Base by Base

Gustavo Barra
  • 3.0 (2)
  • Life Sciences
  • Updated Daily

Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

  1. 8h ago

    413: Rpc34 WH2 dynamics in RNA polymerase III

    Wu J-S et al., PNAS - A PNAS study using smFRET and nano-positioning triangulation maps dynamic positioning of the Rpc34 WH2 domain in yeast Pol III elongation complexes and presents a thiol-capping SPAAC labeling strategy to enable selective site-specific fluorophore attachment. Key terms: RNA polymerase III, Rpc34, winged helix, smFRET, bio-orthogonal labeling. Study Highlights: Using smFRET with ALEX and nano-positioning triangulation, the authors show Rpc34 WH2 occupies three discrete positions across the Pol III DNA-binding cleft and dynamically interconverts among them. A bio-orthogonal labeling workflow—azido-UAA incorporation plus SPAAC with thiol-capping—enabled selective labeling in the cysteine-rich complex. Maf1 binding locks WH2 into the upstream/distal state, validating positional assignments, and HMM dwell-time analysis revealed ordered transitions that proceed through the middle state with characteristic lifetimes. These results indicate Rpc34 WH2 engages the elongation complex via transient, weak DNA and protein contacts, with potential roles in bubble stabilization and rapid reinitiation. Conclusion: Rpc34 WH2 is a mobile, multifunctional cleft-associated module that occupies three ordered positions to transiently engage the Pol III elongation complex, and the thiol-capping SPAAC labeling approach provides a robust route for smFRET studies of large native assemblies. Music: Enjoy the music based on this article at the end of the episode. Article title: Dynamic positioning of Rpc34 winged helix in RNA polymerase III elongation complex for its stability with implications for reinitiation First author: Wu J-S Journal: PNAS DOI: 10.1073/pnas.2601775123 Reference: Wu J-S, Chang W-H, et al. Dynamic positioning of Rpc34 winged helix in RNA polymerase III elongation complex for its stability with implications for reinitiation. Proc Natl Acad Sci U S A. 2026;123(27):e2601775123. doi:10.1073/pnas.2601775123 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at 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/base-by-base-413-rpc34-wh2-pol3-dynamics QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-07-12. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the transcript portions describing Rpc34 WH2 dynamics, labeling strategy, three-state model, Maf1 effects, NPS localization, and rapid reinitiation implications, comparing to the original article. - transcript topics: Rpc34 WH2 dynamics in Pol III elongation complex; smFRET labeling strategy (azido-UAA, SPAAC, MMTS); Maf1 regulation of WH2 mobility; Nano-positioning system (NPS) localization; Three-state model: distal, middle, proximal; Implications for rapid reinitiation and Pol III processivity QC Summary: - factual score: 9/10 - 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 ...

    15 min

  2. 8h ago

    412: Fault Lines in Forensic Proficiency Testing

    Scurich N et al., PNAS - A concise breakdown of a PNAS perspective that analyzes forensic proficiency testing practices using the 2023 CTS firearms test as a case study. The authors identify test design and administration flaws—easy items, consensus scoring, handling of inconclusives, nonblind verification, shot‑to‑shot variability, and contextual bias—that undermine claims about examiner accuracy and the utility of reported error rates for courts and laboratories. Key terms: forensic proficiency testing, firearm identification, false positive rate, test design, cognitive bias. Study Highlights: The authors analyze CTS Test 23‑5262 and report a false‑positive rate of about 20% for bullet comparisons, highlighting broader concerns. They identify structural issues in proficiency testing including ceiling effects from easy items, inconsistent scoring of inconclusives, reliance on consensus rather than ground truth, and nonblind verification. The paper argues these features confound examiner performance with test properties, limiting the tests’ ability to estimate operational error rates and inform court decisions. The authors recommend better test design, blind verification, confidence ratings, and use of objective metrics to improve validation and lab practice. Conclusion: Current forensic proficiency testing practices can conceal fundamental weaknesses in examiner performance and test design; systemic, evidence‑based reform is needed to provide courts and laboratories with meaningful estimates of reliability and to reduce risks of wrongful outcomes. Music: Enjoy the music based on this article at the end of the episode. Article title: Assessing the foundations of forensic identification evidence: A critical examination of proficiency test design and results First author: Scurich N Journal: PNAS DOI: 10.1073/pnas.2528192123 Reference: Scurich N, Albright TD. Assessing the foundations of forensic identification evidence: A critical examination of proficiency test design and results. PNAS. 2026; Vol.123:e2528192123. doi:10.1073/pnas.2528192123 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at 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/fault-lines-forensic-proficiency-testing QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-07-12. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the transcript sections describing CTS proficiency testing (Test 23-5262), the reported false-positive rates, consensus scoring and inconclusives, out-of-class eliminations, shot-to-shot variability and reproducibility, contextual bias and NIBIN leads, nonblind verification, signal detection theory as reform, a - transcript topics: CTS proficiency testing overview and purpose; CTS Test 23-5262 design and ground truth; False-positive rate findings (around 20%; 19.2% excluding item 4; 22% at least one false positive); Consensus scoring and handling of inconclusives; Out-of-class eliminations (Item 4) and associated errors; Class characteristics and reproducibility concerns across tes...

    28 min

  3. 3d ago

    411: EKV cells and the Human Prion Assay: a scalable platform for sCJD infectivity

    Nihata A et al., PNAS - This PNAS study describes the development of EKV, a humanized dividing cell line that propagates bona fide sporadic CJD (sCJD) prions, and the Human Prion Assay (HPA), a cell-based method that quantifies infectivity with sensitivity comparable to transgenic mouse bioassay while enabling rapid therapeutic screening. Key terms: sCJD, EKV cells, Human Prion Assay, prion infectivity, anti-PrP antibody. Study Highlights: The authors engineered EKV cells by reconstituting CAD5 PrP-knockdown cells with human PrP (V129) and iterative single-cell cloning to enrich prion susceptibility. EKV cells propagate de novo infectious sCJD prions that reproduce strain-specific pathology when transmitted to humanized Tg152c mice. The Human Prion Assay (HPA) using EKV cells quantifies sCJD infectivity across a wide dynamic range with sensitivity comparable to mouse bioassay but in weeks rather than years. Persistently infected iEKV clones can be cured by the anti-PrP monoclonal antibody ICSM18, validating the platform for high-throughput therapeutic screens. Conclusion: EKV cells and the HPA provide a renewable, scalable, and faster alternative to animal bioassays for measuring authentic human sCJD infectivity and for screening and validating anti-prion therapeutics, while retaining strain-specific biological properties. Music: Enjoy the music based on this article at the end of the episode. Article title: A scalable, dividing cell model for the robust propagation and quantification of human sporadic Creutzfeldt–Jakob disease prions First author: Nihata A Journal: PNAS DOI: 10.1073/pnas.2600341123 Reference: Nihata A, Collinge J, Linehan J, Brandner S, Mead S, Schmidt C, Rayner MLD, Jat PS, Arora P, et al. A scalable, dividing cell model for the robust propagation and quantification of human sporadic Creutzfeldt–Jakob disease prions. PNAS. 2026;123(27):e2600341123. doi:10.1073/pnas.2600341123. 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at 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/ekv-human-prion-assay QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-07-09. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Substantive audit focused on EKV cell development and validation, in vitro propagation of human sCJD prions, HPA implementation and benchmarking against mouse bioassay, drug-screening demonstration, and documented limitations (codon 129 mismatch, occult infectivity). - transcript topics: Prion biology and strain concepts (PRNP codon 129 polymorphism); Historical barriers to human prion culture and need for cell-based infectivity assays; Engineering EKV cells: CAD5-KDB3, human PrP V129, mouse signal peptide; Iterative single-cell cloning and enrichment to EKV; Infectivity validation via transmission to Tg152c mice; Development and validation of the Human Prion Assay (HPA) QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 6 - claims flagged for review: 0 - metadata checks passed: 4 -...

    27 min

  4. 4d ago

    410: Nucleotide diversity is a poor predictor of short-term adaptive potential

    Abson KL et al., PNAS - A cross-species synthesis and theory paper showing that simple molecular diversity metrics poorly predict short-term adaptive potential. The authors compiled >2,100 quantitative genetics estimates (evolvability and heritability) across ~193 eukaryotic species and compared them to nucleotide diversity (π) and microsatellite heterozygosity (He). They find nucleotide diversity explains only ~1.1% of interspecific variation in evolvability and that doubling π corresponds to a modest ~11.7% increase in evolvability. Theoretical models indicate this weak relationship is expected when trait variance is shaped by stabilizing selection, mutation rates, and effective population size dynamics. Key terms: nucleotide diversity, evolvability, adaptive potential, conservation genetics, microsatellites. Study Highlights: The authors compiled 2,113 evolvability estimates across 193 eukaryotic species and matched these to measures of nucleotide diversity (π) and microsatellite heterozygosity (He). They found no meaningful association between ln(IA) (evolvability) and ln(π): π explained ~1.1% of interspecific variation and doubling π predicts only an ~11.7% increase in evolvability. Microsatellite and nucleotide diversity were uncorrelated across species, and both molecular measures were weak predictors of quantitative genetic variation. Theoretical mutation–selection–drift models show weak associations are expected under stabilizing selection and when VA depends more on mutation rate and selection than on neutral diversity. Conclusion: Simple, genome-wide molecular diversity metrics (π, He) are poor predictors of short-term adaptive potential (evolvability); conservation assessments should not rely on these alone and should incorporate trait-based or functionally informed genomic data. Music: Enjoy the music based on this article at the end of the episode. Article title: Nucleotide diversity is a poor predictor of short-term adaptive potential First author: Abson KL Journal: PNAS DOI: 10.1073/pnas.2536181123 Reference: Abson KL, Zijmers L, Mittell EA, Young EA, Postma E, Eyre-Walker A, Hadfield JD. Nucleotide diversity is a poor predictor of short-term adaptive potential. Proc Natl Acad Sci U S A. 2026;123(27):e2536181123. doi:10.1073/pnas.2536181123 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at 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/nucleotide-diversity-poor-predictor-adaptive-potential QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-07-08. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the transcript's coverage of core scientific claims: relationship between π and IA, the π vs He relationship, functional variation (πN/πS), the theoretical basis (stabilizing selection), and conservation implications/policy directions. - transcript topics: Adaptive potential and evolvability (IA) concept; Nucleotide diversity (π) as predictor of evolvability; Microsatellite diversity (He) and its relation to π and IA; Theoretical mutation–selection...

    22 min

  5. 5d ago

    409: A systems-level atlas of carbon-response transcriptional states in Escherichia coli

    Shin J et al., PNAS - This episode examines a large transcriptome compendium (PRECISE-NP881) that profiles E. coli K-12 MG1655 across 43 carbon substrates. Independent component analysis resolved 137 iModulons, including 25 carbon-catabolism modules that organize substrates into four activity-defined groups tied to growth rate, substrate chemistry, metabolic entry routes, and proteome allocation. The study integrates growth phenotyping, FBA/ME-modeling, targeted knockouts, and reanalysis of a starvation/refeeding time course to connect transcriptional modules to physiological context. Key terms: carbon response, iModulon, Escherichia coli, carbon catabolite repression, transcriptional regulatory network. Study Highlights: The authors assembled PRECISE-NP881 (881 transcriptomes) and used ICA to define 137 iModulons, 25 of which are carbon-catabolism modules whose activities cluster substrates into four groups. Faster-growing sugars showed limited CRP-linked remodeling while slower-growth, non-glycolytic substrates activated CRP-linked, NtrC-1, Propionate, and SgcABCEQX iModulons. Targeted knockouts (e.g., ΔprpC) demonstrated conditional growth defects on Group C/D substrates supporting a role for methylcitrate-mediated propionyl-CoA processing. Proteome-allocation modeling and projection of an independent starvation/refeeding dataset corroborated links between carbon-response modules, growth/stress physiology, and metabolite dynamics. Conclusion: The paper provides a quantitative atlas of carbon-responsive transcriptional states in E. coli, decomposing CCR into separable CRP-linked and substrate-specific modules and linking these modules to growth rate, metabolic context, proteome allocation, and conditional physiological relevance. Music: Enjoy the music based on this article at the end of the episode. Article title: A systems-level atlas of carbon-response transcriptional states in Escherichia coli First author: Shin J Journal: PNAS DOI: 10.1073/pnas.2531884123 Reference: Shin J, Son HF, Krishnan J, Hefner Y, Szubin R, Sung J, Patel A, Lou XA, Catoiu EA, Palsson BØ, Zielinski DC. A systems-level atlas of carbon-response transcriptional states in Escherichia coli. PNAS. 2026;123(27):e2531884123. doi:10.1073/pnas.2531884123. 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at 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/atlas-carbon-response-transcriptional-states-e-coli QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-07-07. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the transcript sections describing PRECISE-NP881 atlas construction ( ICA/iModulons ), four substrate groups (A–D), CRP decomposition into Crp-1/Crp-2/Crp-3, NtrC-1 and Propionate iModulons linked to propionyl-CoA stress, methylcitrate pathway (prpC/astC), SgcABCEQX prophage iModulon, starvation/refeeding dynam - transcript topics: ICA-based iModulon analysis; CRP-linked iModulons decomposition (Crp-1, Crp-2, Crp-3); Four substrate groups (A–D) and growth phenotypes; NtrC-1 and Propiona...

    27 min

  6. 6d ago

    408: Tau, mitochondria, and the fusion switch

    Tsakiria E et al., Proceedings of the National Academy of Sciences (PNAS) - Using Tau knockout mice and the C. elegans PTL-1 deletion, this study shows that loss of wild-type Tau promotes a conserved shift toward mitochondrial fusion, increases respiratory activity, membrane potential and mitophagy, raises ROS, and enhances stress resilience. The adaptive phenotypes depend on mitofusin/FZO-1 and are phenocopied by FZO-1 overexpression. Key terms: Tau protein, mitochondrial fusion, mitofusin (FZO-1), mitophagy, neurodegeneration. Study Highlights: Across mouse and nematode models, Tau/PTL-1 deficiency increased basal and ATP-linked respiration, mitochondrial membrane potential, and ROS while enhancing mitophagy. Loss of Tau shifted mitochondrial morphology toward a pro-fusion state with increased mitofusin (Mfn1/2/FZO-1) localization and reduced Drp1 recruitment. Genetic removal of the mitofusin FZO-1 abolished the enhanced bioenergetics, motility, longevity under stress, and stress resistance, whereas FZO-1 overexpression phenocopied key Tau-loss features. These results identify a conserved, mitofusin-dependent mechanism by which wild-type Tau restrains mitochondrial fusion and functional adaptation. Conclusion: Wild-type Tau acts as a conserved negative regulator of mitochondrial fusion and functional adaptation; its loss triggers FZO-1/mitofusin-dependent mitochondrial remodeling that elevates bioenergetics and stress resilience in a context-dependent manner. Music: Enjoy the music based on this article at the end of the episode. Article title: Tau protein as a regulator of mitochondrial function and dynamics First author: Tsakiria E Journal: Proceedings of the National Academy of Sciences (PNAS) DOI: 10.1073/pnas.2521642123 Reference: Tsakiria E., Campos-Marques C., Ferreira I.L., Trougakos I.P., Dioli C., Gianniou D.D., Silva J.M., Skourti K., Roussos A., Samiotaki M., Sotiropoulos I., Palikaras K., et al. Tau protein as a regulator of mitochondrial function and dynamics. Proc Natl Acad Sci U S A. 2026; doi:10.1073/pnas.2521642123. 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at 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/tau-mitochondrial-fusion-episode-408 QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-07-06. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Substantively audited sections covering: WT Tau localization and baseline role; Tau/PTL-1 deficiency effects on respiration and mitophagy; pro-fusion shift and changes in fission/fusion proteins; ROS dynamics and hormetic effects; dependency on FZO-1 and rescue via FZO-1 overexpression; implications for Tau-lowering th - transcript topics: Tau deficiency and mitochondrial respiration (Seahorse data in Tau-KO mice and PTL-1 KO worms); Mitochondrial morphology and fusion/fission regulators (DRP-1, MFN1/MFN2, form factor); Mitophagy dynamics in Tau/PTL-1 deficiency; ROS production and membrane potential changes; ROS-mediated hormesis and antioxidant effects (NAC) across conditions; Genetic dissection...

    25 min

  7. Jul 5

    407: SLC11A2 withholds metals from Salmonella in the gut epithelium

    Norberg ES et al., Proceedings of the National Academy of Sciences - Using metal‑responsive fluorescent Salmonella reporters, calf intestinal loops, and CRISPR edited epithelial cells, this study shows that the divalent metal transporter SLC11A2 is recruited to Salmonella‑containing vacuoles and restricts Fe2+ and Mn2+, limiting intracellular bacterial replication. Key terms: SLC11A2, nutritional immunity, Salmonella enterica, iron and manganese, intestinal epithelium. Study Highlights: The authors used metal‑sensing GFP reporters in Salmonella and a calf ligated ileal loop model to map metal availability and found a subpopulation of bacteria in IECs and lamina propria cells exposed to ≤0.1 µM Fe2+ and Zn2+, and possibly Mn2+, early in infection. SLC11A2 localized to the apical surface and endosomal network of IECs and was recruited to maturing Salmonella‑containing vacuoles; CRISPR knockout of SLC11A2 in HCT116 epithelial cells increased bacterial replication. Fluorescent reporters and ICP‑MS indicate vacuolar STm are less starved for Fe2+ and Mn2+ in the absence of SLC11A2, while Zn2+ and Mg2+ sensing was unchanged. Salmonella counters SLC11A2‑mediated restriction through the Mn2+/Fe2+ transporter MntH and siderophore production. Conclusion: SLC11A2 mediates epithelial nutritional immunity by sequestering Fe2+ and Mn2+ in Salmonella‑containing vacuoles, reducing vacuolar metal availability and limiting intracellular Salmonella replication. Music: Enjoy the music based on this article at the end of the episode. Article title: SLC11A2 withholds divalent metals from Salmonella in the gut epithelium First author: Norberg ES Journal: Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.2532675123 Reference: Norberg ES, Knodler LA, et al. SLC11A2 withholds divalent metals from Salmonella in the gut epithelium. PNAS. 2026;123:e2532675123. doi:10.1073/pnas.2532675123 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 is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at 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/slc11a2-withholds-divalent-metals-from-salmonella QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-07-05. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited transcript sections covering nutritional immunity concepts, IEC-localized SLC11A2 function, calf ileal loop in vivo model, metal-responsive STm reporters, SLC11A2 recruitment to SCVs, SLC11A2 knockout effects in HCT116 cells, bacterial countermeasures (MntH and siderophores), intracellular niches (SCV vs cytoso - transcript topics: Nutritional immunity and trace metal tug-of-war; SLC11A2 (NRAMP2) in intestinal epithelial cells; Calf ligated ileal loop model and metal availability; Metal-responsive Salmonella reporters (iroN, sitA, zinT); SLC11A2 recruitment to Salmonella-containing vacuoles; SLC11A2 knockout in HCT116 cells and impact on Salmonella replication QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 6 - claims flagged for review: 0 - metadata chec...

    22 min

  8. Jul 1

    406: Temperature & Age Shape Gut Susceptibility to HCoV-229E

    Synowiec A et al., Proceedings of the National Academy of Sciences (PNAS) - This episode examines a PNAS study using fetal, pediatric, and adult human intestinal enteroids to show that physiological temperature and developmental stage jointly determine susceptibility to HCoV-229E, with implications for extrapulmonary coronavirus infection and therapeutic testing. Key terms: HCoV-229E, intestinal enteroids, temperature sensitivity, age-dependent susceptibility, ANPEP/TMPRSS2. Study Highlights: The authors used age-stratified human intestinal enteroids (HIEs) and compared infection at 32 °C and 37 °C, finding temperature-dependent transcriptional reprogramming. HCoV-229E productively infected HIEs from all ages at 32 °C, but at 37 °C replication was largely restricted to fetal and some pediatric tissues. Enterocytes were identified as the primary target cells and viral progeny were released apically. Inhibition of serine proteases with camostat significantly reduced HCoV-229E replication, supporting a TMPRSS2-like entry dependency. Conclusion: Physiological temperature and developmental maturity create a dual barrier that limits intestinal replication of HCoV-229E in adults at 37 °C while permitting broader replication at cooler, upper-airway-like temperatures; HIEs provide a platform to probe host determinants and test entry-directed inhibitors such as camostat. Music: Enjoy the music based on this article at the end of the episode. Article title: Temperature and developmental stage govern intestinal susceptibility to human coronavirus 229E First author: Synowiec A Journal: Proceedings of the National Academy of Sciences (PNAS) DOI: 10.1073/pnas.2600632123 Reference: Synowiec A., Lie L.K., Szczepański A., et al. Temperature and developmental stage govern intestinal susceptibility to human coronavirus 229E. Proc. Natl. Acad. Sci. U.S.A. 2026;123(26):e2600632123. https://doi.org/10.1073/pnas.2600632123 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/temp-age-hcov-229e-ep406 QC: This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-07-01. QC Scope: - article metadata and core scientific claims from the narration - excludes analogies, intro/outro, and music - transcript coverage: Audited the portions of the transcript describing: experimental design (age-stratified HIEs at 32°C vs 37°C), replication patterns of HCoV-229E (32°C broad permissivity; 37°C restricted), cell tropism (enterocytes as primary target), entry mechanism (ANPEP receptor, TMPRSS2 proteases), and protease inhibition (camostat - transcript topics: HCoV-229E infection in age-stratified human intestinal enteroids (HIEs); Temperature effects (32 °C vs 37 °C) on replication; Age dependence and donor variability; Cell type tropism and ANPEP/TMPRSS2 entry; Camostat inhibition and entry pathways; Limitations of the HIE model and translational implications QC Summary: - factual score: 10/10 - metadata score: 10/10 - supported core claims: 4 - 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: - Three age groups of HIEs used: fetal, pediatric, adult - Seasonal HCoV...

    20 min
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Ratings & Reviews

3
out of 5
2 Ratings

About

Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

Information

  • Creator
    Gustavo Barra
  • Years Active
    2025 - 2026
  • Episodes
    415
  • Rating
    Clean
  • Copyright
    © Gustavo Barra
  • Show Website
    Base by Base

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