1.
Flavoparmelia caperata
–
Flavoparmelia caperata, the common greenshield lichen, is a medium to large foliose lichen that has a very distinctive pale yellow green upper cortex when dry. The rounded lobes, measuring 3–8 mm wide, usually have patches of granular soredia arising from pustules, the lobes of the thallus may be smooth, but quite often have a wrinkled appearance especially in older specimens. The lower surface is black except for a margin, rhizomes attached to the lower surface are black. Cortex, PD-, K-, KC+ yellowish, C-, medulla, PD+ red-orange, K-, KC+ pink, C-. On bark of trees, but occasionally on rock, the very similar Flavoparmelia baltimorensis grows mainly on rock and has globose, pustular outgrowths on the upper surface of the lobes, but does not produce granular soredia. A cumulative checklist for the lichen-forming, lichenicolous and allied fungi of the continental United States, British Lichens - List of Lichens & Lichenicolous Fungi. Checklist to Norwegian lichens, Accepted names, checklist of the Lichens of Australia and its Island Territories. The Lichen Herbarium, University of Oslo, Norway, recent Literature on Lichens and Matticks Literature Search. Brodo, I. M. S. D. Sharnoff, yale University Press, New Haven,795 pages. Published by the author, Don Flenniken,2273 Blachleyville Rd. Wooster, Flavoparmelia, a new genus in the lichen family Parmeliaceae. Purvis, O. W. B. J. Coppins, D. L. Hawksworth, the lichen flora of Great Britain and Ireland. The British Lichen Society, Cromwell Road, London SW7 5BD
2.
Lichen
–
A lichen is a composite organism that arises from algae or cyanobacteria living among filaments of multiple fungi in a symbiotic relationship. The combined lichen has properties different from those of its component organisms, Lichens come in many colours, sizes, and forms. The properties are sometimes plant-like, but lichens are not plants, Lichens may have tiny, leafless branches, flat leaf-like structures, flakes that lie on the surface like peeling paint, or other growth forms. A macrolichen is a lichen that is either bush-like or leafy, here, macro and micro do not refer to size, but to the growth form. Common names for lichens may contain the word moss, and lichens may superficially look like and grow with mosses, Lichens do not have roots that absorb water and nutrients as plants do, but like plants, they produce their own food by photosynthesis. When they grow on plants, they do not live as parasites, Lichens occur from sea level to high alpine elevations, in many environmental conditions, and can grow on almost any surface. Lichens are abundant growing on bark, leaves, mosses, on other lichens and they grow on rock, walls, gravestones, roofs, exposed soil surfaces, and in the soil as part of a biological soil crust. Different kinds of lichens have adapted to survive in some of the most extreme environments on Earth, arctic tundra, hot dry deserts, rocky coasts and they can even live inside solid rock, growing between the grains. It is estimated that 6% of Earths land surface is covered by lichen, there are about 20,000 known species of lichens. Some lichens have lost the ability to reproduce sexually, yet continue to speciate, Lichens may be long-lived, with some considered to be among the oldest living things. They are among the first living things to grow on fresh rock exposed after an event such as a landslide, the long life-span and slow and regular growth rate of some lichens can be used to date events. In American English, lichen is pronounced the same as the verb liken, in British English, both this pronunciation and one rhyming with kitchen /ˈlɪtʃən/) are used. Lichens grow in a range of shapes and forms. The shape of a lichen is determined by the organization of the fungal filaments. The nonreproductive tissues, or vegetative body parts, is called the thallus, Lichens are grouped by thallus type, since the thallus is usually the most visually prominent part of the lichen. Thallus growth forms typically correspond to a few basic internal structure types, Common names for lichens often come from a growth form or color that is typical of a lichen genus. When a crustose lichen gets old, the center may start to crack up like old-dried paint, old-broken asphalt paving and this is called being rimose or areolate, and the island pieces separated by the cracks are called areolas. The areolas appear separated, but are connected by an underlying prothallus or hypothallus, when a crustose lichen grows from a center and appears to radiate out, it is called crustose placodioid
3.
Symbiosis
–
Symbiosis is any type of a close and long-term biological interaction between two different species, be it mutualistic, commensalistic, or parasitic. In 1879, Heinrich Anton de Bary defined it as the living together of unlike organisms, Symbiosis can be obligatory, which means that one or both of the symbionts entirely depend on each other for survival, or facultative when they can generally live independently. When one organism lives on another such as mistletoe, it is called ectosymbiosis, or endosymbiosis when one partner lives inside the tissues of another, as in Symbiodinium in corals. In 1877, Albert Bernhard Frank used the term symbiosis which previously had used to depict people living together in community to describe the mutualistic relationship in lichens. In 1879, the German mycologist Heinrich Anton de Bary defined it as the living together of unlike organisms, symbiotic relationships can be obligate, meaning that one or both of the symbionts entirely depend on each other for survival. For example, in lichens, which consist of fungal and photosynthetic symbionts, the algal or cyanobacterial symbionts in lichens, such as Trentepohlia, can generally live independently, and their symbiosis is, therefore, facultative. Endosymbiosis is any relationship in which one symbiont lives within the tissues of the other, either within the cells or extracellularly. Mutualism or interspecies reciprocal altruism is a relationship between individuals of different species where both individuals benefit, in general, only lifelong interactions involving close physical and biochemical contact can properly be considered symbiotic. Mutualistic relationships may be either obligate for both species, obligate for one but facultative for the other, or facultative for both, a large percentage of herbivores have mutualistic gut flora to help them digest plant matter, which is more difficult to digest than animal prey. This gut flora is made up of cellulose-digesting protozoans or bacteria living in the herbivores intestines, coral reefs are the result of mutualisms between coral organisms and various types of algae which live inside them. Most land plants and land ecosystems rely on mutualisms between the plants, which fix carbon from the air, and mycorrhyzal fungi, which help in extracting water, an example of mutual symbiosis is the relationship between the ocellaris clownfish that dwell among the tentacles of Ritteri sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protect the clownfish from its predators, a special mucus on the clownfish protects it from the stinging tentacles. A further example is the fish, which sometimes lives together with a shrimp. The shrimp digs and cleans up a burrow in the sand in which both the shrimp and the fish live. The shrimp is almost blind, leaving it vulnerable to predators when outside its burrow, in case of danger the goby fish touches the shrimp with its tail to warn it. When that happens both the shrimp and goby fish quickly retreat into the burrow, different species of gobies also exhibit mutualistic behavior through cleaning up ectoparasites in other fish. Another non-obligate symbiosis is known from encrusting bryozoans and hermit crabs, the bryozoan colony develops a cirumrotatory growth and offers the crab a helicospiral-tubular extension of its living chamber that initially was situated within a gastropod shell. A spectacular examples of mutualism is between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps
4.
Fungus
–
A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from the other eukaryotic life kingdoms of plants, a characteristic that places fungi in a different kingdom from plants, bacteria and some protists, is chitin in their cell walls. Similar to animals, fungi are heterotrophs, they acquire their food by absorbing dissolved molecules, growth is their means of mobility, except for spores, which may travel through the air or water. Fungi are the principal decomposers in ecological systems and this fungal group is distinct from the structurally similar myxomycetes and oomycetes. The discipline of biology devoted to the study of fungi is known as mycology, in the past, mycology was regarded as a branch of botany, although it is now known fungi are genetically more closely related to animals than to plants. Abundant worldwide, most fungi are inconspicuous because of the size of their structures. Fungi include symbionts of plants, animals, or other fungi and they may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform a role in the decomposition of organic matter and have fundamental roles in nutrient cycling. Since the 1940s, fungi have been used for the production of antibiotics, Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, the fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans, losses of crops due to fungal diseases or food spoilage can have a large impact on human food supplies and local economies. The fungus kingdom encompasses a diversity of taxa with varied ecologies, life cycle strategies. However, little is known of the biodiversity of Kingdom Fungi. Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, phylogenetic studies published in the last decade have helped reshape the classification within Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla. The English word fungus is directly adopted from the Latin fungus, used in the writings of Horace, a group of all the fungi present in a particular area or geographic region is known as mycobiota, e. g. the mycobiota of Ireland. Like plants, fungi grow in soil and, in the case of mushrooms, form conspicuous fruit bodies. The fungi are now considered a kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago. Fungi have membrane-bound cytoplasmic organelles such as mitochondria, sterol-containing membranes and they have a characteristic range of soluble carbohydrates and storage compounds, including sugar alcohols, disaccharides, and polysaccharides
5.
Photosynthesis
–
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organisms activities. In most cases, oxygen is released as a waste product. Most plants, most algae, and cyanobacteria perform photosynthesis, such organisms are called photoautotrophs, in plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances, such as water, in the Calvin cycle, atmospheric carbon dioxide is incorporated into already existing organic carbon compounds, such as ribulose bisphosphate. Using the ATP and NADPH produced by the light-dependent reactions, the compounds are then reduced and removed to form further carbohydrates. Cyanobacteria appeared later, the oxygen they produced contributed directly to the oxygenation of the Earth. Today, the rate of energy capture by photosynthesis globally is approximately 130 terawatts. Photosynthetic organisms also convert around 100–115 thousand million tonnes of carbon into biomass per year. Photosynthetic organisms are photoautotrophs, which means that they are able to synthesize food directly from carbon dioxide, however, not all organisms that use light as a source of energy carry out photosynthesis, photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon. In plants, algae, and cyanobacteria, photosynthesis releases oxygen and this is called oxygenic photosynthesis and is by far the most common type of photosynthesis used by living organisms. Although there are differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. There are also varieties of anoxygenic photosynthesis, used mostly by certain types of bacteria. Carbon dioxide is converted into sugars in a process called carbon fixation, photosynthesis provides the energy in the form of free electrons that are used to split carbon from carbon dioxide that is then used to fix that carbon once again as carbohydrate. Carbon fixation is a redox reaction, so photosynthesis supplies the energy that drives both process. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP, during the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide. Most organisms that utilize oxygenic photosynthesis use visible light for the light-dependent reactions, some organisms employ even more radical variants of photosynthesis. Some archea use a method that employs a pigment similar to those used for vision in animals. The bacteriorhodopsin changes its configuration in response to sunlight, acting as a proton pump and this produces a proton gradient more directly, which is then converted to chemical energy
6.
Algae
–
Algae is an informal term for a large, diverse group of photosynthetic organisms which are not necessarily closely related, and is thus polyphyletic. Included organisms range from unicellular genera, such as Chlorella and the diatoms, to forms, such as the giant kelp. Most are aquatic and autotrophic and lack many of the cell and tissue types, such as stomata, xylem, and phloem. No definition of algae is generally accepted, one definition is that algae have chlorophyll as their primary photosynthetic pigment and lack a sterile covering of cells around their reproductive cells. Some authors exclude all prokaryotes thus do not consider cyanobacteria as algae, Algae constitute a polyphyletic group since they do not include a common ancestor, and although their plastids seem to have a single origin, from cyanobacteria, they were acquired in different ways. Green algae are examples of algae that have primary chloroplasts derived from endosymbiotic cyanobacteria, diatoms and brown algae are examples of algae with secondary chloroplasts derived from an endosymbiotic red alga. Algae exhibit a range of reproductive strategies, from simple asexual cell division to complex forms of sexual reproduction. Algae lack the various structures that characterize land plants, such as the phyllids of bryophytes, rhizoids in nonvascular plants, and the roots, leaves, and other organs found in tracheophytes. Most are phototrophic, although some are mixotrophic, deriving energy both from photosynthesis and uptake of organic carbon either by osmotrophy, myzotrophy, or phagotrophy. Some other heterotrophic organisms, such as the apicomplexans, are derived from cells whose ancestors possessed plastids. Fossilized filamentous algae from the Vindhya basin have been dated back to 1.6 to 1.7 billion years ago, the singular alga is the Latin word for seaweed and retains that meaning in English. Although some speculate that it is related to Latin algēre, be cold, a more likely source is alliga, binding, entwining. The Ancient Greek word for seaweed was φῦκος, which could mean either the seaweed or a red dye derived from it, the Latinization, fūcus, meant primarily the cosmetic rouge. It could be any color, black, red, green, accordingly, the modern study of marine and freshwater algae is called either phycology or algology, depending on whether the Greek or Latin root is used. The name Fucus appears in a number of taxa, most algae contain chloroplasts that are similar in structure to cyanobacteria. Chloroplasts contain circular DNA like that in cyanobacteria and presumably represent reduced endosymbiotic cyanobacteria, however, the exact origin of the chloroplasts is different among separate lineages of algae, reflecting their acquisition during different endosymbiotic events. The table below describes the composition of the three groups of algae. Their lineage relationships are shown in the figure in the upper right, many of these groups contain some members that are no longer photosynthetic
7.
Thallus
–
Many of these organisms were previously known as the thallophytes, a polyphyletic group of distantly related organisms. An organism or structure resembling a thallus is called thalloid, thallodal, thalliform, thalline, a thallus usually names the entire body of a multicellular non-moving organism in which there is no organization of the tissues into organs. Even though thalli do not have organized and distinct parts as do the vascular plants, the analogous structures have similar function or macroscopic structure, but different microscopic structure, for example, no thallus has vascular tissue. In exceptional cases such as the Lemnoideae, where the structure of a plant is in fact thallus-like, it is referred to as having a thalloid structure. Although a thallus is largely undifferentiated in terms of its anatomy, there can be visible differences, a kelp, for example, may have its thallus divided into three regions. The parts of a kelp thallus include the holdfast, stipe, the thallus of a fungus is usually called a mycelium. The term thallus is also used to refer to the vegetative body of a lichen. In seaweed, thallus is also called frond. The gametophyte of some non-thallophyte plants -- clubmosses, horsetails, and ferns is termed prothallus
8.
Hyphae
–
A hypha is a long, branching filamentous structure of a fungus, oomycete, or actinobacterium. In most fungi, hyphae are the mode of vegetative growth. Yeasts are unicellular fungi that do not grow as hyphae, a hypha consists of one or more cells surrounded by a tubular cell wall. In most fungi, hyphae are divided into cells by internal cross-walls called septa, septa are usually perforated by pores large enough for ribosomes, mitochondria and sometimes nuclei to flow between cells. The major structural polymer in fungal cell walls is typically chitin, in contrast to plants, some fungi have aseptate hyphae, meaning their hyphae are not partitioned by septa. Hyphae have a diameter of 4-6 µm. During tip growth, cell walls are extended by the assembly and polymerization of cell wall components. The spitzenkörper is an intracellular organelle associated with tip growth and it is composed of an aggregation of membrane-bound vesicles containing cell wall components. The spitzenkörper is part of the system of fungi, holding and releasing vesicles it receives from the Golgi apparatus. These vesicles travel to the membrane via the cytoskeleton and release their contents outside the cell by the process of exocytosis. Vesicle membranes contribute to growth of the membrane while their contents form new cell wall. As a hypha extends, septa may be formed behind the tip to partition each hypha into individual cells. Hyphae can branch through the bifurcation of a tip, or by the emergence of a new tip from an established hypha. The direction of growth can be controlled by environmental stimuli. Hyphae can sense reproductive units from some distance, and grow towards them, hyphae can weave through a permeable surface to penetrate it. Hyphae may be modified in different ways to serve specific functions. Some parasitic fungi form haustoria that function in absorption within the host cells, the arbuscules of mutualistic mycorrhizal fungi serve a similar function in nutrient exchange, so are important in assisting nutrient and water absorption by plants. Hyphae are found enveloping the gonidia in lichens, making up a part of their structure
9.
Cortex (botany)
–
A cortex is the outermost layer of a stem or root in a plant, or the surface layer or skin of the nonfruiting part of the body of some lichens. In botany, the cortex is the outermost layer of the stem or root of a plant, bounded on the outside by the epidermis, in plants, it is composed mostly of differentiated cells, usually large thin-walled parenchyma cells of the ground tissue system. The outer cortical cells often acquire irregularly thickened walls, and are called collenchyma cells. Some of the cortical cells may contain chloroplasts. It is responsible for the transportation of materials into the cylinder of the root through diffusion. On a lichen, the cortex is the skin, or outer layer of tissue that covers the undifferentiated cells of the medulla
10.
Gas exchange
–
Gas exchange is a biological process through which different gases are transferred in opposite directions across a specialized respiratory surface. Gases are constantly required by, and produced as a by-product of, cellular and metabolic reactions and it is linked with respiration in animals, and both respiration and photosynthesis in plants, bacteria and some protista. In respiration, oxygen is required to enter cells, while carbon dioxide must be excreted. Respiration, which place in the mitochondria has four main steps, glycolysis, pyruvate oxidation. During the process of respiration, glucose is broken down into carbon dioxide and water, photosynthesis, is the process by which plants, bacteria and some protista use light energy to produce glucose from CO2 and O2. This conversion is facilitated by the pigment called chlorophyll, found in the chloroplast organ of these organisms. In multicellular organisms, diffusion alone is not efficient, so specialised respiratory systems and this is the case for mammals, fish, invertebrates, amphibians, reptiles and protista, which have evolved circulatory systems. These systems transport gases to and from the surface and maintain a continuous concentration gradient. Some multicellular organisms such as flatworms are large but very thin, another example of an organism which uses diffusion as a mechanism of gas exchange is the sponge. In order to produce ATP to survive, single-celled organisms organisms such as amoeba must be able to perform gas exchange, however, these organisms do not have specialised gas exchange surface, so single-celled organisms must take advantage of their high surface area. Their high surface area allows for gases to pass across the cell membrane, as organisms increase in size, so does the distance gases must travel across. In the case of single-celled organisms, the cell membrane distance will be 0. 1mm. It is a process, meaning that no energy is required. The alveolar and pulmonary capillary gases equilibrate across the blood–air barrier, the pulmonary alveoli consist of the alveolar epithelial cells, their basement membranes and the endothelial cells of the pulmonary capillaries. This blood gas barrier is thin but extremely strong. This strength comes from the type IV collagen in between the endothelial and epithelial cells, damage can occur to this barrier at a pressure difference of around 5.3 kPa. The large surface area of the membrane comes from the folding of the membrane into 300 million alveoli, the branching of from the bronchioles in the lungs also contributes to the extremely large surface area across which gas exchange can occur. The lungs of a person can contain between 2.5 and 3 liters of alveolar air
11.
Crustose lichen
–
Crustose lichens form a crust that strongly adheres to the substrate, making separation from the substrate impossible without destruction. The basic structure of crustose lichens consists of a layer, an algal layer. The upper cortex layer is differentiated and is usually pigmented, the algal layer lies beneath the cortex. The medulla fastens the lichen to the substrate and is made up of fungal hyphae, the surface of crustose lichens is characterized by branching cracks that periodically close in response to climatic variations such as alternate wetting and drying regimes. Powdery – considered as the simplest subtype due to the absence of an organized thallus, genera Lepraria, Vezdaea Endolithic – grows inside the rock, usually in interstitial spaces between mineral grains. The upper cortex is usually developed, genus Lecidea Epilithic – grows on top of the rock without penetrating the rock substrate. Acarospora fuscata Epiphloeodal – grows only on the surface of plants, lecania naegelii Endophloeodic – grows underneath the cuticle of leaves or stems. Amandinea punctata Squamulose – has a scale-like appearance resulting from partial separation from substrate and it is an intermediate form between crustose and foliose. Genus Psora, Catapyrenium, Coriscium Peltate – similar to squamulose, peltula euploca Bullate – has an extremely inflated appearance. Genus Mobergia Effigurate - has radially arranged marginal lobes that are prolonged, genera Acarospora, Pleopsidium Lobate – characterized by a thallus that radially arranged with lobes that are partially raised. Genera Caloplaca, Lecanora Suffruticose – clusters of coralloid cushions, peltula clavata Crustose lichen forms a thin crust adhering closely to the substratum. In some cases, this crust may be thick and lumpy, the thallus of a crustose lichen is usually only discernible because of the discolouration of the substrate. Some crustose lichens have thalli consisting of scattered or loosely grouped granules, Crustose lichens differ from the leprose lichen by having an upper cortex and algal cells that are located directly beneath the cortex. The thallus of a lichen has a patchwork or crazy-paving appearance. The patches, or areolae, can be as large as 1 cm in diameter or very small and raised, the surface of the thallus is generally smooth, however it is sometimes broken up by “rimose” cracks. These cracks are a by-product of thallus surface shrinkage, which is caused by alternate wetting and drying, an underlayer of fungal hyphae, the hypothallus, is present on some species of crustose lichens. A dark rim on the areolae may form in areas where the hypothallus is exposed and this may also be present on the thallus itself. These fungal hyphae are usually what attach the thallus firmly to the substrate, in general, lichens do not grow very quickly
12.
Fruticose lichen
–
A fruticose lichen is a form of lichen fungi that is characterized by a coral-like shrubby or bushy growth structure. It is composed of a thallus and a holdfast, the lichen is formed from a symbiotic relationship of a photobiont such as cyanobacteria and two mycobionts such as fungus. Fruticose lichen is characterized by an ascending, bushy or pendulous appearance, while lichen communities are mainly controlled by water and light, vegetative dispersal and filamentous growth in fruticose lichen is often associated with areas of low elevation. Fruticose lichens can endure high degrees of desiccation and they grow very slowly and will often occur in extreme habitats such as on tree barks, on rock surfaces and on soils in the Arctic and mountain regions. Fruticose lichen is a form of composed of a shrubby or bushy thallus. The thallus is the body of a lichen that does not have true leaves, stems. Thallus colour of the lichen can be attributed to the amount of light in its environment, a light thallus color is associated with lower light conditions within the growing environment. Fruticose lichen is characterized by photobionts, the mode of dispersal, growth form. The lichens ability to survive extreme desiccation is due to its ability to quench excess light energy, characteristic of fruticose lichen is the shape of the thallus. Like crustose lichen, fruticose lichen is composed of a holdfast which will act as an anchor for the lichen to grow in rock fissures, over loose sand or soil. Fruticose or ‘shrubby’ lichen differ from other forms of lichen based on their form that is attached to the ground only at the base of the lichen. The most important difference that distinguishes fruticose lichen from other forms of lichen is the algal layer that grows around the circumference of the branches of the lichen. The thallus may be rounded or flattened, unbranched or branched. Fruticose lichens have a fine, round, hair-like structures and are attached to rocks. Although fruticose lichens are defined as being bushy, they can exhibit a flattened. Highly branched fruticose lichen have a surface to volume ratio that results in a rapid drying and wetting pattern compared to lichens that have a lower surface to volume ratio. The internal structure of lichen is composed of a dense outer cortex, a thin algal layer, a medulla. The structure of fruticose lichens depends also on their mycobionts, lichen undergoes diffuse growth and the thallus elongates over time
13.
Chlorophyll
–
Chlorophyll is any of several closely related green pigments found in cyanobacteria and the chloroplasts of algae and plants. Its name is derived from the Greek words χλωρός, chloros and φύλλον, chlorophyll is essential in photosynthesis, allowing plants to absorb energy from light. Chlorophyll absorbs light most strongly in the portion of the electromagnetic spectrum. Conversely, it is a poor absorber of green and near-green portions of the spectrum, chlorophyll molecules are specifically arranged in and around photosystems that are embedded in the thylakoid membranes of chloroplasts. Two types of chlorophyll exist in the photosystems of green plants, chlorophyll was first isolated and named by Joseph Bienaimé Caventou and Pierre Joseph Pelletier in 1817. Chlorophyll is vital for photosynthesis, which plants to absorb energy from light. Chlorophyll molecules are arranged in and around photosystems that are embedded in the thylakoid membranes of chloroplasts. In these complexes, chlorophyll serves two primary functions, the two currently accepted photosystem units are photosystem II and photosystem I, which have their own distinct reaction centres, named P680 and P700, respectively. These centres are named after the wavelength of their red-peak absorption maximum, the identity, function and spectral properties of the types of chlorophyll in each photosystem are distinct and determined by each other and the protein structure surrounding them. Once extracted from the protein into a solvent, these chlorophyll pigments can be separated into chlorophyll a, the function of the reaction center of chlorophyll is to absorb light energy and transfer it to other parts of the photosystem. The absorbed energy of the photon is transferred to an electron in a process called charge separation, the removal of the electron from the chlorophyll is an oxidation reaction. The chlorophyll donates the high energy electron to a series of molecular intermediates called a transport chain. The charged reaction center of chlorophyll is reduced back to its ground state by accepting an electron stripped from water. The electron that reduces P680+ ultimately comes from the oxidation of water into O2 and this reaction is how photosynthetic organisms such as plants produce O2 gas, and is the source for practically all the O2 in Earths atmosphere. Electron transfer reactions in the membranes are complex, however. NADPH is an agent used to reduce CO2 into sugars as well as other biosynthetic reactions. Thus, the other chlorophylls in the photosystem and antenna pigment proteins all cooperatively absorb, besides chlorophyll a, there are other pigments, called accessory pigments, which occur in these pigment–protein antenna complexes. Chlorophyll is a pigment, which is structurally similar to
14.
Phaeophytin
–
In both PS II and RC P870, light drives electrons from the reaction center through pheophytin, which then passes the electrons to a quinone in RC P870 and RC P680. The overall mechanisms, roles, and purposes of the molecules in the two transport chains are analogous to each other. In biochemical terms, pheophytin is a chlorophyll molecule lacking a central Mg2+ ion and it can be produced from chlorophyll by treatment with a weak acid, producing a dark bluish waxy pigment. The probable etymology comes from this description, with pheo meaning dusky and this discovery was met with fierce opposition, since many believed pheophytin to be a byproduct of chlorophyll degradation. Therefore, more experiments ensued to prove that pheophytin is indeed the primary electron acceptor of PSII, the data that was obtained is as follows, Photo-reduction of pheophytin has been observed in various mixtures containing PSII reaction centers. The quantity of pheophytin is in proportion to the number of PSII reaction centers. Photo-reduction of pheophytin occurs at temperatures as low as 100K, and is observed after the reduction of plastoquinone and these observations are all characteristic of photo-conversions of reaction center components. Pheophytin is the first electron carrier intermediate in the center of purple bacteria. Its involvement in this system can be broken down into 5 basic steps, the first step is excitation of the bacteriochlorophylls 2 or the special pair of chlorophylls. This can be seen in the following reaction,2 +1 photon → 2* The second step involves the 2 passing an electron to pheophytin, producing a negatively charged radical and a positively charged radical, which results in a charge separation. 2* + Pheo → ·2+ + ·Pheo− The third step is the electron movement to the tightly bound menaquinone, QA. Two electron transfers convert QB to its reduced form, 2·Pheo− + 2H+ + QB → 2Pheo + QBH2 The fifth and final step involves the filling of the “hole” in the special pair by an electron from a heme in cytochrome c. This regenerates the substrates and completes the cycle, allowing for subsequent reactions to take place, in photosystem II, pheophytin plays a very similar role. It again acts as the first electron carrier intermediate in the photosystem, after P680 becomes excited to P680*, it transfers an electron to pheophytin, which converts the molecule into a negatively charged radical. The negatively charged pheophytin radical quickly passes its extra electron to two consecutive plastoquinone molecules, eventually, the electrons pass through the cytochrome b6f molecule and leaves photosystem II. The reactions outlined above in the section concerning purple bacteria give an illustration of the actual movement of the electrons through pheophytin. The overall scheme is, Excitation Charge separation Plastoquinone reduction Regeneration of substrates Photosynthesis Photosystem Chlorophyll Reaction center P680 Klimov VV, discovery of pheophytin function in the photosynthetic energy conversion as the primary electron acceptor of Photosystem II. Nelson, David L. Cox, Michael M. Lehninger Principles of Biochemistry,22 April 2007 Xiong, Ling, and Richard Sayre
15.
Weathering
–
Weathering is the breaking down of rocks, soil, and minerals as well as wood and artificial materials through contact with the Earths atmosphere, waters, and biological organisms. Two important classifications of weathering processes exist – physical and chemical weathering, mechanical or physical weathering involves the breakdown of rocks and soils through direct contact with atmospheric conditions, such as heat, water, ice and pressure. While physical weathering is accentuated in very cold or very dry environments, chemical reactions are most intense where the climate is wet, however, both types of weathering occur together, and each tends to accelerate the other. For example, physical abrasion decreases the size of particles and therefore increases their surface area, the various agents act in concert to convert primary minerals to secondary minerals and release plant nutrient elements in soluble forms. The materials left over after the rock breaks down combined with organic material creates soil, in addition, many of Earths landforms and landscapes are the result of weathering processes combined with erosion and re-deposition. Physical weathering, also recognized as mechanical weathering, is the class of processes that causes the disintegration of rocks without chemical change, the primary process in physical weathering is abrasion. However, chemical and physical weathering often go hand in hand, physical weathering can occur due to temperature, pressure, frost etc. For example, cracks exploited by physical weathering will increase the area exposed to chemical action. Abrasion by water, ice, and wind loaded with sediment can have tremendous cutting power, as is amply demonstrated by the gorges, ravines. In glacial areas, huge moving ice masses embedded with soil and rock fragments grind down rocks in their path, plant roots sometimes enter cracks in rocks and pry them apart, resulting in some disintegration, Burrowing animals may help disintegrate rock through their physical action. However, such influences are usually of importance in producing parent material when compared to the drastic physical effects of water, ice, wind. Physical weathering is called mechanical weathering or disaggregation. Thermal stress weathering results from the expansion and contraction of rock, for example, heating of rocks by sunlight or fires can cause expansion of their constituent minerals. As some minerals expand more than others, temperature changes set up differential stresses that cause the rock to crack apart. Because the outer surface of a rock is often warmer or colder than the more protected inner portions and this process may be sharply accelerated if ice forms in the surface cracks. When water freezes, it expands with a force of about 1465 Mg/m^2, disintegrating huge rock masses, thermal stress weathering comprises two main types, thermal shock and thermal fatigue. Thermal stress weathering is an important mechanism in deserts, where there is a diurnal temperature range, hot in the day. The repeated heating and cooling exerts stress on the layers of rocks
16.
Organic acid
–
An organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acids, whose acidity is associated with their carboxyl group –COOH, sulfonic acids, containing the group –SO2OH, are relatively stronger acids. Alcohols, with –OH, can act as acids but they are very weak. The relative stability of the base of the acid determines its acidity. Other groups can also confer acidity, usually weakly, the thiol group –SH, the group. In biological systems, organic compounds containing these groups are referred to as organic acids. In general, organic acids are acids and do not dissociate completely in water. Lower molecular mass organic acids such as formic and lactic acids are miscible in water, on the other hand, most organic acids are very soluble in organic solvents. P-Toluenesulfonic acid is a strong acid used in organic chemistry often because it is able to dissolve in the organic reaction solvent. Exceptions to these solubility characteristics exist in the presence of other substituents that affect the polarity of the compound. The pKa a logarithmic measure of the dissociation constant, categorizes the strength of an acid, the lower or more negative the number. It should not be confused with pH, the measure of actual hydrogen ion concentration. Phenol C6H5OH The 19th century name carbolic acid came from the original German name karbolsäure and it is a weak, non-carboxylic acid, but is corrosive and causes chemical burns on the skin due to a protein-degenerating effect. Uric acid C5H4N4O3 Uric acid is a purine derivative which is a diprotic acid but not a carboxylic one. Taurine C2H7NO3S One of the few natural sulfonic acids, discovered in bile, p-Toluenesulfonic acid CH3C6H4SO3H A strong acid that, unlike some strong mineral acids, is non-oxidizing. Trifluoromethanesulfonic acid CF3SO3H One of the strongest acids in existence, organic or inorganic, about a thousand times stronger than sulfuric acid, first synthesized in 1954, it also resists oxidation/reduction reactions and does not sulfonate substrates like sulfuric or chlorosulfonic acid. Aminomethylphosphonic acid A strong phosphonic acid Simple organic acids like formic or acetic acids are used for oil and these organic acids are much less reactive with metals than are strong mineral acids like hydrochloric acid or mixtures of HCl and hydrofluoric acid. For this reason, organic acids are used at temperatures or when long contact times between acid and pipe are needed
17.
Iron oxide
–
Iron oxides are chemical compounds composed of iron and oxygen. All together, there are sixteen known iron oxides and oxyhydroxides, common rust is a form of iron oxide. Iron oxides are used as inexpensive, durable pigments in paints, coatings. Colors commonly available are in the end of the yellow/orange/red/brown/black range. When used as a coloring, it has E number E172. Limonite Iron oxide nanoparticles List of inorganic pigments Information from Nano-Oxides, http, //chemed. chem. purdue. edu/demos/demosheets/12.3. html http, //minerals. usgs. gov/minerals/pubs/commodity/iron_oxide/ CDC - NIOSH Pocket Guide to Chemical Hazards de
18.
Aluminosilicate
–
Aluminosilicate minerals are minerals composed of aluminium, silicon, and oxygen, plus countercations. They are a component of kaolin and other clay minerals. Andalusite, kyanite, and sillimanite are naturally occurring minerals that have the composition Al2SiO5. The triple point of the three polymorphs is located at a temperature of 500 °C and a pressure of 0.4 GPa and these three minerals are commonly used as index minerals in metamorphic rocks. Hydrated aluminosilicate minerals are referred to as zeolites and are porous structures that are naturally occurring materials, the catalyst silica-alumina is an amorphous substance which is not an aluminosilicate compound. There exist a variety of glass types. The characteristics of different types depend on the chemical composition of the glass with a special focus on the oxide composition. Glasses can be categorized into different groups, one of them including the so-called aluminosilicate glasses. This glass type can be differentiated, Characteristically, these glasses are free of alkali oxides and contain 15-25% AI2O3, 52-60% SiO2. Very high transformation temperatures and softening points are typical features, main fields of application are glass bulbs for halogen lamps, high-temperature thermometers and thermally and electrically highly loadable film resistors. The AI2O3 content of alkali aluminosilicate glasses is typically 10-25% and the content over 10%. The high alkali content prepares the glass for ion exchange with bigger alkali ions in order to improve the surface compressive strength, due to this particular feature, this glass type is especially suitable for the use in touch displays, solar cells cover glass and laminated safety glass. High transformation temperatures and outstanding properties, e. g. hardness. Aluminium silicate Silicate minerals Calcium aluminosilicate Sodium aluminosilicate
19.
Zygote
–
A zygote, is an eukaryotic cell formed by a fertilization event between two gametes. The zygotes genome is a combination of the DNA in each gamete, in multicellular organisms, the zygote is the earliest developmental stage. In single-celled organisms, the zygote can divide asexually by mitosis to produce identical offspring, oscar Hertwig and Richard Hertwig made some of the first discoveries on animal zygote formation. In fungi, the fusion of haploid cells is called karyogamy. The result of karyogamy is a diploid cell called a zygote or zygospore and this cell may then enter meiosis or mitosis depending on the life cycle of the species. In plants, the zygote may be polyploid if fertilization occurs between meiotically unreduced gametes, in land plants, the zygote is formed within a chamber called the archegonium. In seedless plants, the archegonium is usually flask-shaped, with a long hollow neck through which the cell enters. As the zygote divides and grows, it does so inside the archegonium, in human fertilization, a release ovum and a haploid sperm cell —combine to form a single 2n diploid cell called the zygote. The other product of meiosis is the polar body with only chromosomes. In the fertilized daughter, DNA is then replicated in the two separate pronuclei derived from the sperm and ovum, making the zygotes chromosome number temporarily 4n diploid. After approximately 30 hours from the time of fertilization, fusion of the pronuclei, between the stages of fertilization and implantation, the developing human is a preimplantation conceptus. However, the National Institute of Health has made the determination that the classification of pre-implantation embryo is still correct. After fertilization, the travels down the oviduct towards the uterus while continuing to divide mitotically without actually increasing in size. After four divisions, the conceptus consists of 16 blastomeres, through the processes of compaction, cell division, and blastulation, the conceptus takes the form of the blastocyst by the fifth day of development, just as it approaches the site of implantation. When the blastocyst hatches from the zona pellucida, it can implant in the lining of the uterus. The human zygote has been edited in experiments designed to cure inherited diseases. In the amoeba, reproduction occurs by division of the parent cell
20.
Ascocarp
–
An ascocarp, or ascoma, is the fruiting body of an ascomycete phylum fungus. It consists of tightly interwoven hyphae and may contain millions of asci. Ascocarps are most commonly bowl-shaped but may take a spherical or flask-like form, the ascocarp is classified according to its placement. It is called if it grows above ground, as with the morels, while underground ascocarps. The form of the hymenium is divided into the following types, apothecia can be relatively large and fleshy, whereas the others are microscopic — about the size of flecks of ground pepper. An apothecium is a wide, open, saucer-shaped or cup-shaped fruit body, the structure of the apothecium chiefly consists of three parts, hymenium, hypothecium, and excipulum. The asci are present in the hymenium layer, the asci are freely exposed at maturity. An example are the members of Dictyomycetes, here the fertile layer is free, so that many spores can be dispersed simultaneously. The morel, Morchella, an edible ascocarp, not a mushroom, the genera Helvella and Gyromitra are similar. A cleistothecium is a globose, completely closed fruit body with no opening to the outside. The ascomatal wall is called peridium and typically consists of interwoven hyphae or pseudoparenchyma cells. It may be covered with hyphal outgrowth called appendages, the asci are globose, deliquescent, and scattered throughout the interior cavity i. e. as in Eurotium or arising in tufts from the basal region of ascocarps as in Erysiphe. The truffles, for instance, have solved this problem by attracting animals such as wild boars, cleistothecia are found mostly in fungi that have little room available for their ascocarps, for instance those that live under tree bark, or underground like truffles. Similar to a cleistothecium, a gymnothecium is an enclosed structure containing globose or pear-shaped. However, unlike the cleistothecium, the wall of a gymnothecium consists of a loosely woven tuft of hyphae. Examples are the Gymnoascus, Talaromyces and the dermatophyte Arthroderma, perithecium, These are flask shaped structures opening by a pore or ostiole through which the ascospores escape. The ostiolar canal may be lined by hair-like structures called periphyses, the unitunicate asci are usually cylindrical in shape, borne on a stipe, released from a pore, developed from the inner wall of the perithecium and arise from a basal plectenchyma-centrum. Examples are members of Sphaeriales and Hypocreales, perithecia are also found in Xylaria and Nectria
21.
Vegetative reproduction
–
Vegetative reproduction is a form of asexual reproduction in plants. It is a process by which new organisms arise without production of seeds or spores and it can occur naturally or be induced by horticulturists. Although most plants normally reproduce sexually, many have the ability for vegetative propagation and this is because meristematic cells capable of cellular differentiation are present in many plant tissues. Horticulturalists are interested in understanding how meristematic cells can be induced to reproduce an entire plant, success rates and difficulty of propagation vary greatly. For example, willow and coleus can be propagated merely by inserting a stem in water or moist soil, on the other hand, monocotyledons, unlike dicotyledons, typically lack a vascular cambium and therefore are harder to propagate. In a wide sense, methods of propagation include cutting, vegetative apomixis, layering, division, budding, grafting. Cutting exploits the ability of plants to grow adventitious roots under certain conditions, vegetative propagation is usually considered a cloning method. However, there are cases where vegetatively propagated plants are not genetically identical. Root cuttings of thornless blackberries will revert to type because the adventitious shoot develops from a cell that is genetically thorny. Thornless blackberry is a chimera, with the epidermal layers genetically thornless, similarly, leaf cutting propagation of certain chimeral variegated plants, such as snake plant, will produce mainly nonvariegated plants. Grafting is often not a complete cloning method because seedlings are used as rootstocks, in that case only the top of the plant is clonal. In some crops, particularly apples, the rootstocks are vegetatively propagated so the entire graft can be if the scion. Apomixis is a type of reproduction that does not involve fertilisation, in flowering plants, unfertilized seeds are involved, or plantlets that grow instead of flowers. Hawkweed, dandelion, some citrus and many such as Kentucky blue grass all use this form of asexual reproduction. Bulbils are sometimes formed instead of the flowers of garlic, virtually all types of shoots and roots are capable of vegetative propagation, including stems, basal shoots, tubers, rhizomes, stolons, corms, bulbs, and buds. In a few species, leaves are involved in vegetative reproduction, the rhizome is a modified underground stem serving as an organ of vegetative reproduction, e. g. Polypodium, iris, couch grass and nettles, prostrate aerial stems, called runners or stolons are important vegetative reproduction organs in some species, such as the strawberry, numerous grasses, and some ferns. Adventitious buds form on roots near the surface, on damaged stems
22.
Isidium
–
An isidium is a vegetative reproductive structure present in some lichens. Isidia are outgrowths of the surface, and are corticated, usually with a columnar structure. They are fragile structures and may break off and be distributed by wind, animals, in terms of structure, isidia may be described as warty, cylindrical, clavate, scale-like, coralloid, simple, or branched. Examples of isidiate lichens include members of the genera Parmotrema and Peltigera
23.
Old-growth forest
–
Old-growth features include diverse tree-related structures that provide diverse wildlife habitat that increases the biodiversity of the forested ecosystem. The concept of tree structure includes multi-layered canopies and canopy gaps, greatly varying tree heights and diameters. Old-growth forests are valuable, and logging of these forests has been a point of contention between the logging industry and environmentalists. Old-growth forests tend to have trees and standing dead trees, multi-layered canopies with gaps that result from the deaths of individual trees. Depending on the forest, this may take anywhere from a century to several millennia, hardwood forests of the eastern United States can develop old-growth characteristics in one or two generations of trees, or 150–500 years. In British Columbia, Canada, old growth is defined as 120 to 140 years of age in the interior of the province where fire is a frequent and natural occurrence. In British Columbia’s coastal rainforests, old growth is defined as more than 250 years. In Australia, eucalypt trees rarely exceed 350 years of age due to frequent fire disturbance, Forest types have very different development patterns, natural disturbances and appearances. Levels of biodiversity may be higher or lower in old-growth forests compared to that in second-growth forests, depending on circumstances, environmental variables. Logging in old-growth forests is an issue in many parts of the world. Excessive logging reduces biodiversity, affecting not only the old-growth forest itself, a forest in old-growth stage has a mix of tree ages, due to a distinct regeneration pattern for this stage. New trees regenerate at different times from other, because each one of them has different spatial location relative to the main canopy. The mixed age of the forest is an important criterion in ensuring that the forest is a stable ecosystem in the long term. A climax stand that is uniformly aged becomes senescent and degrades within a relatively short time-period to result in a new cycle of forest succession, thus, uniformly aged stands are a less stable ecosystem. Forest canopy gaps are essential in creating and maintaining mixed-age stands, also, some herbaceous plants only become established in canopy openings, but persist beneath an understory. Openings are a result of death due to small impact disturbances such as wind, low-intensity fires. Because old-growth forest is structurally diverse it provides higher-diversity habitat than forests in other stages, thus, sometimes higher biological diversity can be sustained in old-growth forest, or at least a biodiversity that is different from other forest stages. The characteristic topography of much old-growth forest consists of pits and mounds, mounds are caused by decaying fallen trees, and pits by the roots pulled out of the ground when trees fall due to natural causes, including being pushed over by animals
24.
Desiccation
–
Desiccation is the state of extreme dryness, or the process of extreme drying. A desiccant is a substance that induces or sustains such a state in its local vicinity in a moderately sealed container. A desiccator is a glass or plastic container used in practical chemistry for making or keeping small amounts of materials very dry. The material is placed on a shelf, and an agent or desiccant. Often some sort of humidity indicator is included in the desiccator to show, by color changes and these indicators are in the form of indicator plugs or indicator cards. The active chemical is cobalt chloride, when it bonds with two water molecules, it turns purple. Further hydration results in the pink hexaaquacobalt chloride complex 2+, ecologists frequently study and assess various organisms susceptibility to desiccation. Several bacterial species have shown to accumulate DNA damages upon desiccation. Deinococcus radiodurans is extremely resistant to ionizing radiation, the functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. Radiation resistance is considered to be a consequence of the organism’s evolutionary adaptation to dehydration. The chromosomal DNA from desiccated D. radiodurans revealed increased DNA double-strand breaks, DNA double-strand breaks are repaired principally by a RecA-dependent recombination process that requires the presence of two genome copies. By this process D. radiodurans can survive thousands of double-strand breaks per cell, NHEJ appears to be the preferred pathway for repairing double-strand breaks caused by desiccation during stationary phase. NHEJ can repair double-strand breaks even when only one chromosome is present in a cell, upon exposure to extreme dryness, Bacillus subtilis spores acquire DNA-double strand breaks and DNA-protein crosslinks. In broadcast engineering, a desiccator may be used to pressurize the feedline of a high-power transmitter, because it carries a large amount of energy from the transmitter to the antenna, the feedline must have low dielectric losses. Because it must also be lightweight so as not to overload the radio tower, since moisture can condense in these lines, desiccated air or nitrogen gas is pumped in. This pressure also keeps water or other dampness from coming in the line at any point along its length, list of desiccants Hygroscopy Mummy A Desiccant Requirements Calculator
25.
Lobaria pulmonaria
–
Its population has declined across Europe and L. pulmonaria is considered endangered in many lowland areas. The species has a history of use in medicines. It is a foliose lichen and its leaf-like thallus is green, leathery and lobed with a pattern of ridges, bright green under moist conditions, it becomes brownish and papery when dry. This species often has a fine layers of hairs, a tomentum, the cortex, the outer protective layer on the thallus surface, is roughly comparable to the epidermis of a green plant. The thallus is typically 5–15 centimetres in diameter, with individual lobes 1–3 centimetres wide, the asexual reproductive structures soredia and isidia are present on the thallus surface. Minute cephalodia—pockets of cyanobacteria—are often present on the surface of the thallus. Like other foliose lichens, the thallus is only attached to the surface on which it grows. The thallus contains internal structures known as cephalodia, characteristic of three-membered lichen symbioses involving two photobionts and these internal cephalodia, found between the ribs of the thallus surface, arise when blue-green algae on the thallus surface are enveloped during mycobiont growth. Blue-green cyanobacteria can fix nitrogen, enhancing nutrient availability for the lichen. The other photobiont of L. pulmonaria is the green algae Dictyochloropsis reticulata, L. pulmonaria has the ability to form both vegetative propagation and sexual propagules at an age of about 25 years. In sexual reproduction, the species produces small reddish-brown discs known as apothecia containing asci, based on studies of ascospore germination, it has been suggested that L. Dispersal by vegetative propagules has been determined as the predominant mode of reproduction in L. pulmonaria. In this method, the protruding propagules become dry and brittle during the regular wet/dry cycles of the lichen and these fragments may develop into new thalli, either at the same locale or at a new site after dispersal by wind or rain. This steps lead to an increase in pressure which eventually breaks through the cortex. Continued growth leads to these granules being pushed upwards and out of the thallus surface and it has a wide distribution in Europe, Asia, North America and Africa, preferring damp habitats with high rainfall, especially coastal areas. It is the most widely distributed and most common Lobaria species in North America, associated with old-growth forests, its presence and abundance may be used as an indicator of forest age, at least in the Interior Cedar-Hemlock biogeoclimatic zone in eastern British Columbia. It is also found in pasture-woodlands and it usually grows on the bark of broad-leaved trees such as oak, beech and maple but will also grow on rocks. In the laboratory, L. pulmonaria has been grown on nylon microfilaments, various environmental factors are thought to affect the distribution of L. pulmonaria, such as temperature, moisture, sunlight exposure, and levels of air pollution. Due to declining population, L. pulmonaria is considered to be rare or threatened in parts of the world
