The Structure of
Scientific Papers
Pre-reading Task
Put
the following sections in the order that they appear in a scientific paper.
a) Results, b) Materials and Methods, c) Acknowledgements, d) Introduction, e) Abstract, f) Discussion, g) References
i) _____ ii) _____ iii) _____ iv) _____ v)
_____ vi) _____ vii) _____
Task
1:
Below are parts of six sections of a scientific paper. With a
partner, put them in order and label them in the chart below. Add any clues
that led you to your conclusions Remember, only a part of each section has been
reproduced. Also, in this paper the results and discussion section were
combined. The paper was titled
Bioinformatic analysis of exon
repetition, exon scrambling and trans-splicing in
humans.
by Xiang Shao, Valery Shepelev,
and Alexei Fedorov
Taken from Bioinformatics:Vol. 22 no. 6 2006, pages 692–698
Section
A:
In order to detect and to characterize exon scrambling (ExScram) and exon repetition (ExRep) events in
ESTs, we developed a program package, SCRAMBLING, for
comparison of all currently available human EST sequences (5 992 495) with the
entire set of 20 342 human intron-containing genes.
SCRAMBLING begins computations from establishing a correspondence between each
EST sequence and the gene it was produced from. As a result, 3 221 193 ESTs were linked unambiguously with their native genes.
Next, we mapped the beginning and the end of each EST onto the corresponding
mRNA sequence and calculated the length of the mRNA fragment between these two
mapped positions. If the length of this mRNA fragment differed from the length
of EST sequence by >40 nt,
that EST was processed further to test for possible ExScram
and ExRep events. The threshold of 40 nt is high enough to discard all
small variations in length due to inaccuracy of EST sequencing as well as most
of the cases of alternative splicing with alternative usage of nearby 50- or
30-splice sites. At the same time, the 40 nt
threshold is relatively low in comparison with the average human exon length (125 nt). So the vast
majority of known cases of ExScram and ExRep would exceed this threshold. When we obtained several
mapping positions of EST termini onto corresponding mRNA (due to exon duplication or repetitive segments within mRNA), we
considered all possible combinations between mapped EST beginnings and ends.
There were a total of 182 100 EST sequences that passed this initial selection
(Table 1).
Section
B:
We would like to thank Dr Robert Blumenthal,
Medical University of Ohio, for discussion and valuable suggestions on our
manuscript. Support for this work was provided by the Medical University of
Ohio Foundation and the Stranahan Foundation, through
the Program in Bioinformatics and Proteomics/Genomics. Conflict of Interest:
none declared.
Section
C:
Human genomic sequences were obtained from GenBank, Build 35.1. After processing this database with
the Exon-Intron Database (EID) toolkit (Saxonov et al., 2000), a comprehensive collection of human
gene, mRNA, and individual exon and intron sequences was obtained based on annotations in GenBank. This secondary database (human genome EID) is
publicly available from our EID website http://www.meduohio.edu/bioinfo/eid/
(file hs35p1.EID.tar.gz), and is accompanied with a description of the database(see README file at
http://www.meduohio.edu/bioinfo/eid/word/ README_Sept05.DOC). The advantages to
using EID in our project include a convenient representation of exon/intron gene structures and availability of each gene
sequence together with the related sequences of its mRNA, exons
and introns that share a common EID identifier. The
order of genes in EID strictly follows that of GenBank,
and therefore corresponds to the physical order of genes in chromosomes.
Several programs within the EID toolkit check the original input database and
report possible errors and problems with primary sources.
Section
D:
Excision of introns from
pre-mRNA is a complex process in which several types of small nuclear RNAs and several dozens of proteins assemble into a spliceosomal complex (Maniatis
and Reed, 2002). The precise recognition of exon–intron junctions by a spliceosome
is crucial for the production of functional mRNAs. However, there is often
ambiguity in the choice of exon–intron
junctions. This results in a process known as alternative splicing, which
occurs in _50% of mammalian genes and enables production of multiple mRNA isoforms from the same gene, often in a tissue-specific or
development-stage-specific manner (Modrek and Lee,
2002; Stamm, 2002). There are three other types of
splicing-associated peculiarities reported to result in abnormal exon arrangement within mRNA molecules. The first of these
is called exon repetition (ExRep)
and was first characterized by Caudevilla et al.
(1998).
Section E:
Akopian,A.N. et al. (1999)
Trans-splicing of a voltage-gated sodium channel is
regulated
by nerve growth factor. FEBS
Lett., 445, 177–182.
Benson,D.A. et al. (1999)
GenBank. Nucleic Acids Res.,
27, 12–17.
Boguski,M.S. et al. (1993)
dbEST—database for ‘expressed sequence tags’. Nat.
Genet., 4, 332–333.
Bonen,L. (1993) Trans-splicing of pre-mRNA in plants,
animals, and protists.
FASEB
J., 7, 40–46.
Caldas,C. et al. (1998)
Exon scrambling of MLL transcripts occur commonly and
mimic
partial genomic duplication of the gene. Gene, 208, 167–176.
Caudevilla,C. et al. (2001)
Localization of an exonic splicing enhancer
responsible for
mammalian
natural trans-splicing. Nucleic
Acids Res., 29, 3108–3115.
Section
F:
Motivation: Using bioinformatic
approaches we aimed to characterize poorly understood abnormalities in splicing
known as exon scrambling,exon repetition and trans-splicing.
Results: We developed a software package that allows
large-scale comparison of all human expressed sequence tags (EST) sequences to
the entire set of human gene sequences. Among 5 992 495 ESTsequences, 401 cases of exon
repetition and 416 cases of exon scramblingwere
found. The vast majority of identifiedESTs
contain fragments rather than full-length repeated or scrambled exons. Their structures suggest that the scrambled or
repeated exon fragments may have arisen in the
process of cDNA cloning and not from splicing
abnormalities. Nevertheless, we found 11 cases of full-length exon repetition showing that this phenomenon is real yet
very rare. In searching for examples of trans-splicing, we looked only at
reproducible events where at least two independent ESTs
represent the same putative trans-splicing event. We found 15 ESTs representing five types of putative trans-splicing.
However, all 15 cases were derived from human malignant tissues and could have
resulted from genomic rearrangements. Our results provide support for a very
rare but physiological occurrence of exon repetition,
but suggest that apparent exon scrambling and
trans-splicing result, respectively, from in vitro artifact and gene-level
abnormalities.
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4) Section |
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5) Section |
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6) Section |
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Task
2: In groups discuss any features you think are found in each section.
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