Codon Digest: Moore's Law
Codon Digest: Moore's Law
Papers, news, and press releases in bio+tech.
“Some things may have been tried before their time, but if these things don't violate the laws of physics they are likely to prove possible the next time around.”
— Gordon Moore
AI + Bio
Cue: a deep-learning framework for structural variant discovery and genotyping. Popic V. Nature Methods. Link
EGGNet, a generalizable geometric deep learning framework for protein complex pose scoring. Wang Z. bioRxiv. Link
Basic Science
*Genomic analyses of hair from Ludwig van Beethoven. Begg T.J.A. Current Biology. Link
Probing metabolism in an E. coli-based cell-free system reveals a trade-off between transcription and translation. Kapasiawala M & Murray R.M. bioRxiv. Link
Experimental Tests of the Virtual Circular Genome Model for Nonenzymatic RNA Replication. Ding D. JACS. Link
Global detection of human variants and isoforms by deep proteome sequencing. Meyer J.G. Nature Biotechnology. Link
Evolutionary conservation of the fidelity of transcription. Chung C. Nature Communications. Link
Elucidation of the pathway for biosynthesis of saponin adjuvants from the soapbark tree. Reed J. Science. Link
Single-molecule visualization of stalled replication-fork rescue by the Escherichia coli Rep helicase. Whinn K.S. Nucleic Acids Research. Link
The genomic landscape of reference genomes of cultivated human gut bacteria. Lin X. Nature Communications. Link
U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes. Mimoso C.A. Molecular Cell. Link
The molecular grammar of protein disorder guiding genome-binding locations. Jonas F. Nucleic Acids Research. Link
Genome mining unveils a class of ribosomal peptides with two amino termini. Ren H. Nature Communications. Link
A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth. Wang C. Nature Communications. Link
A naturally occurring mini-alanyl-tRNA synthetase. Antika T.R. Communications Biology. Link
Biological Engineering
*Photosynthesis re-wired on the pico-second timescale. Baikie T.K. Nature. Link
*Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis. Park J.H. ACS Synthetic Biology. Link
Using LanM Enzymes to Modify Glucagon-Like Peptides 1 and 2 in E.coli. Larsen C.K. bioRxiv. Link
DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access. Bögels B.W.A. bioRxiv. Link
Semi-rational evolution of a recombinant DNA polymerase for modified nucleotide incorporation efficiency. Zhai L. bioRxiv. Link
Transmembrane signaling by a synthetic receptor in artificial cells. Søgaard A.B. Nature Communications. Link
A Genetic Programming Approach to Engineering MRI Reporter Genes. Bricco A.R. ACS Synthetic Biology. Link
A stretchable wireless wearable bioelectronic system for multiplexed monitoring and combination treatment of infected chronic wounds. Sani E.S. Science Advances. Link
Genetically encoded, noise-tolerant, auxin biosensors in yeast facilitate metabolic engineering and directed evolution. Chaisupa P. bioRxiv. Link
Direct reprogramming of human fibroblasts into insulin-producing cells using transcription factors. Fontcuberta-PiSunyer M. Communications Biology. Link
Point-of-Care Peptide Hormone Production Enabled by Cell-Free Protein Synthesis. DeWinter M.A. ACS Synthetic Biology. Link
A generalizable nanopore sensor for highly specific protein detection at single-molecule precision. Ahmad M. Nature Communications. Link
Small molecule-nanobody conjugate induced proximity controls intracellular processes and modulates endogenous unligandable targets. Sun X. Nature Communications. Link
Production of 130 diterpenoids by combinatorial biosynthesis in yeast. Bathe U. bioRxiv. Link
Complete bio-degradation of poly(butylene adipate-co-terephthalate) via engineered cutinases. Yang Y. Nature Communications. Link
Biological research and self-driving labs in deep space supported by artificial intelligence. Sanders L.M. Nature Machine Intelligence. Link
Toward sustainable space exploration: a roadmap for harnessing the power of microorganisms. Santomartino R. Nature Communications. Link
Ketosynthase mutants enable short-chain fatty acid biosynthesis in E. coli. Mains K & Fox J.M. Metabolic Engineering. Link
Dynamic upregulation of the rate-limiting enzyme for valerolactam biosynthesis in Corynebacterium glutamicum. Zhao X. Metabolic Engineering. Link
The Brain
Ultra-flexible endovascular probes for brain recording through micron-scale vasculature. Zhang A. bioRxiv. Link
Catalyzing next-generation Artificial Intelligence through NeuroAI. Zador A. Nature Communications. Link
Functional neurological restoration of amputated peripheral nerve using biohybrid regenerative bioelectronics. Rochford A.E. Science Advances. Link
New AAV tools fail to detect Neurod1-mediated neuronal conversion of Müller glia and astrocytes in vivo. Xie Y. eBioMedicine. Link
Determinants of functional synaptic connectivity among amygdala-projecting prefrontal cortical neurons in male mice. Printz Y. Nature Communications. Link
Full-scale scaffold model of the human hippocampus CA1 area. Gandolfi D. Nature Computational Science. Link
Gene Editing, CRISPR & Genetic Control
*Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases. Lampe G.D. bioRxiv. Link
Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system. Qin C. Nature Communications. Link
Orthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells. Ding Y. bioRxiv. Link
Bacterial genome engineering using CRISPR RNA-guided transposases. Gelsinger D.R. bioRxiv. Link
CRISPR-induced DNA reorganization for multiplexed nucleic acid detection. Karlikow M. Nature Communications. Link
Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems. Rubio A. Science Advances. Link
Health
*Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. Tsuchida C.A. bioRxiv. Link
*Human T cell generation is restored in CD3δ severe combined immunodeficiency through adenine base editing. McAuley G.E. Cell. Link
*Immunization against Zika by entrapping live virus in a subcutaneous self-adjuvanting hydrogel. Hao H. Nature Biomedical Engineering. Link
Evaluation of repRNA vaccine for induction and in utero transfer of maternal antibodies in a pregnant rabbit model. Khandhar A.P. Molecular Therapy. Link
Dual targeting of CD19 and CD22 against B-ALL using a novel high-sensitivity aCD22 CAR. Kokalaki E. Molecular Therapy. Link
Pseudoknot-targeting Cas13b combats SARS-CoV-2 infection by suppressing viral replication. Yu D. Molecular Therapy. Link
An ASO therapy for Angelman syndrome that targets an evolutionarily conserved region at the start of the UBE3A-AS transcript. Dindot S.V. Science Translational Medicine. Link
Wastewater concentrations of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, rhinovirus, and seasonal coronavirus nucleic-acids during the COVID-19 pandemic: a surveillance study. Boehm A.B. The Lancet Microbe. Link
Immunotherapy targeting plasma ASM is protective in a mouse model of Alzheimer’s disease. Choi B.J. Nature Communications. Link
A protective measles virus-derived vaccine inducing long-lasting immune responses against influenza A virus H7N9. Hörner C. npj Vaccines. Link
Modular-designed engineered bacteria for precision tumor immunotherapy via spatiotemporal manipulation by magnetic field. Ma X. Nature Communications. Link
Diagnostic classification of childhood cancer using multiscale transcriptomics. Comitani F. Nature Medicine. Link
Artificial-intelligence-based molecular classification of diffuse gliomas using rapid, label-free optical imaging. Hollon T. Nature Medicine. Link
Highly-sensitive label-free deep profiling of N-glycans released from biomedically-relevant samples. Marie A-L. Nature Communications. Link
Epigenetic state determines the in vivo efficacy of STING agonist therapy. Falahat R. Nature Communications. Link
Activatable near-infrared probes for the detection of specific populations of tumour-infiltrating leukocytes in vivo and in urine. He S. Nature Biomedical Engineering. Link
Amplification-Free COVID-19 Detection by Digital Droplet REVEALR. Yang K & Chaput J.C. ACS Synthetic Biology. Link
Plants
A Gγ protein regulates alkaline sensitivity in crops. Zhang H. Science. Link
Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice. Yu Z. Molecular Plant. Link
Plant-based biopharmaceutical engineering. Eidenberger L. Nature Reviews Bioengineering. Link
Software & Computational Models
Performance Prediction of Fundamental Transcriptional Programs. Milner P.T. ACS Synthetic Biology. Link
A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics. Li H. Nature Communications. Link
High Accuracy Prediction of PROTAC Complex Structures. Ignatov M. JACS. Link
Elucidating yeast glycolytic dynamics at steady state growth and glucose pulses through kinetic metabolic modeling. Lao-Martil D. Metabolic Engineering. Link
Tools and Methods
Transgene Expression in Cultured Cells Using Unpurified Recombinant Adeno-Associated Viral Vectors. Benyamini B. bioRxiv. Link
Mammalian cell characterisation by non-invasive plate reader assay. Grob A. bioRxiv. Link
Thermogenetic control of Ca2+ levels in cells and tissues. Ermakova Y.G. bioRxiv. Link
Multicellular PD Control in Microbial Consortia. Martinelli V. bioRxiv. Link
A quantitative fluorescence-based approach to study mitochondrial protein import. Jain N. EMBO Reports. Link
Spatial transcriptomics using multiplexed deterministic barcoding in tissue. Wirth J. Nature Communications. Link
Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. Stahl K. Nature Biotechnology. Link
A new method to synthesize multiple gRNA libraries and functional mapping of mammalian H3K4me3 regions. Pan C. Nucleic Acids Research. Link
Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers. Maingi V. Nature Communications. Link
📰 News
Gordon E. Moore, Intel Co-Founder Behind Moore’s Law, Dies at 94. Noble H.B. & Hafner K. The New York Times. Link
GPT-4. OpenAI. Link
ChatGPT Plugins. OpenAI. Link
CoPilot X. GitHub. Link
FACT SHEET: Biden-Harris Administration Announces New Bold Goals and Priorities to Advance American Biotechnology and Biomanufacturing. The White House. Link
Top FDA official: Agency needs to start using accelerated approval for gene therapies. Mast J. STAT. Link
[Podcast] Making more mammoths with Ben Lamm from Colossal. Szkutak R & Etherington D. Tech Crunch. Link
Beethoven’s genome, sequenced for first time, yields clues on cause of death. Ouellette J. Ars Technica. Link
Pets could be gene-edited under new English law, says RSPCA. Horton H. The Guardian. Link
California’s Plan for Cheaper Insulin Collides With Big Pharma’s Price Cuts. Ryan B. The New York Times. Link
The Unpredictable Abilities Emerging From Large AI Models. Ornes S. Quanta Magazine. Link
Strife at eLife: inside a journal’s quest to upend science publishing. Abbott A. Nature. Link
FDA to convene advisory panel for Sarepta’s gene therapy for Duchenne. Mast J & Feuerstein A. STAT. Link
A Nonprofit Wants Your DNA Data to Solve Crimes. Mullin E. WIRED. Link
Science Museums Take Stock of 1.1 Billion Objects From Around the World. Zimmer C. The New York Times. Link
Abel Prize Goes to Mathematician Who Studied Equations That Describe Nature. Chang K. The New York Times. Link
Major shake-up coming for Fermilab, the troubled U.S. particle physics center. Cho A. Science. Link
I grew up down the street from Fermilab, and sometimes visited as a kid to talk with the physicists there. I never had any clue what they were talking about.
This Is the Lightest Paint in the World. Levy M.G. WIRED. Link
Made by physicists, the paint has “no pigments, and it keeps the surface beneath it 30 degrees cooler.”
Starbucks’s new CEO will work in cafes once a month. Telford T. The Washington Post. Link
Like Undercover Boss, except they publicize it in major news outlets.
🏭 Industry
Pragma Bio is searching for cancer treatments hidden in our microbiome. Coldewey D. Tech Crunch. Link
The company raised $10 million.
Cultivated meat is closer to our plate now that Good Meat also gets FDA blessing. Hall C. Tech Crunch. Link
Bayer, with new leadership stepping in, deprioritizes women's health R&D. Bayer M. Fierce Biotech. Link
This VC built a lab to make building biotech startups easier. Kamps H.J. Tech Crunch. Link
The VC is called Portal Innovations.
6 cultured meat companies making waves. Shah-Neville W. Labiotech. Link
The companies are Mosa Meat, Eat Just (GOOD Meat), UPSIDE Foods, Believer Meats, Multus Biotechnology, and BioBetter Ltd.
Microbiome therapeutics biotech mbiomics raises €13M. Cornall J. Labiotech. Link
Return of the megaround: Is biotech back from the brink? Armstrong A. Fierce Biotech. Link
Fierce Biotech Layoff Tracker 2023: Another layoff wave at Evofem; Neoleukin cuts 70% of staff, CEO. Armstrong A, Masson G & Bayer M. Fierce Biotech. Link
Including layoffs for 280 employees at Genentech’s San Francisco biologics plant.
Flare Therapeutics Announces Oversubscribed $123 Million Series B Financing. Press Release. Link
67% five-year survival rate in glioblastoma therapy, according to CANbridge Pharmaceuticals study. Peter R.M. Labiotech. Link
SpyBiotech receives more than $4 million to develop vaccine platform. Peter R.M. Labiotech. Link
Campbell Neurosciences creates saliva-based test for suicidal thoughts. Cornall J. Labiotech. Link
TeselaGen Offers its Starter Edition to Help BioTech Startups Scale Efficiently. Press Release. Link
Gilead scoops up Nurix's IRAK4 degrader for up to $445M, plucking first fruit grown from 2019 collab. Bayer M. Fierce Biotech. Link
Elegen Launches ENFINIA™ DNA, Rapid Long DNA Synthesis to Power the Bioeconomy. Press Release. Link
Black is the New Green: AIRCARBON STRAWS IN BLACK Now Available. Newlight Technologies. Press Release. Link
Arzeda, the Protein Design Company™, Announces Collaboration with Takeda to Accelerate Protein Biologics Optimization. Press Release. Link
Ichnos Sciences Receives Orphan Drug Designation for First-in-Class Bispecific (CD38 x CD47) Antibody Innate Cell Modulator, ISB 1442. Press Release. Link
L'Oréal Becomes Third Global Company to Invest in Geno-led Venture for Sustainably Sourced Ingredients. Press Release. Link
Thanks for skimming,
— Niko McCarty