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Dupree EJ, Manzoor Z, Alwine S, Crimmins BS, Holsen TM, Darie CC. Proteomic analysis of the lake trout (Salvelinus namaycush) heart and blood: The beginning of a comprehensive lake trout protein database. Proteomics 2021; 22:e2100146. [PMID: 34676671 DOI: 10.1002/pmic.202100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022]
Abstract
Lake trout (Salvelinus namaycush) are a top-predator species in the Laurentian Great Lakes that are often used as bioindicators of chemical stressors in the ecosystem. Although many studies are done using these fish to determine concentrations of stressors like legacy persistent, bioaccumulative and toxic chemicals, there are currently no proteomic studies on the biological effects these stressors have on the ecosystem. This lack of proteomic studies on Great Lakes lake trout is because there is currently no complete, comprehensive protein database for this species. Here, we employed proteomics approaches to develop a lake trout protein database that could aid in future research on this fish, in particular exposomics and adductomics. The current study utilized heart tissue and blood from two lake trout. Our previous work using lake trout liver revealed 4194 potential protein hits in the NCBI databases and 3811 potential protein hits in the UniProtKB databases. In the current study, using the NCBI databases we identified 838 proteins for the heart and 580 proteins for the blood tissues in the biological replicate 1 (BR1) and 1180 potential protein hits for the heart and 561 potential protein hits for the blood in BR2. Similar results were obtained using the UniProtKB databases. This study builds on our previous work by continuing to build the first comprehensive lake trout protein database and provides insight into protein homology through evolutionary relationships. This data is available via the PRIDE partner repository with the dataset identifier PXD023970.
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Affiliation(s)
- Emmalyn J Dupree
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
| | - Zaen Manzoor
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
| | - Shelby Alwine
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
| | - Bernard S Crimmins
- Department of Civil and Environmental Engineering, Clarkson University, Potsdam, New York, USA
- AEACS, LLC, New Kensington, Pennsylvania, USA
| | - Thomas M Holsen
- Department of Civil and Environmental Engineering, Clarkson University, Potsdam, New York, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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Dupree EJ, Darie CC. Examination of a non-invasive biomarker for the diagnosis of prodromal Alzheimer's disease and Alzheimer's disease Dementia. EBioMedicine 2020; 57:102882. [PMID: 32650274 PMCID: PMC7341362 DOI: 10.1016/j.ebiom.2020.102882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, USA, 13699-5810
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, USA, 13699-5810; To whom inquiries should be addressed:.
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Dupree EJ, Crimmins BS, Holsen TM, Darie CC. Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Liver Identifies Proteins from Evolutionarily Close and -Distant Fish Relatives. Proteomics 2019; 19:e1800429. [PMID: 31578773 DOI: 10.1002/pmic.201800429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 09/12/2019] [Indexed: 12/20/2022]
Abstract
Lake trout are used as bioindicators for toxics exposure in the Great Lakes ecosystem. Here the first lake trout (Salvelinus namaycush) liver proteomics study is performed and searched against specific databases: (NCBI and UniProtKB) Salvelinus, Salmonidae, Actinopterygii, and Oncorhynchus mykiss, and the more distant relative, Danio rerio. In the biological replicate 1 (BR1), technical replicate 1 (TR1), (BR1TR1), a large number of lake trout liver proteins are not in the Salvelinus protein database, suggesting that lake trout liver proteins have homology to some proteins from the Salmonidae family and Actinopterygii class, and to Oncorhynchus mykiss and Danio rerio, two more highly studied fish. In the NCBI search, 4194 proteins are identified: 3069 proteins in Actinopterygii, 1617 in Salmonidae, 68 in Salvelinus, 568 in Oncorhynchus mykiss, and 946 in Danio rerio protein databases. Similar results are observed in the UniProtKB searches of BR1RT1, as well as in a technical replicate (BR1TR2), and then in a second biological replicate experiment, with two technical replicates (BR2TR1 and BR2TR2). This study opens the possibility of identifying evolutionary relationships (i.e., adaptive mutations) between various groups (i.e., zebrafish, rainbow trout, Salmonidae, Salvelinus and lake trout) through evolutionary proteomics. Data are available via the PRIDE Q2 (PXD011924).
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Affiliation(s)
- Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA
| | - Bernard S Crimmins
- Department of Environmental Engineering, Clarkson University, Potsdam, NY, 13699-5708, USA.,AEACS, LLC, New Kensington, PA, 15068, USA
| | - Thomas M Holsen
- Department of Environmental Engineering, Clarkson University, Potsdam, NY, 13699-5708, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA
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Ngounou Wetie AG, Sokolowska I, Channaveerappa D, Dupree EJ, Jayathirtha M, Woods AG, Darie CC. Proteomics and Non-proteomics Approaches to Study Stable and Transient Protein-Protein Interactions. Advances in Experimental Medicine and Biology 2019; 1140:121-142. [DOI: 10.1007/978-3-030-15950-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mihăşan M, Babii C, Aslebagh R, Channaveerappa D, Dupree EJ, Darie CC. Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics. Advances in Experimental Medicine and Biology 2019; 1140:515-529. [DOI: 10.1007/978-3-030-15950-4_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
Fatigue is a common and poorly understood problem that impacts approximately 45% of the United States (US) population. Fatigue has also been associated with fatigue-related driving accidents, school absences, decline in school performance and negative health outcomes. Fatigue has been linked to many diseases and is consistently underreported in medical care. Despite these high financial and societal costs, fatigue is a poorly understood problem and there is no consensus on how to measure fatigue. Proteomics is one of the most unbiased approach to measure differences in the protein levels from various biological fluids in two conditions, i.e. before and after mental exercise, aka fatigue. There are, however, challenges associated with such analyses: proteomics experiments are usually expensive and time consuming and also require a large number of participants. Here, we performed a proteomics experiment of three (pre- and post-fatigue) samples and also three matched controls (pre- and post-non-fatigue). We found no particular protein that has significant changes in fatigue sample upon treatment. We did note a potential association between changes in mental energy and Annexin A1. However, the study has value simply because it is an extra study in the field of fatigue, but also allows other to correlate our results with their results.
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Affiliation(s)
- Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Aurora Goodwin
- Applied Physiology and Psychology Lab, Department of Physical Therapy, Clarkson University, Potsdam, NY, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Ali Boolani
- Applied Physiology and Psychology Lab, Department of Physical Therapy, Clarkson University, Potsdam, NY, USA.
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Woods AG, Sokolowska I, Ngounou Wetie AG, Channaveerappa D, Dupree EJ, Jayathirtha M, Aslebagh R, Wormwood KL, Darie CC. Mass Spectrometry for Proteomics-Based Investigation. Advances in Experimental Medicine and Biology 2019; 1140:1-26. [DOI: 10.1007/978-3-030-15950-4_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Wormwood KL, Aslebagh R, Channaveerappa D, Dupree EJ, Borland MM, Ryan JP, Darie CC, Woods AG. Salivary proteomics and biomarkers in neurology and psychiatry. Proteomics Clin Appl 2015; 9:899-906. [PMID: 25631118 DOI: 10.1002/prca.201400153] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/04/2014] [Accepted: 01/27/2015] [Indexed: 12/30/2022]
Abstract
Biomarkers are greatly needed in the fields of neurology and psychiatry, to provide objective and earlier diagnoses of CNS conditions. Proteomics and other omics MS-based technologies are tools currently being utilized in much recent CNS research. Saliva is an interesting alternative biomaterial for the proteomic study of CNS disorders, with several advantages. Collection is noninvasive and saliva has many proteins. It is easier to collect than blood and can be collected by professionals without formal medical training. For psychiatric and neurological patients, supplying a saliva sample is less anxiety-provoking than providing a blood sample, and is less embarrassing than producing a urine specimen. The use of saliva as a biomaterial has been researched for the diagnosis of and greater understanding of several CNS conditions, including neurodegenerative diseases, autism, and depression. Salivary biomarkers could be used to rule out nonpsychiatric conditions that are often mistaken for psychiatric/neurological conditions, such as fibromyalgia, and potentially to assess cognitive ability in individuals with compromised brain function. As MS and omics technology advances, the sensitivity and utility of assessing CNS conditions using distal human biomaterials such as saliva is becoming increasingly possible.
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Affiliation(s)
- Kelly L Wormwood
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Roshanak Aslebagh
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Devika Channaveerappa
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Emmalyn J Dupree
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Megan M Borland
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Jeanne P Ryan
- Department of Psychology, SUNY Plattsburgh, Plattsburgh, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Alisa G Woods
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.,Center for Neurobehavioral Health, SUNY Plattsburgh, Plattsburgh, NY, USA
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