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Draft:Original research/Genetics

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This is an image of Bob, the guinea pig. Credit: selbst.

Genetics involves the expression, transmission, and variation of inherited characteristics.

Genetics studies how living organisms inherit features from their ancestors; for example, children often look like their parents. Genetics seeks to identify which features are inherited, and explain how these features are passed from generation to generation.

In genetics, a feature of an organism is called a "trait". Some traits are features of an organism's morphology or physical appearance; for example, a person's eye-color, height or weight. There are many other trait types, and these range from aspects of behavior to resistance to disease. Traits are often inherited, for example tall and thin people tend to have tall and thin children. Other traits come from the interaction between inherited features and the environment. For example a child might inherit the tendency to be tall, but if little food is available and the child is poorly nourished, it will still be short. The way genetics and environment interact to produce a trait can be complicated: for example, the chances of somebody dying of cancer or heart disease seem to depend on both their family history and their lifestyle.

Genetic information is carried by a long molecule called DNA which is copied and inherited across generations. Traits are carried in DNA as instructions for constructing and operating an organism. These instructions are contained in segments of DNA called genes. DNA is made of a sequence of simple units, with the order of these units spelling out instructions in the genetic code. This is similar to the order of letters spelling out words. The organism "reads" the sequence of these units and decodes the instruction.

Not all the genes for a particular instruction are exactly the same. Different forms of one type of gene are called different alleles of that gene. As an example, one allele of a gene for hair color could carry the instruction to produce a lot of the pigment in black hair, while a different allele could give a garbled version of this instruction, so that no pigment is produced and the hair is white. Mutations are random events that change the sequence of a gene and therefore create a new allele. Mutations can produce a new trait, such as turning an allele for black hair into an allele for white hair. The appearance of new traits is important in evolution.

Heredity

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Main pages: Draft:Original research/Heredity and Heredity

Def. gene "transmission of the physical and [genetic] qualities of parents to their offspring; the biological law by which living beings tend to repeat their characteristics in their descendants"[1] is called heredity.

In humans, eye color is an example of an inherited characteristic: an individual might inherit the "brown-eye trait" from one of the parents.[2] Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype.[3]

The complete set of observable traits (phenotype) arise from the interaction of its genotype with the environment.[4] As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's phenotype and sunlight;[5] thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in their genotype:[6] a striking example is people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn.[7]

Heritable traits are known to be passed from one generation to the next via DNA.[3] The sequence of bases along a particular DNA molecule specifies the genetic information: this is comparable to a sequence of letters spelling out a passage of text.[8]

If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism.[9]

While this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by a quantitative trait locus (multiple interacting genes) within and among organisms.[10][11] Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlie some of the mechanics in developmental plasticity and canalization.[12]

Recent findings have confirmed important examples of heritable changes that cannot be explained by direct agency of the DNA molecule.[13]

DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference, and the three dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level.[14][15]

Heritability may also occur at even larger scales such as ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effect that modifies and feeds back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors.[16] Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits, group heritability, and symbiogenesis.[17][18][19] These examples of heritability that operate above the gene are covered broadly under the title of multilevel or hierarchical selection, which has been a subject of intense debate in the history of evolutionary science.[18][20]

Phenotypes

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Main resources: Genetics/Phenotypes and Phenotypes

Def. the "appearance of an organism based on a multifactorial combination of genetic traits and environmental factors, especially used in pedigrees"[21] is called a phenotype.

Theory of genetics

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This guinea pig has gorgeous long hair and was a prize winner at the Puyallup, WA fair. Credit: Christine from Washington State, USA.

Def. a "branch of biology that deals with the transmission and variation of inherited characteristics, in particular chromosomes and DNA"[22] is called genetics.

Evolutionary genetics

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Main pages: Draft:Original research/Evolution and Evolutionary genetics

Molecular genetics

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Main resources: Genetics/Molecules and Molecular genetics

Def. a "field of biology which studies the structure and function of genes at a molecular level"[23] is called molecular genetics.

Optogenetics

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Main resources: Genetics/Optogenetics and Optogenetics

Def. a "science that combines optics and genetics to probe neural circuits"[24] is called optogenetics.

Population genetics

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Main resources: Genetics/Populations and Population genetics

Def. the "study of the allele frequency distribution and change under the influence of the four evolutionary processes: natural selection, genetic drift, mutation and gene flow"[25] is called population genetics.

Quantitative genetics

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Main resources: Genetics/Quantitatives and Quantitative genetics

Epigenetics

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Main pages: Draft:Original research/Epigenetics and Epigenetics
This is a schematic representation of a nucleosome. Credit: Zephyris.
The flow chart shows recommendations for the design and analysis of epigenome-wide association studies. Credit: BLASToize.

Epigenetics is the study of genome or epigenome changes resulting from external rather than genetic influences.

Inside each eukaryote nucleus is genetic material (DNA) surrounded by protective and regulatory proteins. These protective and regulatory proteins and the dynamic changes to them that occur during the course of a eukaryote's existence are the epigenome.

Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.[26]

There are "nearly 50,000 acetylated sites [punctate sites of modified histones] in the human genome that correlate with active transcription start sites and CpG islands and tend to cluster within gene-rich loci."[26]

Cytogenetics

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Main resource: Cytogenetics
This is a spectral karyotype (SKY) of a human female. Credit: National Human Genome Research Institute, USA.

Cytogenetics is a study of structure, function, behavior and pathology of chromosomes.

Reverse genetics

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Main resource: Reverse genetics
Avian Flu vaccine development was by Reverse Genetics techniques. Courtesy: National Institute of Allergy and Infectious Diseases.

Reverse genetics is an approach to discovering the function of a gene by analyzing the phenotypic effects of specific gene sequences obtained by DNA sequencing. This investigative process proceeds in the opposite direction of so-called forward genetic screens of classical genetics. Simply put, while forward genetics seeks to find the genetic basis of a phenotype or trait, reverse genetics seeks to find what phenotypes arise as a result of particular genes.

Automated DNA sequencing generates large volumes of genomic sequence data relatively rapidly. Many genetic sequences are discovered in advance of other, less easily obtained, biological information. Reverse genetics attempts to connect a given genetic sequence with specific effects on the organism.

Hypotheses

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Main resource: Hypotheses
  1. Individual breeding preferences coupled with geographical isolation may produce new species.
  2. Cavia porcellus may be derived from Cavia tschudii.

See also

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References

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  1. ↑ Poccil (20 October 2004). heredity. San Francisco, California: Wikimedia Foundation, Inc. https://en.wiktionary.org/wiki/heredity. Retrieved 2016-10-04. 
  2. ↑ Sturm RA; Frudakis TN (2004). "Eye colour: portals into pigmentation genes and ancestry". Trends Genet. 20 (8): 327–32. doi:10.1016/j.tig.2004.06.010. PMID 15262401. 
  3. ↑ 3.0 3.1 Pearson H (2006). "Genetics: what is a gene?". Nature 441 (7092): 398–401. doi:10.1038/441398a. PMID 16724031. 
  4. ↑ Visscher PM; Hill WG; Wray NR (2008). "Heritability in the genomics era—concepts and misconceptions". Nat. Rev. Genet. 9 (4): 255–66. doi:10.1038/nrg2322. PMID 18319743. 
  5. ↑ Shoag J; Haq, Rizwan; Zhang, Mingfeng; Liu, Laura; Rowe, Glenn C.; Jiang, Aihua; Koulisis, Nicole; Farrel, Caitlin et al. (Jan 2013). "PGC-1 coactivators regulate MITF and the tanning response". Mol Cell 49 (1): 145–57. doi:10.1016/j.molcel.2012.10.027. PMID 23201126. PMC 3753666. //www.ncbi.nlm.nih.gov/pmc/articles/PMC3753666/. 
  6. ↑ Pho LN; Leachman SA (Feb 2010). "Genetics of pigmentation and melanoma predisposition". G Ital Dermatol Venereol 145 (1): 37–45. PMID 20197744. http://www.minervamedica.it/en/journals/dermatologia-venereologia/article.php?cod=R23Y2010N01A0037. 
  7. ↑ Oetting WS; Brilliant MH; King RA (1996). "The clinical spectrum of albinism in humans and by action". Molecular Medicine Today 2 (8): 330–5. doi:10.1016/1357-4310(96)81798-9. PMID 8796918. 
  8. ↑ Griffiths, Anthony, J. F.; Wessler, Susan R.; Carroll, Sean B.; Doebley J (2012). Introduction to Genetic Analysis (10th ed.). New York: W. H. Freeman and Company. p. 3. ISBN 978-1-4292-2943-2. 
  9. ↑ Douglas J. Futuyma (2005). Evolution. Sunderland, Massachusetts: Sinauer Associates, Inc.. ISBN 0-87893-187-2. 
  10. ↑ Phillips PC (2008). "Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems". Nat. Rev. Genet. 9 (11): 855–67. doi:10.1038/nrg2452. PMID 18852697. PMC 2689140. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2689140/. 
  11. ↑ Wu R; Lin M (2006). "Functional mapping â€“ how to map and study the genetic architecture of dynamic complex traits". Nat. Rev. Genet. 7 (3): 229–37. doi:10.1038/nrg1804. PMID 16485021. 
  12. ↑ Jablonka, E.; Lamb, M. J. (2002). "The changing concept of epigenetics". Annals of the New York Academy of Sciences 981 (1): 82–96. doi:10.1111/j.1749-6632.2002.tb04913.x. PMID 12547675. https://web.archive.org/web/20110511122654/http://a-c-elitzur.co.il/uploads/articlesdocs/Jablonka.pdf. Retrieved 2011-05-11. 
  13. ↑ Jablonka, E.; Raz, G. (2009). "Transgenerational epigenetic inheritance: Prevalence, mechanisms, and implications for the study of heredity and evolution". The Quarterly Review of Biology 84 (2): 131–176. doi:10.1086/598822. PMID 19606595. http://compgen.unc.edu/wiki/images/d/df/JablonkaQtrRevBio2009.pdf. 
  14. ↑ Bossdorf, O.; Arcuri, D.; Richards, C. L.; Pigliucci, M. (2010). "Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana". Evolutionary Ecology 24 (3): 541–553. doi:10.1007/s10682-010-9372-7. http://www.springerlink.com/content/c847255ur67w2487/. 
  15. ↑ Jablonka, E.; Lamb, M. (2005). Evolution in four dimensions: Genetic, epigenetic, behavioural, and symbolic. MIT Press. ISBN 0-262-10107-6. https://books.google.com/books?id=EaCiHFq3MWsC&printsec=frontcover. 
  16. ↑ Laland, K. N.; Sterelny, K. (2006). "Perspective: Seven reasons (not) to neglect niche construction". Evolution 60 (8): 1751–1762. doi:10.1111/j.0014-3820.2006.tb00520.x. Archived from the original on 2011-08-19. https://web.archive.org/web/20110819190949/http://lalandlab.st-andrews.ac.uk/pdf/laland_Evolution_2006.pdf. 
  17. ↑ Chapman, M. J.; Margulis, L. (1998). "Morphogenesis by symbiogenesis". International Microbiology 1 (4): 319–326. PMID 10943381. Archived from the original on 2014-08-23. https://web.archive.org/web/20140823062546/http://www.im.microbios.org/04december98/14%20Chapman.pdf. 
  18. ↑ 18.0 18.1 Wilson, D. S.; Wilson, E. O. (2007). "Rethinking the theoretical foundation of sociobiology". The Quarterly Review of Biology 82 (4): 327–48. doi:10.1086/522809. PMID 18217526. https://web.archive.org/web/20110511235639/http://evolution.binghamton.edu/dswilson/wp-content/uploads/2010/01/Rethinking-sociobiology.pdf. Retrieved 2011-05-11. 
  19. ↑ Bijma, P.; Wade, M. J. (2008). "The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection". Journal of Evolutionary Biology 21 (5): 1175–1188. doi:10.1111/j.1420-9101.2008.01550.x. PMID 18547354. 
  20. ↑ Vrba, E. S.; Gould, S. J. (1986). "The hierarchical expansion of sorting and selection: Sorting and selection cannot be equated". Paleobiology 12 (2): 217–228. http://www.explorelifeonearth.org/cursos/VrbaGould1986sorting.pdf. 
  21. ↑ phenotype. San Francisco, California: Wikimedia Foundation, Inc. 12 September 2016. https://en.wiktionary.org/wiki/phenotype. Retrieved 2016-10-04. 
  22. ↑ genetics. San Francisco, California: Wikimedia Foundation, Inc. April 16, 2014. https://en.wiktionary.org/wiki/genetics. Retrieved 2014-05-07. 
  23. ↑ Pumpie (27 August 2005). molecular genetics. San Francisco, California: Wikimedia Foundation, Inc. https://en.wiktionary.org/wiki/molecular_genetics. Retrieved 2016-01-09. 
  24. ↑ optogenetics. San Francisco, California: Wikimedia Foundation, Inc. January 30, 2014. https://en.wiktionary.org/wiki/optogenetics. Retrieved 2014-05-07. 
  25. ↑ population genetics. San Francisco, California: Wikimedia Foundation, Inc. August 18, 2009. https://en.wiktionary.org/wiki/population_genetics. Retrieved 2014-05-07. 
  26. ↑ 26.0 26.1 Bradley E. Bernstein, Alexander Meissner, Eric S. Lander (February 23, 2007). "The Mammalian Epigenome". Cell 128 (4): 669–81. doi:10.1016/j.cell.2007.01.033. http://www.sciencedirect.com/science/article/pii/S0092867407001286. Retrieved 19 December 2011. 
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