Base by Base

Spakmana D et al., Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2406949123 - Optical tweezers and fluorescence imaging show human Topoisomerase IIIα–RMI1–RMI2 (TRR) processively relaxes highly negatively supercoiled DNA faster than PICH loops. Key terms: topoisomerase IIIα, TRR complex, DNA supercoiling, optical tweezers, ultrafine anaphase bridges.

Study Highlights:
Using torsionally constrained end-closed λ-DNA in a multichannel flow cell, the authors combined Optical DNA Supercoiling (ODS), dual-trap optical tweezers, and fluorescence imaging to measure supercoiling density and visualize TRR binding in real time. They find TRR relaxes hyper-negatively supercoiled DNA in a highly processive manner, with single TRR complexes performing thousands (>3,000) of strand-passage reactions and exhibiting a force-dependent rate described by an Arrhenius relation (δ ≈ 1.1–1.4 nm in ensemble and single-molecule fits). Ensemble TRR activity was ~10-fold lower than E. coli TopoI under the same conditions, while single- complex rates indicate a single TRR can relax PICH-generated negative loops within the reported loop lifetime. These results support a mechanistic role for TRR in relaxing PICH-generated negative supercoils that could facilitate ultrafine anaphase bridge resolution.

Conclusion:
Human topoisomerase IIIα–RMI1–RMI2 (TRR) relaxes highly negatively supercoiled DNA in a force-dependent, highly processive manner and can act within the lifetime of PICH-generated negative loops, supporting a role in ultrafine anaphase bridge resolution.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-25.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantive auditing of the transcript's presentation of TRR mechanism, speed and processivity, binding preferences, dwell times, single-molecule assay setup, relation to PICH loop dynamics, and implications for ultrafine anaphase bridge resolution.
- transcript topics: TRR mechanistic relaxation of negatively supercoiled DNA; Single-molecule optical DNA supercoiling (ODS) assay with dual-trap optical tweezers; TRR processivity and burst dynamics; Force dependence and Arrhenius behavior (δ values); AT-rich sequence binding preferences of TRR; PICH loop dynamics and ultrafine bridge context

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- TRR relaxes hyper-negatively supercoiled DNA in a highly processive manner
- A single TRR complex can catalyze thousands of strand passages (>3,000 Lk) without dissociating
- Ensemble relaxation rate ~35 Lk/s; TRR is ~10-fold slower than EcTopoI; δ ~ 1.1 nm
- Single TRRmCherry complexes exhibit force-dependent relaxation with δ ~ 1.4 nm
- TRR binds preferentially to AT-rich sequences and melted bubbles
- TRR remains bound to DNA for tens of minutes after relaxation

QC result: Pass.

Palacio T et al., Proc. Natl. Acad. Sci. U.S.A. 2025.122:e2528670122 - Reconstituted Saccharomyces cerevisiae mismatch repair shows the Mlh1–Pms1 endonuclease directly generates single-strand gaps to excise mispairs independent of Exo1 and Rad27. Key terms: Mlh1-Pms1, mismatch repair, single-strand gaps, Exo1, APOBEC3A.

Study Highlights:
We reconstituted Saccharomyces cerevisiae mismatch repair with purified Msh2–Msh6 or Msh2–Msh3, Mlh1–Pms1, PCNA, RFC, RPA, and DNA polymerases and analyzed products by restriction mapping, Mung Bean nuclease, electron microscopy, and APOBEC3A deamination. The Mlh1–Pms1 endonuclease, activated by RFC-loaded PCNA and Mn2+, generates strand-specific single-strand gaps on the preexisting nicked strand. Electron microscopy and deamination mapping revealed a broad distribution of gap sizes with a peak around 128 ± 17 nucleotides and most gaps under 500 nucleotides. These gaps can be filled by DNA Polε or low levels of DNA Polδ, providing an Exo1- and Rad27-independent route for mispair excision and explaining redundancy among excision pathways.

Conclusion:
Mlh1–Pms1 catalyzes strand-specific single-strand gap formation that mediates Exo1- and Rad27-independent mispair excision in reconstituted S. cerevisiae mismatch repair.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-24.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited sections: Exo1/Rad27 independence, MLH1-Pms1 endonuclease role, Mn2+ activation, gap formation and sizes, EM evidence, APOBEC3A gap mapping, and the proposed three-pathway MMR model.
- transcript topics: Background on mismatch repair and Exo1/Rad27 roles; Exo1- and Rad27-independent MMR reconstitution; MLH1-Pms1 endonuclease activity and Mn2+ activation; Formation and types of single-stranded gaps; Electron microscopy evidence of gap sizes; APOBEC3A mapping of excision gaps

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Combined Exo1- and Rad27-independent repair accounts for a small fraction (5–13%) of MMR when Exo1/Rad27 pathways are deleted, with Exo1/Rad27 contributing the remainder via redund
- MLH1–Pms1 endonuclease can drive mispair excision independently of Exo1 and Rad27.
- MLH1–Pms1–mediated repair generates strand-specific single-stranded gaps on the nicked strand.
- Gap sizes are broadly distributed with a peak at 128 ± 17 nucleotides; most gaps are under 500 nucleotides.
- Gaps can be filled by DNA Polε or low levels of DNA Polδ, enabling Exo1- and Rad27-independent repair.
- Mn2+ activates MLH1–Pms1 endonuclease; Mg2+ alone does not support robust activity.

QC result: Pass.

Cail RC et al., Proc. Natl. Acad. Sci. U.S.A. 2025.122:e2521561122 - Recombinant human β-cardiac myosin M493I studied by optical trapping and stopped-flow kinetics disrupts the super-relaxed state and increases actin attachment and contractile force. Key terms: β-cardiac myosin, M493I, super-relaxed state, actin attachment, optical trap.

Study Highlights:
System: recombinant human β-cardiac heavy meromyosin (cHMM) expressed in C2C12 cells. Methods: ensemble actin gliding, stopped-flow kinetics, NADH ATPase, mantATP single-turnover, and single-molecule three-bead optical trap assays. Main results: M493I preserves Pi release and the two-step 4.7–5 nm working stroke but slows ADP release ~5-fold, doubles steady-state ATPase Vmax, reduces SRX occupancy (KSRX/DRX from ~0.33 to ~0.53), and prolongs actin attachment with increased high-force, long-duration interactions. Functional implication: the combined increase in DRX head availability and prolonged AM·ADP lifetimes produce higher sustained force and faster actin reattachment consistent with a mechanism for HCM hypercontractility and impaired relaxation.

Conclusion:
The M493I relay-helix mutation disrupts the SRX off state and, together with slowed ADP release and prolonged actin attachment, increases myosin head availability and force production, explaining its hypercontractile HCM phenotype.

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-23.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited transcript sections covering the M493I mutation in the relay helix, SRX/DRX equilibrium and head availability, ADP release kinetics and duty ratio, actin gliding and power stroke, isometric high-force attachments, single-molecule actin reattachment dynamics, and mavacamten/therapeutic implications.
- transcript topics: M493I mutation in relay helix and mechanistic role; SRX/DRX equilibrium and head availability; ADP release kinetics and duty ratio; Actin gliding velocity and power stroke; Isometric high-force attachments under hindering load; Single-molecule actin reattachment dynamics

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- M493I slows ADP release ~5-fold (ADP release ~12 s−1 vs ~69 s−1 for WT).
- Actin gliding velocity reduced ~70% (WT ~1.6 μm/s; M493I ~0.46 μm/s).
- SRX/DRX disruption: SRX/DRX equilibrium constant ~0.53 (M493I) vs ~0.33 (WT); DRX heads ~35% vs ~25%.
- Duty ratio increases from ~0.017 (WT) to ~0.20 (M493I).
- Power output under hindering load (0–10 pN) nearly twofold higher for M493I vs WT.
- Single-molecule actin reattachment fastest component ~1.62 s−1 (M493I) vs ~0.83 s−1 (WT).

QC result: Pass.

Englander SW et al., Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2520855122 - Hydrogen exchange (H-T and NMR H-H) on DNA and RNA reveals two distinct base-pair opening modes: single-base microsecond openings and multi-base millisecond soliton-like loops. Key terms: hydrogen exchange, DNA dynamics, base pair opening, soliton, H-T exchange.

Study Highlights:
Systems studied include long polynucleotides (DNA, duplex RNA, synthetic long duplexes) and short oligonucleotides; key methods are H-T (tritium) exchange, stopped-flow H-D, and NMR H-H (water relaxation) measurements. H-T exchange of long polymers reports opening-limited EX1 imino exchange with kop ~1/s, reclosing kcl ~20/s and Kop ~10^-2 consistent with multi-base open loops with ms lifetimes. NMR H-H on short oligos reports catalyzable EX2 behavior dominated by single base-pair openings with kcl ~10^6/s and Kop ~10^-6 and microsecond lifetimes. The selective detection implies short oligonucleotides cannot host extensive loops while multi-base soliton-like loops in polynucleotides could dynamically expose sequences for protein or nucleic acid recognition.

Conclusion:
Both H-T and NMR H-H exchange provide accurate but complementary views: long polynucleotides exhibit frequent multi-base, ms-lived open loops (Kop ~10^-2, kcl ~20/s) while short oligonucleotides reveal rare single-base, μs-lived openings (Kop ~10^-6, kcl ~10^6/s).

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-22.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited transcript portions describing hydrogen exchange theory, EX1/EX2, the two base-pair opening modes, the soliton traveling loop hypothesis, length dependence, and biological implications as presented in the article.
- transcript topics: Hydrogen exchange theory and Eigen proton-transfer foundations; H-T exchange in long polynucleotides (1000+ bp) and EX1 vs EX2 interpretation; H-H exchange by NMR in short oligonucleotides and its constraints; Two base-pair opening modes: single-base openings (EX1-dominated) and multi-base open loops (EX2-dominated); Soliton traveling loop hypothesis and migration along DNA; Length dependence reconciles datasets (native long DNA vs short oligonucleotides)

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 5
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- There are two base-pair opening modes: single-base openings detected by NMR on short oligonucleotides and multi-base open loops observed in long polynucleotides
- HT (tritium) exchange reports ms-lived open loops with Kop ~ 10^-2 and kcl ~ 20 s^-1 in long polynucleotides, with open-state population Kop ~ 10^-2 (~1%)
- HH-NMR exchange on short oligonucleotides reports μs-lived single-base openings with Kop ~ 10^-6 and very low open-state population
- A traveling soliton-like loop mechanism is proposed to explain how open states migrate along DNA and expose sequences
- Length of nucleic acid dictates which HX method observes which opening mode, reconciling historical discrepancies
- Cryo-EM is proposed as a future method to visualize soliton-like waves and validate the hypothesis

QC result: Pass.

Vatsa A et al., Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2526296123 - In HPV31-positive keratinocytes (CIN612), TOP1α and TOP3β are upregulated and required for viral transcription and replication, acting via distinct effects on R-loop accumulation and topoisomerase-mediated DNA breaks. Key terms: HPV31, TOP1α, TOP3β, R-loops, DNA breaks.

Study Highlights:
Using HPV31-positive CIN612 cells and primary HFK controls, the authors applied ChIP, RADAR, DRIP, alkaline COMET, RNA-seq, and shRNA knockdown to map topoisomerase binding and function. They found TOP1α and TOP3β, but not TOP3α, are elevated in HPV-positive cells and bind the viral URR, and that shRNA depletion of TOP1α or TOP3β reduced episomal viral DNA and early viral transcripts. Knockdown decreased DNA breaks (~50% reduction in COMET tail formation and reduced γH2AX) and altered R-loop levels differentially, with TOP1α depletion increasing viral R-loops by ~50% and TOP3β depletion causing >3-fold R-loop accumulation at viral and cellular loci. Transcriptome changes included reduced IL6/STAT3-AKT signaling after TOP1α loss and marked downregulation of EGR3 (>5-fold) after TOP3β loss, linking distinct mechanistic effects to impaired viral replication.

Conclusion:
TOP1α and TOP3β are differentially required for maintenance of HPV episomes and viral gene expression through distinct regulation of DNA breaks, R-loop dynamics, and specific host signaling pathways.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Differential roles of type I topoisomerases in regulating HPV pathogenesis

First author:
Vatsa A

Journal:
Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2526296123

DOI:
10.1073/pnas.2526296123

Reference:
Vatsa A, Templeton CW, Laimins L. Differential roles of type I topoisomerases in regulating HPV pathogenesis. Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2526296123. https://doi.org/10.1073/pnas.2526296123

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/top1alpha-top3beta-hpv-replication

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-21.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited sections covering HPV biology and torsional stress, TOP1α/TOP3β (and TOP3α) roles, URR binding and episomal maintenance, knockdown effects on viral DNA and transcription, R-loop dynamics (DRIP), DNA breaks (COMET, γH2AX, TOP1cc/TOP3cc), DDR involvement, and host signaling changes (IL-6/STAT3-AKT, EGR3).
- transcript topics: HPV-induced torsional stress and topoisomerase roles; TOP1α, TOP3β, and TOP3α expression in HPV-positive cells; Binding of TOP1α and TOP3β to the HPV URR and episomal maintenance; shRNA knockdown effects on HPV genome levels and viral transcription; R-loop dynamics and DRIP analyses; DNA damage and TOP1cc/TOP3cc formation; γH2AX and COMET results

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- TOP1α and TOP3β are elevated in HPV-positive cells and bound to the HPV genome URR, while TOP3α is not bound to URR and is not essential for replication/transcription.
- Knockdown of TOP1α or TOP3β reduces HPV episome DNA and early viral transcripts (E1, E2, E6, E7).
- TOP1α depletion increases viral R-loops; TOP3β depletion increases R-loops more dramatically (greater than 3-fold).
- TOP1α and TOP3β knockdown reduces DNA breaks (COMET tail moment ~50% reduction; γH2AX decreases).
- TOP1α and TOP3β depletion reduces TOP1cc/TOP3cc formation; R-loop recruitment factors (DHX9, POLR3H) are modulated accordingly.
- Expression of HPV oncoproteins E6 and E7 upregulates TOP1α and TOP3β.

QC result: Pass.

Yu C et al., Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2522417123 - Genetic mapping and comparative genomics show the lncRNA ANTSR multiallelic locus in Aculeata directs female development via heterozygosity despite lacking sequence homology. Key terms: ANTSR, Aculeata, lncRNA, complementary sex determination, heterozygosity.

Study Highlights:
The study analyzed 41 hymenopteran genomes and performed whole-genome resequencing and genetic mapping in Bombus terrestris and Vespa velutina nigrithorax to locate the sex-determining region. The ANTSR locus is a multiallelic noncoding interval between CRELD2 and THUMPD3 that is highly polymorphic and heterozygous in females but homozygous in diploid males across ants, bumblebees, and hornets. Comparative synteny shows the CRELD2–THUMPD3 block originated ~160–200 Mya and the locus has functioned as a zygosity-based female determinant for over 150 million years. Despite this deep functional conservation, alignments and phastCons analyses reveal no detectable sequence homology among distant aculeate lineages, and heterozygosity at ANTSR provides an actionable molecular sex marker for breeding and conservation.

Conclusion:
The ANTSR multiallelic noncoding locus is an ancient, positionally conserved zygosity-based sex determinant across Aculeata that has retained function for over 150 million years despite complete sequence divergence.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Deep evolutionary conservation of a sex-determining locus without sequence homology

First author:
Yu C

Journal:
Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2522417123

DOI:
10.1073/pnas.2522417123

Reference:
Yu C, Moog S, Pan Q, Keller Valsecchi CI, Dupont S, Darrouzet E, Darras H, Hodapp D, Colgan TJ, et al. Deep evolutionary conservation of a sex-determining locus without sequence homology. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2522417123. https://doi.org/10.1073/pnas.2522417123

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/antsr-aculeata-sex-locus

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-20.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Substantive audit of the transcript sections describing: (1) haplodiploid sex determination in Hymenoptera; (2) ANTSR locus and its position between CRELD2 and THUMPD3; (3) heterozygosity-dependent female development demonstrated in Bombus terrestris and Vespa velutina; (4) ANTSR as a long noncoding RNA; (5) absence of
- transcript topics: haplodiploid sex determination in Hymenoptera; ANTSR locus and CRELD2–THUMPD3 synteny; heterozygosity-based female determination at ANTSR; Bombus terrestris: lab crosses and diploid male production; Vespa velutina nigrithorax: field data and haplotype diversity; ANTSR as a long noncoding RNA

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 8
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- ANTSR locus is a multiallelic noncoding region that determines female development via heterozygosity.
- ANTSR locus is located between CRELD2 and THUMPD3; synteny preserved across Aculeata with origin ~160–200 Myr ago.
- In Bombus terrestris, crosses yield diploid males; females are heterozygous at the ANTSR locus and diploid males are homozygous at that region.
- In Vespa velutina nigrithorax, a 13.3 kb interval on chromosome 23 shows female–heterozygous/diploid male–homozygous patterns; four haplotypes observed in France.
- ANTSR encodes a long noncoding RNA; sequence conservation across Aculeata is not detectable.
- Honey bees lost the ANTSR system and use csd as the primary sex determiner.

QC result: Pass.

Sengstack J et al., Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2515183123 - TRDP with Perturb-seq in human fibroblasts found that manipulating TFs (EZH2, E2F3, STAT3, ZFX) reversed aging hallmarks, and EZH2 overexpression rejuvenated aged mouse livers. Key terms: EZH2, E2F3, Perturb-seq, liver rejuvenation, transcription factor.

Study Highlights:
The study used passaged human neonatal dermal fibroblasts and aged mouse liver as model systems and applied the Transcriptional Rejuvenation Discovery Platform (TRDP) with Perturb-seq and CRISPRa/CRISPRi screens. Overexpressing E2F3 or EZH2 and repressing STAT3 or ZFX reversed global gene expression toward earlier passage states and ameliorated cellular aging hallmarks including increased proliferation, proteasome activity, and mitochondrial function. In aged mice, AAV8-mediated liver-specific EZH2 overexpression (log2fc ≈ 2.9) reversed thousands of age-associated gene changes (R_rej = -0.42), reduced steatosis and fibrosis, and improved glucose tolerance. Downstream transcriptional programs converged across perturbations, suggesting shared molecular requirements for cellular and tissue rejuvenation.

Conclusion:
Single transcription factor perturbations identified by TRDP can reverse cellular aging hallmarks in human fibroblasts and, in the case of EZH2 overexpression, partially rejuvenate aged mouse liver with improved histology and glucose tolerance.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Systematic identification of single transcription factor perturbations that drive cellular and tissue rejuvenation

First author:
Sengstack J

Journal:
Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2515183123

DOI:
10.1073/pnas.2515183123

Reference:
Sengstack J, Li H, Aghayev T, Bier G, Mobaraki M, Zheng J, Lin J, Deng C, Villeda SA, et al. Systematic identification of single transcription factor perturbations that drive cellular and tissue rejuvenation. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2515183123. Published January 9, 2026. https://doi.org/10.1073/pnas.2515183123

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/ezh2-liver-rejuvenation

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-19.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited sections describing the TRDP platform, identification of four rejuvenating TF perturbations, in vitro cellular aging hallmarks, in vivo liver experiments with EZH2, safety considerations, and broader implications of aging as a programmable, reversible state.
- transcript topics: TRDP platform and Perturb-seq workflow; Top rejuvenating TF perturbations: E2F3, EZH2, STAT3, ZFX; In vitro reversal of aging hallmarks in late-passage fibroblasts; In vivo liver rejuvenation in aged mice via EZH2 overexpression; Cancer risk considerations and mesenchymal drift; Broader implications and potential organ-wide applications of TRDP

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- TRDP identifies single TF perturbations that promote rejuvenation without dedifferentiation
- Four TF perturbations (E2F3, EZH2, STAT3, ZFX) reverse aging hallmarks in late-passage human fibroblasts
- EZH2 overexpression in aged mouse liver reverses aging-associated gene expression and improves steatosis, fibrosis, and glucose tolerance within three weeks
- TF perturbations do not induce cancer-like transcriptome changes; no resemblance to oncogenic programs
- Aging may reflect an epigenetic/operating-system-like state that can be reset by targeted TF perturbations
- TRDP has potential for translation to other organs, per discussion in the article

QC result: Pass.

Perera J et al., Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2507065123 - Gamma-PNA triplet ligands with Janus bases selectively bind expanded rCUG repeats, displace MBNL1, and show length-dependent cooperativity with partial splicing rescue. Key terms: rCUG repeats, gamma PNA, Janus bases, MBNL1 displacement, myotonic dystrophy type 1.

Study Highlights:
The authors designed compact three-unit bifacial nucleic acid ligands (Janus bases on a γPNA backbone) and evaluated them against rCUG repeat duplexes and DM1 patient-derived myotubes using molecular dynamics, EMSA, SPR, AFM, and cellular splicing assays. MD and EMSA/SPR show cooperative, length-dependent binding with Kd values decreasing to ~0.56 µM for rCUG98 and Hill coefficients rising to ~5, driven by enhanced hydrogen-bonding and π–π stacking between adjacent ligands. AFM revealed a 0.348 nm increase in RNA helix contour height on binding, consistent with a pothole-filling insertion mechanism that selectively recognizes hairpin duplexes over single-stranded RNA. Functionally, a cell-permeable LG2c analog reduced nuclear foci and partially restored mis-splicing of Serca1, cTNT, and IR in DM1 myotubes, though cellular uptake remains limiting.

Conclusion:
Short bifacial γPNA triplet ligands selectively recognize pathogenic rCUG hairpins via a pothole-filling mechanism, displace MBNL1, and can partially restore splicing in DM1 myotubes while cellular delivery requires further optimization.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1

First author:
Perera J

Journal:
Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2507065123

DOI:
10.1073/pnas.2507065123

Reference:
Perera J. D. R., Thadke S. A., Thrikawala S. W., Wilson W. D., Tan K. W. R., Chand N. Z. W., Phan A. T., Ly D. H., et al. A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2507065123. https://doi.org/10.1073/pnas.2507065123

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/pothole-filling-rcug-gamma-pna

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-18.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript portions describing (a) design of bifacial Janus bases on a gammaPNA backbone, (b) pothole-filling mechanism and cooperative binding to rCUG repeats, (c) selectivity for long pathogenic repeats vs. short normal repeats, (d) displacement of MBNL1, (e) splicing rescue in DM1 patient-derived myotube
- transcript topics: Janus bases and gammaPNA backbone design; Pothole-filling mechanism and RNA hairpin targeting; Cooperativity and length-dependent binding to rCUG repeats; Pathogenic vs normal repeat selectivity (rCUG98 vs rCUG33); MBNL1 displacement by LG2b; LG2c: cell uptake and rescue of splicing in DM1 myotubes

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- DM1 is driven by expanded rCUG repeats that sequester MBNL1 and disrupt splicing
- Bifacial Janus base ligands on a gammaPNA backbone enable targeted RNA recognition via hydrogen-bonding on two faces
- LG2b binds longer pathogenic rCUG repeats with cooperativity (N ~ 5) and shows length-dependent binding (Kd decreases with longer repeats; e.g., rCUG98 ~0.56 µM)
- LG2b selectively binds pathogenic repeats (rCUG98) and ignores normal repeats (rCUG33)
- AFM evidence shows a 0.348 nm height increase upon LG2b binding, supporting a pothole-filling mechanism
- LG2b can displace MBNL1 from rCUG98 and can prevent binding in competitive formats

QC result: Pass.

Strobl et al., Nature Communications - Human epidermal Langerhans cells exposed to Ixodes ricinus tick saliva and Borrelia burgdorferi adopt a tolerogenic state with CXCR4/CCR7-driven emigration that impairs T cell priming. Key terms: Langerhans cells, tick saliva, Borrelia burgdorferi, CXCR4/CCR7 migration, immune tolerance.

Study Highlights:
The study uses clinical human tick bite biopsies, an ex vivo human skin tick bite model, in vitro monocyte- and CD34-derived Langerhans cells, immune spheroid cultures and single-cell RNA-sequencing of erythema migrans lesions, employing imaging, migration assays, co-cultures and scRNA-seq. Tick salivary gland extract (SGE) up-regulates CXCR4 and CCR7 on LCs, promotes emigration from the epidermis into dermis and lymphatic vessels, and reduces keratinocyte TGF-β consistent with migration. SGE and Borrelia burgdorferi drive up-regulation of tolerogenic transcription factors IDO1 and IRF4 while blunting immunogenic IRF1/NFκB programs, and SGE-primed LCs induce Treg and Th2 bias with reduced Tfh, Th17 and Th9 induction. Functionally, these changes dampen protective adaptive responses in lymphoid models and in patient lesions, which may reduce bacterial clearance and memory formation.

Conclusion:
Tick saliva reprograms human epidermal Langerhans cells to migrate to lymphatics and adopt a tolerogenic program that impairs protective T cell responses and may facilitate Borrelia transmission.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Human epidermal Langerhans cells induce tolerance and hamper T cell function upon tick-borne pathogen transmission

First author:
Strobl

Journal:
Nature Communications

DOI:
10.1038/s41467-025-66821-6

Reference:
Strobl, J., Kleissl, L., Eder, J., Conolly, S., Frey, T., Gail, L. M., Kopf, A., Weninger, S., Markowicz, M., Bartíková, P., Freystätter, C., Schmetterer, K., Strobl, H., Stockinger, H., Wijnveld, M. & Stary, G. Human epidermal Langerhans cells induce tolerance and hamper T cell function upon tick-borne pathogen transmission. Nature Communications. 2025. https://doi.org/10.1038/s41467-025-66821-6

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/langerhans-tick-saliva-tolerance

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-17.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the scientific content conveyed in the transcript, focusing on LC migration (CXCR4/CCR7), tolerogenic programming (IDO1/IRF4), and T cell polarization in skin infection and ex vivo models, plus vaccine implications.
- transcript topics: LC migration from epidermis to dermis/lymphatics via CXCR4/CCR7; Tolerogenic transcription factors IDO1 and IRF4 upregulation in LCs; Impact of Borrelia burgdorferi and Staphylococcus aureus on LC polarization; Ex vivo human skin tick bite model and single-cell RNA sequencing findings; Immune spheroid culture model and T cell polarization outcomes; Vaccine implications: targeting tick saliva to prevent transmission

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Tick saliva induces emigration of Langerhans cells from epidermis to dermis and lymphatics (CXCR4/CCR7 upregulation)
- SGE promotes LCs to adopt tolerogenic transcriptional program (IDO1 and IRF4)
- TL interactions shift T cell responses toward Tregs and Th2; dampen Th17/Th9 and Tfh
- Borrelia burgdorferi co-stimulation maintains tolerogenic LC polarization; SGE effects persist
- Lesional erythema migrans skin shows reduced LC density with migratory/tolerogenic signatures
- Ex vivo and scRNA-seq and spheroid models reveal mechanistic LC-T cell interactions that impair protective immunity

QC result: Pass.

Girelli et al., Nature Communications - MHz-XPCS of ferritin solutions at EuXFEL shows anomalous, cage-trapped protein diffusion with reduced long-time transport and ~1.2 nm rattling at high concentration. Key terms: ferritin, MHz-XPCS, anomalous diffusion, cage effects, hydrodynamic function.

Study Highlights:
The study probes crowded ferritin solutions using megahertz X-ray Photon Correlation Spectroscopy (MHz-XPCS) at EuXFEL combined with SAXS and δγ-theory modeling. Intensity autocorrelation functions g2(q,t) become non-exponential at high concentrations, and double-exponential analysis yields short- and long-time diffusion components with Dlong/Dshort ≈ 0.12 ± 0.04 at 730 mg/ml and an interaction time estimated near 4.25 µs. δγ-theory of hydrodynamically interacting spheres reproduces the q-dependent hydrodynamic function only when a scaling factor tied to direct protein interactions is included, indicating hydrodynamics set the q-dependence while direct forces reduce overall self-diffusion. Cage analysis finds an average rattling displacement δ ≈ 1.0 ± 0.3 nm for ≈89% of proteins, implying cage-trapping substantially slows molecular transport with consequences for ferritin-based drug delivery.

Conclusion:
MHz-XPCS measurements and δγ-theory modeling demonstrate that crowded ferritin solutions exhibit anomalous, cage-trapped diffusion with separate short- and long-time components and markedly reduced self-diffusion, indicating slower molecular transport under crowding.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Coherent X-rays reveal anomalous molecular diffusion and cage effects in crowded protein solutions

First author:
Girelli

Journal:
Nature Communications

DOI:
10.1038/s41467-025-66972-6

Reference:
Girelli, A., Bin, M., Filianina, M. et al. Coherent X-rays reveal anomalous molecular diffusion and cage effects in crowded protein solutions. Nat Commun (2025). https://doi.org/10.1038/s41467-025-66972-6

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/ferritin-anomalous-diffusion-xpcs

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-16.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the spoken content for the central findings and methods: crowded diffusion in ferritin solutions, MHz-XPCS techniques at EuXFEL, evidence for cage trapping, two diffusion regimes (Dshort and Dlong), interaction time, cage displacement, δγ-theory modeling with a scaling factor, and implications for diffusion in
- transcript topics: Crowding and diffusion in cellular-like environments; MHz-XPCS methodology at EuXFEL; Ferritin as a model system; Anomalous diffusion and cage effects; Short-time vs long-time diffusion; Two-component diffusion: Dshort and Dlong

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- Anomalous diffusion observed in crowded ferritin solutions
- Cage trapping as a mechanism for constrained diffusion under crowding
- Two diffusion components: short-time Dshort and long-time Dlong
- Interaction time τi for ferritin ~ 4.25 µs in crowded conditions
- Cage occupancy A0 ≈ 89% of proteins
- Cage displacement δ ≈ 1.0 ± 0.3 nm (with discussion suggesting δ ≈ 1.2 ± 0.6 nm)

QC result: Pass.