Molecular determinants of condensate composition

Molecular Cell, Journal Year: 2025, Volume and Issue: 85(2), P. 290 - 308

Published: Jan. 1, 2025

Language: Английский

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The evolution of developmental biology through conceptual and technological revolutions

Cell, Journal Year: 2024, Volume and Issue: 187(14), P. 3461 - 3495

Published: June 20, 2024

Developmental biology-the study of the processes by which cells, tissues, and organisms develop change over time-has entered a new golden age. After molecular genetics revolution in 80s 90s diversification field early 21st century, we have phase when powerful technologies provide approaches open unexplored avenues. Progress has been accelerated advances genomics, imaging, engineering, computational biology emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary led remarkable progress understanding animal development. describe classic questions gene regulation, pattern formation, morphogenesis, organogenesis, stem cell are being revisited. discuss connections development with evolution, self-organization, metabolism, time, ecology. speculate developmental might evolve an era synthetic biology, artificial intelligence, human engineering.

Language: Английский

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Evolution of Thylakoid Structural Diversity

Annual Review of Cell and Developmental Biology, Journal Year: 2024, Volume and Issue: 40(1), P. 169 - 193

Published: July 1, 2024

Oxygenic photosynthesis evolved billions of years ago, becoming Earth's main source biologically available carbon and atmospheric oxygen. Since then, phototrophic organisms have diversified from prokaryotic cyanobacteria into several distinct clades eukaryotic algae plants through endosymbiosis events. This diversity can be seen in the thylakoid membranes, complex networks lipids, proteins, pigments that perform light-dependent reactions photosynthesis. In this review, we highlight structural thylakoids, following evolutionary history species. We begin with a molecular inventory different components then illustrate how these building blocks are integrated to form membrane diverse architectures. conclude an outlook on understanding thylakoids remodel their architecture organization during dynamic processes such as biogenesis, repair, environmental adaptation.

Language: Английский

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In-cell structure and snapshots of copia retrotransposons in intact tissue by cryoelectron tomography

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Long terminal repeat (LTR) retrotransposons belong to the transposable elements (TEs), autonomously replicating genetic that integrate into host's genome. Among animals, Drosophila melanogaster serves as an important model organism for TE research and contains several LTR retrotransposons, including Ty1-copia family, which is evolutionarily related retroviruses forms virus-like particles (VLPs). In this study, we use cryo-focused ion beam (FIB) milling lift-out approaches visualize copia VLPs in ovarian cells intact egg chambers, resolving situ capsid structure 7.7 Å resolution by cryoelectron tomography (cryo-ET). Although cytoplasmic vary size, nuclear are homogeneous form densely packed clusters, supporting a import acts size selector. Analyzing flies deficient TE-suppressing PIWI-interacting RNA (piRNA) pathway, observe copia's translocation nucleus during spermatogenesis. Our findings provide insights replication cycle cellular structural biology of active retrotransposon.

Language: Английский

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Molecular architecture of thylakoid membranes within intact spinach chloroplasts

Published: March 25, 2025

Thylakoid membranes coordinate the light reactions of photosynthesis across multiple scales, coupling architecture an elaborate membrane network to spatial organization individual protein complexes embedded within this network. Previously, we used in situ cryo- electron tomography (cryo-ET) reveal native thylakoid green alga Chlamydomonas reinhardtii [1] and then map molecular these thylakoids with single-molecule precision [2]. However, it remains be shown how generalizable algal blueprint is vascular plants, which possess distinct subdivided into grana stacks interconnected by non-stacked stromal lamellae. Here, continue our cryo-ET investigation intact chloroplasts isolated from spinach ( Spinacia oleracea ). We visualize fine ultrastructural details membranes, as well interactions between plastoglobules. apply further develop AI-based computational approaches for automated segmentation picking [3], enabling us quantify photosynthetic plane adjacent stacked membranes. Our analysis reveals that, despite different 3D architecture, plants algae strikingly similar. In contrast plant thylakoids, where semi- crystalline arrays photosystem II (PSII) appear hold some together, find that PSII non-crystalline has uniform concentration both Similar C. , observe strict lateral heterogeneity PSI at boundary appressed non-appressed domains, no evidence a margin region have been proposed intermix. Based on measurements, support simple two-domain model plants.

Language: Английский

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Diatom pyrenoids are encased in a protein shell that enables efficient CO2 fixation

Cell, Journal Year: 2024, Volume and Issue: 187(21), P. 5919 - 5934.e19

Published: Oct. 1, 2024

Language: Английский

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TOMOMAN: a software package for large scale cryo-electron tomography data preprocessing, community data sharing, and collaborative computing

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 3, 2024

Abstract Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are becoming the preferred methodologies for investigating subcellular macromolecular structures in native or near-native environments. While cryo-ET is amenable to a wide range of biological problems, these problems often have data processing requirements that need be individually optimized, precluding notion one-size-fits-all pipeline. Cryo-ET also progressively more complex due an increasing number packages each step. Though package has its own strengths weaknesses, independent development different formats makes them difficult interface with one another. TOMOMAN (TOMOgram MANager) extensible streamlining interoperability packages, enabling users develop project-specific workflows. does this by maintaining internal metadata format wrapping external manage perform preprocessing, from raw tilt-series reconstructed tomograms. can export between various STA packages. includes tools archiving projects repositories; allowing subsequent download directly resume where it was previously left off. By tracking essential metadata, streamlines sharing, which improves reproducibility published results, reduces computational costs minimizing reprocessing, enables distributed multiple groups institutions. provides way test software workflows meet specific needs their questions distribute results broader scientific community.

Language: Английский

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TOMOMAN: a software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing

Journal of Applied Crystallography, Journal Year: 2024, Volume and Issue: 57(6), P. 2010 - 2016

Published: Nov. 22, 2024

Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are becoming the preferred methodologies for investigating subcellular macromolecular structures in native or near-native environments. Although cryo-ET is amenable to a wide range of biological problems, these problems often have data-processing requirements that need be individually optimized, precluding notion one-size-fits-all processing pipeline. Cryo-ET data also progressively more complex due increasing number packages each step. Though package has its strengths weaknesses, independent development different formats make them difficult interface with one another. TOMOMAN ( TOMOgram MANager ) an extensible streamlining interoperability packages, enabling users develop project-specific workflows. does this by maintaining internal metadata format wrapping external manage perform preprocessing, from raw tilt-series reconstructed tomograms. can export between various STA packages. includes tools archiving projects repositories, allowing subsequent download directly resume processing. By tracking essential metadata, streamlines sharing, which improves reproducibility published results, reduces computational costs minimizing reprocessing, enables distribution multiple groups institutions. provides way test software order workflows meet specific needs their questions distribute results broader scientific community.

Language: Английский

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Electron Tomography of Organelles and Vesicles in the Investigation of SNARE Function and Localization

Methods in molecular biology, Journal Year: 2025, Volume and Issue: unknown, P. 237 - 247

Published: Jan. 1, 2025

Language: Английский

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Frontiers in integrative structural modeling of macromolecular assemblies

QRB Discovery, Journal Year: 2025, Volume and Issue: 6

Published: Jan. 1, 2025

Abstract Integrative modeling enables structure determination for large macromolecular assemblies by combining data from multiple experiments with theoretical and computational predictions. Recent advancements in AI-based prediction cryo electron-microscopy have sparked renewed enthusiasm integrative modeling; structures methods can be integrated situ maps to characterize assemblies. This approach previously allowed us others determine the architectures of diverse assemblies, such as nuclear pore complexes, chromatin remodelers, cell–cell junctions. Experimental spanning several scales was used these studies, ranging high-resolution data, X-ray crystallography AlphaFold structure, low-resolution cryo-electron tomography co-immunoprecipitation experiments. Two recurrent challenges emerged across a range studies. First, contained significant fractions disordered regions, necessitating development new regions context ordered regions. Second, needed developed utilize information tomography, timely challenge structural biology is increasingly moving towards characterization. Here, we recapitulate recent developments proteins analysis highlight other opportunities method modeling.

Language: Английский

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