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Li Q, Gao L, Liu L, Wang L, Hu L, Wang L, Song L. Marine thermal fluctuation induced gluconeogenesis by the transcriptional regulation of CgCREBL2 in Pacific oysters. MARINE POLLUTION BULLETIN 2024; 207:116906. [PMID: 39217871 DOI: 10.1016/j.marpolbul.2024.116906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Marine thermal fluctuation profoundly influences energy metabolism, physiology, and survival of marine life. In the present study, short-term and long-term high-temperature stresses were found to affect gluconeogenesis by inhibiting PEPCK activity in the Pacific oyster (Crassostrea gigas), which is a globally distributed species that encounters significant marine thermal fluctuations in intertidal zones worldwide. CgCREBL2, a key molecule in the regulation of gluconeogenesis, plays a critical role in the transcriptional regulation of PEPCK in gluconeogenesis against high-temperature stress. CgCREBL2 was able to increase the transcription of CgPEPCK by either binding the promoter of CgPEPCK gene or activating CgPGC-1α and CgHNF-4α after short-term (6 h) high-temperature stress, while only by binding CgPEPCK after long-term (60 h) high-temperature stress. These findings will further our understanding of the effect of marine thermal fluctuation on energy metabolism on marine organisms.
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Affiliation(s)
- Qingsong Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Lei Gao
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China.
| | - Lu Liu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Ling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Li Hu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China.
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Vello F, Filippini F, Righetto I. Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research. Viruses 2024; 16:1425. [PMID: 39339901 PMCID: PMC11437414 DOI: 10.3390/v16091425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/21/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Computer-aided analysis of proteins or nucleic acids seems like a matter of course nowadays; however, the history of Bioinformatics and Computational Biology is quite recent. The advent of high-throughput sequencing has led to the production of "big data", which has also affected the field of virology. The collaboration between the communities of bioinformaticians and virologists already started a few decades ago and it was strongly enhanced by the recent SARS-CoV-2 pandemics. In this article, which is the first in a series on how bioinformatics can enhance virus research, we show that highly useful information is retrievable from selected general and dedicated databases. Indeed, an enormous amount of information-both in terms of nucleotide/protein sequences and their annotation-is deposited in the general databases of international organisations participating in the International Nucleotide Sequence Database Collaboration (INSDC). However, more and more virus-specific databases have been established and are progressively enriched with the contents and features reported in this article. Since viruses are intracellular obligate parasites, a special focus is given to host-pathogen protein-protein interaction databases. Finally, we illustrate several phylogenetic and phylodynamic tools, combining information on algorithms and features with practical information on how to use them and case studies that validate their usefulness. Databases and tools for functional inference will be covered in the next article of this series: Bioinformatics goes viral: II. Sequence-based and structure-based functional analyses for boosting virus research.
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Affiliation(s)
| | - Francesco Filippini
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, 35131 Padua, Italy; (F.V.); (I.R.)
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Yilmaz S, Moulahoum H, Tok K, Zihnioglu F. Discarded CHO cells as a valuable source of bioactive peptides for sustainable biotechnological applications. Int J Biol Macromol 2024; 272:132869. [PMID: 38838895 DOI: 10.1016/j.ijbiomac.2024.132869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/15/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024]
Abstract
Repurposing discarded cells stands as a groundbreaking paradigm shift in sustainable biotechnology, with profound implications across diverse industrial sectors. Our study proposes a transformative concept by harnessing histone proteins from discarded CHO cells to produce bioactive peptides. We systematically isolated and hydrolyzed histones using Trypsin and Neutrase enzymes, optimizing reaction conditions. Ultrafiltration yielded distinct peptide fractions (<3 kDa and 3-10 kDa), which we analyzed for DPP-IV inhibition, antioxidant potential, and other activities. Furthermore, LC-Q-TOF-MS analysis and in silico tools unveiled the structural composition of bioactive peptides within these fractions. Three peptide sequences with high bioactivity potential were identified: KLPFQR, VNRFLR, and LSSCAPVFL. Our findings demonstrated exceptional DPP-IV inhibition, potent antioxidant effects, and effective anti-lipid peroxidation activities, surpassing reference compounds. Hemolytic activity assessment indicated promising biocompatibility, enhancing therapeutic application prospects. Pioneering the strategic repurposing of discarded cells, this research addresses cost-efficiency in cell-based studies and promotes sustainable use of biological resources across sectors. This novel approach offers an efficient, eco-friendly method for bioactive molecule procurement and resource management, revolutionizing cell culture studies and biotechnological applications.
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Affiliation(s)
- Sude Yilmaz
- Biochemistry Department, Faculty of Science, Ege University, Bornova 35040, Izmir, Turkey
| | - Hichem Moulahoum
- Biochemistry Department, Faculty of Science, Ege University, Bornova 35040, Izmir, Turkey.
| | - Kerem Tok
- Biochemistry Department, Faculty of Science, Ege University, Bornova 35040, Izmir, Turkey
| | - Figen Zihnioglu
- Biochemistry Department, Faculty of Science, Ege University, Bornova 35040, Izmir, Turkey.
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Puerta-Arias JD, Isaza Agudelo JP, Naranjo Preciado TW. Identification and production of novel potential pathogen-specific biomarkers for diagnosis of histoplasmosis. Microbiol Spectr 2023; 11:e0093923. [PMID: 37882565 PMCID: PMC10714873 DOI: 10.1128/spectrum.00939-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/08/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Histoplasmosis is considered one of the most important mycoses due to the increasing number of individuals susceptible to develop severe clinical forms, particularly those with HIV/AIDS or receiving immunosuppressive biological therapies, the high mortality rates reported when antifungal treatment is not initiated in a timely manner, and the limitations of conventional diagnostic methods. In this context, there is a clear need to improve the capacity of diagnostic tools to specifically detect the fungal pathogen, regardless of the patient's clinical condition or the presence of other co-infections. The proposed novel pathogen-specific biomarkers have the potential to be used in immunodiagnostic platforms and antifungal treatment monitoring in histoplasmosis. In addition, the bioinformatics strategy used in this study could be applied to identify potential diagnostic biomarkers in other models of fungal infection of public health importance.
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Affiliation(s)
- Juan David Puerta-Arias
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB-UdeA-UPB-UDES), Medellín, Colombia
- School of Health Sciences, Universidad Pontificia Bolivariana, Medellín, Colombia
- Universidad de Santander (UDES), Facultad de Ciencias Médicas y de la Salud, Bucaramanga, Colombia
| | | | - Tonny Williams Naranjo Preciado
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB-UdeA-UPB-UDES), Medellín, Colombia
- School of Health Sciences, Universidad Pontificia Bolivariana, Medellín, Colombia
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Abstract
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2023). The UniProt website receives about 800,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides four main tools. These are the "BLAST" tool for sequence similarity searching, the "Align" tool for multiple sequence alignment, the "Peptide Search" tool for retrieving proteins containing a short peptide sequence, and the "Retrieve/ID Mapping" tool for using a list of identifiers to retrieve UniProt Knowledgebase (UniProtKB) proteins and to convert database identifiers from UniProt to external databases or vice versa. This article provides four basic protocols and seven alternate protocols for using UniProt tools. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Basic local alignment search tool (BLAST) in UniProt Alternate Protocol 1: BLAST through UniProt text search results pages Alternate Protocol 2: BLAST through UniProt basket Basic Protocol 2: Multiple sequence alignment in UniProt Alternate Protocol 3: Align tool through UniProt results pages and entry pages Alternate Protocol 4: Align tool through UniProt basket Basic Protocol 3: Peptide search in UniProt Basic Protocol 4: Batch retrieval and ID mapping in UniProt Alternate Protocol 5: Retrieve/ID Mapping tool through UniProt text search results pages and BLAST and Align results pages Alternate Protocol 6: Retrieve/ID Mapping tool through UniProt basket Alternate Protocol 7: Retrieve/ID Mapping tool through UniProt search box.
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Affiliation(s)
- Rossana Zaru
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - The UniProt Consortium
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Swiss Institute of Bioinformatics, University Medical Center, Geneva, Switzerland
- Protein Information Resource, Georgetown University Medical Center, Washington, D.C
- Protein Information Resource, University of Delaware, Newark, Delaware
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6
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In silico analysis decodes transthyretin (TTR) binding and thyroid disrupting effects of per- and polyfluoroalkyl substances (PFAS). Arch Toxicol 2023; 97:755-768. [PMID: 36566436 PMCID: PMC9968702 DOI: 10.1007/s00204-022-03434-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/13/2022] [Indexed: 12/26/2022]
Abstract
Transthyretin (TTR) is a homo-tetramer protein involved in the transport of thyroid hormone (thyroxine; T4) in the plasma and cerebrospinal fluid. Many pollutants have been shown to bind to TTR, which could be alarming as disruption in the thyroid hormone system can lead to several physiological problems. It is also indicated that the monomerization of tetramer and destabilization of monomer can lead to amyloidogenesis. Many compounds are identified that can bind to tetramer and stabilize the tetramer leading to the inhibition of amyloid fibril formation. Other compounds are known to bind tetramer and induce amyloid fibril formation. Among the pollutants, per- and polyfluoroalkyl substances (PFAS) are known to disrupt the thyroid hormone system. The molecular mechanisms of thyroid hormone disruption could be diverse, as some are known to bind with thyroid hormone receptors, and others can bind to membrane transporters. Binding to TTR could also be one of the important pathways to alter thyroid signaling. However, the molecular interactions that drive thyroid-disrupting effects of long-chain and short-chain PFASs are not comprehensively understood at the molecular level. In this study, using a computational approach, we show that carbon chain length and functional group in PFASs are structural determinants, in which longer carbon chains of PFASs and sulfur-containing PFASs favor stronger interactions with TTR than their shorter-chained counterparts. Interestingly, short-chain PFAS also showed strong binding capacity, and the interaction energy for some was as close to the longer-chain PFAS. This suggests that short-chain PFASs are not completely safe, and their use and build-up in the environment should be carefully regulated. Of note, TTR homologs analysis suggests that thyroid-disrupting effects of PFASs could be most likely translated to TTR-like proteins and other species.
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Pereira J, Alva V. How do I get the most out of my protein sequence using bioinformatics tools? Acta Crystallogr D Struct Biol 2021; 77:1116-1126. [PMID: 34473083 PMCID: PMC8411974 DOI: 10.1107/s2059798321007907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet-laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure using HHpred, internal repeats using HHrepID, coiled coils using PCOILS and DeepCoil, and transmembrane segments using Quick2D are focused on.
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Affiliation(s)
- Joana Pereira
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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8
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Gabler F, Nam S, Till S, Mirdita M, Steinegger M, Söding J, Lupas AN, Alva V. Protein Sequence Analysis Using the MPI Bioinformatics Toolkit. ACTA ACUST UNITED AC 2020; 72:e108. [DOI: 10.1002/cpbi.108] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Felix Gabler
- Department of Protein Evolution Max Planck Institute for Developmental Biology Tübingen Germany
| | - Seung‐Zin Nam
- Department of Protein Evolution Max Planck Institute for Developmental Biology Tübingen Germany
| | - Sebastian Till
- Department of Protein Evolution Max Planck Institute for Developmental Biology Tübingen Germany
| | - Milot Mirdita
- Quantitative Biology and Bioinformatics Max Planck Institute for Biophysical Chemistry Göttingen Germany
| | - Martin Steinegger
- Quantitative Biology and Bioinformatics Max Planck Institute for Biophysical Chemistry Göttingen Germany
- Present address: Department of Biology Seoul National University Seoul South Korea
| | - Johannes Söding
- Quantitative Biology and Bioinformatics Max Planck Institute for Biophysical Chemistry Göttingen Germany
| | - Andrei N. Lupas
- Department of Protein Evolution Max Planck Institute for Developmental Biology Tübingen Germany
| | - Vikram Alva
- Department of Protein Evolution Max Planck Institute for Developmental Biology Tübingen Germany
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King KM, Van Doorslaer K. Building (Viral) Phylogenetic Trees Using a Maximum Likelihood Approach. ACTA ACUST UNITED AC 2018; 51:e63. [PMID: 30265446 DOI: 10.1002/cpmc.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Phylogenetic analyses allow for inferring a hypothesis about the evolutionary history of a set of homologous molecular sequences. This hypothesis can be used as the basis for further molecular and computational studies. In this unit, we offer one specific method to construct a Maximum Likelihood phylogenetic tree. We outline how to identify homologous sequences and construct a multiple sequence alignment. Following alignment, sequences are screened for potentially confounding factors such as recombination and genetic saturation. Finally, a Maximum Likelihood phylogenetic tree can be constructed implementing a rigorously tested model of evolution. The workflow outlined in this unit provides sufficient background for inferring a robust phylogenetic tree starting from a particular gene of interest. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kelly M King
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona.,Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, BIO5 Institute, and the University of Arizona Cancer Center, University of Arizona, Tucson, Arizona
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10
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Ladunga I. Installing, Maintaining, and Using a Local Copy of BLAST for Compute Cluster or Workstation Use. ACTA ACUST UNITED AC 2018; 63:e54. [PMID: 30168910 DOI: 10.1002/cpbi.54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Basic Local Alignment Search Tool (BLAST) is the first resource to computationally characterize a novel amino acid or nucleic acid sequence. BLAST plays important roles in genomics, transcriptomics, and protein science. For numerous academic and commercial researchers, neither BLAST Web servers nor cloud resources satisfy the requirements of high-throughput comparative genomic pipelines or company policies. For such users, this unit describes how to install BLAST locally, either on a standalone workstation, or preferably on a compute cluster. We provide practical guidance for the planning and the installation under the LINUX, Windows, and Mac OS X operating systems. We propose strategies for downloading existing and generating new sequence databases in BLAST format. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Istvan Ladunga
- Departments of Statistics, Biochemistry, and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska
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Reiser L, Subramaniam S, Li D, Huala E. Using the
Arabidopsis
Information Resource (TAIR) to Find Information About
Arabidopsis
Genes. ACTA ACUST UNITED AC 2017; 60:1.11.1-1.11.45. [DOI: 10.1002/cpbi.36] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | - Donghui Li
- Phoenix Bioinformatics Fremont California
| | - Eva Huala
- Phoenix Bioinformatics Fremont California
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