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Martin CA, Sheppard EC, Ali HAA, Illera JC, Suh A, Spurgin LG, Richardson DS. Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci? Mol Ecol 2024; 33:e17365. [PMID: 38733214 DOI: 10.1111/mec.17365] [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: 02/26/2023] [Accepted: 03/01/2024] [Indexed: 05/13/2024]
Abstract
When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million-ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | | | - Hisham A A Ali
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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Rizzo M, Varnier L, Pezzicoli G, Pirovano M, Cosmai L, Porta C. IL-8 and its role as a potential biomarker of resistance to anti-angiogenic agents and immune checkpoint inhibitors in metastatic renal cell carcinoma. Front Oncol 2022; 12:990568. [PMID: 36059687 PMCID: PMC9437355 DOI: 10.3389/fonc.2022.990568] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/01/2022] [Indexed: 11/24/2022] Open
Abstract
The therapeutic armamentarium of metastatic Renal Cell Carcinoma (mRCC) has consistently expanded in recent years, with the introduction of VEGF/VEGFR (Vascular Endothelial Growth Factor/Vascular Endothelial Growth Factor Receptor) inhibitors, mTOR (mammalian Target Of Rapamycin) inhibitors and Immune Checkpoint (IC) inhibitors. Currently, for the first-tline treatment of mRCC it is possible to choose between a VEGFR-TKI (VEGFR-Tyrosine Kinase Inhibitor) monotherapy, an ICI-ICI (Immune Checkpoint Inhibitor) combination and an ICI-VEGFRTKI combination. However, a consistent part of patients does not derive benefit from first-line therapy with ICIs; moreover, the use of combination regimens exposes patients to significant toxicities. Therefore, there is a critical need to develop prognostic and predictive biomarkers of response to VEGFR-TKIs and ICIs, and measurement of serum IL-8 is emerging as a potential candidate in this field. Recent retrospective analyses of large phase II and phase III trials found that elevated baseline serum IL-8 correlated with higher levels of tumor and circulating immunosuppressive myeloid cells, decreased T cell activation and poor response to treatment. These findings must be confirmed in prospective clinical trials; however, they provide evidence for a potential use of serum IL-8 as biomarker of resistance to VEGFR-TKIs and ICIs. Considering the amount of new agents and treatment regimens which are transforming the management of metastatic renal cell carcinoma, serum IL-8 could become a precious resource in tailoring the best therapy for each individual patient with the disease.
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Affiliation(s)
- Mimma Rizzo
- Division of Medical Oncology, Azienda Ospedaliero Universitaria Consorziale Policlinico di Bari, Bari, Italy
- *Correspondence: Mimma Rizzo,
| | - Luca Varnier
- Department of Pediatrics, Meyer’ Childrens University Hospital, Florence, Italy
| | - Gaetano Pezzicoli
- Department of Interdisciplinary Medicine, School of Medicine, University of Bari “A. Moro”, Bari, Italy
| | - Marta Pirovano
- Division of Nephrology and Dialysis, Azienda Socio-Sanitaria Territoriale (ASST) Fatebenefratelli-Sacco, Fatebenefratelli Hospital, Milan, Italy
| | - Laura Cosmai
- Division of Nephrology and Dialysis, Azienda Socio-Sanitaria Territoriale (ASST) Fatebenefratelli-Sacco, Fatebenefratelli Hospital, Milan, Italy
| | - Camillo Porta
- Division of Medical Oncology, Azienda Ospedaliero Universitaria Consorziale Policlinico di Bari, Bari, Italy
- Chair of Oncology, Interdisciplinary Department of Medicine, University of Bari “A. Moro”, Bari, Italy
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Public Transport COVID-19-Safe: New Barriers and Policies to Implement Effective Countermeasures under User’s Safety Perspective. SUSTAINABILITY 2022. [DOI: 10.3390/su14052945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The COVID-19 emergency forced cities worldwide to adopt measures to restrict travel and implement new urban public transport solutions. The discontinuity and reduction of services made users recognize public transport systems as contamination vectors, and the decrease in the number of passengers can already be seen in several places. Thus, this study assessed the impact of the COVID-19 pandemic on urban public transport. We used hybrid choice models (HCMs) to identify the new barriers and potential solutions to increase users’ perception of safety, considering preexistent perceptions of public transportation quality. We used data from an online survey with users of public transportation in a metropolitan area in southern Brazil. We identified that the main barriers to using public transport during virus transmission are related to the system characteristics that force constant interaction with other passengers. Crowded vehicles and crowded stops/stations were considered the most detrimental factor in feeling safe while riding in the COVID-19 outbreak. Countermeasures that reduce the contact with other passengers—directly (limit the number of passengers in vehicles) or indirectly (operate with large vehicles)—and increase offers are possible solutions to make users feel safe while riding. The results of this research might help reduce passenger evasion and migration to more unsustainable transport modes.
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Abstract
CO2 reutilization processes contribute to the mitigation of CO2 as a potent greenhouse gas (GHG) through reusing and converting it into economically valuable chemical products including methanol, dimethyl ether, and methane. Solar thermochemical conversion and photochemical and electrochemical CO2 reduction processes are emerging technologies in which solar energy is utilized to provide the energy required for the endothermic dissociation of CO2. Owing to the surface-dependent nature of these technologies, their performance is significantly reliant on the solid reactant/catalyst accessible surface area. Solid porous structures either entirely made from the catalyst or used as a support for coating the catalyst/solid reactants can increase the number of active reaction sites and, thus, the kinetics of CO2 reutilization reactions. This paper reviews the principles and application of porous materials for CO2 reutilization pathways in solar thermochemical, photochemical, and electrochemical reduction technologies. Then, the state of the development of each technology is critically reviewed and evaluated with the focus on the use of porous materials. Finally, the research needs and challenges are presented to further advance the implementation of porous materials in the CO2 reutilization processes and the commercialization of the aforementioned technologies.
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Shah MA, Rasul A, Yousaf R, Haris M, Faheem HI, Hamid A, Khan H, Khan AH, Aschnar M, Batiha GES. Combination of natural antivirals and potent immune invigorators: A natural remedy to combat COVID-19. Phytother Res 2021; 35:6530-6551. [PMID: 34396612 PMCID: PMC8441799 DOI: 10.1002/ptr.7228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/14/2021] [Accepted: 04/10/2021] [Indexed: 12/23/2022]
Abstract
The flare‐up in severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) that emerged in December 2019 in Wuhan, China, and spread expeditiously worldwide has become a health challenge globally. The rapid transmission, absence of anti‐SARS‐CoV‐2 drugs, and inexistence of vaccine are further exacerbating the situation. Several drugs, including chloroquine, remdesivir, and favipiravir, are presently undergoing clinical investigation to further scrutinize their effectiveness and validity in the management of COVID‐19. Natural products (NPs) in general, and plants constituents specifically, are unique sources for various effective and novel drugs. Immunostimulants, including vitamins, iron, zinc, chrysin, caffeic acid, and gallic acid, act as potent weapons against COVID‐19 by reinvigorating the defensive mechanisms of the immune system. Immunity boosters prevent COVID‐19 by stimulating the proliferation of T‐cells, B‐cells, and neutrophils, neutralizing the free radicals, inhibiting the immunosuppressive agents, and promoting cytokine production. Presently, antiviral therapy includes several lead compounds, such as baicalin, glycyrrhizin, theaflavin, and herbacetin, all of which seem to act against SARS‐CoV‐2 via particular targets, such as blocking virus entry, attachment to host cell receptor, inhibiting viral replication, and assembly and release.
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Affiliation(s)
- Muhammad Ajmal Shah
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Azhar Rasul
- Department of Zoology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Rimsha Yousaf
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Muhammad Haris
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Hafiza Ishmal Faheem
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Ayesha Hamid
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdul Haleem Khan
- Department of Pharmacy, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Michael Aschnar
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Al-Beheira, Egypt
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Pereira L, Sapkota M, Alonge M, Zheng Y, Zhang Y, Razifard H, Taitano NK, Schatz MC, Fernie AR, Wang Y, Fei Z, Caicedo AL, Tieman DM, van der Knaap E. Natural Genetic Diversity in Tomato Flavor Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:642828. [PMID: 34149747 PMCID: PMC8212054 DOI: 10.3389/fpls.2021.642828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/23/2021] [Indexed: 05/22/2023]
Abstract
Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5, ALMT9, AAT1, CXE1, and LoxC. The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium, the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum. High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels.
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Affiliation(s)
- Lara Pereira
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Manoj Sapkota
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, NY, United States
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Hamid Razifard
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Nathan K. Taitano
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, United States
- U.S. Department of Agriculture, Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Ana L. Caicedo
- Biology Department, University of Massachusetts Amherst, Amherst, MA, United States
| | - Denise M. Tieman
- Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
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Mutations and Epidemiology of SARS-CoV-2 Compared to Selected Corona Viruses during the First Six Months of the COVID-19 Pandemic: A Review. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus (CoV) disease 2019 (COVID-19). This study compared the genome, mutations, and infectivity/transmissibility of SARS-CoV-2 with selected betacoronaviruses (beta-CoVs). This study further examined the origin, risk factors, and outbreaks caused by beta-CoVs. We searched the following databases for relevant studies: PubMed, Google Scholar, and the World Health Organization COVID-19 database. A close relationship between SARS-CoV-2 and SARS bat-like CoV RaTG13 (98.9%) was found at the amino acid level, followed by pangolin CoVs. Non-synonymous mutations occur at high frequencies in the open reading frame (ORF) 1ab, spike (S) protein, and nucleocapsid. Mutations P323L and D614G in the RNA-dependent RNA polymerase (RdRp) and S protein, respectively, occur at a high frequency globally. Mutations at position 3037 in the nonstructural protein (Nsp) 3, 14408 (RdRp), and 23403 (S) confer transmissibility to SARS-CoV-2. SARS-CoV-2 has higher infectivity and transmissibility than SARS-CoV, which shares the same receptor. Although bats are confirmed reservoirs, intermediate hosts are currently unknown. Smoking, old age, diabetes, cardiovascular diseases, and hypertension have all been associated with COVID-19. Within six months of its outbreak, COVID-19 was reported in all countries worldwide, whereas SARS was reported in 28 countries and Middle East respiratory syndrome (MERS) in 5 countries. However, the fatality rate of MERS (65%) was higher than that of COVID-19 (4.9%) and SARS (6.6%). Identifying the SARS-CoV-2 intermediate hosts will help prevent future outbreaks. Attention should be given to the pangolin CoVs. Variations in the S gene may confer transmissibility and infectivity.
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Methane Cracking for Hydrogen Production: A Review of Catalytic and Molten Media Pyrolysis. ENERGIES 2021. [DOI: 10.3390/en14113107] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Currently, hydrogen is mainly generated by steam methane reforming, with significant CO2 emissions, thus exacerbating the greenhouse effect. This environmental concern promotes methane cracking, which represents one of the most promising alternatives for hydrogen production with theoretical zero CO/CO2 emissions. Methane cracking has been intensively investigated using metallic and carbonaceous catalysts. Recently, research has focused on methane pyrolysis in molten metals/salts to prevent both reactor coking and rapid catalyst deactivation frequently encountered in conventional pyrolysis. Another expected advantage is the heat transfer improvement due to the high heat capacity of molten media. Apart from the reaction itself that produces hydrogen and solid carbon, the energy source used in this endothermic process can also contribute to reducing environmental impacts. While most researchers used nonrenewable sources based on fossil fuel combustion or electrical heating, concentrated solar energy has not been thoroughly investigated, to date, for pyrolysis in molten media. However, it could be a promising innovative pathway to further improve hydrogen production sustainability from methane cracking. After recalling the basics of conventional catalytic methane cracking and the developed solar cracking reactors, this review delves into the most significant results of the state-of-the-art methane pyrolysis in melts (molten metals and salts) to show the advantages and the perspectives of this new path, as well as the carbon products’ characteristics and the main factors governing methane conversion.
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Wang W, Zhu Y, Abraham N, Li XZ, Kimber M, Zhou T. The Ribosome-Binding Mode of Trichothecene Mycotoxins Rationalizes Their Structure-Activity Relationships. Int J Mol Sci 2021; 22:1604. [PMID: 33562610 PMCID: PMC7914836 DOI: 10.3390/ijms22041604] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Trichothecenes are the most prevalent mycotoxins contaminating cereal grains. Some of them are also considered as the virulence factors of Fusarium head blight disease. However, the mechanism behind the structure-activity relationship for trichothecenes remains unexplained. Filling this information gap is a crucial step for developing strategies to manage this large family of mycotoxins in food and feed. Here, we perform an in-depth re-examination of the existing structures of Saccharomyces cerevisiae ribosome complexed with three different trichothecenes. Multiple binding interactions between trichothecenes and 25S rRNA, including hydrogen bonds, nonpolar pi stacking interactions and metal ion coordination interactions, are identified as important binding determinants. These interactions are mainly contributed by the key structural elements to the toxicity of trichothecenes, including the oxygen in the 12,13-epoxide ring and a double bond between C9 and C10. In addition, the C3-OH group also participates in binding. The comparison of three trichothecenes binding to the ribosome, along with their binding pocket architecture, suggests that the substitutions at different positions impact trichothecenes binding in two different patterns. Moreover, the binding of trichothecenes induced conformation changes of several nucleotide bases in 25S rRNA. This then provides a structural framework for understanding the structure-activity relationships apparent in trichothecenes. This study will facilitate the development of strategies aimed at detoxifying mycotoxins in food and feed and at improving the resistance of cereal crops to Fusarium fungal diseases.
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Affiliation(s)
- Weijun Wang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (W.W.); (Y.Z.); (N.A.); (X.-Z.L.)
| | - Yan Zhu
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (W.W.); (Y.Z.); (N.A.); (X.-Z.L.)
| | - Nadine Abraham
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (W.W.); (Y.Z.); (N.A.); (X.-Z.L.)
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Xiu-Zhen Li
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (W.W.); (Y.Z.); (N.A.); (X.-Z.L.)
| | - Matthew Kimber
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Ting Zhou
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada; (W.W.); (Y.Z.); (N.A.); (X.-Z.L.)
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Martin CA, Armstrong C, Illera JC, Emerson BC, Richardson DS, Spurgin LG. Genomic variation, population history and within-archipelago adaptation between island bird populations. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201146. [PMID: 33972847 PMCID: PMC8074581 DOI: 10.1098/rsos.201146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/11/2021] [Indexed: 05/13/2023]
Abstract
Oceanic island archipelagos provide excellent models to understand evolutionary processes. Colonization events and gene flow can interact with selection to shape genetic variation at different spatial scales. Landscape-scale variation in biotic and abiotic factors may drive fine-scale selection within islands, while long-term evolutionary processes may drive divergence between distantly related populations. Here, we examine patterns of population history and selection between recently diverged populations of the Berthelot's pipit (Anthus berthelotii), a passerine endemic to three North Atlantic archipelagos. First, we use demographic trees and f3 statistics to show that genome-wide divergence across the species range is largely shaped by colonization and bottlenecks, with evidence of very weak gene flow between populations. Then, using a genome scan approach, we identify signatures of divergent selection within archipelagos at single nucleotide polymorphisms (SNPs) in genes potentially associated with craniofacial development and DNA repair. We did not detect within-archipelago selection at the same SNPs as were detected previously at broader spatial scales between archipelagos, but did identify signatures of selection at loci associated with similar biological functions. These findings suggest that similar ecological factors may repeatedly drive selection between recently separated populations, as well as at broad spatial scales across varied landscapes.
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Affiliation(s)
- Claudia A. Martin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Claire Armstrong
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Juan Carlos Illera
- Oviedo University, Campus of Mieres, Research Unit of Biodiversity (UO-CSIC-PA), Research Building, 5th floor, c/Gonzalo Gutiérrez Quirós, s/n, 33600 Mieres, Asturias, Spain
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain
| | - David S. Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Lewis G. Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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Cerda-Troncoso C, Varas-Godoy M, Burgos PV. Pro-Tumoral Functions of Autophagy Receptors in the Modulation of Cancer Progression. Front Oncol 2021; 10:619727. [PMID: 33634029 PMCID: PMC7902017 DOI: 10.3389/fonc.2020.619727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
Cancer progression involves a variety of pro-tumorigenic biological processes including cell proliferation, migration, invasion, and survival. A cellular pathway implicated in these pro-tumorigenic processes is autophagy, a catabolic route used for recycling of cytoplasmic components to generate macromolecular building blocks and energy, under stress conditions, to remove damaged cellular constituents to adapt to changing nutrient conditions and to maintain cellular homeostasis. During autophagy, cells form a double-membrane sequestering a compartment termed the phagophore, which matures into an autophagosome. Following fusion with the lysosome, the cargo is degraded inside the autolysosomes and the resulting macromolecules released back into the cytosol for reuse. Cancer cells use this recycling system during cancer progression, however the key autophagy players involved in this disease is unclear. Accumulative evidences show that autophagy receptors, crucial players for selective autophagy, are overexpressed during cancer progression, yet the mechanisms whereby pro-tumorigenic biological processes are modulated by these receptors remains unknown. In this review, we summarized the most important findings related with the pro-tumorigenic role of autophagy receptors p62/SQSTM1, NBR1, NDP52, and OPTN in cancer progression. In addition, we showed the most relevant cargos degraded by these receptors that have been shown to function as critical regulators of pro-tumorigenic processes. Finally, we discussed the role of autophagy receptors in the context of the cellular pathways implicated in this disease, such as growth factors signaling, oxidative stress response and apoptosis. In summary, we highlight that autophagy receptors should be considered important players of cancer progression, which could offer a niche for the development of novel diagnosis and cancer treatment strategies.
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Affiliation(s)
- Cristóbal Cerda-Troncoso
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Manuel Varas-Godoy
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Patricia V. Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Saawarn B, Hait S. Occurrence, fate and removal of SARS-CoV-2 in wastewater: Current knowledge and future perspectives. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:104870. [PMID: 33282675 PMCID: PMC7706426 DOI: 10.1016/j.jece.2020.104870] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/12/2020] [Accepted: 11/29/2020] [Indexed: 05/03/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a pandemic of global concern, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently, many studies have documented the detection of SARS-CoV-2 in human excreta and wastewater. The presence of SARS-CoV-2 in human excreta and wastewater poses serious implications for wastewater treatment. Thus, this review aims to understand the fate of SARS-CoV-2 in the urban water cycle and its inactivation in different stages of treatment in wastewater treatment plants (WWTPs) for effective control to prevent any recurrence of the outbreak. The viral load of SARS-CoV-2 in feces of individuals tested positive has been reported to be in the range of 104-108 copies/L depending on the infection stages. In the wastewater, dilution of feces results in the decrease of the viral load in the range of 102-106.5 copies/L. Monitoring of SARS-CoV-2 in WWTP samples following the wastewater-based epidemiology (WBE) can complement real epidemiological data from clinical testing to help to monitor disease outbreaks in a community. Though promising, high uncertainty involved with the WBE technique warrants further research for reliable and quantitative information. Inactivation of SARS-CoV-2 in WWTPs depends on the operational parameters and is generally enhanced by the tertiary treatment and disinfection techniques with a higher dosage. However, the risk of SARS-CoV-2 dissemination by the treated effluent intended to be disposed of or reused in the urban water cycle needs to be assessed with respect to the extent of viral infectivity.
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Affiliation(s)
- Bhavini Saawarn
- Department of Civil and Environmental Engineering, Indian Institute of Technology Patna, Bihar 801 106, India
| | - Subrata Hait
- Department of Civil and Environmental Engineering, Indian Institute of Technology Patna, Bihar 801 106, India
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Han C, Li M, Haihambo N, Babuna P, Liu Q, Zhao X, Jaeger C, Li Y, Yang S. Mechanisms of recurrent outbreak of COVID-19: a model-based study. NONLINEAR DYNAMICS 2021; 106:1169-1185. [PMID: 33758464 PMCID: PMC7972336 DOI: 10.1007/s11071-021-06371-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 05/07/2023]
Abstract
Recurrent outbreaks of the coronavirus disease 2019 (COVID-19) have occurred in many countries around the world. We developed a twofold framework in this study, which is composed by one novel descriptive model to depict the recurrent global outbreaks of COVID-19 and one dynamic model to understand the intrinsic mechanisms of recurrent outbreaks. We used publicly available data of cumulative infected cases from 1 January 2020 to 2 January 2021 in 30 provinces in China and 43 other countries around the world for model validation and further analyses. These time series data could be well fitted by the new descriptive model. Through this quantitative approach, we discovered two main mechanisms that strongly correlate with the extent of the recurrent outbreak: the sudden increase in cases imported from overseas and the relaxation of local government epidemic prevention policies. The compartmental dynamical model (Susceptible, Exposed, Infectious, Dead and Recovered (SEIDR) Model) could reproduce the obvious recurrent outbreak of the epidemics and showed that both imported infected cases and the relaxation of government policies have a causal effect on the emergence of a new wave of outbreak, along with variations in the temperature index. Meanwhile, recurrent outbreaks affect consumer confidence and have a significant influence on GDP. These results support the necessity of policies such as travel bans, testing of people upon entry, and consistency of government prevention and control policies in avoiding future waves of epidemics and protecting economy.
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Affiliation(s)
- Chuanliang Han
- State Key Laboratory of Cognitive Neuroscience and Learning and IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875 China
| | - Meijia Li
- Faculty of Psychology and Center for Neuroscience, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Naem Haihambo
- Faculty of Psychology and Center for Neuroscience, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Pius Babuna
- School of Environment, Beijing Normal University, Beijing, 100875 China
- Department of Geography and Environmental Science, The University of Reading, Whiteknights, Reading, RG6 6AB UK
- Colledge of Agriculture and Natural Resources, Kwame Nkrumah University of Science and Technology, PMB KNUST, Kumasi, Ghana
| | - Qingfang Liu
- Department of Psychology, The Ohio State University, Columbus, OH 43210 USA
| | - Xixi Zhao
- Beijing Anding Hospital, Capital Medical University, Beijing, 100088 China
- The National Clinical Research Center for Mental Disorders and Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, 100088 China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100191 China
| | - Carlo Jaeger
- Global Climate Forum, 10178 Berlin, Germany
- Academy of Disaster Reduction and Emergency Management, Ministry of Emergency Management and Ministry of Education, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875 China
| | - Ying Li
- Academy of Disaster Reduction and Emergency Management, Ministry of Emergency Management and Ministry of Education, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875 China
- Key Laboratory of Environmental Change and Natural Disaster, Ministry of Education, Beijing Normal University, Beijing, 100875 China
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Beijing, 100875 China
| | - Saini Yang
- Academy of Disaster Reduction and Emergency Management, Ministry of Emergency Management and Ministry of Education, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875 China
- Key Laboratory of Environmental Change and Natural Disaster, Ministry of Education, Beijing Normal University, Beijing, 100875 China
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Beijing, 100875 China
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Cag Y, Erdem H, Gormez A, Ankarali H, Hargreaves S, Ferreira-Coimbra J, Rubulotta F, Belliato M, Berger-Estilita J, Pelosi P, Blot S, Lefrant JY, Mardani M, Darazam IA, Cag Y, Rello J. Anxiety among front-line health-care workers supporting patients with COVID-19: A global survey. Gen Hosp Psychiatry 2021; 68:90-96. [PMID: 33418193 PMCID: PMC7749993 DOI: 10.1016/j.genhosppsych.2020.12.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE We aimed to explore anxiety status across a broad range of HCWs supporting patients with COVID-19 in different global regions. METHOD This was an international online survey in which participation was on voluntary basis and data were submitted via Google Drive, across a two-week period starting from March 18, 2020. The Beck Anxiety Inventory was used to quantify the level of anxiety. RESULTS 1416 HCWs (70.8% medical doctors, 26.2% nurses) responded to the survey from 75 countries. The distribution of anxiety levels was: normal/minimal (n = 503, 35.5%), low (n = 390, 27.5%); moderate (n = 287, 20.3%), and severe (n = 236, 16.7%). According to multiple generalized linear model, female gender (p = 0.001), occupation (ie, being a nurse dealing directly with patients with COVID-19 [p = 0.017]), being younger (p = 0.001), reporting inadequate knowledge on COVID-19 (p = 0.005), having insufficient personal protective equipment (p = 0.001) and poor access to hand sanitizers or liquid soaps (p = 0.008), coexisting chronic disorders (p = 0.001) and existing mental health problems (p = 0.001), and higher income of countries where HCWs lived (p = 0.048) were significantly associated with increased anxiety. CONCLUSIONS Front-line HCWs, regardless of the levels of COVID-19 transmission in their country, are anxious when they do not feel protected. Our findings suggest that anxiety could be mitigated ensuring sufficient levels of protective personal equipment alongside greater education and information.
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Affiliation(s)
- Yasemin Cag
- Department of Infectious Diseases and Clinical Microbiology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey.
| | | | - Aynur Gormez
- Department of Psychiatry, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Handan Ankarali
- Department of Biostatistics and Medical Informatics, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Sally Hargreaves
- Institute for Infection and Immunity, St George's University of London, London, United Kingdom
| | | | - Francesca Rubulotta
- Department of Intensive Care Medicine Charing Cross Hospital Imperial College NHS Trust London, United Kingdom
| | - Mirko Belliato
- UOC Anestesia e Rianimazone 1, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Joana Berger-Estilita
- Department of Anaesthesiology and Pain Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Paolo Pelosi
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy,San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Stijn Blot
- Department of Internal Medicine & Pediatrics, Faculty of Medicine & Health Science Ghent University, Ghent, Belgium
| | - Jean Yves Lefrant
- Department of Anaesthesia Critical Care Emergency and Pain Medicine, University Hospital of Nimes, Montpellier University, Nimes, France
| | - Masoud Mardani
- Department of Infectious Diseases, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ilad Alavi Darazam
- Department of Infectious Diseases, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yakup Cag
- University of Health Sciences, Department of Pediatrics, Dr. Lutfi Kirdar Kartal Training and Research Hospital, Istanbul, Turkey
| | - Jordi Rello
- Department of Anaesthesia Critical Care Emergency and Pain Medicine, University Hospital of Nimes, Montpellier University, Nimes, France,Clinical Research and Epidemiology in Pneumonia and Sepsis, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Premraj A, Aleyas AG, Nautiyal B, Rasool TJ. Nucleic Acid and Immunological Diagnostics for SARS-CoV-2: Processes, Platforms and Pitfalls. Diagnostics (Basel) 2020; 10:E866. [PMID: 33114057 PMCID: PMC7690661 DOI: 10.3390/diagnostics10110866] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 12/26/2022] Open
Abstract
Accurate diagnosis at an early stage of infection is essential for the successful management of any contagious disease. The coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is a pandemic that has affected 214 countries affecting more than 37.4 million people causing 1.07 million deaths as of the second week of October 2020. The primary diagnosis of the infection is done either by the molecular technique of RT-qPCR by detecting portions of the RNA of the viral genome or through immunodiagnostic tests by detecting the viral proteins or the antibodies produced by the host. As the demand for the test increased rapidly many naive manufacturers entered the market with novel kits and more and more laboratories also entered the diagnostic arena making the test result more error-prone. There are serious debates globally and regionally on the sensitivity and specificity of these tests and about the overall accuracy and reliability of the tests for decision making on control strategies. The significance of the test is also complexed by the presence of asymptomatic carriers, re-occurrence of infection in cured patients as well as by the varied incubation periods of the infection and shifting of the viral location in the host tissues. In this paper, we review the techniques available for SARS-CoV-2 diagnosis and probable factors that can reduce the sensitivity and specificity of the different test methods currently in vogue. We also provide a checklist of factors to be considered to avoid fallacious practices to reduce false positive and false negative results by the clinical laboratories.
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Affiliation(s)
| | | | | | - Thaha J Rasool
- Camel Biotechnology Center, Presidential Camels and Camel Racing Affairs Centre, Department of the President’s Affairs, P.O. Box 17292, Al Ain 17292, UAE; (A.P.); (A.G.A.); (B.N.)
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COVID-19 and Disruption in Management and Education Academics: Bibliometric Mapping and Analysis. SUSTAINABILITY 2020. [DOI: 10.3390/su12187362] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
COVID-19, What to do now? This issue has had devastating effects in all domains of society worldwide. Lockdowns, the lack of freedom and social distancing meant the closure of a country’s entire activity. Having effects at all levels, beside incalculable ones in health, it is argued that scientific activity in education, business, economics and management suffered some of the most drastic impacts of this pandemic. This study aims to map the scientific literature in these areas in the context of COVID-19 and analyze its content through bibliometrics, which made it possible to highlight the scarcity of studies on the topic, namely empirical studies on the effects of this pandemic on scientific research and teaching/education. The results show there is a lack of peer-reviewed publications on this topic, with the studies covered (93) via the threads used revealing only 28 articles coming within the proposed objective. The bibliometrics corroborates that shortage. Finally, the contributions and implications for theory and practice are presented, followed by the limitations and suggestions for future research.
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Jafarian M, Chisti Y, Nathan GJ. Gas-lift circulation of a liquid between two inter-connected bubble columns. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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