“The sky broke
like an egg into full sunset and the water
caught fire.” -- Pamela Hansford Johnson (American Critic, Author and
Writer, 1912-1981)
EAWAG, the Swiss Federal Institute of Aquatic Science and Technology, offers an
interesting database. Labeled Biocatalysis/Biodegradation Database, it enables
a quick search for pathways to degradation on a number of substances.
For example, enter the following search string in the database’s search box …
dibenzothiophene desulfurization
… and you will see the following:
///////
Dibenzothiophene
Desulfurization Map
This pathway was contributed by
Dr. Margie Romine, Pacific Northwest National Lab, and updated by Dr. Kevin
Gray, Energy BioSystems Corp., The Woodlands, TX. Jennifer Lockhart, Williams
College, assisted with HTML and graphics.
This pathway is the first that purposely does not continue to intermediary
metabolism. Dibenzothiophene (DBT) is a model compound for organic sulfur in
fossil fuels, and its desulfurization pathway removes this sulfur (Gray et al.,
1996). The EAWAG-BBD has a separate DBT degradation pathway, but in the words
of Dr. Kevin Gray (personal communication, 1996):
"We know that in this species of Rhodococcus the pathway does not
continue; i.e., it stops at 2-hydroxybiphenyl (HBP) and the HBP is released
into the medium. The sulfur product is incorporated into cellular biomass via
sulfur assimilation pathways. That actually is the beauty of this system as far
as desulfurization of fossil fuels is concerned: we do not decrease the carbon
content (the 'fuel value') of our substrate molecule. If all we wanted to do
was degrade the dibenzothiophene (DBT) to carbon (and energy) we would have
chosen an easier and more efficient enzyme system like the biphenyl or
naphthalene degradation pathways (which will mineralize DBT). However we don't
want to 'degrade' DBT just 'transform' it into another molecule that can then
go back into the fuel while at the same time removing the sulfur. The
physiological role of this enzyme system is to obtain sulfur for growth; in
fact, Rhodococcus sp. IGTS8 can use dibenzothiophene as a sole source of
sulfur."
The following is a text-format dibenzothiophene desulfurization pathway map. An
organism which can initiate the pathway is given, but other organisms may also
carry out later steps. Follow the links for more information on compounds or
reactions. This is the first pathway to have its map also available in graphic
(12k) format.
Page Author(s): Kevin Gray
June 30, 2014
Click this hyperlink to see the entire detailed pathway: http://eawag-bbd.ethz.ch/dbt/dbt_map.html
///////
TIP: Google® dibenzothiophene
OR thiophene OR thiophenic and browse the results for additional interesting
results.
Showing posts with label BIOCATALYSIS. Show all posts
Showing posts with label BIOCATALYSIS. Show all posts
Friday, September 25, 2015
Thursday, August 14, 2014
Literature Searches (Part 1): Introduction
“I like to browse
in occult bookshops if for no other reason than to refresh my
commitment to science.” -- Dr. Heinz R. Pagels, a physicist and
popularizer of science and executive director of the New York Academy of
Sciences (1939-1988)
A literature search is the starting point of any serious research project. Before you spend valuable time and money on
physical research, you will want to determine who has already spent their own
valuable time and money researching the same topic.
This is the first post in a series designed to serve as a refresher on how to conduct a
literature search.
“A Systems
Approach to Conduct an Effective Literature Review in Support of Information
Systems Research,” by Yair Levy and Timothy J. Ellis, provides “a
framework for conducting and writing an effective literature review.” Don’t be
misled by the title. While the authors focus on information systems, the
approach is equally valid for any area of scientific or technical research. We
will use the article as a framework for this series of posts. Incidentally,
while it is 32 pages long, it is well worth the time it takes to read it. And, amazingly, it is available at no cost
at:
According to Levy and Ellis, a good literature search …
1. Delineates
the existing body of knowledge, including where excess research exists and
where new research is needed
2. Provides a theoretical foundation for the
proposed study
3. Substantiates the presence of the research
problem
4. Justifies the proposed study as one that
contributes something new to the body of knowledge
5. Frames the valid research methodologies,
approach, goals, and research questions for the proposed study
The steps in a literature search include …
- Identifying key words
- Searching using those key words
- Identifying new key words, based on the results of the initial key word search
- Conducting backward reference searches
- Conducting forward reference searchers
- Processing search results to relate them to your research topic
The posts that follow will address each of these points.
To illustrate the points, we will use the following article as a starting
point:
Mohebali, G., & Ball, A. S. (2008). Biocatalytic desulfurization (BDS) of
petrodiesel fuels. Microbiology (Reading, England), 154(Pt 8), 2169–2183.
doi:10.1099/mic.0.2008/017608-0phene; 4, cis-4-[2-(3 ... Rhodococcus sp ...
Cited by 46
Free Full Text Source: http://mic.sgmjournals.org/content/154/8/2169.short
The next post will cover the key word search process.
Visit www.JeanSteinhardtConsulting.com
for more tips and tricks.
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