Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

<p>Abstract</p> <p>Background</p> <p>To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering.</p> <p>Results</p> <p>An interactive <b>Alignment Viewer </b>allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The <b>Construct Design Module </b>enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned <it>in silico </it>into defined expression vectors. The <b>Gene Design Module </b>uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies.</p> <p>Conclusion</p> <p>We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies.</p

Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer

<p>Abstract</p> <p>Background</p> <p>With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript.</p> <p>Results</p> <p>In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38α), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both <it>E. coli </it>and a cell-free wheat germ translation system. We also compare the protein expression levels in <it>E. coli </it>for a set of 11 different proteins with greatly varied G:C content and codon bias.</p> <p>Conclusion</p> <p>The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from <it>Bacillus subtilis</it>. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.</p

Gene Composer in a structural genomics environment

For structural biology applications, protein-construct engineering is guided by comparative sequence analysis and structural information, which allow the researcher to better define domain boundaries for terminal deletions and nonconserved regions for surface mutants. A database software application called Gene Composer has been developed to facilitate construct design

The Allen Telescope Array Fly's Eye Survey for Fast Radio Transients

The relatively unexplored fast radio transient parameter space is known to be home to a variety of interesting sources, including pulsars, pulsar giant pulses and non-thermal emission from planetary magnetospheres. In addition, a variety of hypothesized but as-yet-unobserved phenomena, such as primordial black hole evaporation and prompt emission associated with coalescing massive objects have been suggested. The 2007 announcement by Lorimer et al. of the detection of a bright (30 Jy) radio pulse that was inferred to be of extragalactic origin and the subsequent consternation have demonstrated both the potential utility of bright radio pulses as probes of the interstellar medium and intergalactic medium, as well as the need for wide-field surveys characterizing the fast-transient parameter space. Here we present results from the 450 hour, 150 deg^2 Fly's Eye survey for bright dispersed radio pulses at the Allen Telescope Array (ATA). The Fly's Eye spectrometer produces 128 channel power spectra over a 209 MHz bandwidth, centered at 1430 MHz, on 44 independent signals paths originating with 30 independent ATA antennas. Data were dedispersed between 0 and 2000 pc cm^-3 and searched for pulses with dispersion measures greater than 50 pc cm^-3 between 625 us and 5 s in duration. No pulses were detected in the survey, implying a limiting rate of less than 2 sky^-1 hour^-1 for 10 millisecond duration pulses having apparent energy densities greater than 440 kJy us, or mean flux densities greater than 44 Jy. Here we present details of the instrument, experiment and observations, including a discussion of our results in light of other single pulse searches.Comment: 23 pages, 11 figures, 4 tables. Accepted for publication in Ap

Never waste a good crisis: a review of progress since Rethinking Construction and thoughts for our future

Never waste a good crisis: a review of progress since Rethinking Construction and thoughts for our futur

The importance of making testable predictions: A cautionary tale.

We found a startling correlation (Pearson ρ &gt; 0.97) between a single event in daily sea surface temperatures each spring, and peak fish egg abundance measurements the following summer, in 7 years of approximately weekly fish egg abundance data collected at Scripps Pier in La Jolla California. Even more surprising was that this event-based result persisted despite the large and variable number of fish species involved (up to 46), and the large and variable time interval between trigger and response (up to ~3 months). To mitigate potential over-fitting, we made an out-of-sample prediction beyond the publication process for the peak summer egg abundance observed at Scripps Pier in 2020 (available on bioRxiv). During peer-review, the prediction failed, and while it would be tempting to explain this away as a result of the record-breaking toxic algal bloom that occurred during the spring (9x higher concentration of dinoflagellates than ever previously recorded), a re-examination of our methodology revealed a potential source of over-fitting that had not been evaluated for robustness. This cautionary tale highlights the importance of testable true out-of-sample predictions of future values that cannot (even accidentally) be used in model fitting, and that can therefore catch model assumptions that may otherwise escape notice. We believe that this example can benefit the current push towards ecology as a predictive science and support the notion that predictions should live and die in the public domain, along with the models that made them

The importance of making testable predictions: A cautionary tale.

We found a startling correlation (Pearson ρ &gt; 0.97) between a single event in daily sea surface temperatures each spring, and peak fish egg abundance measurements the following summer, in 7 years of approximately weekly fish egg abundance data collected at Scripps Pier in La Jolla California. Even more surprising was that this event-based result persisted despite the large and variable number of fish species involved (up to 46), and the large and variable time interval between trigger and response (up to ~3 months). To mitigate potential over-fitting, we made an out-of-sample prediction beyond the publication process for the peak summer egg abundance observed at Scripps Pier in 2020 (available on bioRxiv). During peer-review, the prediction failed, and while it would be tempting to explain this away as a result of the record-breaking toxic algal bloom that occurred during the spring (9x higher concentration of dinoflagellates than ever previously recorded), a re-examination of our methodology revealed a potential source of over-fitting that had not been evaluated for robustness. This cautionary tale highlights the importance of testable true out-of-sample predictions of future values that cannot (even accidentally) be used in model fitting, and that can therefore catch model assumptions that may otherwise escape notice. We believe that this example can benefit the current push towards ecology as a predictive science and support the notion that predictions should live and die in the public domain, along with the models that made them