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Snyman M, Xu S. Transcriptomics and the origin of obligate parthenogenesis. Heredity (Edinb) 2023:10.1038/s41437-023-00628-3. [PMID: 37280308 PMCID: PMC10382572 DOI: 10.1038/s41437-023-00628-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 06/08/2023] Open
Abstract
Despite the presence of obligately parthenogenetic (OP) lineages derived from sexual ancestors in diverse phylogenetic groups, the genetic mechanisms giving rise to the OP lineages remain poorly understood. The freshwater microcrustacean Daphnia pulex typically reproduces via cyclical parthenogenesis. However, some populations of OP D. pulex have emerged due to ancestral hybridization and introgression events between two cyclically parthenogenetic (CP) species D. pulex and D. pulicaria. These OP hybrids produce both subitaneous and resting eggs parthenogenetically, deviating from CP isolates where resting eggs are produced via conventional meiosis and mating. This study examines the genome-wide expression and alternative splicing patterns of early subitaneous versus early resting egg production in OP D. pulex isolates to gain insight into the genes and mechanisms underlying this transition to obligate parthenogenesis. Our differential expression and functional enrichment analyses revealed a downregulation of meiosis and cell cycle genes during early resting egg production, as well as divergent expression patterns of metabolism, biosynthesis, and signaling pathways between the two reproductive modes. These results provide important gene candidates for future experimental verification, including the CDC20 gene that activates the anaphase-promoting complex in meiosis.
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Affiliation(s)
- Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, 75235, USA
| | - Sen Xu
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
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2
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Guo Z. The Structural Diversity of Natural Glycosphingolipids (GSLs). J Carbohydr Chem 2022; 41:63-154. [PMID: 36561362 PMCID: PMC9770679 DOI: 10.1080/07328303.2022.2063308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glycosphingolipids (GSLs) are a subclass of glycolipids made of a glycan and a ceramide that, in turn, is composed of a sphingoid base moiety and a fatty acyl group. GSLs represent the vast majority of glycolipids in eukaryotes, and as an essential component of the cell membrane, they play an important role in many biological and pathological processes. Therefore, they are useful targets for the development of novel diagnostic and therapeutic methods for human diseases. Since sphingosine was first described by J. L. Thudichum in 1884, several hundred GSL species, not including their diverse lipid forms that can further amplify the number of individual GSLs by many folds, have been isolated from natural sources and structurally characterized. This review tries to provide a comprehensive survey of the major GSL species, especially those with distinct glycan structures and modification patterns, and the ceramides with unique modifications of the lipid chains, that have been discovered to date. In particular, this review is focused on GSLs from eukaryotic species. This review has listed 251 GSL glycans with different linkages, 127 glycans with unique modifications, 46 sphingoids, and 43 fatty acyl groups. It should be helpful for scientists who are interested in GSLs, from isolation and structural analyses to chemical and enzymatic syntheses, as well as their biological studies and applications.
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3
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Characterization of lipid composition in the muscle tissue of four shrimp species commonly consumed in China by UPLC−Triple TOF−MS/MS. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109469] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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4
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Lopalco P, Lobasso S, Lopes-Dos-Santos RMA, Van Stappen G, Corcelli A. Lipid Profile Changes During the Development of Artemia franciscana, From Cysts to the First Two Naupliar Stages. Front Physiol 2019; 9:1872. [PMID: 30723418 PMCID: PMC6349733 DOI: 10.3389/fphys.2018.01872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/11/2018] [Indexed: 11/18/2022] Open
Abstract
The brine shrimp Artemia is an interesting experimental system for studies of developmental processes. Hatching of dormant cysts gives rise to shrimp larvae called nauplii, characterized by numerous naupliar stages representing the first forms of brine shrimp life cycle. Here combined Thin Layer Chromatography (TLC) and Matrix-Assisted Laser Desorption Ionization-Time-of-Flight/Mass Spectrometry (MALDI-TOF/MS) analyses have been performed to gain information on the lipid profiles of cysts and two naupliar stages. Lipid bands isolated after preparative TLC of the lipid extracts have been analyzed to detect various species of each lipid class; in addition Post-Source Decay (PSD) analyses allowed the identification of phospholipid chains. We compared the relative abundance of various polar and neutral lipid species in the lipid extracts, proving for the first time that during the development of nauplii there is an increase of cardiolipin (CL) and lysophospholipid levels; in parallel, the amount of phosphatidylcholine (PC) decreases. In addition, as regards neutral lipids, we found an increase of diacylglycerols (DAGs) in correspondence of the decrease of triacylglycerols (TAGs). Data reflect the fact that naupliar stages, being an active form of life, are more metabolically active and offer a platform to develop further studies on the importance of lipid metabolic pathways and bioactive lipids during the development.
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Affiliation(s)
- Patrizia Lopalco
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Simona Lobasso
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | | | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Ghent, Belgium
| | - Angela Corcelli
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
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5
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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Itonori S, Hashimoto K, Nakagawa M, Harada M, Suzuki T, Kojima H, Ito M, Sugita M. Structural analysis of neutral glycosphingolipids from the silkworm Bombyx mori and the difference in ceramide composition between larvae and pupae. J Biochem 2018; 163:201-214. [PMID: 29069405 DOI: 10.1093/jb/mvx072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 09/08/2017] [Indexed: 01/06/2023] Open
Abstract
Glycosphingolipids (GSLs) from the silkworm Bombyx mori were identified and GSL expression patterns between larvae and pupae were compared. The structural analysis of neutral GSLs from dried pupae revealed the following predominant species: Glcβ1Cer, Manβ4Glcβ1Cer, GlcNAcβ3Manβ4Glcβ1Cer, Galβ3Manβ4Glcβ1Cer, GalNAcα4Galβ3Manβ4Glcβ1Cer, GlcNAcβ3Galβ3Manβ4Glcβ1Cer, Galα4Galβ3Manβ4Glcβ1Cer and (GalNAcα4)1-4 GalNAcα4Galβ3Manβ4Glcβ1Cer. Lin-ear elongation of α4-GalNAc was observed at the non-reducing end of Galβ3Manβ4Glcβ1Cer with up to five GalNAc repeats. The arthro-series GSL GlcNAcβ3Manβ4Glcβ1Cer, a characteristic GSL-glycan sequence of other Arthropoda, was detected in silkworms. The main ceramide species in each purified GSL fraction were h20:0-d14:1 and h22:0-d14:1. GSL expression patterns in larvae and pupae were compared using thin-layer chromatography, which demonstrated differences among acidic, polar and neutral GSL fractions, while the zwitterionic fraction showed no difference. Neutral GSLs such as ceramides di-, tri- and tetrasaccharides in larvae showed less abundant than those in pupae. MALDI-TOF MS analysis revealed that larval GSLs contained four types of ceramide species, whereas pupal GSLs contained only two types. The structural analysis of neutral GSLs from silkworms revealed a novel series of GSLs. The comparison of GSL expression patterns between larvae and pupae demonstrated differences in several fractions. Alterations in GSL ceramide composition between larvae and pupae were observed by MALDI-TOF MS analysis.
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Affiliation(s)
- Saki Itonori
- Department of Chemistry, Faculty of Liberal Arts and Education, Shiga University, 2-5-1, Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Kyouhei Hashimoto
- Department of Chemistry, Faculty of Liberal Arts and Education, Shiga University, 2-5-1, Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Mika Nakagawa
- Department of Chemistry, Faculty of Liberal Arts and Education, Shiga University, 2-5-1, Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Masashi Harada
- Department of Chemistry, Faculty of Liberal Arts and Education, Shiga University, 2-5-1, Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Takae Suzuki
- Department of Chemistry, Faculty of Liberal Arts and Education, Shiga University, 2-5-1, Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Hisao Kojima
- Department of Bioinformatics, Institute of Science and Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Masahiro Ito
- Department of Bioinformatics, Institute of Science and Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Mutsumi Sugita
- Department of Chemistry, Faculty of Liberal Arts and Education, Shiga University, 2-5-1, Hiratsu, Otsu, Shiga 520-0862, Japan
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The total and mitochondrial lipidome of Artemia franciscana encysted embryos. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1727-1735. [DOI: 10.1016/j.bbalip.2016.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/22/2016] [Accepted: 08/15/2016] [Indexed: 01/12/2023]
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8
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Ramachandran GK, Yong WP, Yeow CH. Identification of Gastric Cancer Biomarkers Using 1H Nuclear Magnetic Resonance Spectrometry. PLoS One 2016; 11:e0162222. [PMID: 27611679 PMCID: PMC5017672 DOI: 10.1371/journal.pone.0162222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/18/2016] [Indexed: 12/16/2022] Open
Abstract
Existing gastric cancer diagnosing methods were invasive, hence, a reliable non-invasive gastric cancer diagnosing method is needed. As a starting point, we used 1H NMR for identifying gastric cancer biomarkers using a panel of gastric cancer spheroids and normal gastric spheroids. We were able to identify 8 chemical shift biomarkers for gastric cancer spheroids. Our data suggests that the cancerous and non-cancerous spheroids significantly differ in the lipid composition and energy metabolism. These results encourage the translation of these biomarkers into in-vivo gastric cancer detection methodology using MRI-MS.
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Affiliation(s)
| | - Wei Peng Yong
- Department of Haematology-Oncology, National University Cancer Institute, Singapore (NCIS), Singapore
| | - Chen Hua Yeow
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
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Scanlan LD, Loguinov AV, Teng Q, Antczak P, Dailey KP, Nowinski DT, Kornbluh J, Lin XX, Lachenauer E, Arai A, Douglas NK, Falciani F, Stapleton HM, Vulpe CD. Gene transcription, metabolite and lipid profiling in eco-indicator daphnia magna indicate diverse mechanisms of toxicity by legacy and emerging flame-retardants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7400-10. [PMID: 25985095 PMCID: PMC4835823 DOI: 10.1021/acs.est.5b00977] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The use of chemical flame-retardants (FR) in consumer products has steadily increased over the last 30 years. Toxicity data exist for legacy FRs such as pentabromodiphenyl ether (pentaBDE), but less is known about effects of new formulations. To address this issue, the toxicity of seven FR chemicals and formulations was assessed on the freshwater crustacean Daphnia magna. Acute 48-h nominal LC50 values for penta- and octabromodiphenyl ether (pentaBDE, octaBDE), Firemaster 550 (FM550), Firemaster BZ-54 (BZ54), bis(2-ethylhexyl) tetrabromophthalate (BEH-TEBP), triphenyl phosphate (TPhP), and nonbrominated BEH-TEBP analog bis(2-ethylhexyl) phthalate (BEHP) ranged from 0.058 mg/L (pentaBDE) to 3.96 mg/L (octaBDE). mRNA expression, (1)H NMR-based metabolomic and lipidomic profiling at 1/10 LC50 revealed distinct patterns of molecular response for each exposure, suggesting pentaPBDE affects transcription and translation, octaBDE and BEH-TEBP affect glycosphingolipid biosynthesis and BZ54 affects Wnt and Hedgehog signal pathways as well as glycosaminoglycan degradation. Brominated components of FM550 (i.e., BZ54) were significantly higher in Daphnia after 48 h following 1/10 LC50 exposure. FM550 elicited significant mRNA changes at five concentrations across a range from 1/10(6) LC50 to 1/2 LC50. Analyses suggest FM550 impairs nutrient utilization or uptake in Daphnia.
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Affiliation(s)
- Leona D. Scanlan
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
| | - Alexandre V. Loguinov
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
| | - Quincy Teng
- U.S. EPA, National Exposure Research Laboratory, Athens, Georgia 30605, United States
| | - Philipp Antczak
- University of Liverpool Institute for Integrative Biology, Liverpool, L69 7ZB, United Kingdom
| | - Kathleen P. Dailey
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
| | - Daniel T. Nowinski
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
| | - Jonah Kornbluh
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
| | - Xin Xin Lin
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
| | - Erica Lachenauer
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
| | - Audrey Arai
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
| | - Nora K. Douglas
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
| | - Francesco Falciani
- University of Liverpool Institute for Integrative Biology, Liverpool, L69 7ZB, United Kingdom
| | - Heather M. Stapleton
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27708, United States
| | - Chris D. Vulpe
- University of California Berkeley, Department of Nutritional Sciences and Toxicology, Berkeley, California 94720, United States
- Corresponding Author.
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Gallo A, Costantini M. Glycobiology of reproductive processes in marine animals: the state of the art. Mar Drugs 2012; 10:2861-92. [PMID: 23247316 PMCID: PMC3528131 DOI: 10.3390/md10122861] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/23/2012] [Accepted: 11/29/2012] [Indexed: 10/31/2022] Open
Abstract
Glycobiology is the study of complex carbohydrates in biological systems and represents a developing field of science that has made huge advances in the last half century. In fact, it combines all branches of biomedical research, revealing the vast and diverse forms of carbohydrate structures that exist in nature. Advances in structure determination have enabled scientists to study the function of complex carbohydrates in more depth and to determine the role that they play in a wide range of biological processes. Glycobiology research in marine systems has primarily focused on reproduction, in particular for what concern the chemical communication between the gametes. The current status of marine glycobiology is primarily descriptive, devoted to characterizing marine glycoconjugates with potential biomedical and biotechnological applications. In this review, we describe the current status of the glycobiology in the reproductive processes from gametogenesis to fertilization and embryo development of marine animals.
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Affiliation(s)
| | - Maria Costantini
- Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy; E-Mail:
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