User:Jaltenb/sandbox

Article evaluation
article:Base pair
 * Is everything in the article relevant to the article topic? Is there anything that distracted you?
 * talking about the amount of carbon in the atmosphere is distracting since it is completely unrelated
 * Is the article neutral? Are there any claims, or frames, that appear heavily biased toward a particular position?
 * the article does not appear to be biased
 * Are there viewpoints that are overrepresented, or underrepresented?
 * there could be more information on DNA and RNA in particular to balance the large portion on unnatural base pairs.
 * Check a few citations. Do the links work? Does the source support the claims in the article?
 * the links work, but citation 4 does not support the claim being made that the human genome is estimated to be 3.2Gb long, it instead refers to the genome as 3.1Gb.
 * Is each fact referenced with an appropriate, reliable reference?       Where does the information come from? Are these neutral sources?        If biased, is that bias noted?
 * not all facts have a reference, there is a large block of text involving hydrogen bonding and stability with only one reference in the first paragraph.
 * Is any information out of date? Is anything missing that could be added?
 * there is length measurements for base pairs, no mention about how many in a turn of the helix, no talk about anything functionally relevant to do with the base pair distance
 * Check out the Talk page of the article. What kinds of conversations,       if any, are going on behind the scenes about how to represent this topic?
 * they are mostly people asking questions about the information and someone changing the article or saying the article is fine in response
 * How is the article rated? Is it a part of any WikiProjects?
 * the article is rated c and top importance
 * How does the way Wikipedia discusses this topic differ from the way we've talked about it in class?
 * it seems....jumbled, it is hard to figure out what information is important because it is all mixed together in areas

== Inbred strain maybe, they only talk about rats, but i believe i have read in behavioural genetics that there are other species that are used as inbred strains, they are very useful in the laboratory. they mention quite a few inbred strains that are not linked or listed...though they might be in the one article, there is no reference to the linked wikipedia page, so it should be difficult to find out.

other species with inbred strains:

Rabits- http://www.sciencedirect.com/science/article/pii/S0079610716300335?via%3Dihub

Japanese medaka, Oryzias latipes-http://www.genetics.org/content/199/4/905.long

i can also talk more about the areas of genetics and developmental studies, and other areas of science where inbred strains are useful, go over some assays and experiments where they have been used etc

Notes: i want to rewrite this entire paragraph, it is chunky and confusing and hard to read. i should also create a small section for outbred strains, crosses between two inbred strains, and

just pasting the old article here so i don't need to keep flipping pages, everything bellow this line is from the Inbred strain wikipedia page from tuesday october 24 2017. if this is not okay tell me and i will remove it. i am also adding in comments that are underlined to help direct my thoughts

Laboratory benefits to using inbred strains
As stated by Elizabeth M.C. Fisher et al in their paper "Genealogies of mouse inbred strains":"Inbred strains have long been used for genetic and immunological studies because of the isogenicity within a strain or F1 hybrid and the genetic heterogeneity between inbred strains. Several Nobel Prizes have been awarded for work which probably could not have been done without inbred strains; examples include Medawar's research of immunological tolerance, Kohler and Milstein's development of monoclonal antibodies, and Doherty and Zinkernagel's studies of major histocompatibility complex (MHC) restriction. The use of inbred strains contributed to the Nobel prize-winning work of George Snell in dissecting the biology of the mouse MHC (ref. 6) and developing the backcrossing methodology, which is now an important tool in genetic mapping studies."Isogenic organisms have identical, or near identical genotypes. which is certainly true of inbred strains, since they normally have atleast 98.6% similarity by generation 20

Breeding of inbred strains is often towards specific phenotypes of interest such as behavioural traits like alcohol preference or physical traits like aging. or they can be selected for traits that make them easier to use in experiments like being easy to use in transgenic experiments. One of the key strengths of using inbred strains as a model is that strains are readily available for whatever study one is performing and that there are resources such as the Jackson Laboratory, and Flybase, where one can look up strains with specific phenotypes or genotypes, from among inbred lines, recombinant lines, and Coisogenic strains. Jackson Laboratory has additional features to maintaining mice, one can order mice that have been altered with genetic tools such as Gal4/UAS or CRISPR, meaning that even if the strain does not currently exist, you can still obtain a line of mouse that is useful to your research

Coisogenic strains are one type of inbred strain that either has been altered, or naturally mutated so that it is different at a single locus

Medaka:

zebrafish:

There are relatively few Inbred strains of zebrafish possibly because they experience greater effects from inbreeding depression than mice or Medaka fish, but it is unclear if the effects of inbreeding can be over come so an isogenic strain can be created for laboratory use

Inbred strains (original article)
Inbred strains (also called inbred lines, or rarely for animals linear animals) are individuals of a particular species which are nearly identical (I need to double check this and specify whether it is for the whole genome or just for specific traits) to each other in genotype due to long inbreeding ( give quick mention of what inbreeding is). Inbred strains of animals are frequently used in laboratories for experiments where for reproducibility of conclusions all the test animals should be as similar ( similar how? ) as possible (removing this sentence and replacing with "due to the nature of an inbred strain, where each individual is near identical to any of its siblings, inbred strains are a popular if not necessary choice for test subjects in the lab so that genetic variability is at a minimum and others can replicate the results of the tester" ). However, for some experiments, genetic diversity in the test population may be desired. Thus outbred strains (give definition of an outbred strain) of most laboratory animals are also available.

Notes: i want to rewrite this entire paragraph, it is chunky and confusing and hard to read. i should also create a small section for outbred strains, crosses between two inbred strains, and

Certain plants including the genetic model organism Arabidopsis thaliana naturally self pollinate, which makes it quite easy to create inbred strains in the laboratory (other plants, including important genetic models such as Maize require transfer of pollen from one flower to another). For most animals, the usual procedure is mating of brother-sister pairs for a minimum of 20 generations, which will result in lines that are roughly 99% genetically identical. Many inbred strains have been inbred for many more generations and are in effect isogenic.

Effects
Inbreeding animals will sometimes lead to genetic drift. The continuous overlaying of like genetics exposes recessive gene patterns that often lead to changes in reproduction performance, fitness, and ability to survive. A decrease in these areas is known as inbreeding depression. A hybrid between two inbred strains can be used to cancel out deleterious recessive genes resulting in an increase in the mentioned areas. This is known as heterosis.

Inbred strains, because they are small populations of homozygous individuals, are susceptible to the fixation of new mutations through genetic drift, Jackson laboratory in a information session on genetic drift in mice, calculated a quick estimate of the rate of mutation based on observed traits to be 1 phenotypic mutation every 1.8 generations, though they caution that this is likely an under representation because the data they used was for visible phenotypic changes and not phenotype changes inside of mice strains. they further add that statistically every 6-9 generations, a mutation in the coding sequence is fixed, leading to the creation of a new substrain. Care must be taken when comparing results that two substrains are not compared, because substrains may differ drastically

Rats and mice
"The period before World War I led to the initiation of inbreeding in rats by Dr Helen King in about 1909 and in mice by Dr C. C. Little in 1909. The latter project led to the development of the DBA strain of mice, now widely distributed as the two major sub-strains DBA/1 and DBA/2, which were separated in 1929-1930. DBA mice were nearly lost in 1918, when the main stocks were wiped out by murine paratyphoid, and only three un-pedigreed mice remained alive. Soon after World War I, inbreeding in mice was started on a much larger scale by Dr L. C. Strong, leading in particular to the development of strains C3H and CBA, and by Dr C. C. Little, leading to the C57 family of strains (C57BL, C57BR and C57L). Many of the most popular strains of mice were developed during the next decade, and some are closely related. Evidence from the uniformity of mitochondrian DNA suggests that most of the common inbred mouse strains were probably derived from a single breeding female about 150-200 years ago."

"Many of the most widely used inbred strains of rats were also developed during this period, several of them by Curtis and Dunning at the Columbia University Institute for Cancer Research. Strains dating back to this time include F344, M520 and Z61 and later ACI, ACH, A7322 and COP. Tryon's classic work on selection for maze-bright and dull rats led to the development of the TMB and TMD inbred strains, and later to the common use of inbred rats by experimental psychologists."

okay, alot of this seems like history, but hows and why's would be nice. why did they choose rats and mice? why were they doing these experiments? what is the purpose of all of this?!

Inbred strains of rats

 * Wistar as a generic name for inbred strains such as Wistar-Kyoto, developed from the Wistar outbred strains. interesting, how about a little elaboration?!

Inbred strains of mice
• A/J

• C3H

• C57BL/6

• CBA

• DBA/2

• BALB/c I want to explain what these mice are for

add in sections for other inbred species

divide the strains section into mammals and plants since each are used for different purposes

add sections for laboratory techniques for making inbred strains and selecting individuals for the strains or phenotypes to work with.

Guinea pigs
G.M. Rommel first started conducting inbreeding experiments on guinea-pigs in 1906. Strain 2 and 13 guinea-pigs, were derived from these experiments and are still in use today. Sewall Wright took over the experiment in 1915. He was faced with the task of analyzing all of the accumulated data produced by Rommel. Wright became seriously interested in constructing a general mathematical theory of inbreeding. By 1920 Wright had developed his method of path coefficients, which he then used to develop his mathematical theory of inbreeding. Wright introduced the inbreeding coefficient F as the correlation between uniting gametes in 1922, and most of the subsequent theory of inbreeding has been developed from his work. The definition of the inbreeding coefficient now most widely used is mathematically equivalent to that of Wright.

Medaka
The Japanese Medaka fish has a high tolerance for inbreeding, one line having been bred brother-sister for as many as 100 generations without evidence of inbreeding depression, providing a ready tool for laboratory research and genetic manipulations. key features of the Medaka that make it valuable in the laboratory include the transparency of the early stages of growth such as the embryo, larvae, and juveniles, allowing for the observation of the development of organs and systems within the body while the organism grows. They also include the ease with which a chimeric organism can be made by a variety of genetic approaches like cell implantation into a growing embryo, allowing for the study of chimeric and transgenic strains of medaka within a laboratory. As stated in "The Genomic and Genetic Toolbox of the Teleost Medaka (Oryzias latipes)" "Currently >60 wild strains from both the northern and southern populations and ∼14 derived inbred strains are available at the Japanese Medaka Stock Center (National BioResource Project Medaka, NBRP Medaka; http://www.shigen.nig.ac.jp ). Apart from genomic polymorphisms, these inbred strains also exhibit strain-specific differences in behavior, body shape, brain morphology, and susceptibility to mutagens (Ishikawa et al. 1999; Kimura et al. 2007). Heritability of craniofacial traits has been demonstrated, indicating that the inbreeding of polymorphic populations in medaka reveals the genetic contribution to variability of these traits (Kimura et al. 2007). To further exploit the tolerance to inbreeding combined with genetic polymorphism, recently a detailed analysis of wild populations has been carried out with the aim to establish a panel of >100 inbred lines derived from a single polymorphic wild population (Spivakov et al. 2014). Such a panel of inbred lines with sequenced genomes will serve as a genetic source for genome-wide association studies (GWAS)."

Zebrafish
Though there are many traits about zebrafish that are worthwhile to study including their regeneration, there are relatively few Inbred strains of zebrafish possibly because they experience greater effects from inbreeding depression than mice or Medaka fish, but it is unclear if the effects of inbreeding can be over come so an isogenic strain can be created for laboratory use