Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3' Terminal Structures for Enzymatic De Novo DNA Synthesis.

Enzymatic oligonucleotide synthesis methods based on the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) promise to enable the de novo synthesis of long oligonucleotides under mild, aqueous conditions. Intermediates with a 3' terminal structure (hairpins) will inevitably arise during synthesis, but TdT has poor activity on these structured substrates, limiting its usefulness for oligonucleotide synthesis. Here, we described two parallel efforts to improve the activity of TdT on hairpins: (1) optimization of the concentrations of the divalent cation cofactors and (2) engineering TdT for enhanced thermostability, enabling reactions at elevated temperatures. By combining both of these improvements, we obtained a ~10-fold increase in the elongation rate of a guanine-cytosine hairpin

The 1967 Iowa corn yield test

The results of the Iowa Corn Yield Test are published to aid Iowa farmers in selecting corn varieties adapted to their farms. This is the forty-eighth consecutive year for the Iowa Corn Yield Test since it began in 1920. A picker-sheller has been used to harvest a majority of fields since 1960 and on all fields since 1965. Individual-year yield data are presented for corn varieties entered two or more consecutive years in a district. One-, 2- and 3-year yield averages are presented in tables 1 through 6 for both high and moderate plant populations for each district. Information concerning other attributes of the entries tested also are listed in tables 1 through 6. This is the fifth year of the district arrangement shown in fig. 1 and the fifth year in which all entries are compared at both high and moderate plant populations at each location. The presentation of data for the varieties tested does not imply approval or endorsement by the authors or by the agencies sponsoring or conducting the test. The entry names listed in the tables are their brand and variety designations

The 1965 Iowa corn yield test

The results of the Iowa Corn Yield Test are published to aid Iowa farmers in selecting corn varieties adapted to their farms. This is the forty-sixth consecutive year for the Iowa Corn Yield Test- since its beginning in 1920 and the sixth consecutive year in which a picker-sheller has been used to harvest a majority of the test fields. Individual year yield data are presented for corn varieties entered two or more consecutive years in a district. One-, two- and three-year yield averages are presented in tables 1 to 6 for both high and normal plant populations for each district. Information concerning other attributes of the entries tested are listed in tables 1 to 6. This is the third year of the district arrangement shown in fig. 1 and the third year in which all entries are compared at both high and normal plant populations at each location. The presentation of data for the varieties tested does not imply approval or endorsement by the authors or by the agencies sponsoring or conducting the test. The entry names listed in the tables are their brand and variety designations

Adenosine Triphosphate and Carbon Efficient Route to Second Generation Biofuel Isopentanol.

Climate change necessitates the development of CO2 neutral or negative routes to chemicals currently produced from fossil carbon. In this paper we demonstrate a pathway from the renewable resource glucose to next generation biofuel isopentanol by pairing the isovaleryl-CoA biosynthesis pathway from Myxococcus xanthus and a butyryl-CoA reductase from Clostridium acetobutylicum. The best plasmid and Escherichia coli strain combination makes 80.50 ± 8.08 (SD) mg/L of isopentanol after 36 h under microaerobic conditions with an oleyl alcohol overlay. In addition, the system also shows a strong preference for isopentanol production over prenol in microaerobic conditions. Finally, the pathway requires zero adenosine triphosphate and can be paired theoretically with nonoxidative glycolysis, the combination being redox balanced from glucose thus avoiding unnecessary carbon loss as CO2. These pathway properties make the isovaleryl-CoA pathway an attractive isopentanol production route for further optimization

DeviceEditor visual biological CAD canvas

<p>Abstract</p> <p>Background</p> <p>Biological Computer Aided Design (bioCAD) assists the <it>de novo </it>design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly.</p> <p>Results</p> <p>We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs.</p> <p>Conclusions</p> <p>DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.</p

Choosing project risk management techniques. A theoretical framework

The pressure for increasing quality while reducing time and costs places particular emphasis on managing risk in projects. To this end, several models and techniques have been developed in literature and applied in practice, so that there is a strong need for clarifying when and how each of them should be used. At the same time, knowledge about risk management is becoming of paramount importance to effectively deal with the complexity of projects. However, communication and knowledge creation are not easy tasks, especially when dealing with uncertainty, because decision-making is often fragmented and a comprehensive perspective on the goals, opportunities, and threats of a project is missing. With the purpose of providing guidelines for the selection of risk techniques taking into account the most relevant aspects characterising the managerial and operational scenario of a project, a theoretical framework to classify these techniques is proposed. Based on a literature review of the criteria to categorise risk techniques, three dimensions are defined: the phase of the risk management process, the phase of the project life cycle, and the corporate maturity towards risk. The taxonomy is then applied to a wide selection of risk techniques according to their documented applications. This work helps to integrate the risk management and the knowledge management processes. Future research efforts will be directed towards refining the framework and testing it in multiple industrie

An integrated approach to supply chain risk analysis

Despite the increasing attention that supply chain risk management is receiving by both researchers and practitioners, companies still lack a risk culture. Moreover, risk management approaches are either too general or require pieces of information not regularly recorded by organisations. This work develops a risk identification and analysis methodology that integrates widely adopted supply chain and risk management tools. In particular, process analysis is performed by means of the standard framework provided by the Supply Chain Operations Reference Model, the risk identification and analysis tasks are accomplished by applying the Risk Breakdown Structure and the Risk Breakdown Matrix, and the effects of risk occurrence on activities are assessed by indicators that are already measured by companies in order to monitor their performances. In such a way, the framework contributes to increase companies' awareness and communication about risk, which are essential components of the management of modern supply chains. A base case has been developed by applying the proposed approach to a hypothetical manufacturing supply chain. An in-depth validation will be carried out to improve the methodology and further demonstrate its benefits and limitations. Future research will extend the framework to include the understanding of the multiple effects of risky events on different processe

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DNAConstructor scripts.zip. Zip file containing files gfp_DNAConstructor.txt and rfp_DNAConstructor.txt, input script files for DNA Constructor. (ZIP 1.7 kb