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Codon Digest: Bacteria Resist Every Virus
Papers, news, and press releases in bio+tech.
Papers, news, and press releases in gene-editing, synthetic biology, longevity, software, and neurotechnology. I don’t send these digests via email, because links are boring. Dates: March 13-20, 2023.
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AI + Bio
Protein-specific signal peptides for mammalian vector engineering. O’Neill P. bioRxiv.
Automated assembly of molecular mechanisms at scale from text mining and curated databases. Bachman JA. Molecular Systems Biology.
AlphaFold2 and its applications in the fields of biology and medicine (Review). Yang Z. Signal Transduction and Targeted Therapy.
Discovering highly potent antimicrobial peptides with deep generative model HydrAMP. Szymczak P. Nature Communications.
Bacteria require phase separation for fitness in the mammalian gut. Krypotou E. Science.
The molecular grammar of protein disorder guiding genome-binding locations. Jonas F. Nucleic Acids Research.
Evolutionary conservation of the fidelity of transcription. Chung C. Nature Communications.
Generation of functional oocytes from male mice in vitro. Murakami K. Nature.
A swapped genetic code prevents viral infections and gene transfer. Nyerges A. Nature.
Point-of-care peptide hormone production enabled by cell-free protein synthesis. DeWinter MA. ACS Synthetic Biology.
Marine biofilm engineered to produce current in response to small molecules. Bird LJ. ACS Synthetic Biology.
A novel system for glycosylation engineering by natural and artificial miRNAs. Klingler F. Metabolic Engineering.
Performance prediction of fundamental transcriptional programs. Milner PT. ACS Synthetic Biology.
Biomolecular glass with amino acid and peptide nanoarchitectonics. Xing R. Science Advances.
A generalizable nanopore sensor for highly specific protein detection at single-molecule precision. Ahmad M. Nature Communications.
Self-regulating living material with temperature-dependent light absorption. Xiong LL. bioRxiv.
A genetic engineering toolbox for the lignocellulolytic anaerobic gut fungus Neocallimastix frontalis. Hooker CA. ACS Synthetic Biology.
Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers. Maingi V. Nature Communications.
Ribozyme-mediated RNA synthesis and replication in a model Hadean microenvironment. Salditt A. Nature Communications.
Synthetic maize centromeres transmit chromosomes across generations. Dawe RK. Nature Plants.
Optogenetic closed-loop feedback control of the unfolded protein response optimizes protein production. Benisch M. Metabolic Engineering.
Assembly of metabolons in yeast using Cas6-mediated RNA scaffolding. Pham A. ACS Synthetic Biology.
Directed evolution of aerotolerance in sulfide-dependent thiazole synthases. Van Gelder K. ACS Synthetic Biology.
Krishna V. Shenoy (1968–2023). Churchland MM & Nuyujukian P. Nature Neuroscience.
An optical design enabling lightweight and large field-of-view head-mounted microscopes. Scherrer JR. Nature Methods.
Analyzing CRISPR screens in non-conventional microbes. Trivedi V. Journal of Industrial Microbiology and Biotechnology.
CRISPR-induced DNA reorganization for multiplexed nucleic acid detection. Karlikow M. Nature Communications.
Precise excision of HTLV-1 provirus with a designer-recombinase. Rojo-Romanos T. Molecular Therapy.
Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds. Lin J-L. Nature Plants.
Autocatalytic base editing for RNA-responsive translational control. Gayet RV. Nature Communications.
A new method to synthesize multiple gRNA libraries and functional mapping of mammalian H3K4me3 regions. Pan C. Nucleic Acids Research.
Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity. Rostain W. Nucleic Acids Research.
Generating minimum set of gRNA to cover multiple targets in multiple genomes with MINORg. Lee RRQ. Nucleic Acids Research.
Single-cell transcriptomic atlas-guided development of CAR-T cells for the treatment of acute myeloid leukemia. Gottschlich A. Nature Biotechnology.
From a genome-wide screen of RNAi molecules against SARS-CoV-2 to a validated broad-spectrum and potent prophylaxis. Yogev O. Communications Biology.
Ide-cel or Standard Regimens in Relapsed and Refractory Multiple Myeloma. Rodriguez-Otero P. The New England Journal of Medicine.
Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics. Geng Z. Science Advances.
Genetic association analysis of 77,539 genomes reveals rare disease etiologies. Greene D. Nature Medicine.
Software & Models
Data integration across conditions improves turnover number estimates and metabolic predictions. Wendering P. Nature Communications.
Neural-network solutions to stochastic reaction networks. Tang Y. Nature Machine Intelligence.
Predicting metabolomic profiles from microbial composition through neural ordinary differential equations. Wang T. Nature Machine Intelligence.
Tools and Methods
Ultra-high throughput mapping of genetic design space. O’Connell RW. bioRxiv.
Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. Stahl K. Nature Biotechnology.
Spatial transcriptomics using multiplexed deterministic barcoding in tissue. Wirth J. Nature Communications.
Spatial profiling of microbial communities by sequential FISH with error-robust encoding. Cao Z. Nature Communications.
CRAPS: Chromosomal-Repair-Assisted Pathway Shuffling in yeast. Dykstra CB. bioRxiv.
A quantitative fluorescence-based approach to study mitochondrial protein import. Jain N. EMBO Reports.
Paul Berg (1926–2023). Friedberg E. Nature.
A new control switch could make RNA therapies easier to program. Trafton A. MIT News Office.
How cell-free processes could speed up vaccine development. Arnold C. Nature.
It’s Official: No More Crispr Babies—for Now. Browne G. WIRED.
A Gene Therapy Cure for Sickle Cell Is on the Horizon. Mullin E. WIRED.
How to build a virus-proof cell. Bundell S & Howe NP. Nature.
Synthetic bacterial genome upgraded for viral defence and biocontainment. Blount BA. Nature.
Eggs made from male mouse stem cells using error-prone culture. Bayerl J & Laird DJ. Nature.
I work in an ultra-clean room on ultra-small chips. Noronha PM. Nature.
How to cold e-mail for a PhD. Hart M. Nature.
Lab Leak or Not? How Politics Shaped the Battle Over Covid’s Origin. Stolberg SG & Mueller B. The New York Times.
5 strategies for biotech startups to outlast a market downturn. Coates J. Tech Crunch.
Growing number of high-security pathogen labs around world raises concerns. Kaiser J. Science.
After misconduct claims, star botanist has second paper retracted. Piller C. Science.
New theory re-ignites debate about identity of Leonardo da Vinci’s mother. Ouellette J. Ars Technica.
Fate of 1,000 trafficked lab monkeys at center of US investigation in limbo. Colley C & Kevany S. The Guardian.
How will gene editing change medicine and who will benefit? Sample I. The Guardian.
Prime Editing Reverses Vision Loss in Mice. Genetic Engineering & Biotechnology News.
Gene Discovery May Help Effort to Breed Climate Resilient Crops. Genetic Engineering & Biotechnology News.
SpyBiotech receives more than $4 million to develop vaccine platform. Peter RM. Labiotech.
Greener Pastures for Biotech? 7 Great Biotechs from Ireland. Gameiro DN. Labiotech.
New Four-Year Data for Genentech’s Evrysdi Reinforce Long-Term Efficacy and Safety Profile in Some of the Most Severely Affected People With Types 2 and 3 Spinal Muscular Atrophy (SMA). Press release.
Thanks for skimming,
— Niko McCarty