The Music of Living Cells: Index #3

"A system for music composition informed by synthetic biology”, in which music is generated via simulations of various cellular processes, including transcription and protein folding, is published.

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Good morning. This week…

The New Yorker’s Raffi Khatchadourian wrote about Jackson Laboratory’s rapid shipments of “designer mice” for SARS-CoV-2 research, NewScientist covered a “radical new theory” on how life began on Earth, and CNN’s Milly Chan wrote a feature on Colorifix’s dyeing of fabrics with synthetic biology.

Meanwhile, the San Francisco Chronicle wrote about how proteins engineered to neutralize SARS-CoV-2 could soon show up in nose sprays, OneZero and Science Friday covered the first genetic edit in a squid, and Sarah Katz wrote a brilliant piece for Discover Magazine explaining why some deaf people oppose a CRISPR cure.

In industry news, Sherlock Biosciences announced a collaboration to launch CRISPR-based tests for SARS-CoV-2 and Mammoth Biosciences inked a deal for Doudna lab’s “miniature” Cas enzyme, CasΦ.

Congratulations to Northwestern’s Center for Synthetic Biology on a $3 million grant from the NSF.

Today is the deadline for iGEM teams to register for the virtual MIT Mammalian Meetup, which will be held on August 27th from 9-12 EDT, featuring keynote speaker Ron Weiss.

This week in research…

Listening to the Music of a Cell

Eduardo Reck Miranda is a professor of computer music at the University of Plymouth. In his latest paper, he introduces “a system for music composition informed by synthetic biology”, in which music is generated via simulations of various cellular processes, including transcription and protein folding. The study was published in Artificial Life.

E. coli Engineered to Grow Solely on Methanol (They must be starving!)

At UCLA, the Liao lab has engineered E. coli to utilize methanol as its sole carbon source. With a paltry doubling time of 8.5 hours, the team began by using “metabolic robustness criteria” to engineer the strain, followed by laboratory evolution, and found that the final organism carefully balanced metabolic flux by tuning gene copy numbers and mutating key enzymes. The work was published in Cell.

Going Deeeep on the SARS-CoV-2 Receptor Binding Domain (Open Access)

Researchers at the University of Washington and the Fred Hutchinson Cancer Research Center, in Seattle, have performed a deep-mutational scan on the SARS-CoV-2 receptor binding domain (RBD), the bit that binds to ACE2 on human cells. They created every single amino-acid substitution in the RBD, and show that, while most mutations are deleterious, some mutations enhance affinity for ACE2. The work was published in Cell.

Boosting Photosynthesis in Plants

At the University of Essex, the Raines lab inserted multiple genes, from red algae and cyanobacteria, into Nicotiana tabacum (tobacco) to stimulate both electron transport and Ribulose 1,5-bisphosphate turnover, increasing photosynthesis. The engineered plants also had an increase in above-ground biomass of up to 52% compared to controls. The study was published in Nature Plants. Read the press release.

E. Coli Gets a 21st Amino Acid (Open Access)

The Xiao lab at Rice University has engineered E. coli to both synthesize a 21st amino acid (5-hydroxyl-tryptophan, or 5HTP) and then site-specifically incorporate it into proteins. The team then used the engineered cell to “serve as a living indicator for reactive oxygen species”, as stated by Xiao in a Rice press release. The work was published in Chem.

More research…

A three-way combinatorial CRISPR screen for analyzing interactions among druggable targets by Zhou, P. et al. in Cell Reports. (Open Access)

Application of CRISPR-Cas12a enhanced fluorescence assay coupled with nucleic acid amplification for the sensitive detection of African swine fever virus by Tao, G. et al. in ACS Synthetic Biology.

A versatile genetic control system in mammalian cells and mice responsive to clinically licensed sodium ferulate by Wang, Y. et al. in Science Advances. (Open Access)

Bacterial mock communities as standards for reproducible cytometric microbiome analysis by Cichocki, N. et al. in Nature Protocols.

Bacterial synthesis of C3-C5 diols via extending amino acid catabolism by Wang, J., et al. in PNAS.

Comprehensive study on Escherichia coli genomic expression: Does position really matter? by Goormans, A.R. et al. in Metabolic Engineering.

CRISPR-Cas13d Induces Efficient mRNA Knockdown in Animal Embryos by Kushawah, G. et al. in Developmental Cell. Read the press release.

De novo rational design of a freestanding, supercharged polypeptide, proton-conducting membrane by Ma, C. et al. in Science Advances. (Open Access)

Developing methods to circumvent the conundrum of chromosomal rearrangements occurring in multiplex gene edition [sic] by Borsenberger, V. et al. in ACS Synthetic Biology.

Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold by Carrasco-López, C. et al. in Nature Communications. (Open Access)

Directed evolution of Pseudomonas fluorescens lipase variants with improved thermostability using error-prone PCR by Guan, L. et al. in Frontiers in Bioengineering and Biotechnology.

DNA Scanner: a web application for comparing DNA synthesis feasibility, price, and turnaround time across vendors by Doçi, G. et al. in Synthetic Biology. (Open Access)

Engineering combinatorial and dynamic decoders using synthetic immediate-early genes by Ravindran, P.T. et al. in Communications Biology. (Open Access)

Engineering designer beta cells with a CRISPR-Cas9 conjugation platform by Lim, D. et al. in Nature Communications. (Open Access)

Engineering isoprenoid quinone production in yeast by Kaur, D. et al. in ACS Synthetic Biology.

Engineering of the 2,3-butanediol pathway of Paenibacillus polymyxa DSM 365 by Schilling, C. et al. in Metabolic Engineering. (Open Access)

Engineering regulatory networks for complex phenotypes in E. coli by Liu, R. et al. in Nature Communications. (Open Access)

Evaluating and engineering Saccharomyces cerevisiae promoters for increased amylase expression and bioethanol production from raw starch by Myburgh, M.W., Rose, S.H. and Viljoen-Bloom, M. in FEMS Yeast Research.

Fully biological production of adipic acid analogs from branched catechols by Kruyer, N.S. et al. in Scientific Reports. (Open Access)

Genetically encoded tags for direct synthesis of EM-visible gold nanoparticles in cells by Jiang, Z. et al. in Nature Methods.

Independent component analysis of E. coli's transcriptome reveals the cellular processes that respond to heterologous gene expression by Tan, J. et al. in Metabolic Engineering. (Open Access)

In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli by de Arroyo Garcia, L. and Jones, P.R. in PLoS Computational Biology. (Open Access)

Metabolically engineered Caldicellulosiruptor bescii as a platform for producing acetone and hydrogen from lignocellulose by Straub, C.T. et al. in Biotechnology and Bioengineering.

One-pot synthesis of adipic acid from guaiacol in Escherichia coli by Suitor, J.T., Varzandeh, S. and Wallace, S. in ACS Synthetic Biology.

Optogenetic control of protein binding using light-switchable nanobodies by Gil, A.A. et al. in Nature Communications. (Open Access)

Preliminary engineering for in situ in vivo bioprinting: a novel micro bioprinting platform for in situ in vivo bioprinting at a gastric wound site by Zhao, W. and Xu, T. in Biofabrication (Open Access)

Regulatory control circuits for stabilizing long-term anabolic product formation in yeast by D’Ambrosio, V. et al. in Metabolic Engineering. (Open Access)

Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes by Sandberg, T.E. et al. in Nature Ecology & Evolution.

Synthetic protease-activated class B GPCRs by Willard, F.S. et al. in Biochemical and Biophysical Research Communications.

Unveiling of swainsonine biosynthesis via a multi-branched pathway in fungi by Luo, F. et al. in ACS Chemical Biology.

This week in reviews and commentary…

Cell-free approach for noncanonical amino acids incorporation into polypeptides by Cui, Z., Johnston, W. and Alexandrox, K. in Frontiers in Bioengineering and Biotechnology.

Computer-aided whole-cell design: Taking a holistic approach by integrating synthetic with systems biology by Marucci, L. et al. in Frontiers in Bioengineering and Biotechnology. (Open Access)

Engineering microbial diagnostics and therapeutics with smart control by Amrofell, M.B., Rottinghaus, A.G. and Moon, T.S. in Current Opinion in Biotechnology.

Heterologous biosynthesis as a platform for producing new generation natural products by Park, D., Swayambhu, G. and Pfeifer, B.A. in Current Opinion in Biotechnology.

Synthetic virus-derived nanosystems (SVNs) for delivery and precision docking of large multifunctional DNA circuitry in mammalian cells by Aulicino, F., Capin, J. and Berger, I. in Pharmaceutics. (Open Access)

Use of cell and genome modification technologies to generate improved “off-the-shelf” CAR T and CAR NK cells by Morgan, M.A. et al. in Frontiers in Immunology (Open Access)

This week in preprints…

An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation by Schoof, M. et al. bioRxiv.

Characterizing and controlling nanoscale self-assembly of suckerin-12 by Hershewe, J.M. et al. bioRxiv.

Coronacept - a potent immunoadhesin against SARS-CoV-2 by Cohen-Dvashi, H. et al. bioRxiv.

dCas9 regulator to neutralize competition in CRISPRi circuits by Huang, H. et al. bioRxiv.

DNA-based nanocarriers to enhance the optoacoustic contrast of tumors in vivo by Joseph, J. et al. bioRxiv.

Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions by Rombouts, J. and Gelens, L. bioRxiv.

Efficacy of Targeting SARS-CoV-2 by CAR-NK Cells by Ma, M.T. et al. bioRxiv.

Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2 by Walls, A.C. et al. bioRxiv.

Engineered sex distortion in the global agricultural pest Ceratitis capitata by Meccariello, A. et al. bioRxiv.

Rational engineering of Kluyveromyces marxianus to create a chassis for the production of aromatic products by Rajkumar, A.S. and Morrissey, J.P. bioRxiv.

Reproducibility in systems biology modelling by Tiwari, K. et al. bioRxiv.

Single-cell lineage and transcriptome reconstruction of metastatic cancer reveals selection of aggressive hybrid EMT states by Simeonov, K.P. et al. bioRxiv.

Systematic engineering of artificial metalloenzymes for new-to-nature reactions by Vornholt T, et al. bioRxiv.