Question: hi can someone explain to what this bio report abstract is saying in plain english!!! help it will only take few mintes!!!!
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gravatar for proxx
4.3 years ago by
proxx0
Canada
proxx0 wrote:

Identification and characterization of up-regulated genes in the halophyte Limoniastrum monopetalum (L.) Boiss grown under crude oil pollution

Abstract

Differential display method was applied to transcripts extracted from leaves of Limoniastrum monopetalumto identify genes that are differentially expressed in response to crude oil pollution. The results showed that 201 bands with different molecular sizes were differentially expressed in polluted plants. Ten cDNA bands were considered to be consistently over-expressed under crude oil stress and selected for sequencing. Comparative analysis of these cDNA sequences allowed us to classify them into six categories: (1) enzymes increase its activity under petroleum stress and were a good marker of petroleum stress (e.g. xanthine dehydrogenase, metallothionein type 2, and arginine decarboxylase), (2) nitrogen metabolism (e.g. glutamine synthetase and amidophosphoribosyltransferase), (3) drought genes (e.g. CPRD2), (4) salinity stress (e.g. retrotransposon protein), (5) plant growth (e.g. aminocyclopropane-1-carboxylic acid and ribulose-1,5-bisphosphate carboxylase oxygenase), and (6) transport related genes like proton-dependent oligopeptide transport (POT) family protein. Coincidently with the differential display results, the amount of the total protein differed significantly between unpolluted and polluted plants (T = 3.687, P < 0.006). The electrophoretic patterns (SDS–PAGE) for water soluble proteins revealed that 11 peptides with different molecular masses disappeared and eight different peptides were synthesized in polluted plants. The results of up-regulated genes identified in this study may explain the way that L. monopetalum populations established on the crude oil polluted soil and vigorous vegetative growth of adult plants.

 

link to full report http://www.sciencedirect.com/science/article/pii/S1687157X1100031X

sequencing rna-seq genome gene • 1.3k views
ADD COMMENTlink modified 4.3 years ago by Obi Griffith17k • written 4.3 years ago by proxx0
1

What parts aren't you sure you understand and what do you think they mean?

ADD REPLYlink written 4.3 years ago by Devon Ryan88k

honestly i'm confused as to what they are trying to investiagte. if you could just explain to me in plain engligh. i.e i'm not quiet sure what the varibles are 

ADD REPLYlink written 4.3 years ago by proxx0
6
gravatar for Obi Griffith
4.3 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

Devon (comment above) is trying to get you to demonstrate that you have at least tried to understand on your own. When someone posts a question like yours there is a concern that they are simply looking for someone to do their homework assignment. Although I can't imagine a class this domain-specific. :-)

The basic idea of this study is pretty straightforward. They are looking for changes in gene expression in a specific plant species as a result of exposure to crude oil. So, the conditions are crude oil stress vs no crude oil stress. The variables are the amount of RNA for different genes/transcripts as measured by the quantification of cDNA bands using the "differential display method". Have you searched the internet for details on that method? There is a basic entry in wikipedia. Here is a reasonable review of the method: http://nar.oxfordjournals.org/content/29/17/3459.full. They chose a few differentially expressed cDNA bands, sequenced them and grouped them by comparative analysis. Without have looked beyond the abstract, I would guess this means that their plant species does not have a very complete genome sequence and/or annotations. So, they compared the sequence of cDNAs to other better characterized species and attempt to assign them to gene classes by homology.

ADD COMMENTlink written 4.3 years ago by Obi Griffith17k
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