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Babich R, Merutka I, Craig E, Harichandara A, De Silva PMCS, Gunasekara TDKSC, Jayasundara N. Transcriptomic and behavioral analyses reveal unique target tissues and molecular pathways associated with embryonic exposure to low level glyphosate and metal mixtures in zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169271. [PMID: 38114029 PMCID: PMC10964846 DOI: 10.1016/j.scitotenv.2023.169271] [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: 09/28/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Investigation of developmental molecular events following exposure to environmentally relevant agrochemical mixtures is critical to predicting their potential long-term ecological and human health risks. Here, we sought to uncover transcriptomic changes during zebrafish (Danio rerio) embryonic development following exposure to glyphosate and co-exposure to metals. Glyphosate is widely used globally with an allowable drinking water limit of 700 ppb. We examined effects of glyphosate (10 ppb) alone and when co-exposed to a metal mixture containing low levels of arsenic (4 ppb), lead (5 ppb), cadmium (2 ppb), and vanadium (15 ppb). This mixture was derived based on behavioral and morphological toxicity findings and environmentally relevant concentrations found in agricultural regions where glyphosate and metals are ubiquitously present. Gene expression patterns coupled to a single-cell transcriptomic dataset revealed that developmental exposure (28-72 h post fertilization) to glyphosate dysregulates expression of developmental genes specific to the central nervous system. Subsequent studies indicated significant suppression of larval zebrafish movement with 10 ppb glyphosate exposure. Studies with glyphosate + metals mixture and metals mixture alone showed unique developmental transcriptomic patterns and behavioral changes compared to glyphosate exposure alone. However, some outcomes (e.g., changes in expression of genes involved in epigenetic regulation and extracellular matrix patterning) were common across all three exposures compared to the control. Notably, glyphosate + metals co-exposure distinctly suppresses lysosomal transcripts and targets renal developmental genes. While further studies are required to uncover the precise nature of the interactions between glyphosate and metals, our study shows that glyphosate at very low levels is a behavioral and neurotoxicant that changes when metals are present. Given this herbicide affects distinctive physiological processes, including renal development and lysosomal dysregulation when co-exposed with metals, we conclude that environmental cation levels should be considered in glyphosate toxicity and risk assessment.
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Affiliation(s)
- Remy Babich
- University of Maine, Orono, ME 14069, United States of America.
| | - Ilaria Merutka
- Nicholas School of the Environment, Duke University, Durham, NC 27708, United States of America
| | - Emily Craig
- University of Maine, Orono, ME 14069, United States of America; Nicholas School of the Environment, Duke University, Durham, NC 27708, United States of America
| | | | | | | | - Nishad Jayasundara
- University of Maine, Orono, ME 14069, United States of America; Nicholas School of the Environment, Duke University, Durham, NC 27708, United States of America
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Allen FI, De Teresa JM, Onoa B. Focused Helium Ion and Electron Beam-Induced Deposition of Organometallic Tips for Dynamic Atomic Force Microscopy of Biomolecules in Liquid. ACS APPLIED MATERIALS & INTERFACES 2024; 16:4439-4448. [PMID: 38244049 DOI: 10.1021/acsami.3c16407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
We demonstrate the fabrication of sharp nanopillars of high aspect ratio onto specialized atomic force microscopy (AFM) microcantilevers and their use for high-speed AFM of DNA and nucleoproteins in liquid. The fabrication technique uses localized charged-particle-induced deposition with either a focused beam of helium ions or electrons in a helium ion microscope (HIM) or scanning electron microscope (SEM). This approach enables customized growth onto delicate substrates with nanometer-scale placement precision and in situ imaging of the final tip structures using the HIM or SEM. Tip radii of <10 nm are obtained and the underlying microcantilever remains intact. Instead of the more commonly used organic precursors employed for bio-AFM applications, we use an organometallic precursor (tungsten hexacarbonyl) resulting in tungsten-containing tips. Transmission electron microscopy reveals a thin layer of carbon on the tips. The interaction of the new tips with biological specimens is therefore likely very similar to that of standard carbonaceous tips, with the added benefit of robustness. A further advantage of the organometallic tips is that compared to carbonaceous tips they better withstand UV-ozone cleaning treatments to remove residual organic contaminants between experiments, which are inevitable during the scanning of soft biomolecules in liquid. Our tips can also be grown onto the blunted tips of previously used cantilevers, thus providing a means to recycle specialized cantilevers and restore their performance to the original manufacturer specifications. Finally, a focused helium ion beam milling technique to reduce the tip radii and thus further improve lateral spatial resolution in the AFM scans is demonstrated.
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Affiliation(s)
- Frances I Allen
- Department of Materials Science and Engineering, University of California, Berkeley, California 97420, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 97420, United States
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 97420, United States
| | - José María De Teresa
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Bibiana Onoa
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 97420, United States
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da Costa RL, Souza IC, Morozesk M, de Carvalho LB, Carvalho CDS, Monferrán MV, Wunderlin DA, Fernandes MN, Monteiro DA. Toxic, genotoxic, mutagenic, and bioaccumulative effects of metal mixture from settleable particulate matter on American bullfrog tadpoles (Lithobates catesbeianus). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122846. [PMID: 37926415 DOI: 10.1016/j.envpol.2023.122846] [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: 07/09/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Amphibians are more susceptible to environmental stressors than other vertebrates due to their semipermeable skin and physiological adaptations to living in very specific microhabitats. Therefore, the aim of the present study was to investigate the effects of a metal mixture from settleable particulate matter (SePM) released from metallurgical industries on Lithobates catesbeianus tadpoles. Endpoints analyzed included metal bioconcentration, morphological (biometrical indices), hematological parameters (hemoglobin and blood cell count), and erythrocyte DNA damage (genotoxicity and mutagenicity). American bullfrog tadpoles (Gosner's stage 25) were kept under control condition (no contaminant addition) or exposed to a sub-lethal and environmentally relevant concentration (1 g.L-1) of SePM for 96 h. Tadpoles exposed to SePM exhibited elevated whole blood levels of Fe56, AL, Sn, Pb, Zn, Cr, Cu, Ti, Rb, V, Ce, La, Ag, As. SePM-exposed tadpoles showed a significant decrease in condition factor (12%) and increases in hepatosomatic index (25%), hemoglobin concentration (17%), and total leukocytes (82%), thrombocytes (90%), and monocytes (78%) abundance. In addition, exposed tadpoles showed higher MN and ENAs (340 and 140%, respectively) frequencies, and erythrocyte DNA damage with approximately 1.2- to 1.8-fold increases in comet parameters. Taken together, these results suggest that the multimetal mixture found in SePM is potentially genotoxic and mutagenic to L. catesbeianus tadpoles, induces stress associated with hematological changes, and negatively affects growth. Although such contamination occurs at sublethal levels, regulatory standards are needed to control the emission of SePM and protect amphibian populations.
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Affiliation(s)
- Regiane Luiza da Costa
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil; Programa de Pós-Graduação Em Ciências Ambientais (PPGCAm), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), Brazil
| | - Iara Costa Souza
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil
| | - Mariana Morozesk
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil
| | - Luana Beserra de Carvalho
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil; Programa de Pós-Graduação Em Ciências Ambientais (PPGCAm), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil
| | - Cleoni Dos Santos Carvalho
- Departamento de Biologia (DBio), Centro de Ciências Humanas e Biológicas (CCHB), Universidade Federal de São Carlos (UFSCar), 18052-780, São Carlos, São Paulo, Brazil
| | - Magdalena Victoria Monferrán
- ICYTAC, Instituto de Ciencia y Tecnología de Alimentos Córdoba, CONICET and Dpto. Qca. Orgánica, Fac. Cs. Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba, Argentina
| | - Daniel Alberto Wunderlin
- ICYTAC, Instituto de Ciencia y Tecnología de Alimentos Córdoba, CONICET and Dpto. Qca. Orgánica, Fac. Cs. Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba, Argentina
| | - Marisa Narciso Fernandes
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil
| | - Diana Amaral Monteiro
- Departamento de Ciências Fisiológicas (DCF), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal de São Carlos (UFSCar), 13565-905, São Carlos, São Paulo, Brazil.
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Manglass LM, Vogel CM, Wintenberg M, Blenner MA, Martinez NE. Flowthrough of 239PU and 55FE during RNA extraction. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2023; 43:013502. [PMID: 36623311 DOI: 10.1088/1361-6498/acb15d] [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: 09/24/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Analysis of gene expression has become an important tool in understanding low-dose effect mechanisms of ionizing radiation at the cellular level. Metal binding to nucleic acids needs to be considered when interpreting these results, as some radioactive metals, particularly actinides, may produce free radicals and cause oxidative stress damage via chemical means at rates much higher than free radical formation related to their radiological properties. Bacteria exposedin situto low dose rates of plutonium-239 (239Pu) and iron-55 (55Fe) were previously analysed for gene expression. The work herein was motivated by an interest in more precisely identifying the distribution of radionuclides in these bacteria as well as the practical need to ensure appropriate transport and handling of the associated ribonucleic acid (RNA) extractions. RNA extractions were performed on bacteria growth media with and without bacteria cells (i.e. with and without RNA) at several different concentrations of239Pu and55Fe to inform the level of specificity of the extraction membrane as well as provide insight into internal (uptake) vs external (sorption) accumulation of these radionuclides in bacteria cells. Results of the study suggest that239Pu and55Fe detected in RNA extraction samples during long term cell studies is the result of binding to RNA prior to the time of extraction, as opposed to flow through or binding after cell lysis, and it highlights the practical importance of nucleic acid sample characterization to radiation protection more generally.
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Affiliation(s)
- Lisa M Manglass
- Department of Physics and Engineering, Francis Marion University, Florence, SC, United States of America
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States of America
| | - Charlotte M Vogel
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Molly Wintenberg
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States of America
| | - Mark A Blenner
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States of America
| | - Nicole E Martinez
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States of America
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Ding Y, Choy LY, Chew MH, Lin Q, Johns PW. Effects of Metal Ions on Cyanocobalamin Stability in Heated Milk
Protein‐Based
Matrices. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.16089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yi Ding
- Abbott Nutrition Research and Development, 20 Biopolis Way, #09‐01/02 Centros Building 138668 Singapore Singapore
| | - Li Yin Choy
- Abbott Nutrition Research and Development, 20 Biopolis Way, #09‐01/02 Centros Building 138668 Singapore Singapore
| | - Min Hui Chew
- Abbott Nutrition Research and Development, 20 Biopolis Way, #09‐01/02 Centros Building 138668 Singapore Singapore
| | - Qi Lin
- Abbott Nutrition Research and Development, 20 Biopolis Way, #09‐01/02 Centros Building 138668 Singapore Singapore
| | - Paul W. Johns
- Abbott Nutrition Research and Development, 20 Biopolis Way, #09‐01/02 Centros Building 138668 Singapore Singapore
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Xia Z, Patchin M, McKay CP, Drndić M. Deoxyribonucleic Acid Extraction from Mars Analog Soils and Their Characterization with Solid-State Nanopores. ASTROBIOLOGY 2022; 22:992-1008. [PMID: 35731031 DOI: 10.1089/ast.2021.0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for in situ biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (e.g., estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Margaret Patchin
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Marija Drndić
- David Rittenhouse Laboratory, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Davies TC. The position of geochemical variables as causal co-factors of diseases of unknown aetiology. SN APPLIED SCIENCES 2022; 4:236. [PMID: 35909942 PMCID: PMC9326422 DOI: 10.1007/s42452-022-05113-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022] Open
Abstract
Abstract The term diseases of unknown aetiology (DUA) or idiopathic diseases is used to describe diseases that are of uncertain or unknown cause or origin. Among plausible geoenvironmental co-factors in causation of DUA, this article focusses on the entry of trace elements, including metals and metalloids into humans, and their involvement in humoral and cellular immune responses, representing potentially toxic agents with implications as co-factors for certain DUA. Several trace elements/metals/metalloids (micronutrients) play vital roles as co-factors for essential enzymes and antioxidant molecules, thus, conferring protection against disease. However, inborn errors of trace element/metal/metalloid metabolisms can occur to produce toxicity, such as when there are basic defects in the element transport mechanism. Ultimately, it is the amount of trace element, metal or metalloid that is taken up, its mode of accumulation in human tissues, and related geomedical attributes such as the chemical form and bioavailability that decisively determine whether the exerted effects are toxic or beneficial. Several case descriptions of DUA that are common worldwide are given to illustrate our knowledge so far of how trace element/metal/metalloid interactions in the immune system may engender its dysregulation and be implicated as causal co-factors of DUA. Article highlights The importance of a proper understanding of geochemical perturbations in human metabolisms is emphasisedIt is proferred that such an understanding would aid greatly in the decipherment of diseases of unknown aetiology (DUA)The thesis presented may pave the way towards better diagnosis and therapy of DUA.
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Affiliation(s)
- Theophilus C. Davies
- Present Address: Faculty of Natural Sciences, Mangosuthu University of Technology, 511 Mangosuthu Highway, 4031, KwaZulu Natal, South Africa
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8
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Mesoscopic model confirms strong base pair metal mediated bonding for T-Hg 2+-T and weaker for C-Ag +-C. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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(MXene)/Au/DNA Aptasensor for the Ultraselective Electrochemical Detection of Lead in Water Samples. ELECTROANAL 2022. [DOI: 10.1002/elan.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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10
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Manglass LM, Wintenberg M, Vogel C, Blenner M, Martinez NE. Accumulation of radio-iron and plutonium, alone and in combination, in Pseudomonas putidagrown in liquid cultures. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2021; 41:1199-1212. [PMID: 34644681 DOI: 10.1088/1361-6498/ac2f86] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The impact of low doses of ionising radiation on biological and environmental systems have been historically difficult to study. Modern biological tools have provided new methods for studying these mechanisms but applying these tools to a dose-response relationship may require refinement of dosimetric techniques that incorporate a detailed understand of radionuclide accumulation in biological cells, particularly when assessing the impact of low doses of ionising radiation. In this workPseudomonas putida (KT2440) grown in liquid culture was exposed to low dose rates (10-20 mGy d-1) of239Pu and55Fe, both alone and in combination, for a period of 20 days, and the accumulation of239Pu and55Fe in cell pellets was analysed via liquid scintillation counting. The study also considered of cells grown with239Pu and stable Fe (primarily56Fe). In addition to the analysis of cell pellet and media samples, this work includes analysis of the radiological content of ribonucleic acid extraction samples to examine uptake of radionuclides. Results indicate that239Pu inhibited the uptake of55Fe, and that the presence of stable and radioactive isotopes of Fe in cultures may promote pathways for Fe accumulation that are used by239Pu. The work herein provides foundational insight into future dosimetric models for our work with environmental bacteria.
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Affiliation(s)
- Lisa M Manglass
- Department of Environmental Engineering and Earth Science, Clemson University, Clemson, SC, United States of America
- Department of Physics and Engineering, Francis Marion University, Florence, SC, United States of America
| | - Molly Wintenberg
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States of America
| | - Charlotte Vogel
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States of America
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States of America
| | - Nicole E Martinez
- Department of Environmental Engineering and Earth Science, Clemson University, Clemson, SC, United States of America
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Zaccaria F, van der Lubbe SCC, Nieuwland C, Hamlin TA, Fonseca Guerra C. How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes. Chemphyschem 2021; 22:2286-2296. [PMID: 34435425 PMCID: PMC9293024 DOI: 10.1002/cphc.202100529] [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: 07/13/2021] [Revised: 08/24/2021] [Indexed: 11/06/2022]
Abstract
The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+, Ca2+, Sr2+, and Ba2+), and (post‐)transition metal (Zn2+, Cd2+, Hg2+, and Pb2+) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+). Importantly, we establish the nature of the cation‐GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.
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Affiliation(s)
- Francesco Zaccaria
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Celine Nieuwland
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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Chan K, Morikawa K, Shibata N, Zinchenko A. Adsorptive Removal of Heavy Metal Ions, Organic Dyes, and Pharmaceuticals by DNA-Chitosan Hydrogels. Gels 2021; 7:112. [PMID: 34449623 PMCID: PMC8395854 DOI: 10.3390/gels7030112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 01/06/2023] Open
Abstract
DNA-chitosan (DNA-CS) hydrogel was prepared by in situ complexation between oppositely charged DNA and chitosan polyelectrolytes via electrostatic cross-linking to study its adsorption characteristics. The DNA-chitosan hydrogel matrix contains (i) cationic (NH3+) and anionic (PO4-) sites for electrostatic binding with ionic species, (ii) -OH and -NH2 groups and heteroaromatic DNA nucleobases for chelation of heavy metal ions, and (iii) DNA double-helix for recognition and binding to small organic molecules of various structures and polarities. DNA-CS hydrogels efficiently bind with Hg2+, Pb2+, Cd2+, and Cu2+ metal cations of significant environmental concern. Adsorption capacities of DNA-CS hydrogels for studied metal ions depend on hydrogel composition and pH of solution and reach ca. 50 mg/g at neutral pHs. Hydrogels with higher DNA contents show better adsorption characteristics and notably higher adsorption capacity to Hg2+ ions. Because of the co-existence of cationic and anionic macromolecules in the DNA-CS hydrogel, it demonstrates an affinity to both anionic (Congo Red) and cationic (Methylene Blue) dyes with moderate adsorption capacities of 12.6 mg/g and 29.0 mg/g, respectively. DNA-CS hydrogel can also be used for adsorptive removal of pharmaceuticals on conditions that their molecules are sufficiently hydrophobic and have ionogenic group(s). Facile preparation and multitarget adsorption characteristics of DNA-CS hydrogel coupled with sustainable and environmentally friendly characteristics render this system promising for environmental cleaning applications.
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Affiliation(s)
- Kayee Chan
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (K.C.); (K.M.)
| | - Kohki Morikawa
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (K.C.); (K.M.)
| | - Nobuyuki Shibata
- Nagoya Municipal Industrial Research Institute, 3-4-41, Rokuban, Atsuta, Nagoya 456-0058, Japan;
| | - Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; (K.C.); (K.M.)
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Li J, Stolee JA, Meda A. Simultaneous quantitation of inorganic ions in oligonucleotides using mixed-mode liquid chromatography coupled with a charged aerosol detector. J Pharm Biomed Anal 2021; 204:114244. [PMID: 34280819 DOI: 10.1016/j.jpba.2021.114244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/23/2021] [Accepted: 07/02/2021] [Indexed: 02/08/2023]
Abstract
The amounts of inorganic ions (e.g. sodium, potassium, magnesium, calcium, chloride, and phosphate) in intrathecally administered oligonucleotide drug products need to be controlled in order to meet the final target formulation composition. During process development, these ions are measured to ensure the solution composition does not change during purification or drug product compounding and to ensure the final drug product targets are achieved. A quantitative method for ion analysis in antisense oligonucleotide (ASO) drugs was developed by mixed-mode anion exchange/cation exchange-hydrophilic interaction liquid chromatography (AEX/CEX-HILIC) with a charged aerosol detector (CAD). This thirteen-minute method measures monovalent and multivalent cations and anions simultaneously. LC separation conditions, CAD parameters, and sample preparation were judiciously optimized to ensure that the method is specific, accurate, precise, linear, robust, and rugged. With this LC-CAD approach, ion analysis for oligonucleotide drugs can be performed in most analytical labs to support drug development.
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Affiliation(s)
- Jiangwei Li
- Department of Analytical Development, Biogen, 225 Binney St, Cambridge, MA 02142, USA.
| | - Jessica A Stolee
- Department of Analytical Development, Biogen, 225 Binney St, Cambridge, MA 02142, USA
| | - Alvin Meda
- Department of Analytical Development, Biogen, 225 Binney St, Cambridge, MA 02142, USA
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Zhou Y, Li X, McBride MB. Aqueous solubility of Pb at equilibrium with hydroxypyromorphite over a range of phosphate concentrations. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:170-178. [PMID: 33399599 DOI: 10.1039/d0em00430h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hydroxypyromorphite (HPM) is a low-solubility Pb phosphate mineral that has the potential to limit solubility and bioavailability of Pb in soils and water. Because of reported uncertainty regarding the solubility product of this important mineral, we re-evaluated the solubility of Pb and activity of the free Pb2+ ion in aqueous suspensions of microcrystalline HPM equilibrated up to 30 days over a wide range of added soluble phosphate. A small addition of phosphate (0.1 mM) reduced Pb solubility as measured by ICP-OES, but greater phosphate additions (up to 50 mM) had no further effect in lowering HPM solubility. However, free Pb2+ ion activity measured by ion-selective electrode progressively decreased from about 10-6.5 with no added phosphate to 10-9 as soluble phosphate was increased. The effect of soluble phosphate in lowering Pb2+ activity is attributed to inhibited dissolution of HPM as well as increased Pb2+-phosphate ion pair formation in solution at higher solution concentrations of phosphate. Measurement of the ion activity products (IAP) of the solutions at equilibrium with HPM gave highly variable IAP values that were sensitive to pH and were generally not consistent with the reported solubility product of this mineral. The high variability of the IAPs for solutions with variable pH and phosphate concentrations indicates that dissolution-precipitation reactions of HPM are not described by a constant solubility product at equilibrium, possibly because of the incongruent dissolution behavior of this mineral at near-neutral pH.
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Affiliation(s)
- Yuting Zhou
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Xinxin Li
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Murray B McBride
- Section of Soil and Crop Sciences, Cornell University, Ithaca, NY 14850, USA.
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Sawan S, Hamze K, Youssef A, Boukarroum R, Bouhadir K, Errachid A, Maalouf R, Jaffrezic-Renault N. Voltammetric study of the affinity of divalent heavy metals for guanine-functionalized iron oxide nanoparticles. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02738-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Lilienthal S, Luo GF, Wang S, Yue L, Fischer A, Ehrlich A, Nahmias Y, Willner I. Constitutional Dynamic Networks-Guided Synthesis of Programmed "Genes", Transcription of mRNAs, and Translation of Proteins. J Am Chem Soc 2020; 142:21460-21468. [PMID: 33290051 DOI: 10.1021/jacs.0c10565] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inspired by nature, where dynamic networks control the levels of gene expression and the activities of transcribed/translated proteins, we introduce nucleic acid-based constitutional dynamic networks (CDNs) as functional modules mimicking native circuits by demonstrating CDNs-guided programmed synthesis of genes, controlled transcription of RNAs, and dictated transcription/translation synthesis of proteins. An auxiliary CDN consisting of four dynamically equilibrated constituents AA', AB', BA', and BB' is orthogonally triggered by two different inputs yielding two different compositionally reconfigured CDNs. Subjecting the parent auxiliary CDN to two hairpins, HA and HB, and two templates TA and TB and a nicking/replication machinery leads to the cleavage of the hairpins and to the activation of the nicking/replication machineries that synthesize two "genes", e.g., the histidine-dependent DNAzyme g1 and the Zn2+-ion-dependent DNAzyme g2. The triggered orthogonal reconfiguration of the parent CDN to the respective CDNs leads to the programmed preferred CDN-guided synthesis of g1 or g2. Similarly, the triggered reconfigured CDNs are subjected to two hairpins HC and HD, the templates I'/I and J'/J, and the RNA polymerase (RNAp)/NTPs machinery. While the cleavage of the hairpins by the constituents associated with the parent CDN leads to the transcription of the broccoli aptamer recognizing the DFHBI ligand and of the aptamer recognizing the malachite green (MG) ligand, the orthogonally triggered CDNs lead to the CDNs-guided enhanced transcription of either the DFHBI aptamer or the MG aptamer. In addition, subjecting the triggered reconfigured CDNs to predesigned hairpins HE and HF, the templates M'/M and N'/N, the RNAp/NTPs machinery, and the cell-free ribosome t-RNA machinery leads to the CDNs-guided transcription/translation of the green fluorescence protein (GFP) or red fluorescence protein (RFP).
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Affiliation(s)
- Sivan Lilienthal
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Guo-Feng Luo
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liang Yue
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Amit Fischer
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Avner Ehrlich
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yaakov Nahmias
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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17
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Dulay H, Tabares M, Kashefi K, Reguera G. Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Front Microbiol 2020; 11:600463. [PMID: 33324382 PMCID: PMC7726332 DOI: 10.3389/fmicb.2020.600463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
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Affiliation(s)
- Hunter Dulay
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Marcela Tabares
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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18
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Tao X, Wang X, Liu B, Liu J. Conjugation of antibodies and aptamers on nanozymes for developing biosensors. Biosens Bioelectron 2020; 168:112537. [PMID: 32882473 DOI: 10.1016/j.bios.2020.112537] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023]
Abstract
Nanozymes are engineered nanomaterials with enzyme-like activities. Over the past decade, impressive progresses on nanozymes in biosensing have been made due to their unique advantages of high stability, low cost, and easy modification compared to natural enzymes. For many biosensors, it is critical to conjugate nanozymes to affinity ligands such as antibodies and aptamers. Since different nanomaterials have different surface properties, conjugation methods need to be compatible with these properties. In addition, the effect of biomolecules on nanozyme activity needs to be considered. In this review, we first categorized nanozyme-based biosensors into four parts, respectively describing noncovalent and covalent modifications with antibodies and aptamers. Meanwhile, recent advances in antibody and aptamer labeled nanozyme biosensors are summarized, and the methods of their conjugation are further illustrated. Finally, conclusions and future perspectives for the development and application of nanozyme bioconjugates are discussed.
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Affiliation(s)
- Xiaoqi Tao
- College of Food Science, Southwest University, Chongqing, 400715, China; Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Xin Wang
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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Rasouli Z, Ghavami R. Facile Approach to Fabricate a Chemical Sensor Array Based on Nanocurcumin-Metal Ions Aggregates: Detection and Identification of DNA Nucleobases. ACS OMEGA 2020; 5:19331-19341. [PMID: 32803026 PMCID: PMC7424583 DOI: 10.1021/acsomega.0c00593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/07/2020] [Indexed: 05/04/2023]
Abstract
Here, a three-channel absorbance sensor array based on the nanocurcumin-metal ion (NCur-MI) aggregates is designed for the detection and identification of deoxyribonucleic acid nucleobases (DNA NBs) for the first time. For this purpose, the binding affinities of some of MIs (i.e., Co2+, Cr3+, Cu2+, Fe2+, Fe3+, Hg2+, Mn2+, Ni2+, V3+, and Zn2+) to the NCur to induce the aggregation were evaluated under various experimental conditions. Further studies reveal that in the presence of DNA NBs, the aggregates of NCur-Co2+, NCur-Ni2+, and NCur-Zn2+ show the diverse absorbance responses to the deaggregation of NCur depending on the binding affinity of each of DNA NBs to the metal ions Co2+, Ni2+, and Zn2+. These responses are distinguishable from one another. Thus, clear differentiation among the DNA NBs is achieved by linear discriminant analysis and hierarchical clustering analysis to generate clustering maps. The discriminatory capacity of the sensor array for the identification of the DNA NBs is tested in the ranges of 2.4-16 and 5.6-10.4 μM. Furthermore, a mixed set of the DNA NBs was prepared for multivariate multicomponent analysis. Finally, the practicability of the sensor array is confirmed by the discrimination of the DNA NBs in an animal DNA sample. It should be noted that the proposed array is the first example to fabricate an NCur-based sensor array for the simultaneous detection of DNA NBs.
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Affiliation(s)
- Zolaikha Rasouli
- Chemometrics Laboratory, Chemistry
Department, Faculty of Science, University
of Kurdistan, P.O. Box 416, Sanandaj 66177-15175, Iran
| | - Raouf Ghavami
- Chemometrics Laboratory, Chemistry
Department, Faculty of Science, University
of Kurdistan, P.O. Box 416, Sanandaj 66177-15175, Iran
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20
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Fond memories of my PhD research in Professor Cris dos Remedios' laboratory. Biophys Rev 2020; 12:789-790. [PMID: 32642927 DOI: 10.1007/s12551-020-00727-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022] Open
Abstract
I completed my PhD in 2013 under the supervision of Prof Cristobal G. dos Remedios, Department of Anatomy and Histology, The University of Sydney. His guidance and exemplary scientific standard in his laboratory ignited an insatiable scientific curiosity that continuously pushes me towards new knowledge through my own research.
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Hammud HH, Holman KT, Al-Noaimi M, Sheikh NS, Ghannoum AM, Bouhadir KH, Masoud MS, Karnati RK. Structures of selected transition metal complexes with 9-(2-hydroxyethyl)adenine: Potentiometric complexation and DFT studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Study of adduct compounds between oxovanadium complexes VO(IV) and some biological relevance using FTIR technique. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00949-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Hall D. A note of appreciation for Prof. Cristobal dos Remedios on behalf of Biophysical Reviews. Biophys Rev 2019; 11:129-130. [PMID: 30783907 DOI: 10.1007/s12551-019-00505-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/11/2019] [Indexed: 12/19/2022] Open
Abstract
Following the initial five-year tenure (2009-2014) of the founding Chief Editor, Dr. Jean Garnier, Prof. Cristobal dos Remedios (University of Sydney) assumed responsibility for Biophysical Reviews as the second Chief Editor (2014-2019). Under his stewardship, Biophysical Reviews has become a six issue per year journal, publishing approximately 100 reviews per year. At the conclusion of his five-year tenure as Chief Editor (and at the age of 78), Cris is stepping down, leaving the journal well placed to apply for (and receive) an impact factor in 2020. On behalf of the journal, I would like to take the occasion of his retirement as Chief Editor to thank Cris for his dedicated service to Biophysical Reviews, and also welcome him to his new position as Emeritus Chief Editor.
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Affiliation(s)
- Damien Hall
- Laboratory for Multiscale Structural Biology, Institute for Protein Research, Osaka University, 3-1-Yamadaoka, Suita, Osaka, 565-0871, Japan.
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