralis, which has an optimum pH of 7.8. Well studied is the sea pansy, Renilla reniformis. In this organism, the luciferase is associated with a luciferin-binding protein as well as a green fluorescent protein. Calcium triggers release of the luciferin from the luciferin binding protein; the substrate is available for oxidation by the luciferase, where it is degraded to coelenteramide with a resultant release of energy. In the absence of GFP, this energy would be released as a photon of blue light. However, due to the associated GFP, the energy released by the luciferase is instead coupled through resonance energy transfer to the fluorophore of the GFP, is subsequently released as a photon of green light.

The catalyzed reaction is: coelenterazine + O2 → coelenteramide + CO2 + photon of light Newer luciferases have been identified that, unlike other luciferases, are secreted molecules. One such example is the Metridia coelenterazine-dependent luciferase, derived from the marine copepod Metridia longa; the Metridia longa secreted luciferase gene encodes a 24 kDa protein containing an N-terminal secretory signal peptide of 17 amino acid residues. The sensitivity and high signal intensity of this luciferase molecule proves advantageous in many reporter studies; some of the benefits of using a secreted reporter molecule like MetLuc is its no-lysis protocol that allows one to be able to conduct live cell assays and multiple assays on the same cell. Bacterial bioluminescence is seen in Photobacterium species, Vibrio fischeri, Vibrio haweyi, Vibrio harveyi. Light emission in some bioluminescent bacteria utilizes'antenna' such as'lumazine protein' to accept the energy from the primary excited state on the luciferase, resulting in an excited lulnazine chromophore which emits light, of a shorter wavelength, while in others use a yellow fluorescent protein with FMN as the chromophore and emits light, red-shifted relative to that from luciferase.

Dinoflagellate luciferase is a multi-domain protein, consisting of an N-terminal domain, three catalytic domains, each of which preceded by a helical bundle domain. The structure of the dinoflagellate luciferase catalytic domain has been solved; the core part of the domain is a 10 stranded beta barrel, structurally similar to lipocalins and FABP. The N-terminal domain is conserved between dinoflagellate luciferin binding proteins, it has been suggested that this region may mediate an interaction between LBP and luciferase or their association with the vacuolar membrane. The helical bundle domain has a three helix bundle structure that holds four important histidines that are thought to play a role in the pH regulation of the enzyme. There is a large pocket in the β-barrel of the dinoflagellate luciferase at pH 8 to accommodate the tetrapyrrole substrate but there is no opening to allow the substrate to enter. Therefore, a significant conformational change must occur to provide access and space for a ligand in the active site and the source for this change is through the four N-terminal histidine residues.

At pH 8, it can be seen that the unprotonated histidine residues are involved in a network of hydrogen bonds at the interface of the helices in the bundle that block substrate access to the active site and disruption of this interaction by protonation or by replacement of the histidine residues by alanine causes a large molecular motion of the bundle, separating the helices by 11Å and opening the catalytic site. Logically, the histidine residues cannot be replaced by alanine in nature but this experimental replacement further confirms that the larger histidine residues block the active site. Additionally, three Gly-Gly sequences, one in the N-terminal helix and two in the helix-loop-helix motif, could serve as hinges about which the chains rotate in order to further open the pathway to the catalytic site and enlarge the active site. A dinoflagellate luciferase is capable of emitting light due to its interaction with its substrate and the luciferin-binding protein in the scintillon organelle found in dinoflagellates.

The luciferase acts in accord