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56. AbGradCon 2021: lessons in digital meetings, international collaboration, and interdisciplinarity in astrobiology

Author

Jia, Tony Z., primary, Johnson-Finn, Kristin N., additional, Alian, Osama M., additional, Bonati, Irene, additional, Fujishima, Kosuke, additional, Grefenstette, Natalie, additional, Heenatigala, Thilina, additional, Li, Yamei, additional, Noda, Natsumi, additional, Penev, Petar I., additional, Prondzinsky, Paula, additional, and Smith, Harrison B., additional

Published
2022
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61. Recent progress in primitive polyester synthesis and membraneless microdroplet assembly.

Author

Jia, Tony Z. and Chandru, Kuhan

Subjects
*ORIGIN of life, *DEHYDRATION reactions, *HYDROXY acids, *CHEMICAL systems, *MONOMERS
Abstract

While it is often believed that the origins of life required participation of early biomolecules, it has been recently proposed that "non-biomolecules", which would have been just as, if not more, abundant on early Earth, could have played a part. In particular, recent research has highlighted the various ways by which polyesters, which do not participate in modern biology, could have played a major role during the origins of life. Polyesters could have been synthesized readily on early Earth through simple dehydration reactions at mild temperatures involving abundant "non-biological" alpha hydroxy acid (AHA) monomers. This dehydration synthesis process results in a polyester gel, which upon further rehydration, can assemble into membraneless droplets proposed to be protocell models. These proposed protocells can provide functions to a primitive chemical system, such as analyte segregation or protection, which could have further led to chemical evolution from prebiotic chemistry to nascent biochemistry. Here, to further shed light into the importance of "non-biomolecular" polyesters at the origins of life and to highlight future directions of study, we review recent studies which focus on primitive synthesis of polyesters from AHAs and assembly of these polyesters into membraneless droplets. Specifically, most of the recent progress in this field in the last five years has been led by laboratories in Japan, and these will be especially highlighted. This article is based on an invited presentation at the 60th Annual Meeting of the Biophysical Society of Japan held in September, 2022 as an 18th Early Career Awardee. [ABSTRACT FROM AUTHOR]

Published
2023
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62. Probing the Limits of Reactant Concentration and Volume in Primitive Polyphenyllactate Synthesis and Microdroplet Assembly Processes

Author

Sithamparam, Mahendran, Afrin, Rehana, Tharumen, Navaniswaran, He, Ming-Jing, Chen, Chen, Yi, Ruiqin, Wang, Po-Hsiang, Jia, Tony Z., and Chandru, Kuhan

Abstract

Polyester microdroplets have been investigated as primitive protocell models that can exhibit relevant primitive functions such as biomolecule segregation, coalescence, and salt uptake. Such microdroplets assemble after dehydration synthesis of alpha-hydroxy acid (αHA) monomers, commonly available on early Earth, via heating at mild temperatures, followed by rehydration in aqueous media. αHAs, in particular, are also ubiquitous in biology, participating in a variety of biochemical processes such as metabolism, suggesting the possible strong link between primitive and modern αHA-based processes. Although some primitive αHA polymerization conditions have been probed previously, including monomer chirality and reaction temperature, relevant factors pertaining to early Earth’s local environmental conditions that would likely affect primitive αHA polymerization are yet to be fully investigated. Hence, probing the entire breadth of possible conditions that could promote primitive αHA polymerization is required to understand the plausibility of polyester microdroplet assembly on early Earth at the origin of life. In particular, there are numerous aqueous environments available on early Earth that could have resulted in varying volumes and concentrations of αHA accumulation, which would have affected subsequent αHA polymerization reactions. Similarly, there were likely varying levels of salt in the various aqueous prebiotic solutions, such as in the ocean, lakes, and small pools, that may have affected primitive reactions. Here, we probe the limits of the dehydration synthesis and subsequent membraneless microdroplet (MMD) assembly of phenyllactic acid (PA), a well-studied αHA relevant to both biology and prebiotic chemistry, with respect to reactant concentration and volume and salinity through mass spectrometry- and microscopy-based observations. Our study showed that polymerization and subsequent microdroplet assembly of PA appear robust even at low reactant concentrations, smaller volumes, and higher salinities than those previously tested. This indicates that PA-polyester and its microdroplets are very much viable under a wide variety of conditions, thus more likely participating in prebiotic chemistries at the origins of life.

Published
2025
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63. Computational Exploration of Lipid Chemical Space: Predicting Assembly Using QSPR Models

Author

Forget, Selene, Cleaves, H. James, Jia, Tony, Gillams, Richard J., and Meringer, Markus

Subjects
machine learning, surfactant molecules, critical micelle concentration, fungi, food and beverages, combinatorial library, quantitative structure-property relationship, Atmosphärenprozessoren
Abstract

Compartmentalization is likely to have been essential for the emergence of life. Compartmentalization allows for the creation of unique chemical conditions that can be maintained out of equilibrium with the environment and the exclusion of parasites. Confining organic molecules also helps limit diffusion, increases concentration and can thus influence both the thermodynamics and kinetics of prebiotic reactions. Biology currently predominantly uses phospholipids to construct cell membranes. However, there are many other types of organic compounds that can form stable compartments in water, and many of these may have been abundant in the prebiotic environment. In this study we explore this alternative lipid chemical space by using structure enumeration algorithms to compute an exhaustive combinatorial library of surfactant molecules. We then predict the propensity of these compounds to self-assemble into membranes using quantitative structure-property relationship (QSPR) models on critical micelle concentration (CMC). Combined with critical packing parameter calculations, these models can allow identification of novel molecule types which can be experimentally assayed as candidates for the emergence of protocells.

Published
2020

72. This white paper is a part of the National Academy of Sciences Astrobiology Science Strategy for the Search for Life in the Universe report assembled by a the world's foremost astrobiology experts, chaired by the University of Toronto's Barbara Sherwood Lollar. Here are links to the report and articles that discuss the paper and the report'http://sites.nationalacademies.org/SSB/CurrentProjects/SSB_180812https://amp.space.com/42086-whats-next-for-astrobiology-at-nasa.htmlhttps://qz.com/1418576/us-scientists-lay-out-plan-to-search-for-life-in-universe/amp

Author

Giri, Chaitanya, Jia, Tony, James, H, Ii, Cleaves, Usui, Tomohiro, Bodas, Dhananjay, Carr, Christopher, Chen, Huan, Fujii, Yuka, Furukawa, Yoshihiro, Genda, Hidenori, Gillams, Richard, Hamano, Keiko, Kameda, Shingo, Krishnamurthy, Ramanarayanan, Meinert, Cornelia, Meringer, Markus, Paknikar, Kishore, Rajamani, Sudha, Shivaji, Sisinthy, Steele, Andrew, Taniguchi, Masateru, Yabuta, Hikaru, Yamagishi, Akihiko, Max Planck Institute for Solar System Research (MPS), Max-Planck-Gesellschaft, Institut de Chimie de Nice (ICN), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Published
2019

73. LIFE-DETECTION TECHNOLOGIES FOR THE NEXT TWO DECADES

Author

Giri, Chaitanya, Jia, Tony, James, H, Ii, Cleaves, Usui, Tomohiro, Bodas, Dhananjay, Carr, Christopher, Chen, Huan, Fujii, Yuka, Furukawa, Yoshihiro, Genda, Hidenori, Gillams, Richard, Hamano, Keiko, Kameda, Shingo, Krishnamurthy, Ramanarayanan, Meinert, Cornelia, Meringer, Markus, Paknikar, Kishore, Rajamani, Sudha, Shivaji, Sisinthy, Steele, Andrew, Taniguchi, Masateru, Yabuta, Hikaru, Yamagishi, Akihiko, Meinert, Cornelia, Max Planck Institute for Solar System Research (MPS), Max-Planck-Gesellschaft, Institut de Chimie de Nice (ICN), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, [SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology, [CHIM.ANAL] Chemical Sciences/Analytical chemistry, [SDU.ASTR]Sciences of the Universe [physics]/Astrophysics [astro-ph], [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDU.STU.PL] Sciences of the Universe [physics]/Earth Sciences/Planetology, [SDU.ASTR] Sciences of the Universe [physics]/Astrophysics [astro-ph]
Published
2019

74. Searches for Technosignatures: The State of the Profession

Author

Wright, Jason, Allen, Veronica, Alvarado-Gómez, Julián D., Angerhausen, Daniel, Apai, Daniel, Atri, Dimitra, Balbi, Amedeo, Barclay, Thomas, Barentsen, Geert, Beasley, Tony, Beatty, Thomas, Behmard, Aida, Berea, Anamaria, Boyajian, Tabetha, Bridge, Joanna S., Bryson, Steve, Bytof, Jeff, Cleaves, Henderson, Colon, Knicole, Cordes, James, Cowing, Keith, Curtis, Jason, Davenport, James, Davies, Paul, DeMarines, Julia, Denning, Kathryn, Dick, Steven, Dong, Chuanfei, Dutil, Yvan, Edmonds, Peter, Enriquez, Emilio, Eubanks, Marshall, Fernandez, Yan, Frank, Adam, De la Torre, Gabriel G., Gajjar, Vishal, Garrett, Michael, Gelino, Dawn, Geller, Harold, Giles, Daniel, Gillum, Eliot, Gomez, Jose L., Graham, R. J., Grimaldi, Claudio, Grinspoon, David, Haqq-Misra, Jacob, Hellbourg, Greg, Helman, Daniel, Horowitz, Paul, Howard, Andrew, Isaacson, Howard, Jackson, Albert, Jia, Tony Z., Kainu, Morgan, Kanodia, Shubham, Kawaler, Steven, Kendall, Shana, Khan, Afshin, Kipping, David, Kite, Edwin, Knuth, Kevin H., Kopparapu, Ravi, Korpela, Eric, Laine, Pauli, Lau, Graham, Lesyna, Larry, Loureiro, Rafael, MacDonald, Mariah, Margot, Jean-Luc, Mendez, Abel, Mishra, Amit, Morrison, Ian, Mullally, Susan, Mullan, Brendan, Nita, Gelu, O'Neil, Karen, Pass, Jim, Paulino-Lima, Ivan Glaucio, Piotelat, Elisabeth, Pope, Benjamin, Raymond, Sean N., Ricker, George, Riley, Crystal S., Robertson, Paul, Rocha, Graça, Rodriguez, Joseph, Rosenthal, Lee, Roy, Arpita, Rybarczyk, Daniel, de Souza, Rafael S., Sallmen, Shauna, Santander, Marcos, Scharf, Caleb, Schwieterman, Edward, Seiler, Douglas, Shabram, Megan, Sheikh, Sofia, Shostak, Seth, Shrestha, Pradipta, Siemion, Andrew, Sigurdsson, Steinn, Sneed, Evan, Socas-Navarro, Hector, Soderblom, David, Solmaz, Arif, Subramaniam, Sadasivan, Suresh, Akshay, Tan, Joshua, Tanner, Angelle, Tarter, Jill, Taylor, Stuart F., Terrien, Ryan, Turner, Jake D., Vakoch, Douglas, Villa, Ciro, Walkowicz, Lucianne, Wang, Sharon Xuesong, Weiss, Lauren, Werthimer, Dan, Williams, David, Winn, Joshua, Wishnow, Ed, Worden, Simon (Pete), Wright, Shelley, Zackrisson, Erik, Zanis, Michael, Zarka, Philippe, Center for Space and Habitability (CSH), University of Bern, Space Telescope Science Institute (STSci), NYUAD Center for Space Science, New York University [Abu Dhabi], NYU System (NYU)-NYU System (NYU), Dipartimento di Fisica, Università di Roma 'Tor Vergata', Università degli Studi di Roma Tor Vergata [Roma], NASA Ames Research Center Cooperative for Research in Earth Science in Technology (ARC-CREST), NASA Ames Research Center (ARC), Department of Geological Sciences [Gainesville] (UF|Geological), University of Florida [Gainesville] (UF), Department of Computer Science [Bath], University of Bath [Bath], Denver Museum of Nature and Science, Princeton University, Department of Physics and Astronomy [Rochester], University of Rochester [USA], Safran Aircraft Engines, Caltech Department of Astronomy [Pasadena], California Institute of Technology (CALTECH), Department of Earth and Planetary Science [UC Berkeley] (EPS), University of California [Berkeley], University of California-University of California, Department of Physics and Astronomy [Iowa City], University of Iowa [Iowa City], Space Sciences Laboratory [Berkeley] (SSL), Department of Biological Sciences (DBS), Central Campus, University of Essex, Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur (LIMSI), Université Paris Saclay (COmUE)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université - UFR d'Ingénierie (UFR 919), Sorbonne Université (SU)-Sorbonne Université (SU)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), ECLIPSE 2019, Laboratoire d'Astrophysique de Bordeaux [Pessac] (LAB), Université de Bordeaux (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Center for Space Research [Cambridge] (CSR), Massachusetts Institute of Technology (MIT), Department of Astronomy [Berkeley], SETI Institute, Université de Montréal (UdeM), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP]
Abstract

International audience; The small size of the SETI workforce is a major problem for NASA and the search for life elsewhere in the universe. The Astro2020 Decadal should address this issue by making nurturing the field an explicit priority for the next decade.

Published
2019

78. Deciphering Biosignatures in Planetary Contexts

Author

Chan, Marjorie A., primary, Hinman, Nancy W., additional, Potter-McIntyre, Sally L., additional, Schubert, Keith E., additional, Gillams, Richard J., additional, Awramik, Stanley M., additional, Boston, Penelope J., additional, Bower, Dina M., additional, Des Marais, David J., additional, Farmer, Jack D., additional, Jia, Tony Z., additional, King, Penelope L., additional, Hazen, Robert M., additional, Léveillé, Richard J., additional, Papineau, Dominic, additional, Rempfert, Kaitlin R., additional, Sánchez-Román, Mónica, additional, Spear, John R., additional, Southam, Gordon, additional, Stern, Jennifer C., additional, and Cleaves, Henderson James, additional

Published
2019
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89. Oligoarginine Peptides Slow Strand Annealing and Assist Nonenzymatic RNA Replication

Author

Jia, Tony Z., Fahrenbach, Albert C., Kamat, Neha P., Adamala, Katarzyna P., and Szostak, Jack W.

Abstract

The nonenzymatic replication of RNA is thought to have been a critical process required for the origin of life. One unsolved difficulty with nonenzymatic RNA replication is that template-directed copying of RNA results in a double-stranded product; following strand separation, rapid strand reannealing outcompetes slow nonenzymatic template copying, rendering multiple rounds of RNA replication impossible. Here we show that oligoarginine peptides slow the annealing of complementary oligoribonucleotides by up to several thousand-fold; however, short primers and activated monomers can still bind to template strands, and template-directed primer extension can still occur within a phase-separated condensed state, or coacervate. Furthermore, we show that within this phase, partial template copying occurs even in the presence of full-length complementary strands. This method for enabling further rounds of replication suggests one mechanism by which short, non-coded peptides could have enhanced early cellular fitness, potentially explaining how longer, coded peptides, i.e. proteins, came to prominence in modern biology.

Published
2016
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90. Peptide-Assisted Nonenzymatic RNA Replication in Coacervate Droplets

Author

Jia, Tony Z.

Subjects
Chemistry, General, Chemistry, Biochemistry
Abstract

Life on earth may have first appeared in the form of a protocell capable of metabolism and containing a self-replicating informational polymer. This polymer was likely to have been RNA due to its ability to serve both as an informational and a catalytic biomolecule in modern life, spawning the “RNA world” hypothesis and suggesting that RNA could have facilitated its own replication without the aid of polymerases. Nonenzymatic replication of RNA was a critical process required for the assembly of the first ribozyme, an essential component for sustained Darwinian evolution. However, template-directed copying of RNA results in a double-stranded product; following strand separation, rapid strand reannealing outcompetes slow nonenzymatic template copying, rendering multiple rounds of RNA replication impossible. The lack of a prebiotically plausible route to an RNA polymerase ribozyme raises questions about a purely RNA world, prompting some to propose a peptide-RNA world wherein peptides and RNA emerged simultaneously and complementarily. Considerable evidence supports the possibility that peptides and RNA were present together on the primitive earth. Arginine-rich peptides are particularly interesting as they can bind strongly to RNA and form coacervate droplets. These droplets can segregate and concentrate biopolymers and can even enhance catalytic activity, leading some to speculate that the earliest protocells may have been membrane-free phase-separated entities similar to coacervate or aqueous two-phase system (ATPS) droplets. We first introduce the processes by which amino acids and peptides could have formed on the abiotic earth and also highlight some prebiotically important features of coacervate droplets. We challenge the broad notion that all peptide-based coacervate droplets should be used as membrane-free protocell models moving forward. We next determine that RNA strands within ATPS and ATP/poly-L-lysine coacervate droplets rapidly exchange with the surrounding aqueous phase, providing once specific example of a coacervate droplet system that is not a suitable membrane-free protocell models. We then show that the annealing of complementary RNA strands is slowed by several orders of magnitude within oligoarginine/RNA coacervate droplets. However, we also observe that primer-template binding and template-directed primer extension can still proceed within these droplets even in the presence of inhibitory strands, providing a pathway by which RNA on the early earth could have replicated and evolved efficiently. This strategy for enabling further rounds of replication suggests one mechanism by which short, non-coded peptides could have enhanced early cellular fitness, potentially explaining how longer, coded peptides, i.e. proteins, came to prominence in modern biology.

Published
2016

92. A General LC-MS-Based Method for Direct and De Novo Sequencing of RNA Mixtures Containing both Canonical and Modified Nucleotides.

Author

Zhang N, Shi S, Yuan X, Ni W, Wang X, Yoo B, Jia TZ, Li W, and Zhang S

Subjects
5-Methylcytosine metabolism, Hydrophobic and Hydrophilic Interactions, Oligonucleotides genetics, Pseudouridine genetics, RNA Processing, Post-Transcriptional genetics, Uridine genetics, Chromatography, Liquid methods, Nucleotides genetics, RNA genetics, Sequence Analysis, RNA methods, Tandem Mass Spectrometry methods
Abstract

Mass spectrometry (MS)-based sequencing has advantages in direct sequencing of RNA, compared to cDNA-based RNA sequencing methods, as it is completely independent of enzymes and base complementarity errors in sample preparation. In addition, it allows for sequencing of different RNA modifications in a single study, rather than just one specific modification type per study. However, many technical challenges remain in de novo MS sequencing of RNA, making it difficult to MS sequence mixed RNAs or to differentiate isomeric modifications such as pseudouridine (Ψ) from uridine (U). Our recent study incorporates a two-dimensional hydrophobic end labeling strategy into MS-based sequencing (2D-HELS MS Seq) to systematically address the current challenges in MS sequencing of RNA, making it possible to directly and de novo sequence purified single RNA and mixed RNA containing both canonical and modified nucleotides. Here, we describe the method to sequence representative single-RNA and mixed-RNA oligonucleotides, each with a different sequence and/or containing modified nucleotides such as Ψ and 5-methylcytosine (m 5 C), using 2D-HELS MS Seq.

Published
2021
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93. Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry.

Author

Chandru K, Mamajanov I, Cleaves HJ 2nd, and Jia TZ

Abstract

A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored., Competing Interests: The authors declare no conflict of interest

Published
2020
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