In This Issue

 

The Parkinson's Institute

 

 

 

  Featured Article

Moving forward: future directions for understanding Parkinson’s disease

The partnership between Life Technologies and The Parkinson’s Institute has produced fully characterized iPSC lines from samples with known clinical histories, setting the stage for further disease-relevant studies.

read more >>

 

New Tools

GeneArt® CRISPR Nuclease Vector Kit—new genome engineering technology

   

All-in-one vector system for CRISPR-based genome editing

read more >>


      Tips & Tricks
gateway cloning    

When using the gene synthesis portal to order gene synthesis and related services read more>>

synthetic biology resources  

Synthetic Biology Resources

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Did you know?

GeneArt® Strings™ DNA Fragments—now bigger and better

We have made two improvements to our GeneArt® Strings™ DNA Fragments. First, we are now offering fragments in sizes up to 3 kb as well as eight new size ranges above 1 kb (the previous maximum size). Second, an error correction step has been added to the gene synthesis process, which helps reduce the error rate and improve the quality of the final synthesized fragment.

Hot From Social

Did you know that, when TAL DNA binding domains are fused to nucleases, they can be used to generate site-specific double-stranded breaks within a genome that can be repaired to knock out an inherent gene function or knock in an exogenous piece of DNA with desirable traits?

Learn more in our on-demand webinar, “TAL effectors toolbox for precision genome editing

 

Featured Article

Next steps include differentiating the iPSCs to dopaminergic neurons (or other relevant cell types) and genome editing using GeneArt® TALs Products and Services to study the impact of specific mutations. Using other analytical tools from Life Technologies, Parkinson’s disease (PD)–relevant phenotypes can then be studied. 

This partnership aims to develop systems that can be useful in the identification of therapeutics that may ameliorate the processes that underlie PD, or that may help us understand the environmental factors that impact the development of PD.

See how TAL effector–based genetic engineering of iPSCs derived from PD samples provides previously unavailable model systems to study disease mechanisms in cell types.

View the on-demand webinar >>

Download the paper >>

Send Us Your Story about how Life Technologies is enabling you to make breakthroughs.


New Tools

 

All-in-one vector system for CRISPR-based genome editing

Transfect, enrich, screen, and publish using our GeneArt® CRISPR Nuclease Vector Kit. The GeneArt® CRISPR kit offers a simple, ready-to-use, all-in-one expression vector system consisting of both the Cas9 nuclease expression cassette and guide RNA cloning cassette for rapid and efficient cloning of a target specific crRNA. The kit includes the reagents needed to generate a target-specific CRISPR/Cas9 expression vector, allowing you to edit a genomic locus of your choice in a sequence-specific manner from a single plasmid.

The cloning efficiency and streamlined workflow offered by the GeneArt® CRISPR kit means that you won’t have to screen as many clones so you can generate results much faster. After relevant targets have been identified with fast and easy-to-use GeneArt® CRISPRs, the biologically relevant mutations can be validated with GeneArt® TALs Products and Services to reduce potential off-targeting.

CRISPR/Cas9 targeted double-strand break at the genomic target site

The Cas9 endonuclease can be programmed with a single gRNA, directing a DNA double-strand break (DSB) at a desired genomic location, resulting in the silencing of that DNA sequence. Similar to DSBs induced by TAL nucleases (GeneArt® Precision TALs), the cell then activates endogenous DNA repair processes, either nonhomologous end joining (NHEJ) or homology-directed repair (HDR), to heal the targeted DSB.

Learn More >>


Q & A - Vector NTI® database frequently asked questions

What types of files can be imported into the Vector NTI database?

The following file types can be imported:

EMBL®, GenBank®, FASTA, SWISS-PROT®, GenPept, Protein FASTA, REBASE®, PROSITE, ASCII, and Vector NTI® DNA/RNA

How do I import files into the Vector NTI® database?

To import files into the Vector NTI® Express or Express Designer database, click on File > Import > (select the type of file such as DNA, protein, oligo, etc.). For the Vector NTI Advance® database , click on Table > Import. You can also simply drag and drop files into the Vector NTI® database explorer in Vector NTI Advance®, Express, or Express Designer.

What is the difference between a static license and dynamic license (DLS)?

A static license activates the product for a particular computer and only requires Internet connectivity at the time of initial activation. The end user is provided with a license that, in conjunction with the computer's hardware ID, generates a key that unlocks the Vector NTI® modules you are entitled to use. One static license seat allows for the use of Vector NTI® software on one machine.

With a dynamic license, a server application called DLS is installed on a client's server, and manages concurrent or floating user licenses for client seats. Clients can run the program on any Windows® or Mac OS® operating system. When an application of the suite is launched from a client, it requests a concurrent license from the DLS web server for that seat. For example, in a two-license/five-client seat configuration, five machines are eligible to use the license, but only two of these five machines at any given time can use the license.

How can I access and search the NCBI database through the Vector NTI® software?

Open Vector NTI® Express or Express Designer, then click on Curate > Entrez Query. In the left pane (called Explorer Viewer), select the NCBI database you wish to access. For example, to search for nucleotide sequences for the gene ILK, change the database to ‘nucleotide’ and in the search term window, type “ILK”. Click Submit. After the search is done, click on the Request ID entry (top right panel) to display the search result files (bottom right panel). To view the sequences and map of a search result file, double-click on a file. This opens the Vector NTI® molecule editor where you can view and edit the graphics map and sequence of the specific search result file. You can also save the file into your database by clicking File > Save As.

How do I report bugs and get help?

Go to the Software Support page, click on “Report a software bug”, and fill in the information. This report will go directly to our tech support team. They will follow up, typically in less than 24 hours.

Tips & Tricks

geneart   

Tips & tricks when using the gene synthesis portal to order gene synthesis and related services.


1). Getting back to the Project Manager after starting a project

After log-in, starting a new project in the Project Manager will immediately direct you to the Project Configurator. Use the navigation chevrons on top and click the blue “Project Manager” section to get back. You can move to the “Project Summary” page the same way.

2). A wild type sequence can be set up in just one minute

Only four inputs are usually required to order a wild type sequence that needs no further edits, and this can be achieved in just one minute. Try it yourself: add the sequence name and sequence, choose the sequence type and biosafety classification, and you’re done. Save and close, then proceed to summary.

Extra tip: for wild type sequences that require subcloning, you do not need to specify cloning sites. Add a subcloning service, give it a name, and choose the vector (from the short list). The Cloning Assistant will automatically recognize flanking cloning sites (if available) in the sequence.

3). Get your correct pricing in the Cart

Adding your project to the Cart allows you to check pricing. You easily can get back from the Cart to the Project Summary; just click “Edit” to go back to the Project Configurator for any adjustments required. Clicking the project name (in blue) or clicking “View” will return you to a view-only mode.

If you have a quote or promotion code, enter it in the upper right corner in Cart view to ensure the pricing shown is correct.

4). Use Batch Upload to speed up entering multiple sequences for gene synthesis or Strings™ DNA fragment requests

Drag and drop the “Batch Upload” icon to benefit from this functionality, which allows you to quickly set up larger orders with more than one sequence. The only requirement is to have the sequences prepared within a single file and in FASTA format. Click the icon—after choosing gene synthesis or Strings™ DNA fragments, a window will open that allows you to paste your FASTA sequences. Further information on the FASTA format and how to easily convert to FASTA can be found here as well.
We will also soon be launching the Large Order Assistant tool, designed to replace Batch Upload for efficient and simple processing of these types of orders.

5). The gene synthesis portal divides subcloning into four categories—each of which is set up to make ordering as easy as possible. All subcloning orders start when you enter a name, then choose either:

  • Subcloning into one of our standard Invitrogen™ expression vectors. Choose directly from our vector short list; cloning will automatically start.
  • Subcloning into a nonstandard Invitrogen™ vector. Order these as you would a custom vector (see next bullet). All of our vectors are available and ready for use in GeneArt® services.
  • Ordering a custom vector for the first time. The first time you order subcloning into your custom vector, choose “Custom vector” from the short list. Fill in the fields requested and either paste in or upload the sequence (since portal performs in silico cloning, the sequence is mandatory), then click on “Start cloning”.
  • Subsequent orders of your custom vector. If we’ve already processed an order for your custom vector, the next time you come to the portal to order your vector will be part of the “My portal vectors” list and can be chosen with one click.

6). Did you know that you can order successive Gateway® pDONR (BP) and pDEST (LR) cloning?

Start by defining a pDONR subcloning (BP reaction) (please follow the generic subcloning procedure). When you choose pDONR221 or pDONR Zeo at the foot of the vector short list, a tick box at the bottom of the subcloning tab will appear. Tick to add a second subcloning, then click on “Save & close”. A second subcloning icon will be added exclusively featuring pDEST cloning (LR reaction) including a number of Gateway® vectors.

7). Quick subcloning setup when more than one gene will always be cloned into the same vector

First, set up all of your required genes. Then set up your subcloning choice only once, and click on “Save & close”. The menu on the top right of the subcloning icon provides a “Copy item” function. Choose that, then open the menu of the next gene synthesis icon. You will find a “Paste” function there. Repeat pasting as often as required.

8). Easy setup for subcloning services that are very similar to each other See tip No. 7 (above).

Instead of copying an item, you can use the “Copy tree” function to copy an entire service workflow. Then make the modifications required.

Have tips and tricks you use in your lab?


Upcoming Events

Watch or register for our synthetic biology webinars

Event  Date
RNA-guided genome editing with an engineered Type II CRISPR/Cas9 system

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Genome editing of iPSCs from Parkinson’s disease patients using TAL technology: design, detect, and quantitate

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TAL effectors tool box for precision genome editing

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Combine expression-optimized genes with an advanced expression system to improve your results

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New easy methods for next-generation cloning for every lab

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Introduction to simplified vector design and integrated gene synthesis ordering through new Vector NTI® Express Designer Software

View now