Optimizing DNA assembly based on statistical language modelling

An Integrated Algorithm for Designing Oligodeoxynucleotides for Gene Synthesis

The design and construction of large synthetic genes can be a slow, difficult, and confusing process, especially in the key step of oligodeoxynucleotide design. Herein we present an integrated algorithm to design oligonucleotide sets for gene synthesis by both ligase chain reaction and polymerase chain reaction. It offers much flexibility with no constraints on the gene to be synthesized. Firstly, it divides the long-input DNA sequence by a greedy algorithm based on the length of the oligodeoxynucleotide overlap region. Secondly, it tunes the length of the overlap region iteratively in an attempt to minimize the melting temperature variance of overlap. Thirdly, dynamic programming algorithm is used to achieve the uniform melting temperature of the oligodeoxynucleotide overlaps. Finally, the oligodeoxynucleotides with homologous melting temperature necessary for ligase chain reaction-based or two-step assembly PCR-based synthesis of the desired gene are outputted.

Construction of a 3A system from BioBrick parts for expression of recombinant hirudin variants III in Corynebacterium glutamicum

Standardized parts can be efficiently assembled into novel biological systems using the three antibiotic (3A) system, ensuring the reusability of components and repeatability of experiments. In this study, we created the 3A expression system for easy construction of gene expression cassettes in Corynebacterium glutamicum (C. glutamicum), which was applied to screen combinations of promoters and signal peptides for improved secreted rhv3 production. We first obtained three strong promoters P₂₂₅₂, P_odhi, and P_yweA from all of promoters, which drive the highest expression of green fluorescent protein (egfp). The three promoters were then assembled with different signal peptides to generate a series of constructs using the 3A expression system developed in this study, from which the highest activity of rhv3 reached 3187.5 ATU/L of P_yweA-CspA-rhv3. Further increased production of rhv3 achieved large-scale fermentation using 5-L jar bioreactor, with the highest rhv3 accumulation 1.21 g/L obtained after 40 h of cultivation, which is higher than 0.95 g/L reported in E. coli. To the best of our knowledge, this is the first report of rhv3 secretory expression in C. glutamicum, which could be applied for the production of other recombinant proteins with significant applications.Key points• We have exploited a 3A system for the genetic manipulation in C. glutamicum.• We constructed element libraries for assembling standard sequence in C. glutamicum.• The secreted expression of rhv3 was realized by 3A system in C. glutamicum.

Scoring Amino Acid Mutations to Predict Avian-to-Human Transmission of Avian Influenza Viruses

Avian influenza virus (AIV) can directly cross species barriers and infect humans with high fatality. Using machine learning methods, the present paper scores the amino acid mutations and predicts interspecies transmission. Initially, 183 signature positions in 11 viral proteins were screened by the scores of five amino acid factors and their random forest rankings. The most important amino acid factor (Factor 3) and the minimal range of signature positions (50 amino acid residues) were explored by a supporting vector machine (the highest-performing classifier among four tested classifiers). Based on these results, the avian-to-human transmission of AIVs was analyzed and a prediction model was constructed for virology applications. The distributions of human-origin AIVs suggested that three molecular patterns of interspecies transmission emerge in nature. The novel findings of this paper provide important clues for future epidemic surveillance.