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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

00:20:26

253: Nap1 and histone acetylation tune chromatin...

Base by Base ·

2026/01/08

Gao J et al., Nat Commun - H4 tail lysine residues drive liquid-liquid phase separation of 12‑mer nucleosome arrays, while H3 tail acetylation and the histone chaperone Nap1 increase internal dynamics and lower droplet viscosity. Key terms: Nap1, H3 acetylation, H4 acetylation, liquid-liquid phase separation, nucleosome arrays. Study Highlights:H4 tail lysine residues are the primary drivers of nucleosome array phase separation, and H4-tail acetylation

en-us

00:18:13

252: Keratinocytes to cSCC: genetic steps

Base by Base ·

2026/01/07

️ Episode 252: Keratinocytes to cSCC: genetic steps In this episode of PaperCast Base by Base, we explore Single-cell and spatial multi-omic profiling maps the genetic and transcriptional changes from normal keratinocytes through actinic keratoses to invasive cutaneous squamous cell carcinoma Study Highlights:Single-cell genotyping of 137 keratinocytes revealed most cells have low mutation burdens (median 1.14 mut/Mb) while keratinocytes with TP53 or

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00:18:13

252: Keratinocytes to cSCC: genetic steps

Base by Base ·

2026/01/07

️ Episode 252: Keratinocytes to cSCC: genetic steps In this episode of PaperCast Base by Base, we explore Single-cell and spatial multi-omic profiling maps the genetic and transcriptional changes from normal keratinocytes through actinic keratoses to invasive cutaneous squamous cell carcinoma Study Highlights:Single-cell genotyping of 137 keratinocytes revealed most cells have low mutation burdens (median 1.14 mut/Mb) while keratinocytes with TP53 or

en-us

00:19:00

251: MuSCs, laminin-α2 and LAMA2 MD

Base by Base ·

2026/01/06

️ Episode 251: MuSCs, laminin-α2 and LAMA2 MD In this episode of PaperCast Base by Base, we explore Activated muscle stem cells express and secrete laminin-α2 to remodel their niche, and loss of MuSC-derived laminin-α2 slows MuSC proliferation and delays regeneration in mouse models and human iPSC-derived precursors Study Highlights:Activated MuSCs upregulate Lama2 and deposit laminin-α2 around proliferating cells during early regeneration. MuSCs from

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00:18:16

250: CIP2A–TOPBP1: Mitotic repair via MiDAS and MMEJ

Base by Base ·

2026/01/05

️ Episode 250: CIP2A–TOPBP1: Mitotic repair via MiDAS and MMEJ In this episode of PaperCast Base by Base, we explore This study shows the CIP2A-TOPBP1 complex coordinates two mitotic double-strand break repair pathways, MiDAS and MMEJ, by recruiting SLX4/SMX components and Polθ to mitotic chromatin. Study Highlights:TOPBP1 BRCT1/2 binds SLX4 phosphorylated at Thr1260, a CDK1-dependent modification that promotes recruitment of SLX4, MUS81 and ERCC1 to

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00:20:40

249: PCM1 links centrosome asymmetry to endosome...

Base by Base ·

2026/01/04

️ Episode 249: PCM1 links centrosome asymmetry to endosome dynamics In this episode of PaperCast Base by Base, we explore In developing neural progenitors PCM1 localizes to the mother centrosome and to Notch ligand-containing endosomes, promoting Par-3/dynein assembly and Rab5-to-Rab11 trafficking to bias posterior-directed endosome segregation and preserve progenitor fate Study Highlights:Pcm1 is asymmetrically enriched at the posterior mother

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00:21:12

248: Disruption of PIKfyve triggers lysosomal repair...

Base by Base ·

2026/01/03

️ Episode 248: Disruption of PIKfyve triggers lysosomal repair and mitochondrial adaptation In this episode of PaperCast Base by Base, we explore Disruption of the PIKfyve/Fig4/Vac14 complex drives ULK1-dependent trafficking of PI4KIIα and ATG9A to lysosomes, elevating lysosomal PI(4)P to promote membrane repair and induce mitochondrial fragmentation with increased respiration Study Highlights:PIKfyve complex disruption or pharmacological inhibition

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00:21:12

248: Disruption of PIKfyve triggers lysosomal repair...

Base by Base ·

2026/01/03

️ Episode 248: Disruption of PIKfyve triggers lysosomal repair and mitochondrial adaptation In this episode of PaperCast Base by Base, we explore Disruption of the PIKfyve/Fig4/Vac14 complex drives ULK1-dependent trafficking of PI4KIIα and ATG9A to lysosomes, elevating lysosomal PI(4)P to promote membrane repair and induce mitochondrial fragmentation with increased respiration Study Highlights:PIKfyve complex disruption or pharmacological inhibition

en-us

00:21:27

247: Genome graphs reveal structural variation in M....

Base by Base ·

2026/01/02

️ Episode 247: Genome graphs reveal structural variation in M. tuberculosis In this episode of PaperCast Base by Base, we explore Long-read assemblies and a pangenome reference graph uncover widespread structural variants that shape Mycobacterium tuberculosis evolution and contribute to drug resistance Study Highlights:The authors built an M. tuberculosis pangenome reference graph from 859 high-quality long-read assemblies and identified 3,077 unique

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00:21:27

247: Genome graphs reveal structural variation in M....

Base by Base ·

2026/01/02

️ Episode 247: Genome graphs reveal structural variation in M. tuberculosis In this episode of PaperCast Base by Base, we explore Long-read assemblies and a pangenome reference graph uncover widespread structural variants that shape Mycobacterium tuberculosis evolution and contribute to drug resistance Study Highlights:The authors built an M. tuberculosis pangenome reference graph from 859 high-quality long-read assemblies and identified 3,077 unique

en-us

00:16:44

246: SV2A structural pharmacology and allosteric...

Base by Base ·

2026/01/01

️ Episode 246: SV2A structural pharmacology and allosteric occlusion In this episode of PaperCast Base by Base, we explore High-resolution cryo-EM structures of human SV2A reveal that orthosteric ligands induce an occluded MFS conformation and a secondary allosteric pocket modulates ligand binding Study Highlights:The authors report sub-3 Å cryo-EM structures of human SV2A in the apo state and in complexes with levetiracetam, UCB-J, padsevonil, and the

en-us

00:16:44

246: SV2A structural pharmacology and allosteric...

Base by Base ·

2026/01/01

️ Episode 246: SV2A structural pharmacology and allosteric occlusion In this episode of PaperCast Base by Base, we explore High-resolution cryo-EM structures of human SV2A reveal that orthosteric ligands induce an occluded MFS conformation and a secondary allosteric pocket modulates ligand binding Study Highlights:The authors report sub-3 Å cryo-EM structures of human SV2A in the apo state and in complexes with levetiracetam, UCB-J, padsevonil, and the

en-us

00:19:10

245: Benchmarking DNA foundation models

Base by Base ·

2025/12/31

️ Episode 245: Benchmarking DNA foundation models In this episode of PaperCast Base by Base, we explore A comprehensive, unbiased benchmark compares five DNA foundation models across 57 datasets and multiple tasks, finding mean token embeddings improve classification and that model strengths vary by task and pre-training. Study Highlights:The study evaluated DNABERT-2, NT-v2, HyenaDNA, Caduceus-Ph, and GROVER on 57 datasets spanning sequence

en-us

00:19:10

245: Benchmarking DNA foundation models

Base by Base ·

2025/12/31

️ Episode 245: Benchmarking DNA foundation models In this episode of PaperCast Base by Base, we explore A comprehensive, unbiased benchmark compares five DNA foundation models across 57 datasets and multiple tasks, finding mean token embeddings improve classification and that model strengths vary by task and pre-training. Study Highlights:The study evaluated DNABERT-2, NT-v2, HyenaDNA, Caduceus-Ph, and GROVER on 57 datasets spanning sequence

en-us

00:17:38

244: NEK7 couples SDHB to preserve mitochondrial...

Base by Base ·

2025/12/30

️ Episode 244: NEK7 couples SDHB to preserve mitochondrial electron transport and limit liver fibrosis In this episode of PaperCast Base by Base, we explore Mitochondrial NEK7 is imported via MTS peptides, binds SDHB to stabilize complex II conformation, prevent reverse electron transport and ROS, and thereby protects against spontaneous and experimentally induced liver fibrosis Study Highlights:NEK7 localizes to hepatocyte mitochondria through two

en-us

00:17:38

244: NEK7 couples SDHB to preserve mitochondrial...

Base by Base ·

2025/12/30

️ Episode 244: NEK7 couples SDHB to preserve mitochondrial electron transport and limit liver fibrosis In this episode of PaperCast Base by Base, we explore Mitochondrial NEK7 is imported via MTS peptides, binds SDHB to stabilize complex II conformation, prevent reverse electron transport and ROS, and thereby protects against spontaneous and experimentally induced liver fibrosis Study Highlights:NEK7 localizes to hepatocyte mitochondria through two

en-us

00:17:41

243: Genome-wide UVB GxE study finds 162 vitamin D...

Base by Base ·

2025/12/29

️ Episode 243: Genome-wide UVB GxE study finds 162 vitamin D variants In this episode of PaperCast Base by Base, we explore A GWIS of 338,977 UK Biobank White British participants using a cumulative weighted ambient UVB measure identified 307 independent loci for 25-hydroxyvitamin D, including 162 novel variants Study Highlights:The study linked a cumulative and weighted ambient UVB (CW-D-UVB) dose from TEMIS to each participant’s residence and blood

en-us

00:17:41

243: Genome-wide UVB GxE study finds 162 vitamin D...

Base by Base ·

2025/12/29

️ Episode 243: Genome-wide UVB GxE study finds 162 vitamin D variants In this episode of PaperCast Base by Base, we explore A GWIS of 338,977 UK Biobank White British participants using a cumulative weighted ambient UVB measure identified 307 independent loci for 25-hydroxyvitamin D, including 162 novel variants Study Highlights:The study linked a cumulative and weighted ambient UVB (CW-D-UVB) dose from TEMIS to each participant’s residence and blood

en-us

00:17:40

242: AAV9-fcMISv2 gene therapy prevents pregnancy in...

Base by Base ·

2025/12/28

️ Episode 242: AAV9-fcMISv2 gene therapy prevents pregnancy in female cats In this episode of PaperCast Base by Base, we explore A single intramuscular injection of an AAV9 vector encoding feline anti‑Müllerian hormone (fcMISv2) in prepubertal kittens produced sustained supraphysiological AMH, was well tolerated, and prevented breeding‑induced ovulation and pregnancy in adult females Study Highlights:Twelve 2–3 month-old kittens received a single IM dose

en-us

00:18:36

241: Wagyu T2T reveals a cattle X neocentromere

Base by Base ·

2025/12/27

️ Episode 241: Wagyu T2T reveals a cattle X neocentromere In this episode of PaperCast Base by Base, we explore A telomere-to-telomere Wagyu assembly uncovers a natural neocentromere on the cattle X formed by inverted repeats and transposable element expansion, adds hundreds of new genes, and improves variant discovery Study Highlights:The UOA_Wagyu_1 haplotype-resolved assembly includes a complete X chromosome and four T2T autosomes, adding 431 Mb

en-us

400 results

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