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.
🧪 Papers
AI + Bio
Protein-specific signal peptides for mammalian vector engineering. O’Neill P. bioRxiv.
Evolutionary-scale prediction of atomic-level protein structure with a language model. Lin Z. Science.
Automated assembly of molecular mechanisms at scale from text mining and curated databases. Bachman JA. Molecular Systems Biology.
DeepBindGCN: Integrating molecular vector representation with graph convolutional neural networks for accurate protein-ligand interaction prediction. Zhang H. bioRxiv.
VariPred: Enhancing pathogenicity prediction of missense variants using protein language models. Lin W. bioRxiv.
How far are we from personalized gene expression prediction using sequence-to-expression deep neural networks? Sasse A. bioRxiv.
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.
Basic Science
A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Wee LM. Cell.
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.
Biological Engineering
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.
Solar-powered multi-organism symbiont mimic system for beyond natural synthesis of polypeptides from CO2 and N2. Yu W. Science Advances.
Self-regulating living material with temperature-dependent light absorption. Xiong LL. bioRxiv.
Plastidial engineering with coupled farnesyl diphosphate pool reconstitution and enhancement for sesquiterpene biosynthesis in tomato fruit. Chen J. Metabolic Engineering.
A genetic engineering toolbox for the lignocellulolytic anaerobic gut fungus Neocallimastix frontalis. Hooker CA. ACS Synthetic Biology.
Engineering the biological conversion of formate into crotonate in Cupriavidus necator. Collas F. bioRxiv.
Design and mathematical analysis of activating amplifiers that expand synthetic juxtacrine receptor control. Lam C. bioRxiv.
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.
Peroxisomal metabolic coupling improves fatty alcohol production from sole methanol in yeast. Zhai X. PNAS.
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.
The Brain
Krishna V. Shenoy (1968–2023). Churchland MM & Nuyujukian P. Nature Neuroscience.
New AAV tools fail to detect Neurod1-mediated neuronal conversion of Müller glia and astrocytes in vivo. Xie Y. eBioMedicine.
An optical design enabling lightweight and large field-of-view head-mounted microscopes. Scherrer JR. Nature Methods.
Genetically encoded sensors for measuring histamine release both in vitro and in vivo. Dong H. Neuron.
Ultrasound as a versatile tool for short- and long-term improvement and monitoring of brain function. Blackmore DG. Neuron.
Genetic Control
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.
Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system. Qin C. Nature Communications.
Autocatalytic base editing for RNA-responsive translational control. Gayet RV. Nature Communications.
Combining fusion of cells with CRISPR-Cas9 editing for the cloning of large DNA fragments or complete bacterial genomes in yeast. Guesdon G. bioRxiv.
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.
Health
Single-cell transcriptomic atlas-guided development of CAR-T cells for the treatment of acute myeloid leukemia. Gottschlich A. Nature Biotechnology.
Human T cell generation is restored in CD3δ severe combined immunodeficiency through adenine base editing. McAuley GE. Cell.
Gene augmentation for autosomal dominant retinitis pigmentosa using rhodopsin genomic loci nanoparticles in the P23H+/− knock-in murine model. Simna SP. Gene Therapy.
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.
Therapeutic immune cell engineering with an mRNA : AAV-Sleeping Beauty composite system. Ye L. bioRxiv.
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.
High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display. Li A. eLife.
Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing. Zhao P. Nature Methods.
A quantitative fluorescence-based approach to study mitochondrial protein import. Jain N. EMBO Reports.
📰 News
Paul Berg (1926–2023). Friedberg E. Nature.
CRISPR? Nah. A new startup bets on an old approach to gene editing. Mast J. STAT.
A Clean Source Of Energy From A Bacterial Protein? Scientists Discover A Remarkably Efficient Enzyme That Turns Air Into Electricity. University of Oxford.
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.
Setting aside the thorniest issues around CRISPR babies, scientists say embryo-editing research should proceed. Molteni M. STAT.
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.
Powerful AI models, and more — this week’s best science graphics. 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.
🏭 Industry
SpyBiotech receives more than $4 million to develop vaccine platform. Peter RM. Labiotech.
Illumina has been ignoring its investors, but it can’t ignore Carl Icahn. Herper M. STAT.
Switch Therapeutics Launches with $52 Million to Advance First-of-its-Kind RNAi Technology. Press release.
Synthetic Biology Startup Molecular Assemblies Ships First DNA From New San Diego Facility. Cumbers J. Forbes.
Greener Pastures for Biotech? 7 Great Biotechs from Ireland. Gameiro DN. Labiotech.
Amyris, Inc. Reports Fourth Quarter and Full Year 2022 Financial Results. Press release.
Synchron to Begin Patient Enrollment for the COMMAND Trial of Brain-Computer Interface at Gates Vascular Institute. Press release.
CHARM Therapeutics Announces Collaboration with Bristol Myers Squibb to Enable and Accelerate Small Molecule Drug Discovery Programs. Press release.
Amylyx Pharmaceuticals Reports Fourth Quarter and Full Year 2022 Financial Results. Press release.
Vertex Announces Publication in New England Journal of Medicine of Results from Phase 2 Study of Inaxaplin (VX-147). Press release.
Aura Biosciences Reports Fourth Quarter and Full Year 2022 Financial Results and Provides Clinical Development and Operational Highlights. Press release.
Checkerspot’s Pollinator™ Kit for Renewable Design wins SXSW Innovation Award in the Design Category. Press release.
Thanks for skimming,
— Niko McCarty