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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Task
2: In groups discuss any features you think are found in each section.