Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration

نویسندگان

  • Lauren B.A. Woodruff
  • Thomas E. Gorochowski
  • Nicholas Roehner
  • Tarjei S. Mikkelsen
  • Douglas Densmore
  • D. Benjamin Gordon
  • Robert Nicol
  • Christopher A. Voigt
چکیده

Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Domestication of Persian Shallot (Allium hirtifolium) as Cultivated Crop

Due to highly consumption of extensive wild germplasm of Allium hirtifolium Boiss (Mooseer) in food and medicinal industry, exploration and domestication process have been done in Golestan province (Gorgan). Economic productions of domesticated Persian Shallot plants need to be improved through breeding process. The successes of domesticated accessions improvement program depend on the availabl...

متن کامل

Using Neural Networks and Genetic Algorithms for Modelling and Multi-objective Optimal Heat Exchange through a Tube Bank

In this study, by using a multi-objective optimization technique, the optimal design points of forced convective heat transfer in tubular arrangements were predicted upon the size, pitch and geometric configurations of a tube bank. In this way, the main concern of the study is focused on calculating the most favorable geometric characters which may gain to a maximum heat exchange as well as a m...

متن کامل

Yard Crane Pools and Optimum Layouts for Storage Yards of Container Terminals

As more and more container terminals open up all over the world, competition for business is becoming very intense for container terminal operators. They are finding out that even to keep their existing Sea Line customers, they have to make them happy by offering higher quality service. The quality of service they can provide depends on their operating policies and the design of the terminal la...

متن کامل

Parallel Coprocessor Architectures for Molecular Dynamics Simulation: a Case Study in Design Space Exploration

The purpose of the paper is to describe a new semi-automated design space exploration method based on genetic programming. A new control/dataflow specification method is proposed as well as appropriate models for hardware parts and algorithms. With this method we are able to test many different hardware architectures and algorithms against cost, speed, computation time and other constraints wit...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره 45  شماره 

صفحات  -

تاریخ انتشار 2017