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PODCAST

Base by Base

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.

science life sciences

All Episodes

00:22:31

332: When Chromatin Filters Force: Age, AP-1, and...

Base by Base ·

2026/04/02

Liao Y et al., PNAS - Human dermal fibroblasts from young and old donors were embedded in 3D collagen and exposed to mechanical tension and TGF-β. Combining bulk RNA‑seq, ATAC‑seq, imaging, and perturbations, the study shows that matrix tension amplifies TGF‑β responses in young but not aged cells and identifies AP‑1 as a central chromatin-associated regulator required for fibroblast activation. Key terms: chromatin accessibility, mechanotransduction,

en-us

00:26:50

331: Bi-allelic NDUFA5 variants and complex I...

Base by Base ·

2026/03/31

Tan et al et al., The American Journal of Human Genetics - This report identifies bi-allelic NDUFA5 variants in four individuals from three families causing an isolated mitochondrial complex I deficiency with variable multisystem features. The study combines genomic, transcriptomic, proteomic, biochemical, structural modeling, and zebrafish functional data to support pathogenicity. Key terms: NDUFA5, complex I deficiency, mitochondriopathy, proteomics,

en-us

00:26:50

331: Bi-allelic NDUFA5 variants and complex I...

Base by Base ·

2026/03/31

Tan et al et al., The American Journal of Human Genetics - This report identifies bi-allelic NDUFA5 variants in four individuals from three families causing an isolated mitochondrial complex I deficiency with variable multisystem features. The study combines genomic, transcriptomic, proteomic, biochemical, structural modeling, and zebrafish functional data to support pathogenicity. Key terms: NDUFA5, complex I deficiency, mitochondriopathy, proteomics,

en-us

00:22:56

330: 5ULTRA: Mapping 5′ UTR variants that alter...

Base by Base ·

2026/03/30

Chaldebas M et al., The American Journal of Human Genetics - Chaldebas et al. present 5ULTRA, a computational pipeline that integrates uORF databases, Kozak-motif features, splicing prediction, and a random-forest score to detect and prioritize 5′ UTR variants predicted to alter protein translation. The score correlates with proteomic and MPRA measures and is applied to population, somatic, GWAS, and rare-disease datasets to nominate candidate functional

en-us

00:22:16

329: Large future genetic diversity losses predicted...

Base by Base ·

2026/03/30

Mualim KS et al., PNAS - This study develops spatiotemporal population-genetic models calibrated with genomic data to predict how habitat loss and fragmentation drive changes in nucleotide diversity (π). The authors translate IUCN, Living Planet Index, and GBF indicators into estimates of current and future genetic diversity loss across thousands of species. Key terms: genetic diversity, habitat loss, fragmentation, WFmoments, conservation indicators.

en-us

00:23:39

328: Variant selection boosts R2 for haptoglobin (HP)...

Base by Base ·

2026/03/27

Zhou A et al., Human Genetics and Genomics Advances - Comparing LD‑pruning, COJO, SuSiE and PCA in haptoglobin (HP) cis‑region data, the study finds including non‑lead variants substantially increases variance explained (R2) and MR precision. Key terms: haptoglobin, cis-Mendelian randomization, LD-pruning, SuSiE, COJO. Study Highlights:The study analyzed circulating haptoglobin (HP) using Fenland protein GWAS summary statistics with LD from UK Biobank,

en-us

00:23:39

328: Variant selection boosts R2 for haptoglobin (HP)...

Base by Base ·

2026/03/27

Zhou A et al., Human Genetics and Genomics Advances - Comparing LD‑pruning, COJO, SuSiE and PCA in haptoglobin (HP) cis‑region data, the study finds including non‑lead variants substantially increases variance explained (R2) and MR precision. Study Highlights:The study analyzed circulating haptoglobin (HP) using Fenland protein GWAS summary statistics with LD from UK Biobank, compared four variant selection methods (modified LD‑pruning, COJO, SuSiE,

en-us

00:19:17

327: Bi-allelic ATG12 variants impair ATG12-ATG5...

Base by Base ·

2026/03/27

Lambton J et al., The American Journal of Human Genetics - Bi-allelic ATG12 variants disrupt ATG12‑ATG5 conjugation and LC3 lipidation, impairing autophagy in patient cells and model systems and causing cerebellar vermis hypoplasia. Study Highlights:The study characterized six affected individuals with bi-allelic ATG12 variants using patient fibroblasts, HeLa ATG12 knockout complementation, yeast complementation, and CRISPR zebrafish models. Methods

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00:24:34

326: DUO-1 protects REC-8 cohesin and synaptonemal...

Base by Base ·

2026/03/25

Strand LG et al., PNAS - In C. elegans germline, the deubiquitinase DUO-1 is required for assembly and active maintenance of the synaptonemal complex and REC-8 cohesin, preventing RAD-51 accumulation and ensuring diakinesis compaction. Study Highlights:Using C. elegans germline as a developmental timecourse model, the authors combined cytological analyses (immunofluorescence, FISH, RAD-51/MSH-5/COSA-1 staining), temporally controlled auxin-inducible

en-us

00:24:34

326: DUO-1 protects REC-8 cohesin and synaptonemal...

Base by Base ·

2026/03/25

Strand LG et al., PNAS - In C. elegans germline, the deubiquitinase DUO-1 is required for assembly and active maintenance of the synaptonemal complex and REC-8 cohesin, preventing RAD-51 accumulation and ensuring diakinesis compaction. Study Highlights:Using C. elegans germline as a developmental timecourse model, the authors combined cytological analyses (immunofluorescence, FISH, RAD-51/MSH-5/COSA-1 staining), temporally controlled auxin-inducible

en-us

00:23:57

325: cis-pcQTL mapping reveals allelic proxitropy...

Base by Base ·

2026/03/24

Lawrence et al., Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants. The American Journal of Human Genetics 113 - Using a cis-principal-component (pcQTL) approach in human GTEx tissues, the authors uncover novel multi-gene regulatory variants and 33% more GWAS colocalizations than single-gene eQTLs. Study Highlights:The study analyzes 13 human GTEx tissues and identifies clusters of co-expressed

en-us

00:23:57

325: cis-pcQTL mapping reveals allelic proxitropy...

Base by Base ·

2026/03/24

Lawrence et al., Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants. The American Journal of Human Genetics 113 - Using a cis-principal-component (pcQTL) approach in human GTEx tissues, the authors uncover novel multi-gene regulatory variants and 33% more GWAS colocalizations than single-gene eQTLs. Study Highlights:The study analyzes 13 human GTEx tissues and identifies clusters of co-expressed

en-us

00:20:16

324: ZSWIM8–CUL3 clamp on AGO2–miR-7 reveals...

Base by Base ·

2026/03/23

Farnung J et al., The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation. Nature ( - Cryo-EM and biochemical reconstitution reveal how the ZSWIM8–CUL3 E3 ligase recognizes human AGO2–miRNA–trigger complexes to polyubiquitylate AGO and drive targeted microRNA degradation. Study Highlights:Using purified human proteins and cellular assays, the authors combined cryo-EM (3.1 Å), in vitro ubiquitylation, co-immunoprecipitation and sRNA-seq

en-us

00:20:16

323: Meat consumption and APOE ε3/ε4–ε4/ε4: slower...

Base by Base ·

2026/03/22

Norgren J et al., JAMA Network Open - Population-based SNAC-K study finds higher meat consumption associated with slower cognitive decline and lower dementia risk in APOE ε3/ε4 and ε4/ε4 older adults. Study Highlights:Using the Swedish National Study on Aging and Care–Kungsholmen (SNAC-K) cohort of older adults and repeated validated food-frequency questionnaires, the authors applied panel data analyses with linear regression for cognitive trajectories

en-us

00:20:16

323: Meat consumption and APOE ε3/ε4–ε4/ε4: slower...

Base by Base ·

2026/03/22

Norgren J et al., JAMA Network Open - Population-based SNAC-K study finds higher meat consumption associated with slower cognitive decline and lower dementia risk in APOE ε3/ε4 and ε4/ε4 older adults. Study Highlights:Using the Swedish National Study on Aging and Care–Kungsholmen (SNAC-K) cohort of older adults and repeated validated food-frequency questionnaires, the authors applied panel data analyses with linear regression for cognitive trajectories

en-us

00:22:50

322: Bi-allelic RNU6ATAC and RNU4ATAC variants cause...

Base by Base ·

2026/03/22

Johnson MB et al., The American Journal of Human Genetics - Bi-allelic variants in snRNAs RNU6ATAC and RNU4ATAC cause infancy-onset autoimmune diabetes in humans, with RNA-seq showing U12 intron retention and impaired B cell development. Study Highlights:In human infants with early-onset diabetes and immune dysregulation, the authors used genome sequencing, RNA-seq, DNA methylation deconvolution, WGCNA, Sanger sequencing, and flow cytometry to define a

en-us

00:29:52

321: Canonical nucleobases in asteroid (162173) Ryugu...

Base by Base ·

2026/03/20

Koga T et al., et al. A complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu. Nature Astronomy ( - Ryugu asteroid samples analyzed by HPLC/ESI-HRMS reveal all five canonical nucleobases (adenine, guanine, cytosine, thymine, uracil) and distribution linked to ammonia. Study Highlights:The team analysed Ryugu aggregate samples A0480 and C0370 and the Orgueil meteorite using water and HCl extraction followed by HPLC/ESI-HRMS,

en-us

00:23:15

320: Sex-stratified cQTL mapping identifies TOX...

Base by Base ·

2026/03/19

Amour C et al., Human Genetics and Genomics Advances, Journal Pre-proof - Sex-stratified cQTL mapping in Tanzanian and Dutch adults identifies sex-specific regulators such as TOX-linked IFN-γ in males and EGFR-linked IL-10 in females, revealing multiple genome-wide cQTLs. Study Highlights:The study analyzed cytokine production after ex vivo stimulation in two human cohorts (Tanzania 300TZFG and Dutch 500FG) using sex-stratified cytokine QTL mapping with

en-us

00:23:15

320: Sex-stratified cQTL mapping identifies TOX...

Base by Base ·

2026/03/19

Amour C et al., Human Genetics and Genomics Advances, Journal Pre-proof - Sex-stratified cQTL mapping in Tanzanian and Dutch adults identifies sex-specific regulators such as TOX-linked IFN-γ in males and EGFR-linked IL-10 in females, revealing multiple genome-wide cQTLs. Study Highlights:The study analyzed cytokine production after ex vivo stimulation in two human cohorts (Tanzania 300TZFG and Dutch 500FG) using sex-stratified cytokine QTL mapping with

en-us

00:23:35

319: Predicting reduced-penetrance TP53 variants from...

Base by Base ·

2026/03/18

Fortuno C et al., Human Genetics and Genomics Advances - TP53 germline variant analysis using functional assays finds reduced-penetrance variants have intermediate activity, higher frequency, later onset, and 106 predicted candidates. Study Highlights:Using ClinVar curation and comparison to benign and pathogenic reference sets, the authors analyzed TP53 germline variants with multiple functional assays, bioinformatic predictors, immune-fitness scores,

en-us

525 results

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