scholarly journals Soot and charcoal are reservoirs of extracellular DNA

2021 ◽  
Author(s):  
Stanislav Jelavic ◽  
Lisbeth Garbrecht Thygesen ◽  
Valerie Magnin ◽  
Nathaniel Findling ◽  
Sascha Müller ◽  
...  
Keyword(s):  
Hydrophobic Interactions ◽  
Antibiotic Resistance Genes ◽  
Solution Concentration ◽  
Low Ph ◽  
Extracellular Dna ◽  
Biological Degradation ◽  
Environmental Matrices ◽  
Solution Composition ◽  
Dna Adsorption ◽  
Insight Into

Soot and charcoal are carbonaceous materials widespread in the environment where they readily can come in contact with extracellular DNA shed from organisms. The adsorption at a surface protects DNA from chemical and biological degradation. However, a comprehensive insight into DNA adsorption at soot and charcoal is lacking. We measured DNA adsorption capacity at soot and charcoal as a function of solution composition, time and DNA length. We observed that the capacity for DNA is the highest at low pH, it increases with solution concentration and cation valency and that the activation energy for DNA adsorption at both soot and charcoal is ~50 kJmol-1. We demonstrate how the interaction between DNA and soot and charcoal partly occurs via terminal basepairs, suggesting that, besides electrostatic forces, hydrophobic interactions play an important role in binding. The importance of hydrophobic interactions increases as the hydrophobicity of a surface increases. Such strong binding and hydrophobic interactions need to be taken into account to improve DNA extraction protocols and for mitigation of the spread of antibiotic resistance genes in environmental matrices that contain soot and charcoal such as aerosol, wastewater and topsoil.

scholarly journals Antibiotic resistance genes and mobile genetic elements removal from treated wastewater by sewage-sludge biochar and iron-oxide coated sand

2020 ◽  
Author(s):  
David Calderón-Franco ◽  
Apoorva Seeram ◽  
Gertjan Medema ◽  
Mark C. M. van Loosdrecht ◽  
David G. Weissbrodt
Keyword(s):  
Antibiotic Resistance ◽  
Iron Oxide ◽  
Sewage Sludge ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Environmental Dna ◽  
Extracellular Dna ◽  
Treated Wastewater ◽  
Dna Adsorption ◽  
Coated Sand

AbstractDisinfection of treated wastewater in wastewater treatment plants (WWTPs) is used to minimize emission of coliforms, pathogens, and antibiotic resistant bacteria (ARB) in the environment. However, the fate of free-floating extracellular DNA (eDNA) that do carry antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) is overlooked. Water technologies are central to urban and industrial ecology for sanitation and resource recovery. Biochar produced by pyrolysis of sewage sludge and iron-oxide-coated sands recovered as by-product of drinking water treatment were tested as adsorbents to remove ARGs and MGEs from WWTP effluent. DNA adsorption properties and materials applicability were studied in batch and up-flow column systems at bench scale. Breakthrough curves were measured with ultrapure water and treated wastewater at initial DNA concentrations of 0.1-0.5 mg mL-1 and flow rates of 0.1-0.5 mL min-1. Batch tests with treated wastewater indicated that the adsorption profiles of biochar and iron-oxide coated sand followed a Freundlich isotherm, suggesting a multilayer adsorption of nucleic acids. Sewage-sludge biochar exhibited higher DNA adsorption capacity (1 mg g-1) and longer saturation breakthrough times (4 to 10 times) than iron-oxide coated sand (0.2 mg g-1). The removal of a set of representative ARGs and MGEs was measured by qPCR comparing the inlet and outlet of the plug-flow column fed with treated wastewater. ARGs and MGEs present as free-floating eDNA were adsorbed by sewage-sludge biochar at 85% and iron-oxide coated sand at 54%. From the environmental DNA consisting of the free-floating extracellular DNA plus the intracellular DNA of the cells present in the effluent water, 97% (sewage-sludge biochar) and 66% (iron-oxide coated sand) of the tested genes present were removed. Sewage-sludge biochar displayed interesting properties to minimize the spread of antimicrobial resistances to the aquatic environment while strengthening the role of WWTPs as resource recovery factories.Graphical abstractHighlightsSewage-sludge biochar and iron oxide coated sands were tested to adsorb DNA and cells.Biochar removed 97% of genes tested from environmental DNA of unfiltered effluent.85% of ARGs and MGEs of free-floating extracellular DNA were retained by biochar.Biochar is a WWTP by-product that can be re-used for public health sanitation.

Structure, anion, and solvent effects on cation response in ESI-MS

2019 ◽  
Author(s):  
Isaac Omari ◽  
Parmissa Randhawa ◽  
Jaiya Randhawa ◽  
Jenny Yu ◽  
J Scott McIndoe
Keyword(s):  
Predictive Power ◽  
Solution Concentration ◽  
High Reactivity ◽  
Chemical Processes ◽  
Ionization Mass ◽  
Solution Composition ◽  
Ionization Mass Spectrum ◽  
Electrospray Ionization Mass Spectrum ◽  
Cation Response ◽  
Insight Into

<p>The abundance of an ion in an electrospray ionization mass spectrum is dependent on many factors beyond just solution concentration. Even in cases where the ions are permanently charged and do not rely on protonation or other chemical processes to acquire the necessary charge, factors such as cation structure, molecular weight, solvent, and the identity of the anion can perturb results. Screening of a variety of combinations of cation, anion and solvent provided insight into some of the more important factors. Rigid cations and high conductivity anions tended to provide the highest responses, while acetonitrile was the most accurate solvent for reflecting solution composition. Functional groups that had affinity for the solvent tended to depress response. These observations will provide predictive power when accounting for ions that for reasons of high reactivity can not be isolated.</p><br>

Structure, anion, and solvent effects on cation response in ESI-MS

2019 ◽  
Author(s):  
Isaac Omari ◽  
Parmissa Randhawa ◽  
Jaiya Randhawa ◽  
Jenny Yu ◽  
J Scott McIndoe
Keyword(s):  
Predictive Power ◽  
Solution Concentration ◽  
High Reactivity ◽  
Chemical Processes ◽  
Ionization Mass ◽  
Solution Composition ◽  
Ionization Mass Spectrum ◽  
Electrospray Ionization Mass Spectrum ◽  
Cation Response ◽  
Insight Into

<p>The abundance of an ion in an electrospray ionization mass spectrum is dependent on many factors beyond just solution concentration. Even in cases where the ions are permanently charged and do not rely on protonation or other chemical processes to acquire the necessary charge, factors such as cation structure, molecular weight, solvent, and the identity of the anion can perturb results. Screening of a variety of combinations of cation, anion and solvent provided insight into some of the more important factors. Rigid cations and high conductivity anions tended to provide the highest responses, while acetonitrile was the most accurate solvent for reflecting solution composition. Functional groups that had affinity for the solvent tended to depress response. These observations will provide predictive power when accounting for ions that for reasons of high reactivity can not be isolated.</p><br>

scholarly journals Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction

Open Biology ◽  
2013 ◽  
Vol 3 (11) ◽  
pp. 130100 ◽  
Author(s):  
Zhisheng Lu ◽  
Julien R. C. Bergeron ◽  
R. Andrew Atkinson ◽  
Torsten Schaller ◽  
Dennis A. Veselkov ◽  
...  
Keyword(s):  
Solution Structure ◽  
Hydrophobic Interactions ◽  
Dynamic Information ◽  
Ubiquitin Ligase Complex ◽  
Biophysical Studies ◽  
Viral Infectivity Factor ◽  
Β Sheet ◽  
Socs Box ◽  
Insight Into ◽  
Hiv 1

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

scholarly journals Extracellular DNA (eDNA): Neglected and Potential Sources of Antibiotic Resistant Genes (ARGs) in the Aquatic Environments

Pathogens ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 874
Author(s):  
Periyasamy Sivalingam ◽  
John Poté ◽  
Kandasamy Prabakar
Keyword(s):  
Antibiotic Resistance ◽  
Health Risk ◽  
Genetic Material ◽  
Antibiotic Resistance Genes ◽  
Extracellular Dna ◽  
Antibiotic Resistant ◽  
Treatment Technologies ◽  
Environmental Bacteria ◽  
Global Threat ◽  
Potential Public Health

Over the past decades, the rising antibiotic resistance bacteria (ARB) are continuing to emerge as a global threat due to potential public health risk. Rapidly evolving antibiotic resistance and its persistence in the environment, have underpinned the need for more studies to identify the possible sources and limit the spread. In this context, not commonly studied and a neglected genetic material called extracellular DNA (eDNA) is gaining increased attention as it can be one of the significant drivers for transmission of extracellular ARGS (eARGs) via horizontal gene transfer (HGT) to competent environmental bacteria and diverse sources of antibiotic-resistance genes (ARGs) in the environment. Consequently, this review highlights the studies that address the environmental occurrence of eDNA and encoding eARGs and its impact on the environmental resistome. In this review, we also brief the recent dedicated technological advancements that are accelerating extraction of eDNA and the efficiency of treatment technologies in reducing eDNA that focuses on environmental antibiotic resistance and potential ecological health risk.

scholarly journals Significance of Mast Cell Formed Extracellular Traps in Microbial Defense

2021 ◽  
Author(s):  
Daniel Elieh Ali Komi ◽  
Wolfgang M. Kuebler
Keyword(s):  
State Of The Art ◽  
Extracellular Dna ◽  
Cellular Mechanisms ◽  
Extracellular Traps ◽  
Synthetic Chemicals ◽  
Dna Strands ◽  
Associated Proteins ◽  
Microbial Defense ◽  
And Function ◽  
Insight Into

AbstractMast cells (MCs) are critically involved in microbial defense by releasing antimicrobial peptides (such as cathelicidin LL-37 and defensins) and phagocytosis of microbes. In past years, it has become evident that in addition MCs may eliminate invading pathogens by ejection of web-like structures of DNA strands embedded with proteins known together as extracellular traps (ETs). Upon stimulation of resting MCs with various microorganisms, their products (including superantigens and toxins), or synthetic chemicals, MCs become activated and enter into a multistage process that includes disintegration of the nuclear membrane, release of chromatin into the cytoplasm, adhesion of cytoplasmic granules on the emerging DNA web, and ejection of the complex into the extracellular space. This so-called ETosis is often associated with cell death of the producing MC, and the type of stimulus potentially determines the ratio of surviving vs. killed MCs. Comparison of different microorganisms with specific elimination characteristics such as S pyogenes (eliminated by MCs only through extracellular mechanisms), S aureus (removed by phagocytosis), fungi, and parasites has revealed important aspects of MC extracellular trap (MCET) biology. Molecular studies identified that the formation of MCET depends on NADPH oxidase-generated reactive oxygen species (ROS). In this review, we summarize the present state-of-the-art on the biological relevance of MCETosis, and its underlying molecular and cellular mechanisms. We also provide an overview over the techniques used to study the structure and function of MCETs, including electron microscopy and fluorescence microscopy using specific monoclonal antibodies (mAbs) to detect MCET-associated proteins such as tryptase and histones, and cell-impermeant DNA dyes for labeling of extracellular DNA. Comparing the type and biofunction of further MCET decorating proteins with ETs produced by other immune cells may help provide a better insight into MCET biology in the pathogenesis of autoimmune and inflammatory disorders as well as microbial defense.

scholarly journals Genome-Guided Characterization of Ochrobactrum sp. POC9 Enhancing Sewage Sludge Utilization—Biotechnological Potential and Biosafety Considerations

2018 ◽  
Vol 15 (7) ◽  
pp. 1501 ◽  
Author(s):  
Krzysztof Poszytek ◽  
Joanna Karczewska-Golec ◽  
Anna Ciok ◽  
Przemyslaw Decewicz ◽  
Mikolaj Dziurzynski ◽  
...  
Keyword(s):  
Sewage Sludge ◽  
Pathogenic Bacteria ◽  
Biogas Production ◽  
Treatment Plant ◽  
Antibiotic Resistance Genes ◽  
Biotechnological Potential ◽  
Sewage Sludge Sample ◽  
Complex Organic ◽  
Insight Into

Sewage sludge is an abundant source of microorganisms that are metabolically active against numerous contaminants, and thus possibly useful in environmental biotechnologies. However, amongst the sewage sludge isolates, pathogenic bacteria can potentially be found, and such isolates should therefore be carefully tested before their application. A novel bacterial strain, Ochrobactrum sp. POC9, was isolated from a sewage sludge sample collected from a wastewater treatment plant. The strain exhibited lipolytic, proteolytic, cellulolytic, and amylolytic activities, which supports its application in biodegradation of complex organic compounds. We demonstrated that bioaugmentation with this strain substantially improved the overall biogas production and methane content during anaerobic digestion of sewage sludge. The POC9 genome content analysis provided a deeper insight into the biotechnological potential of this bacterium and revealed that it is a metalotolerant and a biofilm-producing strain capable of utilizing various toxic compounds. The strain is resistant to rifampicin, chloramphenicol and β-lactams. The corresponding antibiotic resistance genes (including blaOCH and cmlA/floR) were identified in the POC9 genome. Nevertheless, as only few genes in the POC9 genome might be linked to pathogenicity, and none of those genes is a critical virulence factor found in severe pathogens, the strain appears safe for application in environmental biotechnologies.

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