We can draw an analogy between the study of omics and cars- we may know all the parts of a car, but we have to know how to assemble the parts in order for the car to be functional. The same concept can be applied to the use of omics. In order to study the way microorganisms interact with their environment, we must examine interactions at the molecular, cellular, community, and ecosystem level, and different types of omics assess each level. The list below includes many types of omics, along with a general size range:
• Genomics- the classification of organisms based on their 16S rRNA (Wackett, Dodge, & Ellis, 2004; Xu, 2006) o width of DNA is ~2 nm (Audesirk, 2011); molecular
• Metagenomics- the study of genomes in an environmental context (Demanèche et al., 2009; Kimes et al., 2013; Tyson et al., 2004; Vieites, Guazzaroni, Beloqui, Golyshin, & Ferrer, 2009; Xu, 2006) o molecular
• Transcriptomics- the study of gene expression (Sorek & Cossart, 2010; Stewart, Sharma, Bryant, Eppley, & DeLong, 2011; Z. Wang, Gerstein, & Snyder, 2009) o molecular
• Proteomics- study of protein structure and function (VerBerkmoes, Denef, Hettich, & Banfield, 2009) o range in diameter from 1.1-5.21 nm (Erickson, 2009); molecular
• Lipidomics- (German, Gillies, Smilowitz, Zivkovic, & Watkins, 2007) o size 100 µm in diameter x 1 µm depth (Suzuki, Shinohara, Ohsaki, & Fujimoto, 2011); molecular
• Phenomics- study of the genotype-phenotype relationship (Schilling, Edwards, & Palsson, 1999) o cellular
• Metabolomics- the study of the interactions of organisms with their environment by looking at metabolites (Bundy, Davey, & Viant, 2008) o Cellular, community, and ecosystem
The list above contains parts, in terms of the way a microorganism interacts wit...
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...croorganisms, they didn’t look at what these evolutionary patterns mean for ecosystem function.
Omics are tools to be used for system-level understanding of the way organisms interact with their environment. When studying a problem at a molecular scale, it may be easy to forget that the molecular-scale problem can effect an ecosystem scale. In this way, the investigation of molecular-scale problems could have implications on ecosystem scales that are not fully realized without the use of combine omic techniques. In a description of systems biology, Kitano (2002) states that instead of examining characteristics of isolated parts of a cell or organism, we must study the structure and dynamics of cellular and organismal function. I believe that omics are helping us to dive deeper into the world of biogeochemistry, and this hidden world will soon become more exposed.
Miller, K. R., & Levine, J. S. (2010). Miller & Levine biology. Boston, Mass.: Pearson.
Disease and parasitism play a pervasive role in all life. Many of these diseases start with microparasites, which are characterized by their ability to reproduce directly within an individual host. They are also characterized by their small size, short duration of infection, and the production of an immune response in infected and recovered individuals. Microparasites which damage hosts in the course of their association are recognized as pathogens. The level of the interaction and the extent of the resultant damage depends on both the virulence of the pathogen, as well as the host defenses. If the pathogen can overcome the host defenses, the host will be damaged and may not survive. If on the other hand the host defenses overcome the pathogen, the microparasite may fail to establish itself within the host and die.
Hall, Linley Erin. “Understanding Genetics DNA and RNA.” New York: The Rosen Publishing Group, Inc., 2011. Print. 01 Apr. 2014.
Rastogi, G. and Sani, R.K. (2011) 'Chapter 2 :Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment', in Ahmad, I., Ahmad, F. and Pichtel, J. (ed.)Microbes and Microbial Technology. California, USA: Springer Science, pp. 29-57.
Miller, K. R., & Levine, J. S. (2010). Miller & Levine biology. Boston, Mass: Pearson
National Genome Research Institute. "Genetic Information and the Workplace Report." Genetic Information and the Workplace Report. National Genome Research Institute, 20 Jan. 1998. Web. 28 Apr. 2014.
...standing the nature of relationship between the residing microbes inside human cells and about their function is very important to put an end to this war and to live in peace with the natural organisms that are benefitting human body and their survival has become our primary importance.
"Polymerase Chain Reaction (PCR) Fact Sheet." National Human Genome Research Institute. 10 Dec. 2007. National Institutes of Health. .
There are many different techniques involved in gene screening. With the start of the Human Genome Mapping Project some of these techniques have been altered to speed up the screening process. Examples of these techniques include PCR (polymerize chain reaction), RFLP's (restricti...
Schreuder, Jolanda A. H.; Roelen, Corné A. M.; van Zweeden, Nely F.; Jongsma, Dianne; van der Klink, Jac J. L.; Groothoff, Johan W.
David and John Free. (26 Nov 2006). MadSci Network: Chemistry. Retrieved on March 6, 2011, from http://www.madsci.org/posts/archives/2007-02/1171045656.Ch.r.html
23. S. Alwarappan, S. Boyapalle, A. Kumar, C.-Z. Li and S. Mohapatra, J. Phys. Chem. C, 2012, 116, 6556–6559
Madar, Sylvia S., & Windelspecht, Michael. (2014). Inquiry into Life, Metabolism: Energy & Enzymes (pp. 104-107). New York: McGraw Hill.
Microbes are everywhere in the biosphere, and their presence invariably affects the environment in which they grow. The effects
Figure 1: Image of the nanoscale, this illustration shows how small things at the nanoscale really are (nano.gov, 2013).