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## Introduction
Major advances in sequencing technology have produced an avalanche of biological data over the past 12 years. The bottleneck in discovery has consequently shifted from data generation to data analysis,
and it raises the question suggesting that
only a small amount of total much data is
not used to its full potential \cite{Lockhart_Winzeler_2000}.
One Crowdsourcing is one technique to gain more insight from existing biological
data may be crowdsourcing. data. Putting the diverse eyes and hands of the general public to the purpose of
mining, organizing or analyzing biological data has previously surfaced in bioinformatics
is not new \cite{Good_Su_2013}
\cite{ld_Allison_Bonneau_et_al__2012}. Examples of problems approached by crowdsourcing \cite{ld_Allison_Bonneau_et_al__2012}; examples include protein \cite{lane2012milliseconds} and RNA folding, and both paid (Ingenuity® Systems, www.ingenuity.com) and unpaid \cite{hingamp2008metagenome} curation of literature.
Rather than approach a problem strictly as professionals, we
presented developed an Open Source DIY workshop where scientists and the public
could work worked together to tackle
an introductory a synthetic biology project resulting in a publishable outcome. The problem to be solved would need data from completely open
sources, sources and not require difficult
analysis and ideally examine one or more typical bioinformatics data sources. analysis. Thus we decided to
do a survey of plant translation initiation
motifs which could be embodied as motifs, aiming to create an open source parts list for controlling translation in metabolic engineering and synthetic
biology efforts. biology.
Plants offer many advantages as systems to do
fine fine-tuned biological engineering [e.g., modification to enhance production economically valuable terpinoid \cite{moses2013bioengineering}, modification of lignin biosynthesis to expediate biofuel synthesis \cite{li2008improvement}]. There is a paucity of published information, however, on how to control sets of genes working in concert. Use of small sequence motifs as ribosome binding site parts for synthetic biology has been proposed in bacteria [ \cite{Salis_Mirsky_Voigt_2009} see also: http://parts.igem.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Anderson.] and similar parts have been produced for yeast [parts.igem.org].
The half dozen estimates of Estimates for RBS parts in prokaryotic systems show that the translation
level of
the a gene can be
reduced to 3% vs control, suggesting that RBS parts can be used to control gene expression shifted by greater than an order of magnitude, indicating their potential utility in
a synthetic biology
effort, so projects. Generating an estimate of the
regulatory power of plant translation initiation motifs was
conceived thus seen as a useful
goal for our project.
Working meetings were posted through Counter Culture Labs and Berkeley Bio Labs
(two groups (groups with
over 100 >100 members each) on meetup.com and met every week or two over
the course of three months.
In
most eukaryotic
cells, such as plants, plant genes the 5' cap of the mRNA transcript acts as the ribosome binding
site. Another sequence within the mRNA, termed site and the Kozak
sequence, sequence acts as the signal for translation initiation.
Additionally, some genes are encoded within the chloroplast genome. Due to the bacterial origins of the chloroplast,
its transcripts
of genes encoded within the chloroplast genome contain distinct consensus sequences in comparison to transcripts from the
nuclear genome. Thus, instead nucleus. Instead of the 5'
cap, cap there is a short motif called the Shine-Delgarno sequence where the ribosome binds and then initiates
translation translation, generally 8 nucleotides downstream,
but the though this distance
in chloroplasts from the start codon to the Shine-Delgarno motif has been shown to vary. varies. Although there has been some experimental work on ribosome binding sites and Kozak sequences in plants [refs, perhaps Lutcke et al EMBO J 1987],
genomic genomic-scale surveys have not been performed.
Here we use publicly available, combined RNA- and protein expression data for both nuclear and chloroplast genes to estimate the power of the ribosome binding and translation initiation sequence motifs to initiate translation. These are initial
results, but results; experimental confirmation of the motifs will follow.