Writing DNA with GenoCAD™

Chemical synthesis of custom DNA made to order calls for software streamlining the design of synthetic DNA sequences. GenoCAD™ (www.genocad.org) is a free web-based application to design protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks called genetic parts. By capturing design strategies in grammatical models of DNA sequences, GenoCAD guides the user through the design process. By successively clicking on icons representing structural features or actual genetic parts, complex constructs composed of dozens of functional blocks can be designed in a matter of minutes. GenoCAD automatically derives the construct sequence from its comprehensive libraries of genetic parts. Upon completion of the design process, users can download the sequence for synthesis or further analysis. Users who elect to create a personal account on the system can customize their workspace by creating their own parts libraries, adding new parts to the libraries, or reusing designs to quickly generate sets of related constructs

Changes in sulfur in soybean rhizosphere soil and the response of microbial flora in a continuous cropping system mediated by Funneliformis mosseae

Soybean is an S-loving crop, and continuous cropping might cause soil sulfur shortage. The primary objectives of this study are to determine whether Funneliformis mosseae (F. mosseae) can enhance the content of available S in S-deficient soil and thereby improve the sulfur utilization rate in soybean. The experiment used Heinong 48 (HN48), a soybean variety with a vast planting area in Heilongjiang Province, and F. mosseae was inoculated in the soil of soybean that had been continuously cropped for 0 and 3 years. The results of the barium sulfur turbidimetric assay show that the sulfur content in the soil and soybean was reduced by continuous cropping and increased by inoculation with F. mosseae; the results of the macro-genome sequencing technology, show that the diversity and abundance of bacteria in the soil was decreased by continuous cropping and increased by inoculation with F. mosseae. The sulfur-oxidizing bacteria (SOB) activity and sulfur-related gene expression levels were lower in the continuous crop group compared to the control group and higher in the F.mosseae-inoculated group compared to the control group. Continuous cropping reduced the sulfur content and ratio of soybean rhizosphere soil, affecting soil flora activity and thus soybean growth; F. mosseae inoculation increased the sulfur content of soybean root-perimeter soil and plants, increased the diversity and abundance of rhizosphere soil microorganisms, increased the expression of genes for sulfur transport systems, sulfur metabolism, and other metabolic functions related to elemental sulfur, and increased the species abundance and metabolic vigor of most SOB. In summary, continuous cropping inhibits soil sulfur uptake and utilization in soybean while the inoculation with F. mosseae can significantly improve this situation. This study offers a theoretical research foundation for using AMF as a bio-fungal agent to enhance soil sulfur use. It also supports the decrease of chemical fertilizers, their substitution, and the protection of native soil

Automation-aided high-throughput technologies for synthetic biology

Synthetic biology is a research discipline which harnesses technological progress in de novo DNA synthesis as well as combining expertise of biological sciences and engineering research fields to facilitate construction of novel artificial biological systems. Since the past two decades, application of its methodologies has led to significant advances in metabolic engineering, providing alternative biochemical routes for the production of therapeutic products, cosmetics and biofuels. However, several challenges remain to be addressed to support development of synthetic biology applications, notably the demand for faster, cheaper and more reliable DNA manufacturing as well as efficient methods for genome-scale engineering of living organisms. This doctoral thesis proposes new interdisciplinary approaches to these problems, taking advantage of the latest laboratory automation technologies to improve efficiency of modern DNA assembly and genome editing methods. The first results chapter proposes application of a robotic platform for an acoustic liquid transfer for miniaturisation of DNA fabrication. This research, published in 2016, demonstrates the possibility to cost-efficiently assemble DNA in sub-microlitre assembly reactions. The second results chapter presents efforts to develop a method for genome-scale engineering of a model eukaryote, the budding yeast. This work capitalises on the recent progress in on-chip DNA synthesis and the next-generation sequencing (NGS) technology. Finally, the last results chapter demonstrates computational studies to predict and accelerate turnaround times of a commercial DNA supply chain using probabilistic simulations. The developed software is used to estimate sequence-specific DNA manufacturing turnaround times in order to help plan DNA manufacturing and guide decisions regarding further automation of different experimental procedures

Sc3.0: revamping and minimizing the yeast genome

From Springer Nature via Jisc Publications RouterHistory: registration 2020-08-04, pub-electronic 2020-08-13, online 2020-08-13, collection 2020-12Publication status: Publishe

Do people become more proactive at work as they grow older? Examining the mediating roles of intrinsic motivation, emotional exhaustion, and career aspiration

Today, there is an increasingly aging workforce. Previous studies have examined whether aged people exhibit more positive attitudes, better health, and better performance. However, the relationship between age and proactive work behavior has seldom been examined, which is unfortunate since organizations need employee proactivity to deal with uncertainty and unpredictability. Based on socioemotional selectivity theory, we propose that age might be positively related to proactive work behavior through intrinsic motivation and emotional exhaustion because older people tend to manage their emotions and obtain intrinsic enjoyment. But age might be negatively related to proactive work behavior through career aspiration because older people focus less on future development. With a sample of 393 people, we revealed intrinsic motivation and career aspiration. The findings could help us better understand how age is related to organizational outcomes and individual differences in proactive work behavior. They could also further reduce age-related discrimination and encourage organizations to manage older people in wise and better ways

Sequence verification of synthetic DNA by assembly of sequencing reads

Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.or

GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs

One of the foundations of synthetic biology is the project to develop libraries of standardized genetic parts that could be assembled quickly and cheaply into large systems. The limitations of the initial BioBrick standard have prompted the development of multiple new standards proposing different avenues to overcome these shortcomings. The lack of compatibility between standards, the compliance of parts with only some of the standards or even the type of constructs that each standard supports have significantly increased the complexity of assembling constructs from standardized parts. Here, we describe computer tools to facilitate the rigorous description of part compositions in the context of a rapidly changing landscape of physical construction methods and standards. A context-free grammar has been developed to model the structure of constructs compliant with six popular assembly standards. Its implementation in GenoCAD makes it possible for users to quickly assemble from a rich library of genetic parts, constructs compliant with any of six existing standards

Yeast Golden Gate: Standardized Assembly of S. cerevisiae Transcriptional Units

BBF RFC 88 describes a new standard for the assembly of basic Saccharomyces cerevisiae transcriptional units (TUs) consisting of a promoter/5’untranslated region (UTR), open reading frame (ORF), and 3’UTR/terminator. Note that we use the term “promoter” here to refer to both the promoter and the 5’ UTR, which we currently define as a single part. Future iterations of this standard will incorporate subdivision of currently defined parts e.g. into promoter and 5’ UTR. The standard makes use of the type IIS restriction enzyme BsaI to generate standardized and user­‐defined ‘signature overhangs’, thus enabling directional and seamless TU assembly. RFC88 is supported by the Yeast Standardized Collection of Parts for Expression (SCoPE), a repository of subcloned and sequence verified parts compatible with this assembly standard. The Yeast SCoPE is currently populated by a large number of S. cerevisiae promoters and terminators that facilitate expression and characterization of non­‐native ORFs