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Fifer LM, Wong ML. Quantifying the Potential for Nitrate-Dependent Iron Oxidation on Early Mars: Implications for the Interpretation of Gale Crater Organics. ASTROBIOLOGY 2024; 24:590-603. [PMID: 38805190 DOI: 10.1089/ast.2023.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Geological evidence and atmospheric and climate models suggest habitable conditions occurred on early Mars, including in a lake in Gale crater. Instruments aboard the Curiosity rover measured organic compounds of unknown provenance in sedimentary mudstones at Gale crater. Additionally, Curiosity measured nitrates in Gale crater sediments, which suggests that nitrate-dependent Fe2+ oxidation (NDFO) may have been a viable metabolism for putative martian life. Here, we perform the first quantitative assessment of an NDFO community that could have existed in an ancient Gale crater lake and quantify the long-term preservation of biological necromass in lakebed mudstones. We find that an NDFO community would have the capacity to produce cell concentrations of up to 106 cells mL-1, which is comparable to microbes in Earth's oceans. However, only a concentration of <104 cells mL-1, due to organisms that inefficiently consume less than 10% of precipitating nitrate, would be consistent with the abundance of organics found at Gale. We also find that meteoritic sources of organics would likely be insufficient as a sole source for the Gale crater organics, which would require a separate source, such as abiotic hydrothermal or atmospheric production or possibly biological production from a slowly turning over chemotrophic community.
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Affiliation(s)
- Lucas M Fifer
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
- Astrobiology Program, University of Washington, Seattle, Washington, USA
| | - Michael L Wong
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC, USA
- NHFP Sagan Fellow, NASA Hubble Fellowship Program, Space Telescope Science Institute, Baltimore, Maryland, USA
- NASA Nexus for Exoplanet System Science, Virtual Planetary Laboratory Team, University of Washington, Seattle, Washington, USA
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2
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Zhang J, Zhang Y, Ma Z. In silico Prediction of Human Secretory Proteins in Plasma Based on Discrete Firefly Optimization and Application to Cancer Biomarkers Identification. Front Genet 2019; 10:542. [PMID: 31244885 PMCID: PMC6563772 DOI: 10.3389/fgene.2019.00542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022] Open
Abstract
The early control and prevention of cancer contributes effectively interventions and cancer therapies. Secretory protein, one of the richest biomarkers, is proved important as molecular signposts of the physiological state of a cell. In this work, we aim to propose a proteomic high-throughput technology platform to facilitate detection of early cancer by means of biomarkers that secreted into the bloodstream. We compile a new benchmark dataset of human secretory proteins in plasma. A series of sequence-derived features, which have been proved involved in the structure and function of the secretory proteins, are collected to mathematically encode these proteins. Considering the influence of potential irrelevant or redundant features, we introduce discrete firefly optimization algorithm to perform feature selection. We evaluate and compare the proposed method SCRIP (Secretory proteins in plasma) with state-of-the-art approaches on benchmark datasets and independent testing datasets. SCRIP achieves the average AUC values of 0.876 and 0.844 in five-fold the cross-validation and independent test, respectively. Besides that, we also test SCRIP on proteins in four types of cancer tissues and successfully detect 66∼77% potential cancer biomarkers.
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Affiliation(s)
- Jian Zhang
- School of Computer and Information Technology, Xinyang Normal University, Xinyang, China
- Henan Key Laboratory of Education Big Data Analysis and Application, Xinyang, China
| | - Yu Zhang
- Information Engineering College, Huanghuai University, Zhumadian, China
- Henan Key Laboratory of Smart Lighting, Zhumadian, China
| | - Zhiqiang Ma
- Department of Computer Science, College of Humanities & Sciences of Northeast Normal University, Changchun, China
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3
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Merino N, Aronson HS, Bojanova DP, Feyhl-Buska J, Wong ML, Zhang S, Giovannelli D. Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context. Front Microbiol 2019; 10:780. [PMID: 31037068 PMCID: PMC6476344 DOI: 10.3389/fmicb.2019.00780] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/27/2019] [Indexed: 01/21/2023] Open
Abstract
Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.
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Affiliation(s)
- Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, United States
| | - Heidi S Aronson
- Department of Biology, University of Southern California, Los Angeles, CA, United States
| | - Diana P Bojanova
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jayme Feyhl-Buska
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michael L Wong
- Department of Astronomy - Astrobiology Program, University of Washington, Seattle, WA, United States.,NASA Astrobiology Institute's Virtual Planetary Laboratory, University of Washington, Seattle, WA, United States
| | - Shu Zhang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Biology, University of Naples "Federico II", Naples, Italy.,Department of Marine and Coastal Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,Institute for Biological Resources and Marine Biotechnology, National Research Council of Italy, Ancona, Italy
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4
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Venev SV, Zeldovich KB. Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis. Mol Biol Evol 2019; 35:211-224. [PMID: 29106597 PMCID: PMC5850847 DOI: 10.1093/molbev/msx282] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Prokaryotes evolved to thrive in an extremely diverse set of habitats, and their proteomes bear signatures of environmental conditions. Although correlations between amino acid usage and environmental temperature are well-documented, understanding of the mechanisms of thermal adaptation remains incomplete. Here, we couple the energetic costs of protein folding and protein homeostasis to build a microscopic model explaining both the overall amino acid composition and its temperature trends. Low biosynthesis costs lead to low diversity of physical interactions between amino acid residues, which in turn makes proteins less stable and drives up chaperone activity to maintain appropriate levels of folded, functional proteins. Assuming that the cost of chaperone activity is proportional to the fraction of unfolded client proteins, we simulated thermal adaptation of model proteins subject to minimization of the total cost of amino acid synthesis and chaperone activity. For the first time, we predicted both the proteome-average amino acid abundances and their temperature trends simultaneously, and found strong correlations between model predictions and 402 genomes of bacteria and archaea. The energetic constraint on protein evolution is more apparent in highly expressed proteins, selected by codon adaptation index. We found that in bacteria, highly expressed proteins are similar in composition to thermophilic ones, whereas in archaea no correlation between predicted expression level and thermostability was observed. At the same time, thermal adaptations of highly expressed proteins in bacteria and archaea are nearly identical, suggesting that universal energetic constraints prevail over the phylogenetic differences between these domains of life.
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Affiliation(s)
- Sergey V Venev
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation St, Worcester, MA
| | - Konstantin B Zeldovich
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation St, Worcester, MA
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Radiation-Resistant Micrococcus luteus SC1204 and Its Proteomics Change Upon Gamma Irradiation. Curr Microbiol 2016; 72:767-75. [DOI: 10.1007/s00284-016-1015-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/13/2016] [Indexed: 10/22/2022]
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Aridhi S, Sghaier H, Zoghlami M, Maddouri M, Nguifo EM. Prediction of Ionizing Radiation Resistance in Bacteria Using a Multiple Instance Learning Model. J Comput Biol 2016; 23:10-20. [DOI: 10.1089/cmb.2015.0134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Sabeur Aridhi
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
| | - Haïtham Sghaier
- National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Ariana, Tunisia
- Laboratory BVBGR, ISBST, University of Manouba, La Manouba, Tunisia
| | - Manel Zoghlami
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
| | - Mondher Maddouri
- University of Tunis El Manar, Faculty of Sciences of Tunis, LIPAH, Tunis, Tunisia
- Taibah University, Medinah, Saudi Arabia
| | - Engelbert Mephu Nguifo
- Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS)–Université Blaise Pascal (UBP), Clermont Ferrand, France
- Centre National de Recherche Scientifique (CNRS), UMR 6158, LIMOS, Aubière, France
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Vieira HGS, Grynberg P, Bitar M, Pires SDF, Hilário HO, Macedo AM, Machado CR, de Andrade HM, Franco GR. Proteomic analysis of Trypanosoma cruzi response to ionizing radiation stress. PLoS One 2014; 9:e97526. [PMID: 24842666 PMCID: PMC4026238 DOI: 10.1371/journal.pone.0097526] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 04/22/2014] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, is extremely resistant to ionizing radiation, enduring up to 1.5 kGy of gamma rays. Ionizing radiation can damage the DNA molecule both directly, resulting in double-strand breaks, and indirectly, as a consequence of reactive oxygen species production. After a dose of 500 Gy of gamma rays, the parasite genome is fragmented, but the chromosomal bands are restored within 48 hours. Under such conditions, cell growth arrests for up to 120 hours and the parasites resume normal growth after this period. To better understand the parasite response to ionizing radiation, we analyzed the proteome of irradiated (4, 24, and 96 hours after irradiation) and non-irradiated T. cruzi using two-dimensional differential gel electrophoresis followed by mass spectrometry for protein identification. A total of 543 spots were found to be differentially expressed, from which 215 were identified. These identified protein spots represent different isoforms of only 53 proteins. We observed a tendency for overexpression of proteins with molecular weights below predicted, indicating that these may be processed, yielding shorter polypeptides. The presence of shorter protein isoforms after irradiation suggests the occurrence of post-translational modifications and/or processing in response to gamma radiation stress. Our results also indicate that active translation is essential for the recovery of parasites from ionizing radiation damage. This study therefore reveals the peculiar response of T. cruzi to ionizing radiation, raising questions about how this organism can change its protein expression to survive such a harmful stress.
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Affiliation(s)
| | - Priscila Grynberg
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
| | - Mainá Bitar
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Simone da Fonseca Pires
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Heron Oliveira Hilário
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andrea Mara Macedo
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Hélida Monteiro de Andrade
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glória Regina Franco
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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