BLOSSOM STTM HUB:
The Blossom STTM Hub is a tool which designs STTM sequences from miRNA and insert the designed STTM into the required DNA vectors to plot the plasmid map and to get the features and sequencing of the resulting vector. It also display the transgenic lines varying in different characteristics both genotypic and phenotypic. The species mainly under consideration here are rice, maize, arabidopsis and poplar. The customers can purchase the required vectors and plasmids after STTM modification by selecting from the transgenic lines display shown through the Michigan Tech Blossom STTM store.
The STTM Hub application’s Design_STTM phase first accepts miRNA sequence along with a name from the user. Then, the user is given an option to select a DNA vector sequence from a plausible list. The application is automated to design the STTM sequence using the miRNA input provided by the user. The designed STTM is to be inserted into the DNA vector chosen. The user is then given an option whether to transfer the designed STTM into another binary vector. Based on the selection made, the user is made to proceed to STEP 2.
If the designed sttm vector has to be transferred into another binary vector, the origin sequence must be removed from the initial DNA as the binary vector will also have an origin and the resultant DNA cannot have two origin sequences. The primers used to delete the origin segment are displayed and the user then has to select the binary vector, from a list of available vectors, to which the STTM needs to be transferred. A drop down menu is made available to do the same. In this step, the user can add their own binary vector sequence to which they can transfer the STTM. A link to add a new vector to their personal database is made available to fulfil this function.
Once the user selects their desired binary vector, the vector sequence dynamically loads and is displayed. Now, enzymes to be used as cutting sites are to be selected by the user. This is the last step before the plasmid map generation.
After all the inputs are provided, a validation check takes place, which verifies for the correctness of all the input sequences and selections. If everything is valid, the STTM Hub tool generates the plasmid map for the resulting vector containing the designed STTM sequence.
PLASMID MAP GENERATION:
The plasmid map is generated using HTML5 Canvas as the display interface and contains clean labels of all the features, enzymes and the STTM location along with their corresponding positions. Apart from the plasmid map, the resulting vector sequence is also displayed to the user highlighting the STTM sequence specially. A tabular listing of the features and their location in the vector is also displayed. The user is given an option of receiving the PDF report of the generated data through their registered email or other email address
The objective of Material_STTM is to build a web interface to support the distribution of STTM constructs and transgenic lines. It will show the availability of both STTM constructs and transgenic crops lines in which the targeted miRNAs are knocked down and it displays detailed genotypic and phenotypic descriptions of these transgenic lines. Material_STTM is intended to serve as a venue through which homozygous transgenic seeds of each STTM transgene can be distributed to the research community.
The transgenic lines display page contains of the list of STTM constructs made available and are ready to be distributed to interested customers. Every STTM construct in display consists of various genotypic and phenotypic information which show in detail the changes reflected in the corresponding crops as a result of the addition of STTM. Several documentation_images are provided to facilitate the interested customers and researchers to see the changes effected clearly.
A link to the Blossom STTM E-store is provided near each STTM construct and users can use the link to lead to the store from where they can purchase the STTM constructs and the crops they require.
BLOSSOM STTM E-STORE:
The Blossom STTM E-store is setup using the Michigan Tech Touchnet Marketplace Service. The cart functionality is integrated and the user can select the required constructs and crops and place an order for the desired quantity. The order will be recorded and they will be provided with a transaction ID enabling them to keep track of the order. The order will be received and processed by the Blossom Team within the specified time frame subject to availability.
BLOSSOM USER ACCOUNT:
Every user registered into Blossom STTM HUB will be given an account which stores all the plasmid reports and sequences they prepare. This can be referred to anytime when they login and is available to download. The user can remove the files as and when needed.
The STTM HUB has a Contact Us page which can be used to contact the Blossom team for any kind of queries and requests. Users can fill up the Contact Us form with their query and a reply will be issued promptly.