Paper details:
Task
Write up a publication on the work that we have undertaken in the laboratory component of ART. We will be
submitting this paper to the following Journal: Journal of Bacteriology.
Note for figures. Please include these as either incorporated in your word file document or as a separate
powerpoint files. Word count should be a MAXIMUM of 3000 words.
Abstract (max 200 words): The Abstract section should be 200 words or fewer concisely summarizing the
basic content of the paper without extensive experimental details. No references should be included in this
section.
Introduction (800 words). The introduction should supply sufficient background information to allow the
reader to understand and evaluate the results of the present study without referring to previous publications
on the topic. The introduction should also provide the hypothesis that was addressed or the rationale for the
present study. Use only those references required to provide the most salient background rather than an
exhaustive review of the topic.
Some tips as to what to include (You can use your answer to question one of Assignment one as the basis for
this)
1. What is tyrosine phosphorylation?
2. Why is it important? What does it do? Provide at least 2 specific examples. (This can
concentrate on bacterial examples for now. but remember that eukaryotes also use
tyrosine phosphorylation.)
3. How is it predominantly studied now? What is wrong with the current use of mimics?
(Use a Figure if you like)
4. What are we going to do that is different? How?
5. What tyrosine kinase are we using? Why is it a fusion of two proteins?
Materials and Methods (500 words). The Materials and Methods section should include sufficient technical
information to allow the experiments to be repeated. When centrifugation conditions are critical. give enough
information to enable another investigator to repeat the procedure: make of centrifuge. model of rotor.
temperature, time at maximum speed. and centrifugal force (x g rather than revolutions per minute). For
commonly used materials and methods (e.g., media and protein concentration determinations). a simple
reference is sufficient. If several alternative methods are commonly used, it is helpful to identify the method
briefly as well as to cite the reference. For example, it is preferable to state “cells were broken by ultrasonic
treatment as previously described (9)” rather than to state “cells were broken as previously described (9).”
This allows the reader to assess the method without constant reference to previous publications. Describe
new methods completely and give sources of unusual chemicals, equipment, or microbial strains. When large
numbers of microbial strains or mutants are used in a study, include tables identifying the immediate sources
(i.e., sources from whom the strains were obtained) and properties of the strains. mutants, bacteriophages,
and plasmids, etc. Enzyme purifications should be described in this section. but the results of such procedures
should be described in the Results section. A method or strain, etc., used in only one of several experiments
reported in the paper may be described in the Results section or very briefly (one or two sentences) in a table
footnote or figure legend. It is expected
that the sources from whom the strains were obtained will be identified. For instance, you obtained Rosetta
DE3 toxin from Alistair Standish.
Results (700 words). The Results section should include the results of the experiments. Reserve extensive
interpretation of the results for the Discussion section. Present the results as concisely as possible in one of
the following: text, table(s), or figure(s). Number figures and tables in the order in which they are cited in the
text, and be sure to cite all figures and tables.
For guidance as to what to include in your results section, please include the following figures:
Figure 1. A. Amplification of CpsCD from pTriex6:CpsCD. B. PCR check of Rosetta PY.
Figure 2. Plasmid check of pBADHis:ompR, pBADHiszH-NS, pBADHis:Spa47. NOTE: Just do the plasmid that YOU
are going on to purify the protein of.
Figure 3. A. Protein Expression check B. Purification.
Figure 4. Phosphotyrosine Western immunoblot. I would include ALL the proteins here – this will give you
more to discuss in the Discussion and prove whether (OR NOT) the system will work.
Discussion (600 words). The Discussion should provide an interpretation of the results in relation to
previously published work and to the experimental system at hand and should not contain extensive
repetition of the Results section or reiteration of the introduction.
Analysis of the next steps would also provide the possibility to analyse what we are doing. If we are having
problems, describe the possibilities of why, and how we could fix them.
References. Don’t forget this! I will expect at least 10 references, but likely you would be closer to 20.
Figures. All figures should contain a figure legend underneath which describes exactly what is shown in the
figure.
