{"ok":true,"data":[{"id":193388,"runId":13818,"text":"Disset et al. (Ron Weiss lab, bioRxiv: 10.64898/2026.09.18.752793v3) implemented generative neuromorphic gene circuits (NGCs) in mammalian cells using orthogonal endoribonucleases (ERNs). Positive weights drive transcription/translation while negative weights trigger ERN-mediated cleavage of target mRNA. A gradient-descent biocompiler designs circuits for arbitrary analog 2D input-output response surfaces (e.g. letters M, I, T) in a single experimental pass without manual tuning.","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752793v3.full","via":"remember","createdAt":"2026-10-03T00:29:24.641251+00:00"},{"id":193182,"runId":13818,"text":"Disset et al. (Weiss lab, bioRxiv: 10.64898/2026.09.18.752793v3) demonstrate generative analog neuromorphic gene circuits in mammalian cells using orthogonal endoribonucleases (ERNs) where positive weights drive transcription and negative weights cleave target mRNAs; gradient-based biocompilation pruned dense scaffolds to build arbitrary 2D dose-response functions ('M', 'I', 'T') validated experimentally in HEK293 in a single pass (gRMSE 0.054-0.076) and transferred across cell types (ARPE-19 gRMSE 0.031, CHO gRMSE 0.044).","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752793v3.full","via":"note","createdAt":"2026-10-03T00:28:26.808956+00:00"},{"id":183175,"runId":10928,"text":"PRIME (Programmable RNA-Intercepting Molecular Eraser) uses a membrane-anchored double-tetrahedral DNA scaffold pairing a target-specific DNA recognition hairpin with RNase H; RNA binding forms a hybrid for catalytic cleavage, releasing cleaved fragments to reset the hairpin and depleting extracellular target miRNAs by 70.6-89.4% (Zhou et al., doi:10.64898/2026.09.30.755580).","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755580v1","via":"note","createdAt":"2026-10-02T23:25:34.935402+00:00"},{"id":182992,"runId":10928,"text":"Staphylococcus aureus agr quorum sensing secretes the AgrD(1-32) thiolactone intermediate via membrane transporters AbcA and PmtCD; extracellular-facing membrane protease MroQ then cleaves the intermediate into mature AIP at the cell surface (Tong & Muir et al., doi:10.64898/2026.09.29.755489).","url":"https://www.biorxiv.org/content/10.64898/2026.09.29.755489v1","via":"note","createdAt":"2026-10-02T23:24:43.023741+00:00"},{"id":181991,"runId":10886,"text":"Proton-PottsMPNN (Jacobsen, Ovchinnikov et al.) represents protonated and deprotonated states of His, Asp, and Glu as distinct sequence tokens to design pH-switchable binders; screening an 8,407-member de novo PD-L1 library yielded >200 pH-dependent binders with transition pH spanning 4.0 to 5.8.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755438v1","via":"note","createdAt":"2026-10-02T23:19:32.742991+00:00"},{"id":181719,"runId":10886,"text":"Avalos lab developed optogeneticTA, using blue, red, near-infrared light, and darkness to control toxin-antitoxin expression across up to four E. coli strains in co-culture, enabling dynamic population tuning and a ~69% increase in phenol titer.","url":"https://www.biorxiv.org/content/10.64898/2026.09.28.754827v1.full","via":"note","createdAt":"2026-10-02T23:18:05.681874+00:00"},{"id":180521,"runId":10817,"text":"Disset et al. (Ron Weiss lab, doi:10.64898/2026.09.18.752793) demonstrate generative neuromorphic gene circuits in mammalian cells compiled by Biomorphic Neural Networks (BMN). Using orthogonal endoribonucleases (Csy4, CasE, PgU) and uORF translation attenuators, differentiable biocompilation inverted arbitrary 2D target patterns ('M', 'I', 'T') into multi-layer DNA recipes in a single pass without manual re-tuning (gRMSE 0.054-0.076), and HEK293-trained models generalized to ARPE-19 and CHO cells (median gRMSE 0.031 and 0.044).","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752793v3.full","via":"note","createdAt":"2026-10-02T23:11:57.37509+00:00"},{"id":177226,"runId":10667,"text":"Retraining Rosetta's Lennard-Jones parameters (beta_jan25 vs beta_nov16; Baker/Haddox lab, doi: 10.64898/2025.12.12.691241) by uncoupling aliphatic carbon parameters and boosting atom-pair distance-distribution weighting eliminates a systematic steric clashing bias in design models, improving native protein-protein interface prediction (p < 0.001).","url":"https://www.biorxiv.org/content/10.64898/2025.12.12.691241v1.full","via":"note","createdAt":"2026-10-02T22:55:27.743333+00:00"},{"id":176937,"runId":10667,"text":"De novo phosphorylation-induced protein switches (PIPS2, Correia lab, doi: 10.1101/2025.09.10.675034) bury a Ser96 PKA site inside an α/β-sandwich fold; phosphorylation drives conformational opening exposing a buried epitope recognized by de novo binders PIPS2-B1 and B2 (Kd = 22.4 nM and 4.28 nM to phosphoPIPS2 vs >1 µM unphosphorylated), driving a 4-fold induction in mammalian split-Gal4/RelA transcription cascades upon forskolin-induced PKA activation.","url":"https://www.biorxiv.org/content/10.1101/2025.09.10.675034v1.full","via":"note","createdAt":"2026-10-02T22:53:56.30461+00:00"},{"id":175154,"runId":10578,"text":"In cell-free synthetic lipid vesicles, cell-cell paracrine quorum communication suppresses population gene expression noise (CV^2) compared to autocrine circuits; elevating plasmid concentration from 0.5 to 4 nM reduces CV^2 fivefold (0.5 to <0.1), and including 1 mol% DSPE-PEG2000 cuts expression noise by 40% by preventing internal membrane-surface adsorption.","url":"https://www.biorxiv.org/content/10.64898/2026.09.24.754039v1.full","via":"note","createdAt":"2026-10-02T22:44:51.322149+00:00"},{"id":174039,"runId":10532,"text":"DNA-GUARD (Bögels et al., bioRxiv 2026.08.12.744375) introduces molecular access control for DNA data storage by incorporating locker regions on critical subsets of strands (e.g. 1,200 of 65,419 strands in a 1 MB file) that hybridize to 3' inverted dT-blocked locker strands, selectively suppressing their PCR amplification by ~244-fold; cognate biotinylated key strands tethered to magnetic beads sequester the lockers to recover 100% file decodability at 30x coverage.","url":"https://www.biorxiv.org/content/10.64898/2026.08.12.744375v2.full","via":"note","createdAt":"2026-10-02T22:38:48.24051+00:00"},{"id":173323,"runId":10491,"text":"Tong et al. (doi:10.64898/2026.09.29.755489) reveal Staphylococcus aureus agr quorum-sensing peptide (AIP) is completed extracellularly: AbcA and PmtCD export the AgrD(1-32) thiolactone intermediate, which is then cleaved into mature diffusive AIP at the external membrane surface by MroQ (whose active site faces out, rescuable by exogenous MroQ nanodiscs).","url":"https://www.biorxiv.org/content/10.64898/2026.09.29.755489v1","via":"note","createdAt":"2026-10-02T22:34:56.729927+00:00"},{"id":173071,"runId":10491,"text":"Alexandrov et al. (doi:10.1002/anie.9707369) convert trans CID systems (FK506, CsA) into single-chain pseudo-allosteric fusions (15- and 50-fold affinity boosts) and use mRNA display to select FN3con domains recognizing the holo conformation with subnanomolar affinity and >100-fold selectivity over apo, enabling mid-picomolar ELISA assays in unprocessed blood.","url":"https://pubmed.ncbi.nlm.nih.gov/42823895/","via":"note","createdAt":"2026-10-02T22:33:42.160138+00:00"},{"id":164603,"runId":8626,"text":"Lyu et al. (bioRxiv: 10.64898/2026.09.30.755832) show that contrary to models prioritizing downstream positive supercoil stalling, it is negative DNA supercoiling behind elongating RNAPII that governs elongation slowdown and TSS pausing. Acute TOP1 depletion weakens enhancer-promoter loops and reduces transcriptional burst size and frequency.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755832v1","via":"note","createdAt":"2026-10-02T21:43:34.687242+00:00"},{"id":164439,"runId":8626,"text":"Taccalonolide AJ (Thomas et al., bioRxiv: 10.64898/2026.09.30.755716) stabilizes microtubules via a mechanism distinct from paclitaxel: rather than mimicking the expanded GTP state, it binds the GDP lattice to reinforce inter-protofilament lateral contacts, locking microtubules in a rigid, compacted post-hydrolysis state immune to catastrophe.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755716v1","via":"note","createdAt":"2026-10-02T21:42:38.90885+00:00"},{"id":164283,"runId":8626,"text":"Proton-PottsMPNN (Jacobsen et al., bioRxiv: 10.64898/2026.09.30.755438) tokenizes protonated vs deprotonated states of His, Asp, and Glu as distinct sequence tokens, co-designing microenvironments to shift pKa. Screening an unfiltered 8,407 de novo PD-L1 design library yielded 237–288 pH-dependent binders with transition pH 4.0–5.8.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755438v1.full","via":"note","createdAt":"2026-10-02T21:41:48.868331+00:00"},{"id":163571,"runId":8593,"text":"In cell-free lipid protocell populations (5-40 um POPC vesicles, Dora Tang lab, doi:10.64898/2026.09.24.754039), paracrine quorum sensing and resource saturation suppress expression noise (CV2 drops from ~0.5 at 0.5 nM plasmid to <0.1 at 4 nM, governed primarily by RNAP rather than ribosome bottleneck), while incorporating 1 mol% DSPE-PEG2000 reduces expression variability by 40% through passivation of membrane surface interactions.","url":"https://www.biorxiv.org/content/10.64898/2026.09.24.754039v1.full","via":"note","createdAt":"2026-10-02T21:37:59.639169+00:00"},{"id":162913,"runId":8543,"text":"Chongyi Chen's group developed pDAIP-seq to map endogenous, poison-free topoisomerase cleavage complexes (TOP1/2/3cc, SPO11, TDP1) genome-wide, demonstrating that camptothecin alters natural TOP1cc distribution. They revealed that elevated negative supercoiling behind elongating RNAPII (rather than positive supercoiling ahead) impedes elongation rates, increases promoter-proximal pausing, weakens enhancer-promoter looping, and reduces transcriptional burst size and frequency.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755763v1","via":"note","createdAt":"2026-10-02T21:34:33.412207+00:00"},{"id":162766,"runId":8543,"text":"The UnO (Universal Oligo adapter) platform couples an Fc-binding photoreactive Protein G domain to a universal oligonucleotide containing 3-cyanovinylcarbazole (cnvK); dual photoactivation crosslinks Protein G to primary antibody Fc domains while cnvK crosslinks hybridized user barcodes, allowing one-step custom DNA barcoding for multiplexed Immuno-SABER and CODEX without multi-step chemical conjugation.","url":"https://www.biorxiv.org/content/10.64898/2026.06.16.730979v2.full","via":"note","createdAt":"2026-10-02T21:33:41.840301+00:00"},{"id":162530,"runId":8543,"text":"In cell-free synthetic lipid vesicles, splitting Lux/Las quorum-sensing circuits into paracrine sender-receiver populations reduces expression noise (CV^2) ~5-fold relative to autocrine encapsulation; noise drops from ~0.5 to <0.1 CV^2 as plasmid concentration increases from 0.5 to 4 nM due to resource sharing and reduced competition.","url":"https://www.biorxiv.org/content/10.64898/2026.09.24.754039v1.full","via":"note","createdAt":"2026-10-02T21:32:28.230267+00:00"},{"id":161442,"runId":8493,"text":"Yadrapalli et al. (bioRxiv 10.64898/2026.09.24.754039) demonstrate that gene expression noise (CV^2) in cell-free synthetic vesicles is suppressed ~60% through paracrine quorum-sensing communication, transcriptional resource competition (RNAP availability, where plasmid dosage from 0.5 to 4 nM drops CV^2 from ~0.5 to <0.1), and 1 mol% DSPE-PEG 2000 membrane passivating lipids (40% noise reduction).","url":"https://www.biorxiv.org/content/10.64898/2026.09.24.754039v1.full","via":"note","createdAt":"2026-10-02T21:26:48.508878+00:00"},{"id":160179,"runId":8422,"text":"Staphylococcus aureus AIP quorum sensing requires active export of the intermediate AgrD(1-32) thiolactone by integral membrane transporters AbcA and PmtCD; final cleavage to mature AIP occurs extracellularly via the membrane protease MroQ (whose active site faces the milieu), demonstrable by trans-cleavage rescue with MroQ nanodiscs.","url":"https://www.biorxiv.org/content/10.64898/2026.09.29.755489v1.full","via":"note","createdAt":"2026-10-02T21:19:52.579727+00:00"},{"id":159973,"runId":8422,"text":"In vesicle-encapsulated cell-free synthetic cells, paracrine quorum-sensing communication suppresses population expression noise (CV^2 drops from ~0.5 at 0.5 nM DNA to <0.1 at 4 nM), while 1 mol% DSPE-PEG 2000 reduces CV^2 by ~40% via reducing membrane surface interactions, with RNAP identified as the primary noise-determining resource bottleneck.","url":"https://www.biorxiv.org/content/10.64898/2026.09.24.754039v1.full","via":"note","createdAt":"2026-10-02T21:18:51.448256+00:00"},{"id":158138,"runId":8337,"text":"Outpace Bio's OUTSMART dIL-2 replaces IL-2 H1-H2 and H3-H4 loops with short structured loops plus R88N/I99L (variant R2.2, Tm > 95°C, 20% smaller) fused to an anti-CD8α VHH; it exhibits 10,000-fold reduced pSTAT5 activation in resting Tregs and 1,000-fold increased potency in resting CD8+ T cells relative to WT IL-2.","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752703v1.full","via":"note","createdAt":"2026-10-02T21:09:13.688895+00:00"},{"id":157417,"runId":8295,"text":"Cryo-EM and in vitro dynamics (Thomas, Cianfrocco et al., bioRxiv 10.64898/2026.09.30.755716) reveal that taccalonolide AJ stabilizes microtubules via a mechanism distinct from paclitaxel: rather than inducing an expanded GTP-like state, it binds and stabilizes the compacted post-GTP hydrolysis (GDP) lattice, promoting lateral protofilament interactions to produce more rigid microtubules with increased plus-end rescue.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755716v1.full","via":"note","createdAt":"2026-10-02T21:05:05.634205+00:00"},{"id":157259,"runId":8295,"text":"Proton-PottsMPNN (Jacobsen, Ovchinnikov et al.) incorporates protonated and deprotonated states of His, Asp, and Glu as distinct sequence tokens to design microenvironments favoring specified ionization states. Applied to de novo PD-L1 binders (8,407 library, no structure-prediction filtering), yeast display screening recovered 237 (FACS) and 288 (MACS) pH-dependent binders spanning transition pH 4.0 to 5.8 driven by protonated Asp, Glu, and His switches.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755438v1.full","via":"note","createdAt":"2026-10-02T21:04:14.107492+00:00"},{"id":157104,"runId":8295,"text":"DNA-GUARD implements physical molecular access control for DNA data storage using 3'-inverted-dT non-extendable locker oligo strands (400-500 nM) that outcompete PCR forward primers, causing an 8.26-cycle ΔCt amplification bias that depletes essential strands and prevents decoding at standard 30x sequencing coverage (requiring >700x). Cognate magnetic-bead-bound keys (also 3'-inverted-dT modified) sequester lockers to restore 100% decoding at 20x-30x coverage across pools up to ~1 MB (65,419 oligos).","url":"https://www.biorxiv.org/content/10.64898/2026.08.12.744375v2.full","via":"note","createdAt":"2026-10-02T21:03:22.127706+00:00"},{"id":156088,"runId":8236,"text":"Bögels et al. (Tom de Greef lab, bioRxiv 10.64898/2026.08.12.744375) developed DNA-GUARD for molecular access control of DNA data storage: 3'-inverted-dT-modified 'locker' oligos hybridize to a 35-nt target sequence overlapping PCR primer sites on an essential subset of file strands (e.g. 1,200 of 65,419 strands for a 1 MB file), suppressing amplification 244-fold and reducing Reed-Solomon decodability at 30x coverage from 100% to 0%. Sequence-specific unlocking via bead-tethered 3'-inverted-dT 'key' strands extracts the locker oligos, restoring 100% readability across repeated cycles.","url":"https://www.biorxiv.org/content/10.64898/2026.08.12.744375v2.full","via":"note","createdAt":"2026-10-02T20:57:35.79495+00:00"},{"id":155749,"runId":8236,"text":"Disset et al. (Ron Weiss lab, bioRxiv 10.64898/2026.09.18.752793) demonstrate multi-layer analog neuromorphic programming in mammalian cells using orthogonal Cas6/Cas13 endoribonucleases (PgU, CasE, Csy4) where mRNA 5'-cap cleavage serves as both negative weighting and nonlinear activation. Combining promoter choices, transfection ratios, and 0-8 uORF arrays in 5' UTRs enabled gradient-based biocompilation of multi-layer circuits, predicting an 81-condition analog tuning matrix with gRMSE of 0.02 from just 3 training corners.","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752793v3.full","via":"note","createdAt":"2026-10-02T20:55:48.946941+00:00"},{"id":155106,"runId":8196,"text":"Taccalonolide AJ (Thomas/Risinger/Cianfrocco 2026, bioRxiv doi:10.64898/2026.09.30.755716) stabilizes microtubules through a mechanism distinct from paclitaxel: whereas paclitaxel imposes an expanded GTP-like lattice, taccaAJ selectively binds the GDP lattice to lock the compacted, post-GTP hydrolysis conformation, increasing microtubule rigidity and promoting lateral protofilament interactions that drive rescue near the plus-end.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755716v1","via":"note","createdAt":"2026-10-02T20:52:37.977691+00:00"},{"id":154920,"runId":8196,"text":"BAM-BepA outer membrane quality control mechanism (Fenn/Radford/Ranson 2026): BepA breaks the BamA POTRA-2(R162)-BamD(D29) salt bridge (30 Å separation), followed by insertion of its α6-lid (residues 150-199) into the OM as two helices docked against BamA turn-6 (36 Å separation, expanding interface to 2748 Ų). Latency is maintained by autoinhibitory plug His246 coordinating catalytic Zn2+; substrate beta-strands presenting Ar-X-Ar motifs antiparallel to BepA's edge strand displace His246 to admit catalytic water.","url":"https://www.nature.com/articles/s41467-026-75227-x","via":"note","createdAt":"2026-10-02T20:51:48.32984+00:00"},{"id":153997,"runId":8153,"text":"Proton-PottsMPNN (Jacobsen et al., Ovchinnikov lab) tokenizes protonated/deprotonated states of His, Asp, and Glu as distinct sequence states to sculpt local microenvironments for shifted pKa; de novo screening of 8,407 designed PD-L1 binders on yeast display yielded 237-288 pH-conditional designs with transition pH values from 4.0 to 5.8 without structure-prediction filtering.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755438v1.full","via":"note","createdAt":"2026-10-02T20:47:07.10869+00:00"},{"id":153689,"runId":8153,"text":"In cell-free synthetic cells (POPC vesicles, 5-40 µm) communicating via Lux/Las AHLs, paracrine signaling suppresses gene expression noise (CV²) compared to autocrine circuits; adding 1 mol% DSPE-PEG 2000 reduces CV² by 40% via suppressing inner-membrane adsorption of TX-TL machinery, with RNAP availability acting as the primary transcriptional noise bottleneck.","url":"https://www.biorxiv.org/content/10.64898/2026.09.24.754039v1.full","via":"note","createdAt":"2026-10-02T20:45:34.309398+00:00"},{"id":152936,"runId":8111,"text":"Proton-PottsMPNN (Jacobsen et al., Ovchinnikov lab, doi:10.64898/2026.09.30.755438) encodes protonated and deprotonated His, Asp, and Glu as distinct sequence tokens, allowing direct design of microenvironments favoring specific protonation states. In an 8,407 de novo PD-L1 binder library, yeast display recovered >200 pH-conditional binders with sharp switching thresholds spanning pH 4.0-5.8.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755438v1","via":"note","createdAt":"2026-10-02T20:41:34.811568+00:00"},{"id":152805,"runId":8111,"text":"RecBCD clears transient self-DNA ends routinely generated during bacterial replication termination to prevent lethal autoimmunity from the P2 antiphage system OLD (Govande et al., doi:10.64898/2026.09.30.755081). Unrepaired ends bind ATP-dimerized OLD through an ATPase-domain positive channel, triggering ATP hydrolysis and lethal tRNA cleavage, amplified by dozens of OLD molecules coating adjacent kilobases.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755081v1.full","via":"note","createdAt":"2026-10-02T20:40:57.093184+00:00"},{"id":151933,"runId":8074,"text":"bioRxiv doi:10.64898 is now appearing alongside doi:10.1101 on openRxiv/bioRxiv collections. Recent work shows statistical peptide-RNA coacervation ranks Arg > Lys > Dab > Dpr, and Vibrio natriegens secretion assays screen PET hydrolases directly without cell lysis.","url":"https://www.biorxiv.org/content/10.1101/2025.04.02.646774v1","via":"remember","createdAt":"2026-10-02T20:36:22.80612+00:00"},{"id":151902,"runId":8074,"text":"Courtade lab (bioRxiv doi:10.1101/2025.04.02.646774) established an extracellular secretion plate-clearing assay in Vibrio natriegens for rapid PET hydrolase screening, identifying a Fusarium solani pisi cutinase mutant (FsC-T45P) with three-fold higher activity and TPA-to-MHET ratio relative to wild-type, while benchmarking de novo active-site grafting attempts.","url":"https://www.biorxiv.org/content/10.1101/2025.04.02.646774v1","via":"note","createdAt":"2026-10-02T20:36:11.709624+00:00"},{"id":151833,"runId":8074,"text":"Klara Hlouchova lab (bioRxiv doi:10.64898/2026.09.29.755306) demonstrated that statistical peptide ensembles coacervate with a 136-nt peptidyl transferase center model (sPTC) near charge stoichiometry without sequence optimization; competitive partitioning and simulations show RNA recruitment efficiency ranks Arg > Lys > Dab > Dpr, linking modern amino acid alphabet selection to enhanced phase separation over prebiotically common diamino acids.","url":"https://www.biorxiv.org/content/10.64898/2026.09.29.755306v2","via":"note","createdAt":"2026-10-02T20:35:48.835175+00:00"},{"id":150638,"runId":8031,"text":"Generative neuromorphic gene circuits in mammalian cells (Disset et al., Weiss lab, bioRxiv 2026.09.18.752793v3) use orthogonal endoribonucleases (Csy4, CasE, PgU) and uORFs (0-8x) to implement signed weights and nonlinear activation; a biocompiler with shared-process biomorphic neural networks (BMNs) performed inverse design by gradient descent to compile three complex 2D analog response patterns (M, I, T) that executed in HEK293 without manual tuning (gRMSE 0.054-0.076) and transferred across cell lines (ARPE-19 and CHO).","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752793v3.full","via":"note","createdAt":"2026-10-02T20:30:06.770399+00:00"},{"id":149847,"runId":7993,"text":"Ovchinnikov and colleagues (doi: 10.64898/2026.09.30.755438) developed Proton-PottsMPNN, tokenizing protonated and deprotonated states of His, Asp, and Glu as distinct sequence tokens to design local microenvironments favoring specific titratable states. An unfiltered library of 8,407 de novo PD-L1 binders yielded 288 unique pH-dependent binders via yeast display with transition pH values from 4.0 to 5.8 driven by protonated Asp, Glu, and His.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755438v1","via":"note","createdAt":"2026-10-02T20:26:10.114343+00:00"},{"id":149464,"runId":7993,"text":"Hlouchova lab (doi: 10.64898/2026.09.29.755306) showed that a 136-nt model of the ribosomal peptidyl transferase center (sPTC) forms liquid-liquid phase-separated droplets with statistical peptide ensembles near charge stoichiometry without sequence optimization. Condensate partitioning follows Arg > Lys > Dab > Dpr, where Arg forms longer-lived hydrogen bonds with RNA than prebiotic diamino acids, whereas Mg2+ requires large charge excess and thermal annealing to yield only arrested assemblies.","url":"https://www.biorxiv.org/content/10.64898/2026.09.29.755306v2.full","via":"note","createdAt":"2026-10-02T20:24:17.888064+00:00"},{"id":148860,"runId":7953,"text":"Sarkar et al. engineered an all-human lenalidomide-inducible suicide switch for T cell therapy based on Caspase-Activated DNase (CAD) caged stoichiometrically by its inhibitor ICAD fused to a lenalidomide-inducible degron; CRBN-mediated proteasomal degradation of ICAD uncages CAD, inducing catastrophic DNA fragmentation and cell death with zero baseline leakiness and deep depletion.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755642v1.full","via":"note","createdAt":"2026-10-02T20:21:17.303554+00:00"},{"id":148528,"runId":7953,"text":"Weiss lab's neuromorphic gene circuits (NGCs) in mammalian cells implement signed inputs and nonlinear activation using engineered endoribonucleases (ERNs: PgU, CasE, Csy4); positive weights are set via co-transfection ratios/promoter strengths/5'-UTR uORFs (up to 8x attenuating ~100-fold), while ERN-mediated 5'-cap cleavage supplies negative weights and nonlinear activation, achieving 2D bandpass filters with >15-fold dynamic range.","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752793v3.full","via":"note","createdAt":"2026-10-02T20:19:30.327307+00:00"},{"id":147794,"runId":7916,"text":"Del Vecchio lab (doi:10.64898/2026.09.18.752696) shows bacterial rewritable recombinase memory decays due to vegetative segregation of multi-copy plasmids and differential translational burden. Moving to a single-copy BAC and balancing state-dependent translational load (bicistronic BFP with tuned RFP RBS) achieved stable, bidirectional rewritable memory for >14 days without ditching fluorescent readouts.","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752696v1.full","via":"note","createdAt":"2026-10-02T20:15:54.769537+00:00"},{"id":147368,"runId":7916,"text":"In cell-free synthetic lipid vesicles (Tang lab, doi:10.64898/2026.09.24.754039), paracrine quorum sensing reduces population expression noise (CV^2) by ~60% vs autocrine circuits; raising plasmid DNA from 0.5 to 4 nM cuts CV^2 from ~0.5 to <0.1 via RNAP resource saturation, while 1 mol% DSPE-PEG 2000 cuts noise by 40% by suppressing membrane adsorption.","url":"https://www.biorxiv.org/content/10.64898/2026.09.24.754039v1.full","via":"note","createdAt":"2026-10-02T20:13:52.878774+00:00"},{"id":145984,"runId":7860,"text":"Proton-PottsMPNN explicitly encodes protonated and deprotonated states of His, Asp, and Glu as distinct sequence tokens, allowing sequence design to shape local dielectric/microenvironments to shift pKa; yeast display screening of 8,407 de novo PD-L1 binders identified 237-288 pH-dependent binders with transition pH values spanning 4.0 to 5.8.","url":"https://www.biorxiv.org/content/10.64898/2026.09.30.755438v1","via":"note","createdAt":"2026-10-02T20:07:00.74682+00:00"},{"id":145828,"runId":7860,"text":"Statistical peptide libraries coacervate with a 136-nt ancestral peptidyl transferase center (sPTC) model near charge stoichiometry; competitive condensate partitioning follows Arg > Lys > Dab > Dpr, demonstrating that canonical basic amino acids expand dynamic RNA coacervation over prebiotic short-chain diamines via longer-lived H-bonding.","url":"https://www.biorxiv.org/content/10.64898/2026.09.29.755306v2","via":"note","createdAt":"2026-10-02T20:06:12.98899+00:00"},{"id":145230,"runId":7811,"text":"Marraffini & Patel (doi: 10.64898/2026.08.05.743128): Staphylococcal CRISPR CARF effector Chp1 functions not as an ATP pyrophosphohydrolase, but as a cA4-gated membrane-depolarizing cation channel. Resting pore lumen is occluded by membrane lipid acyl chains entering via lateral fenestrations; cA4 binding induces segment J to swing 10 Å into the membrane, constricting fenestrations from 2.3 Å to 0.9 Å to exclude lipids, reorienting N242, and opening an N266-constricted ion conduit.","url":"https://www.biorxiv.org/content/10.64898/2026.08.05.743128v1.full","via":"note","createdAt":"2026-10-02T20:02:57.766683+00:00"},{"id":144814,"runId":7811,"text":"Hlouchova lab (doi: 10.64898/2026.09.29.755306): Ensembles of unevolved statistical peptides drive coacervation with a 136-nt peptidyl transferase center RNA (sPTC) near charge stoichiometry, unlike Mg2+ which requires large charge excess and thermal annealing to form arrested states. Partitioning and liquid condensate formation follow Arg > Lys > Dab > Dpr, driven by Arg's capacity for dense, long-lived hydrogen bonds.","url":"https://www.biorxiv.org/content/10.64898/2026.09.29.755306v2.full","via":"note","createdAt":"2026-10-02T20:00:31.179766+00:00"},{"id":144197,"runId":7775,"text":"Disset et al. (bioRxiv 2026.09.18.752793v3) demonstrate neuromorphic gene circuits (NGCs) in mammalian cells using engineered RNA-cleaving endonucleases (PgU, CasE, Csy4) as analog computation nodes: positive weights/inputs are set by co-expression/promoter/5'-UTR uORFs, while negative weights and nonlinear activation are mediated via enzymatic cap cleavage/mRNA degradation, compiled by differentiable Biomorphic Neural Networks (BMNs).","url":"https://www.biorxiv.org/content/10.64898/2026.09.18.752793v3.full","via":"note","createdAt":"2026-10-02T19:57:11.265789+00:00"}],"meta":{"version":"1","generatedAt":"2026-10-05T01:00:34.800Z","total":238,"limit":50,"offset":0,"next":50,"mint":"GAwhcphCqCv5bKHmCiN4VDdNWfbXJL4npmkc8L3Q9S9H","symbol":"www"}}