Archive:Eduzendium
How to join
- For more specific details about recruitment and specific mechanisms and utilities for collaboration please go to the dedicated Eduzendium Recruitment Page. The page includes the list of classes associated with us and instructions about signing up.
Operational details
How to categorize your pages, how to add templates to the page, how to register and retrieve passwords, etc.
See also
- A list of courses already integrated in Citizendium
- Eduzendium instructors discuss their experiences here.
Eduzendium[1] is a program in which the Citizendium partners with university programs throughout the world to create high-quality, English language entries for the Citizendium.
Some Citizendium articles started in the framework of Eduzendium
 Halobacterium NRC-1: A microorganism from the Archaea kingdom perfectly suited for life in highly saline environments giving biologists an ideal specimen for genetic studies. [e]
Halobacterium sp. NRC-1 is a non-pathogenic, halophilic archaea that thrives all over the world in high salt environments, including salt production facilities, brine inclusions in salt crystals, natural lakes and ponds, and salt marshes. Prior to 1990 H. NRC-1 was classified as an archeabacterium under the prokaryote kingdom in the two-empire system which consisted of eukaryotes and prokaryotes. Since 1990 the prokaryotes were split into bacteria and archaea due to their different evolutionary paths and biochemical differences.[2] Like all archaea H. NRC-1 has no nucleus or organelles within the cell, and like other archaea, have evolved many metabolic pathways to allow it to survive in extreme environments.[3] Halobacterium sp. NRC-1 is motile using both flagella and gas vesicles, and respond to their environment by moving toward or away from chemicals in a process called chemotaxis. Additionally, they can move toward or away from light in a process called phototaxis by utilizing their sensory rhodopsins. Phototaxis is an advantageous ability for halobacteria because it enables them to swim away from the high levels of ultra violet and ionizing radiation that they are exposed to on a daily basis. Halobacterium sp. NRC-1 reproduce by binary fission and grow best in a 42 degree Celsius, aerobic, high salt environment. Halobacterium sp. NRC-1 is very easy to culture in the lab and its genome has been completely mapped and sequenced. Whole-genome DNA microarrays are available to investigate gene expression. This makes it an excellent model microorganism for research in basic cellular processes, gene expression and as well as for teaching. Genome structureThe genome of Halobacterium sp. NRC-1 was published in 2000. Since that time scientists have done extensive research to gain insights into both its extremophilic abilities as well as its biological processes. In order to survive in its environment, H. NRC-1 has developed amazing capabilities to repair its own genome, one being a precise base excision repair system. Homologous recombination plays an important role in DNA repair as well. Its ability to repair its chromosomes after extensive damage is only exceeded by the extremely radiation resistant Deinococcus radioduransbacterium.[4] In fact, H. NRC-1 was found to display a significant number of unique homologs with this bacterium, which suggests that they might have been acquired through lateral gene transfer.[5] This microorganism also displays other types of defense mechanisms. In combination with its saline environment which provides some protection from UV radiation, the proteins that are produced by H. NRC-1 were found to be highly acidic. This low pH helps the proteins resist the denaturing effects of the high concentration of salts that surrounds it.[6] [7] Halobacterium sp. NRC-1 contains the smallest genome to date among the halophiles.[7] It is 2,571,010 bp in size, and is composed of a large GC-rich chromosome (2,014,239 bp, 68 % G+C), and two smaller extrachromosomal replicons, pNRC100 (191,346 bp) and pNRC200 (365,425 bp), with 58–59 % G+C composition. The large chromosome contains 2,111 genes, pNRC200 contains 374, and pNRC100 contains 197. Of the 2,682 genes in the genome, only 1,658 coded for proteins that had significant matches to the genome database. A significantly smaller fraction of the genes on pNRC200 and pNRC100 matched to genes of known function in the databases. The genes on the large chromosome had a 45% match rate, while pNRC200 had a 32% match rate and pNRC100 had only 26% of its genome match up to genes of known function. 52 RNA genes have also been identified. Interestingly, about 40 genes that are located on the small replicons, pNRC100 and pNRC200, code for functions likely to be essential or important for cell livelihood (e.g. thioredoxin and thioredoxin reductase, a cytochrome oxidase, a DNA polymerase, multiple TATA-binding proteins (TBP) and transcription factor B (TFB) transcription factors, and the only arginyl-tRNA synthetase in the genome. In fact, these two replicons share 145,428 base pairs of identical DNA.[5] After the publication of Halobacterium sp. NRC-1’s complete genome, the mapping of another closely related microorganism, Halobacterium H. Salinarum, was published as well. Interestingly, genomic comparisons between these two halophiles showed that the large chromosomes were virtually identical to one another while the smaller replicons carried different genes.[8] This information has cast new light on how the species differ from each other and the role of replicons in these organisms. While much of the published literature on Halobacterium sp. NRC-1 refers to the smaller genetic elements as replicons or megaplasmids, their characteristics don't really fit the definition of these terms. Replicons are considered to be exact copies of specific sequences of an original DNA or RNA genome, or even a whole copy of the original genome. Plasmids are referred to as being small extra chromosomal DNA elements that carry relatively few genes that code for genetic information that is not essential to an organism's biological processes. Considering that the genetic information carried on these replicons not only code for information that is essential to the organism's survival, but also contain nucleotide sequences that are not identical to that of its larger chromosome, scientists are beginning to refer to them as "minichromosomes" rather than megaplasmids or replicons.[7] Cell structure and metabolismHalobacterium sp.NRC-1 is a rod shaped aerobic chemoorganotroph which uses organic molecules as its source of energy, carbon and electrons. This halophile possesses facultative anaerobic and phototrophic capabilities as well. Research has shown that it is unable to metabolize sugars, but instead rely on amino acids that are eventually catabolized by the citric acid cycle during aerobic respiration. It survives on the remains of less halophilic organisms that have lysed due to the overwhelming amounts of salt in the environment. Outside of their natural environment, cells are cultured best in a complex medium. A minimal medium described for Halobacterium includes all but 5 of the 20 amino acids for growth.[5] This microorganism has been studied extensively and has been shown to contain some of the usual features found in halophilic archaea, for example, an S-layer glycoprotein, ether-linked lipids, and purple membrane.[9] This purple membrane consists of the light-driven ion transporters bacteriorhodopsin and halorhodopsin, and the phototaxis receptors, sensory rhodopsins I and II.[5] In order to survive in low oxygen environments, Halobacterium sp. NRC-1 increases its production of Bacteriorhodopsin, which is a unique protein that can use light as an energy source, much like chlorophyll can in cyanobacteria and phototrophic eukaryotes. When the retinal in Bacteriorhodopsin absorbs light, it results in a series of conformational changes that translocates protons through the cell's membrane into the periplasmic space. This light driven proton pumping generates an electrochemical proton gradient which is then used to power the synthesis of ATP. This phototrophic capability is particularly useful to Halobacterium sp. NRC-1 as oxygen is not very soluble in concentrated salt solutions. In addition to its ability to use light as an energy source, it is also capable of anaerobic respiration using dimethyl sulfoxide (DMSO) and trimethylamine-N-oxide (TMAO) as terminal electron acceptors. Arginine fermentation can also be used for anaerobic energy production as well.[10] Halobacterium sp. NRC-1 is also classified as an obligate halophilic microorganism which has adapted to be able to grow in conditions of extremely high salinity, up to 10 times that of seawater.[5] In order to survive under these conditions it maintains a very high concentration of salts internally in the form of KCl to enable it to remain isotonic to its preferred environment.[11] Halorhodopsin plays a very important role in helping to maintain the osmotic balance within the cell. This membrane protein acts as a light driven pump by transporting chloride and potassium ions into the cell. Halorhodopsin saves the organism a large amount of metabolic energy by using the energy of the yellow light that it captures to fuel the movement of these ions.[12] Ecology -Image ISS007-E-13002 from the ISS of the Great Salt Lake showing purple tint due to halobacterium presence and increased bacteriorhodopsin production due to high salt concentration. Image courtesy of the Image Science & Analysis Laboratory, NASA Johnson Space Center Halobacterium NRC-1 is one of many strains of halobacterium which thrive in extremely high salinity environments such as salt lakes, salt marshes and salt drying ponds. Their optimal temperature for reproduction is 42°C. Often these highly saline bodies of water will be tinted red or purple. It is the red/purple color of the bacteriorhodopsins that give the purple color you often see in these highly saline environments. Bacteriorhodopsin consists of a photosensitive protein pigment called retinal. This protein pigment is responsible for NRC-1's colorful properties. The more saline the environment the more colorful the water will be because halobacterium increase their production of bacteriorhodopsin in response to drops in oxygen, which is less soluble in saline solutions. There are not many other organisms that can survive in these high salt environments, in fact one of its primary sources of food is the amino acids of other organisms which have lysed due to the high salt concentration in this environment. Brine shrimp are one of a few other organisms that can survive the high salt concentration, and they feed almost exclusively on the halobacteria. In addition to rhodopsin, Halobacterium NRC-1 produce carotenoids, which are red organic pigments that can also serve as antioxidants. The flamingo, whose pink color comes exclusively from the carotenoids in its diet (it doesn't have the ability to produce these pigments naturally) feed on the brine shrimp (who are capable of producing these pigments). These same brine shrimp have fed on the carotenoid producing halobacteria. So interestingly enough, these small organisms, the brine shrimp and the halobacteria, are the ones responsible for the flamingos beautiful pink coloring. Application to BiotechnologyHalobacterium NRC-1 can easily be analyzed just by placing it in a hypotonic solution. Due to the higher salt concentration within the microorganism in comparison to its less salinic environment, water will flow into the cell following its concentration gradient, causing the cell to swell and undergo lysis. This explosion releases this microorganism's proteins, which then can be used by researchers for genetic analysis. Halobacterium sp. NRC-1 was one of the first Archaea to have its genome fully mapped and published. Since that time several more archaea have been successfully mapped and a few others partially mapped. This allows scientists to analyze the properties of halobacterium in silico to determine the activity of genes. Transformation tools have also been developed to create loss-of-function mutants which aid in research. Mutant strains of Halobacterium sp. NRC-1 are experimentally designed to carry inoperative knockout genes which alter this organism's normal cellular processes. Scientists can then infer the function of the mutated gene by comparing the physical and biochemical characteristics of the original Halobacterium sp. NRC-1 with the characteristics of the new mutant. These gene knockouts are making it possible to analyze this organism's ability to withstand extreme environmental conditions, including high levels of radiation, severe temperature changes, and fluctuations in oxygen levels. [8] The ability of this organism to be easily cultured along with these advanced research tools make Halobacterium sp. NRC-1 an ideal model for the testing of gene functions. In addition, Halobacterium sp. NRC-1 is an ideal study tool because it is an extremophile, it exists in environments that are very unfriendly toward life. This makes it very useful for studying many biological questions especially those involved with adaptation and survival in extreme environments. In fact, much research is being done to investigate whether or not halobacterium could be potential candidates for extraterrestrial life, such as on Mars or Europa. Recent research has shown that Halobacterium sp. NRC-1 can not only survive at temperatures far below its optimal growth temperature, but continue to reproduce as well.[13] Current ResearchProtective effect of cations in extreme environmentsThe extremophillic properties and biological responses of Halobacteruim NRC-1 are currently being investigated to test the organism's survival potential in the harsh environmental conditions that exist on Mars. The recent discoveries that meterorites from Mars contain a mineral form of sodium chloride as well as the isolation of halophilic archaea from ancient rock salt has led scientists to believe that the existence of Halobacterium sp. NRC-1 in a Martian environment is quite possible. Halobacterium are known to be slightly thermophilic organisms, showing optimum growth at 40 degrees Celsius. In this experiment, cells of Halobacterium sp. NRC-1 were freeze dried and suspended in buffers containing specific cations, including Mg++,Ca++,or K+. Results showed that NRC-1 was still capable of slow, yet steady growth at the extremely low temperature of -15 degrees Celsius. All of the cations appeared to show protective qualities during the freeze-drying, with K+ being the most effective. The conditions of Martian environment include very low temperatures and low water availability. Scientists will continue to research NRC-1’s ability to survive in such inhospitable environments such as the one on Mars. Hopefully, these future findings will provide us some further insight in our search for life beyond our planet.[13] Radiation resistanceHalobacterium sp. NRC-1 is known to be extremely radiation resistant due to protection from its pigments, the saline environment it thrives in, and its ability to repair its DNA after extensive damage. In this study the scientists wanted to find out if they could produce a mutant strain that would be even more resistant to ionizing radiation, and determine what genes and mechanisms were responsible for providing the increased resistance. To do this, they exposed cultures of H. NRC-1 to four cycles of irradiation with high doses of 18-20 MeV (mega-electron volt) electrons from a standard medical LINAC (particle accelerator), allowing the cultures to recover between doses. At the end of this process they were able to isolate two mutant strains (named LH5 and LH7a) with an LD50 (median lethal dose) of greater than 11 kGy (kilo-Grays) (standard measure of absorbed radiation dose) which makes them the most radiation resistant organism known, even more resistant than Deinococcus radiodurans (LD50 7.9 kGy). The wild-type H. NRC-1 was found to have an LD50 of 5.4 kGy while the mutant strains were 11.9 kGy for LH5 and 12.1 kGy for LH7a. Unlike most other microbes like D. radiodurans which show the most radiation resistance during their stationary phase, H. NRC-1 is most resistant when in its growth phase. Tests verified that this was true for the mutants as well. They were also able to rule out a slowdown in growth rate, which is one of the methods employed by D. radiodurans, as the reason for the increased resistance. To do this, they compared the doubling rate of the mutant strains with that of the wild-type H. NRC-1 and found it to be the same. They then used whole-genome transcriptome analysis to compare the mutant strains with the wild type H. NRC-1 to determine what had given the mutant strains their increased radiation resistance. They found significant up-regulation of an operon containing two single-stranded DNA-binding protein (RPA-replication protein A) genes, VNG2160 (rfa3) and VNG2162, plus a third gene, VNG2163, which is unknown. While the authors tests did not identify the actual role this operon plays in providing the increased resistance to radiation, they propose that it does facilitate the DNA repair machinery and/or protects the repair intermediates to maximize radiation resistance.[14] Peptide delivery vehicle for biotechnologyHalobacterium sp. NRC-1 is also playing a significant role in the advancement of immunological biotechnology. Recent experimental findings show that recombinant gas vesicles from a mutant strain of Halobacterium sp. NRC-1 have the potential to serve as antigen display/delivery systems. DNA segments of an SIV (simian immunodeficiency virus) gene were inserted into a specific site on a GvpC gene (gas vesicle protein C) in the Halobacterium. The gene was successfully taken up by the microorganism and recombination had been accomplished. Subsequently, the gas vesicles began to express the new recombinant/pathogenic proteins at their surface. Mice were then immunized with these antigen presenting SIV recombinant gas vesicles. Antibody production was monitored, and an increased level of humoral response was observed. After a 12 week period, a booster shot was given. 43 weeks after the booster shot was administered, an elevated number of antibodies still remained and was recorded. Research showed that this increased production of antibodies was long lived even in the absence of an adjuvant, and immunologic memory had been proven. These results indicate that the gas vesicles of Halobacterium sp. NRC-1 show great potential in their possible roles as immunizing agents.[15] References
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| Speech Recognition: The ability to recognize and understand human speech, especially when done by computers. [e] In computer technology, Speech Recognition refers to the recognition of human speech by computers for the performance of speaker-initiated computer-generated functions (e.g., transcribing speech to text; data entry; operating electronic and mechanical devices; automated processing of telephone calls) — a main element of so-called natural language processing through computer speech technology. Speech derives from sounds created by the human articulatory system, including the lungs, vocal cords, and tongue. Through exposure to variations in speech patterns during infancy, a child learns to recognize the same words or phrases despite different modes of pronunciation by different people— e.g., pronunciation differing in pitch, tone, emphasis, intonation pattern. The cognitive ability of the brain enables humans to achieve that remarkable capability. As of this writing (2008), we can reproduce that capability in computers only to a limited degree, but in many ways still useful.
First, speech is not simply spoken text--in the same way that Miles Davis playing So What can hardly be captured by a note-for-note rendition as sheet music. What humans understand as discrete words, phrases or sentences with clear boundaries are actually delivered as a continuous stream of sounds: Iwenttothestoreyesterday, rather than I went to the store yesterday. Words can also blend, with Whaddayawa? representing What do you want? Second, there is no one-to-one correlation between the sounds and letters. In English, there are slightly more than five vowel letters--a, e, i, o, u, and sometimes y and w. There are more than twenty different vowel sounds, though, and the exact count can vary depending on the accent of the speaker. The reverse problem also occurs, where more than one letter can represent a given sound. The letter c can have the same sound as the letter k, as in cake, or as the letter s, as in citrus. In addition, people who speak the same language do not use the same sounds, i.e. languages vary in their phonology, or patterns of sound organization. There are different accents--the word 'water' could be pronounced watter, wadder, woader, wattah, and so on. Each person has a distinctive pitch when they speak--men typically having the lowest pitch, women and children have a higher pitch (though there is wide variation and overlap within each group.) Pronunciation is also colored by adjacent sounds, the speed at which the user is talking, and even by the user's health. Consider how pronunciation changes when a person has a cold. Lastly, consider that not all sounds consist of meaningful speech. Regular speech is filled with interjections that do not have meaning in themselves, but serve to break up discourse and convey subtle information about the speaker's feelings or intentions: Oh, like, you know, well. There are also sounds that are a part of speech that are not considered words: er, um, uh. Coughing, sneezing, laughing, sobbing, and even hiccupping can be a part of what is spoken. And the environment adds its own noises; speech recognition is difficult even for humans in noisy places. (Read more...) | |||||||||||||||||||||||||
| Mashup: A data visualization created by combining data with multiple computer applications. [e] A mashup is a complex form of data visualization. On the web, mashup often refers to an integrated application created by combining of geographical location and other information with a service such as Google maps or Microsoft Virtual Earth. The term has achieved widespread usage in describing this kind of web application since Google introduced its public Google Maps API[1] in 2005. Though not restricted to the web, mashups have become an increasingly popular internet paradigm, leading to the creation of a variety of web based mashups. Tim O'Reilly lists Mashups as one of the Web 2.0 technologies. [2].  An example mashup: Housing Maps.
Thanks to Google Maps, Internet mashups have become popular in recent years; however the concept of mashups has been around for a long time in a context completely unfamiliar to typical Internet engineers. Before internet mashups became popular, mashups referred to music. Music mashups are the fusion of two or more songs by overlaying their tunes and lyrics to form a new song. They have been around since the beginning of recorded music. Before this was a popular buzzword, this was called multi track recording and rerecording, where the Beatles made notable advances. Today, music mashups have been extended to incorporate videos and are still prevalent in the entertainment industry. Websites like http://www.mashup-charts.com/ are used to rate amateur music mashups. (Read more...) |
What does Eduzendium do?
The Citizendium invites university instructors to include the crafting of a Citizendium article as an assignment.
Our project is open for collaborative educational and knowledge generation initiatives with higher education institutions. We strongly believe in the necessity of inviting experts of all kinds to help us build our repository of knowledge.
A distinct approach in this context is our policy of inviting the professors that teach and the students enrolled in advanced courses of the foundational/"fundamentals of" sort to help us seed or build up our entries with high-quality, clearly-argued and -written content. A pilot program involved major universities in the United States and abroad in late 2007, with good success. We hope the program will extend throughout universities in the English-speaking world.
Philosophically, we believe that the individuals who struggle with the meaning of fundamental concepts on a daily basis make excellent authors and editors for entries on those concepts. Advanced foundational courses are an ideal site for recruiting such authors and editors because their primary goal is to redefine and communicate for each generation the meaning of the basic and essential issues of our knowledge world. Furthermore, the activity of these seminars is often directed at producing short and insightful papers about some basic concepts which might or might not be later transformed into more "formal" publications. We believe that opening up the Citizendium to collaborative work on specific topic to students and their professors offers them the opportunity to take their work to another, more socially consequential level, which enhances the educational process on the one hand, while helping the Citizendium to build its socially involved and expert friendly knowledge environment, on the other hand.
In brief, we encourage faculty to use the Citizendium as a platform for their students to write public entries about key terms pertaining to a number of disciplines.
The collaborative process
In inviting the academic community to join us we are aware that we will be successful only to the degree we offer educators and students the opportunity to do what they ought to be doing: teach or learn in an efficient way, with the added excitement, feedback, real life rewards of being part of the Citizendium. We are aware that the primary goal of the education process in academia is to transmit useful knowledge and to train students for success. The Eduzendium program is designed to be extremely flexible and adaptable to the needs of each professor and seminar member. It includes an array of possible collaborative arrangements and the actual editorial process will be shaped according to each seminar's policies.
A very simple and direct collaboration would be where the professor would takes the students to sign up on the Citizendium and perform a certain amount of work or to initiate and actively collaborate on a specific entry. In other situations the professors can charge specific students to write specific entries, which can be evaluated and edited for content and style individually. Editorial changes can be operated by the professor, by a team designated by the professor or by his or her entire class. This can be done using our wiki platform, in which case the topic can be reserved and closed to public access for a limited period of time. (You must ask, however, and make your intentions very clear.) Professors and their students can obtain access to a specific namespace or wiki page, which will be editable and even readable only by them for a period of time (typically, until the assignments are finished). Conceivably, some seminar might decide to work on their topics completely outside the Citizendium technological flow and only provide the Citizendium with the best of their finished products; that would be fine as well.
In a different scenario, the professor can assign the topics to the entire class, asking the members to work on them simultaneously and edit them during a period of time. He or she can intervene in the editorial process when and if needed. This, again, can be done inside or outside of the Citizendium process.
Finally, instructors can decide to work collaboratively on an existing topic in the public view and to assess the fruits of the collaboration through individual student reflection papers.
In those scenarios in which the class works outside the Citizendium process, or within a closed Citizendium environment (such as an ad hoc namespace), the professor or the class can look over the final product and decide if they would like to vet the product and make it into an "approved" Citizendium article. The instructor can then propose the topic to the Citizendium editors for introduction in the editorial flow. Note that it will always be possible to link to a specific version of an article, even after it has been edited. Note that professors need not approve articles; some may not be approvable.
While Citizendium management gives a wide latitude to Eduzendium participants for purposes of choosing topics, professors may be asked not to choose articles that are currently undergoing active editing by Citizendium contributors. This should still permit very wide latitude of topic choice. Indeed, many course topics may not have any articles written at all. (We would love for you to get us started!)
In essence, the Eduzendium program fosters real life conditions for collaborative intellectual projects within the participating seminars, which can result in a diversity of team (group) or individual projects. Instructors and students can get complete control over the degree and nature of the editorial process. Specifically, they can decide the nature of the assignments and the degree to which they will be completed in collaboration with other students or with the Citizendium community, the amount of work allocated to contributing Citizendium, the nature of the rewards and penalties to be used in assessing student work, and the quality standards of this work. Finally, they can decide if, how much and when their work can be officially published on Citizendium.
What are the educational benefits?
Writing a high-quality encyclopedia article about a specific topic requires, and trains, a specific sort of effort or discipline. Simply producing a suitably informative, but neutral, definition of a concept can require a great deal of thought. Crafting a jumble of facts into a coherent narrative, which the Citizendium requires, is a difficult, but rewarding and educational task. Furthermore, it practices a very useful scholarly skill to investigate and decide on what the most reliable bibliography items for an article are.
The educational benefits are plain if a student writes a general, neutral encyclopedia article on a topic, in addition to an opinionated paper about some special aspect of the topic.
References
- ↑ "Google Maps API". Google (2008). Retrieved on 2008-08-16.
- ↑ "Levels of the Game: The Hierarchy of Web 2.0 Applications".
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