© 2026 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
\n\n© The Author(s) 2026. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
\n\nSB gratefully acknowledges funding support from the Caltech Center for Evolutionary Science, grant no. CES.FY2025. JEG gratefully acknowledges support from NASA’s Interdisciplinary Consortia for Astrobiology Research, grant no. 80NSSC23K1357. We dedicate this paper to the memory of Professor Yuk L. Yung (1946-2026), who passed away on March 16, 2026.
\nData related to all proteins analysed in this work are available at accession code: https://doi.org/10.5281/zenodo.18521378. Source data are provided with this paper.
\nProtein sequence design was performed using ProteinMPNN40, which is distributed under the MIT License and is openly available at https://github.com/dauparas/ProteinMPNN. The Colab notebook used in this study is available at https://colab.research.google.com/github/dauparas/ProteinMPNN/blob/main/colab_notebooks/quickdemo.ipynb. The original license and copyright information provided by the authors were retained. Protein structure prediction was performed using AlphaFold2 and ESMFold as implemented in ColabFold39, which is distributed under the Apache License 2.0 and is openly available at https://github.com/sokrypton/ColabFold. The specific notebooks used are available at https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynband https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/ESMFold.ipynb. No modifications were made to the core prediction algorithms. Protein structural similarity metrics were computed using TM-align45, which is freely available for academic use at: https://zhanggroup.org/TM-align/.
\nAI protein design software is used to explore the world of ancient protein structures, and very small, primordial amino acid libraries are found to produce a wide variety of key folds. Data from asteroid analyses and protobiotic chemistry experiments are utilised to constrain several primitive amino acid libraries of varying sizes. Protein design software is then used to construct sequences of these amino acids that could emulate a broad range of key protein folds including metabolic (all enzymes of the reverse tricarboxylic acid cycle), redox, electron-transfer and ribosomal, among others. AlphaFold2 is employed to predict 3D structures from these sequences, which are compared to their native counterparts using the Template Modelling Score. A library of only 6 amino acids-those of highest measured abundance on asteroid Bennu-can reproduce all folds in the test set. Two libraries of just 7 amino acids, constrained by the Miller-Urey experiment and Murchison meteorite data, and one library with 8 amino acids constrained by another Miller-Urey experiment, are also able to produce all folds considered. It is also demonstrated that a 6 amino acid alphabet-the 5 most abundant on Bennu supplemented by cysteine that could have been supplied by atmospheric haze chemistry-can yield a ferredoxin-like protein with a plausible Fe-S binding geometry. Such broad protein folding with very limited amino acid libraries has significant implications for the origins of life, synthetic biology and medical applications.
", "date": "2026-04-03", "date_type": "published", "publication": "Nature Communications", "publisher": "Nature Publishing Group", "issn": "2041-1723", "official_url": "https://authors.library.caltech.edu/records/8x6xr-kp774", "funders": { "items": [ { "grant_number": "CES.FY2025" }, { "grant_number": "80NSSC23K1357" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" }, { "id": "Caltech-Center-for-Evolutionary-Science" } ] }, "doi": "10.1038/s41467-026-71509-6", "primary_object": { "basename": "s41467-026-71509-6_reference.pdf", "url": "https://authors.library.caltech.edu/records/8x6xr-kp774/files/s41467-026-71509-6_reference.pdf" }, "related_objects": [ { "basename": "41467_2026_71509_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/8x6xr-kp774/files/41467_2026_71509_MOESM2_ESM.pdf" }, { "basename": "41467_2026_71509_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/8x6xr-kp774/files/41467_2026_71509_MOESM3_ESM.pdf" }, { "basename": "41467_2026_71509_MOESM4_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/8x6xr-kp774/files/41467_2026_71509_MOESM4_ESM.xlsx" }, { "basename": "41467_2026_71509_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/8x6xr-kp774/files/41467_2026_71509_MOESM1_ESM.pdf" } ], "pub_year": "2026", "author_list": "Bartlett, Stuart; Gupta, Arushi; et al." }, { "id": "https://authors.library.caltech.edu/records/bt3x6-cjk89", "eprint_status": "archive", "datestamp": "2025-07-22 15:19:35", "lastmod": "2025-07-22 15:19:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Flamholz-Avi-I", "name": { "family": "Flamholz", "given": "Avi I." }, "orcid": "0000-0002-9278-5479" }, { "id": "Goyal-Akshit", "name": { "family": "Goyal", "given": "Akshit" }, "orcid": "0000-0002-9425-8269" }, { "id": "Fischer-W-W", "name": { "family": "Fischer", "given": "Woodward W." }, "orcid": "0000-0002-8836-3054" }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "Dianne K." }, "orcid": "0000-0003-1647-1918" }, { "id": "Phillips-R", "name": { "family": "Phillips", "given": "Rob" }, "orcid": "0000-0003-3082-2809" } ] }, "title": "The proteome is a terminal electron acceptor", "ispublished": "pub", "full_text_status": "public", "keywords": "microbial physiology; redox chemistry; metabolism; environmental science; protein evolution", "note": "Source code for models and analyses are available on GitHub (https://github.com/flamholz/redox-proteome) (97). All other data are included in the manuscript and/or supporting information.
\n\nA.I.F., A.G., W.W.F., D.K.N., and R.P. designed research; A.I.F. and A.G. performed research; A.I.F. and A.G. contributed new reagents/analytic tools; A.I.F. and A.G. analyzed data; and A.I.F., A.G., W.W.F., D.K.N., and R.P. wrote the paper.
\n\nAppendix 01 (PDF)
\nDataset S01 (XLSX)
\nDataset S02 (XLSX)
\nDataset S03 (XLSX)
\nDataset S04 (XLSX)
\nDataset S05 (XLSX)
\nDataset S06 (XLSX)
\n", "abstract": "
Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. Escherichia coli, for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of this metabolic flexibility, we developed a coarse-grained mathematical framework coupling redox chemistry with principles of cellular resource allocation. Our models inherit key qualities from both of their antecedents: i) describing diverse metabolic chemistries and ii) enforcing the simultaneous balancing of atom (e.g., carbon), electron, and energy (adenosine triphosphate) flows, as in redox models, while iii) treating biomass as both the product and catalyst of the growth process, as in resource allocation models. Assembling integrated models of respiration, fermentation, and photosynthesis clarified key microbiological phenomena, including demonstrating that autotrophs grow more slowly than heterotrophs because of constraints imposed by the intracellular production of reduced carbon. Our model further predicted that heterotrophic growth is improved by matching the redox state of biomass to the nutrient environment. Through analysis of ≈60,000 genomes and diverse proteomic datasets, we found evidence that proteins indeed accumulate amino acid substitutions promoting redox matching. We therefore propose an unexpected mode of genome evolution where substitutions neutral or even deleterious to the individual biochemical or structural functions of proteins can nonetheless be selected due to a redox-chemical benefit to the population.
", "date": "2025-01-07", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences", "volume": "122", "number": "1", "publisher": "National Academy of Sciences", "pagerange": "e2404048121", "issn": "0027-8424", "official_url": "https://authors.library.caltech.edu/records/bt3x6-cjk89", "funders": { "items": [ { "grant_number": "PHY-1748958" }, { "grant_number": "61-1772" }, {}, { "grant_number": "Ramalingaswami Fellowship" }, { "grant_number": "GBMF4513" }, { "grant_number": "Caltech Center for Evolutionary Science" }, { "grant_number": "1R01AI127850-01A1" }, { "grant_number": "Donna and Benjamin M. Rosen Bioengineering Center" }, { "grant_number": "1R35 GM118043" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" }, { "id": "Division-of-Geological-and-Planetary-Sciences" }, { "id": "Caltech-Center-for-Evolutionary-Science" }, { "id": "Rosen-Bioengineering-Center" } ] }, "doi": "10.1073/pnas.2404048121", "pmcid": "PMC11725909", "primary_object": { "basename": "flamholz-et-al-the-proteome-is-a-terminal-electron-acceptor.pdf", "url": "https://authors.library.caltech.edu/records/bt3x6-cjk89/files/flamholz-et-al-the-proteome-is-a-terminal-electron-acceptor.pdf" }, "related_objects": [ { "basename": "pnas.2404048121.sd03.xlsx", "url": "https://authors.library.caltech.edu/records/bt3x6-cjk89/files/pnas.2404048121.sd03.xlsx" }, { "basename": "pnas.2404048121.sd04.xlsx", "url": "https://authors.library.caltech.edu/records/bt3x6-cjk89/files/pnas.2404048121.sd04.xlsx" }, { "basename": "pnas.2404048121.sd05.xlsx", "url": "https://authors.library.caltech.edu/records/bt3x6-cjk89/files/pnas.2404048121.sd05.xlsx" }, { "basename": "pnas.2404048121.sapp.pdf", "url": "https://authors.library.caltech.edu/records/bt3x6-cjk89/files/pnas.2404048121.sapp.pdf" }, { "basename": "pnas.2404048121.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/bt3x6-cjk89/files/pnas.2404048121.sd01.xlsx" }, { "basename": "pnas.2404048121.sd02.xlsx", "url": "https://authors.library.caltech.edu/records/bt3x6-cjk89/files/pnas.2404048121.sd02.xlsx" }, { "basename": "pnas.2404048121.sd06.xlsx", "url": "https://authors.library.caltech.edu/records/bt3x6-cjk89/files/pnas.2404048121.sd06.xlsx" } ], "pub_year": "2025", "author_list": "Flamholz, Avi I.; Goyal, Akshit; et al." }, { "id": "https://authors.library.caltech.edu/records/8n92k-h7b39", "eprint_status": "archive", "datestamp": "2024-06-18 17:57:42", "lastmod": "2024-06-26 19:45:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kitchen-Sheila-A", "name": { "family": "Kitchen", "given": "Sheila A." }, "orcid": "0000-0003-4402-8139" }, { "id": "Naragon-Thomas-H", "name": { "family": "Naragon", "given": "Thomas H." }, "orcid": "0000-0002-5373-4257" }, { "id": "Br\u00fcckner-Adrian", "name": { "family": "Br\u00fcckner", "given": "Adrian" }, "orcid": "0000-0002-9184-8562" }, { "id": "Ladinsky-Mark-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Quinodoz-Sofia-A", "name": { "family": "Quinodoz", "given": "Sofia A." }, "orcid": "0000-0003-1862-5204" }, { "id": "Badroos-Jean-M", "name": { "family": "Badroos", "given": "Jean M." }, "orcid": "0000-0002-0867-3686" }, { "id": "Viliunas-Joani-W", "name": { "family": "Viliunas", "given": "Joani W." }, "orcid": "0000-0001-7795-4265" }, { "id": "Kishi-Yuriko", "name": { "family": "Kishi", "given": "Yuriko" }, "orcid": "0000-0002-1005-7030" }, { "id": "Wagner-Julian-M", "name": { "family": "Wagner", "given": "Julian M." } }, { "id": "Miller-David-R", "name": { "family": "Miller", "given": "David R." }, "orcid": "0000-0002-7186-2623" }, { "id": "Yousefelahiyeh-Mina", "name": { "family": "Yousefelahiyeh", "given": "Mina" }, "orcid": "0000-0003-0365-3018" }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "Igor A." }, "orcid": "0000-0002-9934-3040" }, { "id": "Eldredge-Ken-Taro", "name": { "family": "Eldredge", "given": "K. Taro" }, "orcid": "0000-0002-2136-2321" }, { "id": "Pirro-Stacy", "name": { "family": "Pirro", "given": "Stacy" }, "orcid": "0000-0002-5642-4203" }, { "id": "Guttman-M", "name": { "family": "Guttman", "given": "Mitchell" }, "orcid": "0000-0003-4748-9352" }, { "id": "Davis-Steven-R", "name": { "family": "Davis", "given": "Steven R." }, "orcid": "0000-0001-5353-1591" }, { "id": "Aardema-Matthew-L", "name": { "family": "Aardema", "given": "Matthew L." }, "orcid": "0000-0002-7206-6311" }, { "id": "Parker-J", "name": { "family": "Parker", "given": "Joseph" }, "orcid": "0000-0001-9598-2454" } ] }, "title": "The genomic and cellular basis of biosynthetic innovation in rove beetles", "ispublished": "pub", "full_text_status": "public", "note": "© 2024 Elsevier.
\n\n© The Author(s), under exclusive licence to Springer Nature Limited 2024.
\n\nWe thank E. Meyerowitz and members of the Meyerowitz Lab Paul Tarr and Carla de Agostini Verna for introducing us to techniques for Arabidopsis maintenance, transgenesis and crossing. This work was supported by a grant to B.A.H. from the Caltech Center for Evolutionary Science (G.O. and M.L.J.) and the Caltech Resnick Sustainability Institute Explorer Grant (G.O.). T.I. was supported by NIH Training grant number 5T32GM007616-39 and with support to B.A.H. from the US Department of Agriculture, National Institute of Food and Agriculture (NIFA) specialty crop initiative under US Department of Agriculture NIFA award number 2012-51181-20086.
\nConceptualization, G.O., T.I. and B.A.H.; methodology, G.O., T.I., M.L.J., I.A. and B.A.H.; investigation, G.O., M.L.J., I.A. and B.A.H.; writing—original draft, G.O. and B.A.H.; writing—review and editing, G.O., T.I., M.L.J., I.A. and B.A.H.; funding acquisition, B.A.H.
\n\nAll data are available in the main text and the Supplementary Information files. Illumina sequencing reads were deposited to SRA (bioproject, PRJNA1074841). The Arabidopsis TAIR 10 genome assembly was used in this study. Constructs and seeds of transgenic plants created in this study are available upon request.
\n\nExtended Data Fig. 2 T3 heterozygous ClvR crosses for (a) female ClvRap and (b) male ClvRap.
\nModelling code and more information on the model, the scripts and parameters used to generate the data, and the data itself can be found at https://github.com/HayLab/Pigss. Plots were generated in R (version 4.2.3) with the ggplot2 package122.
\nThe authors have filed patent applications on ClvR and related technologies (US application numbers 15/970,728 and 16/673,823).
\nGene drive elements promote the spread of linked traits and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Here we demonstrate the essential features of the ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61. Resistant alleles, which can slow or prevent drive, were not observed. Modelling shows plant ClvRs are robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications are discussed.
\n\u00a9 The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/pages/standard-publication-reuse-rights)
\n\nWe thank Erich Schwarz for generously providing early access to unpublished versions of the S. hermaphroditum genome and its annotation; Jennifer Heppert and Heidi Goodrich-Blair for unpublished HGB2511 sequence; Heenam Park and Tsui-Fen Chou for CRISPR reagents and advice; Mengyi Cao for information about Steinernema CRISPR; Barbara Perry, Wilber Palma, and Stephanie Nava for technical assistance; WormBase and WormBase ParaSite for C. elegans and Steinernema genome information; Mona Shagholi of the Caltech Mass Spectrometry service center; and Daniel Semlow and Anton Gartner for advice about the effects of EMS mutagenesis. Some strains were provided by the CGC, funded by P40 OD010440.
\n\nThis work was supported by NSF-EDGE grant 2128267 (to PWS) and Caltech's Center for Evolutionary Science (CES) and Center for Environmental Microbial Interactions (CEMI). This research benefited from the use of instrumentation made available by the Caltech CCE Multiuser Mass Spectrometry Laboratory, enabled by funds from DOW Next Generation Instrumentation.
", "abstract": "The entomopathogenic nematode Steinernema hermaphroditum was recently rediscovered and is being developed as a genetically tractable experimental system for the study of previously unexplored biology, including parasitism of its insect hosts and mutualism with its bacterial endosymbiont Xenorhabdus griffiniae. Through whole-genome re-sequencing and genetic mapping we have for the first time molecularly identified the gene responsible for a mutationally defined phenotypic locus in an entomopathogenic nematode. In the process we observed an unexpected mutational spectrum following EMS mutagenesis in this species. We find that the ortholog of the essential C. elegans peroxidase gene skpo-2 controls body size and shape in S. hermaphroditum. We confirmed this identification by generating additional loss-of-function mutations in the gene using CRISPR-Cas9. We propose that the identification of skpo-2 will accelerate gene targeting in other Steinernema entomopathogenic nematodes used commercially in pest control, as skpo-2 is X-linked and males hemizygous for loss of its function can mate, making skpo-2 an easily recognized and maintained marker for use in co-CRISPR.
", "date": "2024-02-07", "date_type": "published", "publication": "Genetics", "volume": "226", "number": "2", "publisher": "Oxford University Press", "pagerange": "iyad209", "issn": "1943-2631", "official_url": "https://authors.library.caltech.edu/records/n6k3c-dpn19", "funders": { "items": [ { "grant_number": "P40 OD010440" }, { "grant_number": "IOS-2128267" }, { "grant_number": "Dow Next Generation Educator Fund" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Caltech-Center-for-Evolutionary-Science" } ] }, "doi": "10.1093/genetics/iyad209", "primary_object": { "basename": "iyad209.pdf", "url": "https://authors.library.caltech.edu/records/n6k3c-dpn19/files/iyad209.pdf" }, "related_objects": [ { "basename": "iyad209_supplementary_data.zip", "url": "https://authors.library.caltech.edu/records/n6k3c-dpn19/files/iyad209_supplementary_data.zip" } ], "pub_year": "2024", "author_list": "Schwartz, Hillel T.; Tan, Chieh-Hsiang; et al." }, { "id": "https://authors.library.caltech.edu/records/ysv2f-72x76", "eprint_status": "archive", "datestamp": "2025-05-12 19:21:00", "lastmod": "2025-07-03 19:15:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Haoyu", "name": { "family": "Li", "given": "Haoyu" }, "orcid": "0000-0002-7192-2470" }, { "id": "Kipp-Michael-A", "name": { "family": "Kipp", "given": "Michael A." }, "orcid": "0000-0003-1844-3670" }, { "name": { "family": "Kim", "given": "Sora L." }, "orcid": "0000-0002-4900-3101" }, { "name": { "family": "Kast", "given": "Emma R." }, "orcid": "0000-0002-2905-3793" }, { "name": { "family": "Eberle", "given": "Jaelyn J." }, "orcid": "0000-0001-6890-9112" }, { "id": "Tissot-F-L-H", "name": { "family": "Tissot", "given": "Fran\u00e7ois L.H." }, "orcid": "0000-0001-6622-2907" } ] }, "title": "Exploring uranium isotopes in shark teeth as a paleo-redox proxy", "ispublished": "pub", "full_text_status": "public", "keywords": "Uranium isotopes; Diagenesis; Anoxia; Apatite", "note": "© 2023 Elsevier Ltd. All rights reserved.
\n\nData are available through CaltechDATA at https://doi.org/10.22002/xe7v7-c1r13.
\n\nSupplementary data 1 (PDF)
", "abstract": "\u00a9 2023, Li et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
\n\nWe thank Bruce Hay, Arjun Raj, Yujing Yang, Jesus del Rio Salgado, Judah Bates, and Aki Ohdera for feedback and discussions.
\n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
\n\nYutian Li, Conceptualization, Data curation, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing \u2013 original draft, Writing \u2013 review and editing; Anish A Sarma, Formal analysis, Validation, Methodology, Writing \u2013 review and editing; Iris T Lee, Investigation, Writing \u2013 review and editing; Fayth Hui Tan, Michael J Abrams, Zevin J Condiotte, Martin Heithe, Misha Raffiee, John O Dabiri, David A Gold, Writing \u2013 review and editing; Lea Goentoro, Conceptualization, Resources, Data curation, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing \u2013 original draft, Project administration, Writing \u2013 review and editing
\n\nThe raw images of the single fly tracking data are available at CaltechDATA: https://doi.org/10.22002/D1.2157. The raw measurements of the single fly tracking data are available in: https://cdn.elifesciences.org/articles/65092/elife-65092-fig5-data1-v3.xlsx. Matlab code to process the data in the spreadsheet can be downloaded from: https://cdn.elifesciences.org/articles/65092/elife-65092-fig5-code1-v3.zip.
\n\nFayth Hui Tan, Michael J Abrams, Martin Heithe, Lea Goentoro: Has applied for a patent related to the findings reported in this manuscript (US Patent Application No. 17/355,727). The other authors declare that no competing interests exist.
", "abstract": "Previously we reported evidence that a regenerative response in the appendages of moon jellyfish, fruit flies, and mice can be promoted by nutrient modulation (Abrams et al., 2021). Sustar and Tuthill subsequently reported that they had not been able to reproduce the induced regenerative response in flies (Sustar and Tuthill, 2023). Here we discuss that differences in the amputation method, treatment concentrations, age of the animals, and stress management explain why they did not observe a regenerative response in flies. Typically, 30\u201350% of treated flies showed response in our assay.", "date": "2023-06-22", "date_type": "published", "publication": "eLife", "volume": "12", "publisher": "eLife", "pagerange": "e85370", "issn": "2050-084X", "official_url": "https://authors.library.caltech.edu/records/x179p-jhv14", "funders": { "items": [ { "agency": "Max Factor Foundation" }, { "agency": "Caltech Center for Evolutionary Sciences" } ] }, "local_group": { "items": [ { "id": "GALCIT" }, { "id": "Caltech-Center-for-Evolutionary-Science" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/elife.85370", "pmcid": "PMC10287153", "primary_object": { "basename": "elife-65092-fig5-code1-v3.zip", "url": "https://authors.library.caltech.edu/records/x179p-jhv14/files/elife-65092-fig5-code1-v3.zip" }, "related_objects": [ { "basename": "elife-65092-fig5-data1-v3.xlsx", "url": "https://authors.library.caltech.edu/records/x179p-jhv14/files/elife-65092-fig5-data1-v3.xlsx" }, { "basename": "elife-85370.pdf", "url": "https://authors.library.caltech.edu/records/x179p-jhv14/files/elife-85370.pdf" } ], "pub_year": "2023", "author_list": "Li, Yutian; Sarma, Anish A.; et al." }, { "id": "https://authors.library.caltech.edu/records/z5bbf-7xn39", "eprint_id": 121396, "eprint_status": "archive", "datestamp": "2023-08-22 20:33:26", "lastmod": "2026-03-28 00:14:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Ren\u00e9e-Z", "name": { "family": "Wang", "given": "Ren\u00e9e Z." }, "orcid": "0000-0003-3994-3244" }, { "id": "Liu-Albert-K", "name": { "family": "Liu", "given": "Albert K." }, "orcid": "0000-0001-9500-0449" }, { "id": "Banda-Douglas-M", "name": { "family": "Banda", "given": "Douglas M." }, "orcid": "0000-0001-6198-2923" }, { "id": "Fischer-W-W", "name": { "family": "Fischer", "given": "Woodward W." }, "orcid": "0000-0002-8836-3054" }, { "id": "Shih-Patrick-M", "name": { "family": "Shih", "given": "Patrick M." }, "orcid": "0000-0002-2119-3345" } ] }, "title": "A Bacterial Form I' Rubisco Has a Smaller Carbon Isotope Fractionation than Its Form I Counterpart", "ispublished": "pub", "full_text_status": "public", "keywords": "Molecular Biology; Biochemistry", "note": "\u00a9 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\n(This article belongs to the Special Issue Future Prospects in Cyanobacterial Synthetic Biology and Biotechnology) \n\nWe thank Tobias Erb for thoughtful and supportive comments. \n\nR.Z.W. was supported by the National Science Foundation Graduate Research Fellowship Program (NSF GRFP). A.K.L., D.M.B., and P.M.S. were supported by a Society in Science\u2013Branco Weiss fellowship from ETH Z\u00fcrich and a Packard Fellowship from the David Lucile Packard Foundation. W.F.S. and research was supported by NASA Exobiology (80NSSC21K0484), Simons Foundation Collaboration on Origin and Evolution of Life (554187), Schwartz Reisman Collaborative Science Program, Caltech Center for Evolutionary Sciences.\n\nAuthor Contributions. Conceptualization, W.W.F. and P.M.S.; Methodology, R.Z.W., A.K.L., and D.M.B.; Formal Analysis, R.Z.W.; Writing\u2014Original Draft Preparation, R.Z.W.; Writing\u2014Review and Editing, R.Z.W., W.W.F., A.K.L., and P.M.S.; Funding Acquisition, W.W.F. and P.M.S. All authors have read and agreed to the published version of the manuscript. \n\nData Availability Statement. All data used in this study are presented in the supplement. \n\nThe authors declare no conflict of interest.\n\nPublished - biomolecules-13-00596-v2.pdf
Supplemental Material - biomolecules-13-00596-s001.zip
", "abstract": "Form I rubiscos evolved in Cyanobacteria \u2265 2.5 billion years ago and are enzymatically unique due to the presence of small subunits (RbcS) capping both ends of an octameric large subunit (RbcL) rubisco assembly to form a hexadecameric (L8S8) holoenzyme. Although RbcS was previously thought to be integral to Form I rubisco stability, the recent discovery of a closely related sister clade of octameric rubiscos (Form I'; L8) demonstrates that the L8 complex can assemble without small subunits (Banda et al. 2020). Rubisco also displays a kinetic isotope effect (KIE) where the 3PG product is depleted in 13C relative to 12C. In Cyanobacteria, only two Form I KIE measurements exist, making interpretation of bacterial carbon isotope data difficult. To aid comparison, we measured in vitro the KIEs of Form I' (Candidatus Promineofilum breve) and Form I (Synechococcus elongatus PCC 6301) rubiscos and found the KIE to be smaller in the L8 rubisco (16.25 \u00b1 1.36\u2030 vs. 22.42 \u00b1 2.37\u2030, respectively). Therefore, while small subunits may not be necessary for protein stability, they may affect the KIE. Our findings may provide insight into the function of RbcS and allow more refined interpretation of environmental carbon isotope data.", "date": "2023-04", "date_type": "published", "publication": "Biomolecules", "volume": "13", "number": "4", "publisher": "MDPI", "pagerange": "Art. No. 596", "id_number": "CaltechAUTHORS:20230515-138491000.9", "issn": "2218-273X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230515-138491000.9", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship" }, { "agency": "ETH Z\u00fcrich" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "NASA", "grant_number": "80NSSC21K0484" }, { "agency": "Simons Foundation", "grant_number": "554187" }, { "agency": "Schwartz Reisman Collaborative Science Program" }, { "agency": "Caltech Center for Evolutionary Science" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" }, { "id": "Caltech-Center-for-Evolutionary-Science" } ] }, "doi": "10.3390/biom13040596", "pmcid": "PMC10135865", "primary_object": { "basename": "biomolecules-13-00596-v2.pdf", "url": "https://authors.library.caltech.edu/records/z5bbf-7xn39/files/biomolecules-13-00596-v2.pdf" }, "related_objects": [ { "basename": "biomolecules-13-00596-s001.zip", "url": "https://authors.library.caltech.edu/records/z5bbf-7xn39/files/biomolecules-13-00596-s001.zip" } ], "pub_year": "2023", "author_list": "Wang, Ren\u00e9e Z.; Liu, Albert K.; et al." }, { "id": "https://authors.library.caltech.edu/records/44vpf-33p55", "eprint_id": 120725, "eprint_status": "archive", "datestamp": "2023-08-22 19:06:45", "lastmod": "2026-03-27 20:30:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Smith-Benjamin-P", "name": { "family": "Smith", "given": "B. P." }, "orcid": "0000-0003-3189-8717" }, { "id": "Edie-Stewart-M", "name": { "family": "Edie", "given": "S. M." }, "orcid": "0000-0003-2843-7952" }, { "id": "Fischer-W-W", "name": { "family": "Fischer", "given": "W. W." }, "orcid": "0000-0002-8836-3054" } ] }, "title": "Tracing energy inputs into the seafloor using carbonate sediments", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "\u00a9 2023 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY). \n\nB.P.S. acknowledges the support from the Agouron Institute Postdoctoral Fellowship, W.W.F. acknowledges the support from the Caltech's Rothberg Innovative Initiative and the Caltech Center for Evolutionary Science, and S.M.E. thanks the Trimble Fellowship on the Geobiology of Complex Multicellular Life for supporting the early phase of this research. \n\nAuthor contributions: B.P.S. and W.W.F. designed research; B.P.S. and S.M.E. performed research; B.P.S. contributed new reagents/analytic tools; B.P.S. and S.M.E. analyzed data; and B.P.S., S.M.E., and W.W.F. wrote the paper. \n\nThe authors declare no competing interest.\n\nPublished - pnas.2215833120.pdf
Supplemental Material - pnas.2215833120.sapp.pdf
Supplemental Material - pnas.2215833120.sd01.xlsx
", "abstract": "Carbonate rocks provide unique and valuable sedimentary archives for secular changes in Earth's physical, chemical, and biological processes. However, reading the stratigraphic record produces overlapping, nonunique interpretations that stem from the difficulty in directly comparing competing biological, physical, or chemical mechanisms within a common quantitative framework. We built a mathematical model that decomposes these processes and casts the marine carbonate record in terms of energy fluxes across the sediment\u2013water interface. Results showed that physical, chemical, and biological energy terms across the seafloor are subequal and that the energetic dominance of different processes varies both as a function of environment (e.g., onshore vs. offshore) as well as with time-varying changes in seawater chemistry and with evolutionary changes in animal abundance and behavior. We applied our model to observations from the end-Permian mass extinction\u2014a massive upheaval in ocean chemistry and biology\u2014revealing an energetic equivalence between two hypothesized drivers of changing carbonate environments: a reduction in physical bioturbation increased carbonate saturation states in the oceans. Early Triassic occurrences of 'anachronistic' carbonates\u2014facies largely absent from marine environments after the Early Paleozoic\u2014were likely driven more by reduction in animal biomass than by repeated perturbations to seawater chemistry. This analysis highlighted the importance of animals and their evolutionary history in physically shaping patterns in the sedimentary record via their impact on the energetics of marine environments.", "date": "2023-02-28", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "120", "number": "9", "publisher": "National Academy of Sciences", "pagerange": "e2215833120", "id_number": "CaltechAUTHORS:20230411-695015900.5", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230411-695015900.5", "funders": { "items": [ { "agency": "Agouron Institute" }, { "agency": "Rothenberg Innovation Initiative (RI2)" }, { "agency": "Caltech Center for Evolutionary Science" }, { "agency": "Trimble Fellowship" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Evolutionary-Science" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1073/pnas.2215833120", "pmcid": "PMC9992785", "primary_object": { "basename": "pnas.2215833120.pdf", "url": "https://authors.library.caltech.edu/records/44vpf-33p55/files/pnas.2215833120.pdf" }, "related_objects": [ { "basename": "pnas.2215833120.sapp.pdf", "url": "https://authors.library.caltech.edu/records/44vpf-33p55/files/pnas.2215833120.sapp.pdf" }, { "basename": "pnas.2215833120.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/44vpf-33p55/files/pnas.2215833120.sd01.xlsx" } ], "pub_year": "2023", "author_list": "Smith, B. P.; Edie, S. M.; et al." }, { "id": "https://authors.library.caltech.edu/records/n1101-2dq81", "eprint_id": 110679, "eprint_status": "archive", "datestamp": "2023-08-22 13:00:25", "lastmod": "2023-12-22 23:35:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cao-Mengyi", "name": { "family": "Cao", "given": "Mengyi" }, "orcid": "0000-0002-3117-3401" }, { "id": "Schwartz-Hillel-T", "name": { "family": "Schwartz", "given": "Hillel T." }, "orcid": "0000-0002-3448-8652" }, { "id": "Tan-Chieh-Hsiang", "name": { "family": "Tan", "given": "Chieh-Hsiang" }, "orcid": "0000-0002-5432-0160" }, { "id": "Sternberg-P-W", "name": { "family": "Sternberg", "given": "Paul W." }, "orcid": "0000-0002-7699-0173" } ] }, "title": "The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis", "ispublished": "pub", "full_text_status": "public", "keywords": "symbiosis; mutualism; parasitism; entomopathogenic; nematode; hermaphroditism; Steinernema; Xenorhabdus; model\nsystem; genetic screen", "note": "\u00a9 The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). \n\nReceived: 25 August 2021; Accepted: 29 September 2021; Published: 11 October 2021; Corrected and typeset: 17 November 2021. \n\nWe are overwhelmingly grateful for S. hermaphroditum as a generous gift from nature and a superb organism to explore scientific curiosities. We thank Adler Dillman of University of California Riverside for generously sharing the S. hermaphroditum-India strain CS34 and for comments on this manuscript. We also thank Heidi Goodrich-Blair and Jennifer Heppert of the University of Tennessee Knoxville for helpful discussions and editorial suggestions. We are also grateful for valuable suggestions from Zuzana Kocsisova. We appreciate our correspondence with Christine Griffin on the mode of reproduction of S. hermaphroditum-Indonesia. The monoclonal anti-MSP antibody 4A5 developed by David Greenstein of the University of Minnesota was obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH and maintained at The University of Iowa Department of Biology. Bacterial strains HB101 and DA1877 were obtained from the Caenorhabditis Genetics Center (CGC), which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was also facilitated by WormBase and ParaSite, a knowledgebase for nematode research. Figures 2D and 5A are created with BioRender.com. \n\nThis research was supported by National Institutes of Health (NIH) Ruth L. Kirschstein National Research Service Award (NRSA) Individual Postdoctoral Fellowship F32 5F32GM131570 (M.C.); National Science Foundation (NSF) Enabling Discovery through GEnomics (EDGE) grant 2128267, and the Center for Evolutionary Science at California Institute of Technology. \n\nData availability: Strains described in this work are available upon request. 16S rRNA gene sequences of the X. griffiniae bacterial symbionts of the S. hermaphroditum isolate CS34 are available in the Genbank database. The accession numbers for 16S rRNA sequence (including HGB2511) are MZ913116\u2013MZ913125. Supplemental material is available at figshare: https://doi.org/10.25386/genetics.16689217. \n\nThe authors declare that there is no conflict of interest.\n\nSubmitted - 2021.08.26.457822v1.full.pdf
", "abstract": "Entomopathogenic nematodes (EPNs), including Heterorhabditis and Steinernema, are parasitic to insects and contain mutualistically symbiotic bacteria in their intestines (Photorhabdus and Xenorhabdus, respectively) and therefore offer opportunities to study both mutualistic and parasitic symbiosis. The establishment of genetic tools in EPNs has been impeded by limited genetic tractability, inconsistent growth in vitro, variable cryopreservation, and low mating efficiency. We obtained the recently described Steinernema hermaphroditum strain CS34 and optimized its in vitro growth, with a rapid generation time on a lawn of its native symbiotic bacteria Xenorhabdus griffiniae. We developed a simple and efficient cryopreservation method. Previously, S. hermaphroditum isolated from insect hosts was described as producing hermaphrodites in the first generation. We discovered that CS34, when grown in vitro, produced consecutive generations of autonomously reproducing hermaphrodites accompanied by rare males. We performed mutagenesis screens in S. hermaphroditum that produced mutant lines with visible and heritable phenotypes. Genetic analysis of the mutants demonstrated that this species reproduces by self-fertilization rather than parthenogenesis and that its sex is determined chromosomally. Genetic mapping has thus far identified markers on the X chromosome and three of four autosomes. We report that S. hermaphroditum CS34 is the first consistently hermaphroditic EPN and is suitable for genetic model development to study naturally occurring mutualistic symbiosis and insect parasitism.", "date": "2022-01", "date_type": "published", "publication": "Genetics", "volume": "220", "number": "1", "publisher": "Oxford University Press", "pagerange": "Art. No. iyab170", "id_number": "CaltechAUTHORS:20210831-223307133", "issn": "0016-6731", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210831-223307133", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "5F32GM131570" }, { "agency": "NSF", "grant_number": "IOS-2128267" }, { "agency": "Caltech Center for Evolutionary Science" }, { "agency": "NIH", "grant_number": "P40 OD010440" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Evolutionary-Science" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1093/genetics/iyab170", "pmcid": "PMC8733455", "primary_object": { "basename": "2021.08.26.457822v1.full.pdf", "url": "https://authors.library.caltech.edu/records/n1101-2dq81/files/2021.08.26.457822v1.full.pdf" }, "pub_year": "2022", "author_list": "Cao, Mengyi; Schwartz, Hillel T.; et al." } ]