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Stamatakos PV, Fragkoulis C, Zoidakis I, Ntoumas K, Kratiras Z, Mitsogiannis I, Dellis A. A review of urinary bladder microbiome in patients with bladder cancer and its implications in bladder pathogenesis. World J Urol 2024; 42:457. [PMID: 39073494 DOI: 10.1007/s00345-024-05173-0] [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: 03/06/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024] Open
Abstract
PURPOSE The recent discovery of the urinary microbiome has led to an emerging field of investigation about the potential role of microorganisms in the pathogenesis of urinary bladder cancer. Few preliminary data have been reported so far implicating urobiome as causative and prognostic factor of bladder tumorigenesis. In the present study, a review of the current evidence is presented about microbiome composition among patients with bladder cancer and healthy individuals as well as possible implications of microbiome on urothelial carcinoma of the bladder. METHODS A literature review was conducted using PubMed/MEDLINE, Scopus, and the Cochrane library until December 2023. Search algorithm was constructed using the following terms and their associated Mesh terms and Boolean operators: "urinary microbiome" and "urinary microbiota". Studies written in English language, identifying, and comparing urinary microbiome among bladder cancer patients and healthy control group were included in the review. RESULTS A total of 2,356 reports were identified. From this total 16 articles complied with the inclusion criteria were selected for analysis. These articles represent a total of about 486 bladder cancer patients. CONCLUSION Recent studies revealed the colonization of the urinary tract and the bladder by micro-organisms using both enhanced culture- and molecular-based techniques for microbial characterization. However, several limitations exist in the literature decreasing the reliability of the current reports. As a result, urinary microbiome consist an ambitious era in bladder cancer research with an increasing number of evidence about its potential pathogenetic, prognostic and therapeutic role.
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Affiliation(s)
| | - Charalampos Fragkoulis
- Department of Urology, General Hospital of Athens "G. Gennimatas", Leof. Mesogeion 154, Athens, 115 27, Greece
| | - Ieronymos Zoidakis
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Konstantinos Ntoumas
- Department of Urology, General Hospital of Athens "G. Gennimatas", Leof. Mesogeion 154, Athens, 115 27, Greece
| | - Zisis Kratiras
- 3rd Department of Urology, School of Medicine, University of Athens, University Hospital of Athens "Attikon", Athens, Greece
| | - Iraklis Mitsogiannis
- 2nd Department of Urology, School of Medicine, University of Athens, General Hospital of Athens "Sismanogleio", Athens, Greece
| | - Athanasios Dellis
- 1st Department of Urology, School of Medicine, University of Athens, University Hospital of Athens "Aretaieion", Athens, Greece
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Karlo J, Dhillon AK, Siddhanta S, Singh SP. Reverse stable isotope labelling with Raman spectroscopy for microbial proteomics. JOURNAL OF BIOPHOTONICS 2024; 17:e202300341. [PMID: 38010366 DOI: 10.1002/jbio.202300341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Global proteome changes in microbes affect the survival and overall production of commercially relevant metabolites through different bioprocesses. The existing methods to monitor proteome level changes are destructive in nature. Stable isotope probing (SIP) coupled with Raman spectroscopy is a relatively new approach for proteome analysis. However, applying this approach for monitoring changes in a large culture volume is not cost-effective. In this study, for the first time we are presenting a novel method of combining reverse SIP using 13 C-glucose and Deuterium to monitor the proteome changes through Raman spectroscopy. The findings of the study revealed visible changes (blue shifts) in proteome related peaks that can be used for monitoring proteome dynamics, that is, synthesis of nascent amino acids and its turnover with time in a non-destructive, cost-effective, and label-free manner.
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Affiliation(s)
- Jiro Karlo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | | | - Soumik Siddhanta
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Surya Pratap Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
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3
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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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Cheng Y, Zhang J, Ren W, Zhang L, Xu X. Response of a new rumen-derived Bacillus licheniformis to different carbon sources. Front Microbiol 2023; 14:1238767. [PMID: 38029181 PMCID: PMC10646532 DOI: 10.3389/fmicb.2023.1238767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Bacillus licheniformis (B. licheniformis) is a microorganism with a wide range of probiotic properties and applications. Isolation and identification of novel strains is a major aspect of microbial research. Besides, different carbon sources have varying effects on B. licheniformis in regulating the microenvironment, and these mechanisms need to be investigated further. Methods In this study, we isolated and identified a new strain of B. licheniformis from bovine rumen fluid and named it B. licheniformis NXU98. The strain was treated with two distinct carbon sources-microcrystalline cellulose (MC) and cellobiose (CB). A combination of transcriptome and proteome analyses was used to investigate different carbon source effects. Results The results showed that B. licheniformis NXU98 ABC transporter proteins, antibiotic synthesis, flagellar assembly, cellulase-related pathways, and proteins were significantly upregulated in the MC treatment compared to the CB treatment, and lactate metabolism was inhibited. In addition, we used MC as a distinct carbon source to enhance the antibacterial ability of B. licheniformis NXU98, to improve its disease resistance, and to regulate the rumen microenvironment. Discussion Our research provides a potential new probiotic for feed research and a theoretical basis for investigating the mechanisms by which bacteria respond to different carbon sources.
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Affiliation(s)
| | | | | | - Lili Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Xiaofeng Xu
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
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5
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Fernandez M, Callegari EA, Paez MD, González PS, Agostini E. Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress. Biometals 2023; 36:1081-1108. [PMID: 37209221 DOI: 10.1007/s10534-023-00506-9] [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: 01/17/2023] [Accepted: 04/24/2023] [Indexed: 05/22/2023]
Abstract
Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI) + phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (Gel-LC) and gel-free (shotgun) nanoUHPLC-ESI-MS/MS. A total of 400 differentially expressed proteins were identified, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI) + phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was also added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stress-associated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.
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Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María D Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
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Overview of omics applications in elucidating the underlying mechanisms of biochemical and biological factors associated with meat safety and nutrition. J Proteomics 2023; 276:104840. [PMID: 36758853 DOI: 10.1016/j.jprot.2023.104840] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023]
Abstract
Over the years, significant technological discoveries have facilitated the improvement of meat-related research. Recent studies of complex and interactive factors contributing to variations in meat safety are increasingly focused on data-driven omics approaches such as proteomics. This review highlighted omics advances in elucidating the biochemical and biological actions on meat safety. Also, the impacts of the nutritional characteristics of meat and meat products on human health are emphasized. Future perspectives should explore multi-omics and in situ investigations to elucidate the implications in microbiological studies, including nutritional and health-related assessments. Also, creating meat safety assessment and prediction models based on biomarkers of meat safety traits will help to mitigate application constraints, thereby evaluating meat quality more accurately. This could provide a scientific basis for increasing the meat industry's profitability and producing high-quality meat and meat products for consumers. SIGNIFICANCE OF THE REVIEW: This review highlighted omics advances in elucidating underlying mechanisms of biochemical and biological factors associated with meat safety. Also, the impacts of meat proteins on human health are emphasized. Future perspectives should explore multi-omics and in situ investigations to elucidate the implications in microbiological studies, including nutritional and health-related assessments. Also, creating meat safety assessment and prediction models based on biomarkers of meat safety traits will help to mitigate application constraints, thereby evaluating meat quality more accurately. This could provide a scientific basis for increasing the meat industry's profitability and producing high-quality meat and meat products for consumers.
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de Oliveira Silva JV, Meneguello JE, Formagio MD, de Freitas CF, Hioka N, Pilau EJ, Marchiosi R, Machinski Junior M, de Abreu Filho BA, Zanetti Campanerut-Sá PA, Graton Mikcha JM. Proteomic Investigation over the Antimicrobial Photodynamic Therapy Mediated by Rose Bengal Against Staphylococcus aureus. Photochem Photobiol 2022; 99:957-966. [PMID: 36054748 DOI: 10.1111/php.13707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/28/2022] [Indexed: 11/28/2022]
Abstract
In order, to understand the antimicrobial action of photodynamic therapy and how this technique can contribute to its application in the control of pathogens. The objective of the study was to employ a proteomic approach to investigate the protein profile of S. aureus after antimicrobial photodynamic therapy mediated by rose bengal (RB-aPDT). S. aureus was treated with RB (10 nmol/l) and illuminated with green LED (0.17 J/cm2 ) for cell viability evaluation. Afterward, proteomic analysis was employed for protein identification and bioinformatic tools to classify the differentially expressed proteins. The reduction of S. aureus after photoinactivation was ~2.5 log CFU/ml. A total of 12 proteins (four up-regulated and eight down-regulated), correspond exclusively to alteration by RB-aPDT. Functionally these proteins are distributed in protein binding, structural constituent of ribosome, proton transmembrane transporter activity, and ATPase activity. The effects of photodamage include alterations of levels of several proteins resulting in an activated stress response, altered membrane potential, and effects on energy metabolism. These 12 proteins required the presence of both light and RB suggesting a unique response to photodynamic effects. The information about this technique contributes valuable insights into bacterial mechanisms and the mode of action of photodynamic therapy.
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Affiliation(s)
| | - Jean Eduardo Meneguello
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Paraná, Brazil
| | - Maíra Dante Formagio
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Paraná, Brazil
| | - Camila Fabiano de Freitas
- Department of Chemistry, State University of Maringá, Paraná, Brazil.,Departament of Chemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Noboru Hioka
- Department of Chemistry, State University of Maringá, Paraná, Brazil
| | | | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Paraná, Brazil
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Afzaal M, Saeed F, Hussain M, Shahid F, Siddeeg A, Al‐Farga A. Proteomics as a promising biomarker in food authentication, quality and safety: A review. Food Sci Nutr 2022; 10:2333-2346. [PMID: 35844910 PMCID: PMC9281926 DOI: 10.1002/fsn3.2842] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/07/2022] [Accepted: 03/12/2022] [Indexed: 12/18/2022] Open
Abstract
Adulteration and mislabeling have become a very common global malpractice in food industry. Especially foods of animal origin are prepared from plant sources and intentionally mislabeled. This type of mislabeling is an important concern in food safety as the replaced ingredients may cause a food allergy or toxicity to vulnerable consumers. Moreover, foodborne pathogens also pose a major threat to food safety. There is a dire need to develop strong analytical tools to deal with related issues. In this context, proteomics stands out as a promising tool used to report the aforementioned issues. The development in the field of omics has inimitable advantages in enabling the understanding of various biological fields especially in the discipline of food science. In this review, current applications and the role of proteomics in food authenticity, safety, and quality and food traceability are highlighted comprehensively. Additionally, the other components of proteomics have also been comprehensively described. Furthermore, this review will be helpful in the provision of new intuition into the use of proteomics in food analysis. Moreover, the pathogens in food can also be identified based on differences in their protein profiling. Conclusively, proteomics, an indicator of food properties, its origin, the processes applied to food, and its composition are also the limelight of this article.
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Affiliation(s)
- Muhammad Afzaal
- Department of Food ScienceGovernment College University FaisalabadFaisalabadPakistan
| | - Farhan Saeed
- Department of Food ScienceGovernment College University FaisalabadFaisalabadPakistan
| | - Muzzamal Hussain
- Department of Food ScienceGovernment College University FaisalabadFaisalabadPakistan
| | - Farheen Shahid
- Department of Food ScienceGovernment College University FaisalabadFaisalabadPakistan
| | - Azhari Siddeeg
- Department of Food Engineering and TechnologyFaculty of Engineering and TechnologyUniversity of GeziraWad MedaniSudan
| | - Ammar Al‐Farga
- Department of BiochemistryCollege of SciencesUniversity of JeddahJeddahSaudi Arabia
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Hosseini H, Al-Jabri HM, Moheimani NR, Siddiqui SA, Saadaoui I. Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications-a review. J Basic Microbiol 2022; 62:1030-1043. [PMID: 35467037 DOI: 10.1002/jobm.202100504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 11/09/2022]
Abstract
The increase in the human population causes an increase in the demand for nutritional supplies and energy resources. Thus, the novel, natural, and renewable resources became of great interest. Here comes the optimistic role of bioprospecting as a promising tool to isolate novel and interesting molecules and microorganisms from the marine environment as alternatives to the existing resources. Bioprospecting of marine metabolites and microorganisms with high biotechnological potentials has gained wide interest due to the variability and richness of the marine environment. Indeed, the existence of extreme conditions that increases the adaptability of marine organisms, especially planktons, allow the presence of interesting biological species that are able to produce novel compounds with multiple health benefits and high economical value. This review aims to provide a comprehensive overview of marine microbial bioprospecting as a growing field of interest. It emphasizes functional bioprospecting that facilitates the discovery of interesting metabolites. Marine bioprospecting was also discussed from a legal aspect for the first time, focusing on the shortcomings of international law. We also summarized the challenges facing bioprospecting in the marine environment including economic feasibility issues.
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Affiliation(s)
- Hoda Hosseini
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hareb M Al-Jabri
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Navid R Moheimani
- Algae R&D Centre, Harry Buttler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Simil A Siddiqui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Imen Saadaoui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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