scholarly journals The masking effect of extracellular DNA and robustness of intracellular DNA in anaerobic digester NGS studies: A discriminatory study of the total DNA pool

2020 ◽  
Vol 30 (2) ◽  
pp. 438-450
Author(s):  
Magdalena Nagler ◽  
Sabine Marie Podmirseg ◽  
Markus Mayr ◽  
Judith Ascher‐Jenull ◽  
Heribert Insam
Keyword(s):  
Anaerobic Digester ◽  
Extracellular Dna ◽  
Masking Effect ◽  
Total Dna ◽  
Dna Pool

scholarly journals The Molecular Information About Deadwood Bacteriomes Partly Depends on the Targeted Environmental DNA

2021 ◽  
Vol 12 ◽  
Author(s):  
Maraike Probst ◽  
Judith Ascher-Jenull ◽  
Heribert Insam ◽  
María Gómez-Brandón
Keyword(s):  
Environmental Dna ◽  
Extracellular Dna ◽  
Masking Effect ◽  
Differential Analysis ◽  
Intact Cells ◽  
Total Dna ◽  
Dna Types ◽  
Dna Pool ◽  
First Time

Microbiome studies mostly rely on total DNA extracts obtained directly from environmental samples. The total DNA consists of both intra- and extracellular DNA, which differ in terms of their ecological interpretation. In the present study, we have investigated for the first time the differences among the three DNA types using microbiome sequencing of Picea abies deadwood logs (Hunter decay classes I, III, and V). While the bacterial compositions of all DNA types were comparable in terms of more abundant organisms and mainly depended on the decay class, we found substantial differences between DNA types with regard to less abundant amplicon sequence variants (ASVs). The analysis of the sequentially extracted intra- and extracellular DNA fraction, respectively, increased the ecological depth of analysis compared to the directly extracted total DNA pool. Both DNA fractions were comparable in proportions and the extracellular DNA appeared to persist in the P. abies deadwood logs, thereby causing its masking effect. Indeed, the extracellular DNA masked the compositional dynamics of intact cells in the total DNA pool. Our results provide evidence that the choice of DNA type for analysis might benefit a study’s answer to its respective ecological question. In the deadwood environment researched here, the differential analysis of the DNA types underlined the relevance of Burkholderiales, Rhizobiales and other taxa for P. abies deadwood decomposition and revealed that the role of Acidobacteriota under this scenario might be underestimated, especially compared to Actinobacteriota.

scholarly journals DNA secretion and gene-level selection in bacteria

Microbiology ◽  
2006 ◽  
Vol 152 (9) ◽  
pp. 2683-2688 ◽  
Author(s):  
Jeremy A. Draghi ◽  
Paul E. Turner
Keyword(s):  
Mathematical Model ◽  
Population Genetics ◽  
Genetic Material ◽  
Extracellular Dna ◽  
Bacterial Cells ◽  
Gene Level ◽  
Natural Genetic Transformation ◽  
Dna Pool ◽  
Extracellular Environment ◽  
Living Bacteria

Natural genetic transformation can facilitate gene transfer in many genera of bacteria and requires the presence of extracellular DNA. Although cell lysis can contribute to this extracellular DNA pool, several studies have suggested that the secretion of DNA from living bacteria may also provide genetic material for transformation. This paper reviews the evidence for specific secretion of DNA from intact bacteria into the extracellular environment and examines this behaviour from a population-genetics perspective. A mathematical model demonstrates that the joint action of DNA secretion and transformation creates a novel type of gene-level natural selection. This model demonstrates that gene-level selection could explain the existence of DNA secretion mechanisms that provide no benefit to individual cells or populations of bacteria. Additionally, the model predicts that any trait affecting DNA secretion will experience selection at the gene level in a transforming population. This analysis confirms that the secretion of DNA from intact bacterial cells is fully explicable with evolutionary theory, and reveals a novel mechanism for bacterial evolution.

scholarly journals Evasion of Immune Surveillance in Low Oxygen Environments EnhancesCandida albicansVirulence

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
José Pedro Lopes ◽  
Marios Stylianou ◽  
Emelie Backman ◽  
Sandra Holmberg ◽  
Jana Jass ◽  
...  
Keyword(s):  
Cell Wall ◽  
Immune Surveillance ◽  
Oxygen Deprivation ◽  
Extracellular Dna ◽  
Masking Effect ◽  
Infection Model ◽  
Low Oxygen ◽  
Content Type ◽  
Oxygen Levels ◽  
Oxygen Conditions

ABSTRACTMicrobial colonizers of humans have evolved to adapt to environmental cues and to sense nutrient availability. Oxygen is a constantly changing environmental parameter in different host tissues and in different types of infection. We describe howCandida albicans, an opportunistic fungal pathogen, can modulate the host response under hypoxia and anoxia. We found that high infiltration of polymorphonuclear leukocytes (PMNs) to the site of infection contributes to a low oxygen milieu in a murine subdermal abscess. A persistent hypoxic environment did not affect viability or metabolism of PMNs. Under oxygen deprivation, however, infection withC. albicansdisturbed specific PMN responses. PMNs were not able to efficiently phagocytose, produce ROS, or release extracellular DNA traps. Failure to launch an adequate response was caused byC. albicanscell wall masking of β-glucan upon exposure to low oxygen levels which hindered PAMP sensing by Dectin-1 on the surfaces of PMNs. This in turn contributed to immune evasion and enhanced fungal survival. The cell wall masking effect is prolonged by the accumulation of lactate produced by PMNs under low oxygen conditions. Finally, adaptation to oxygen deprivation increased virulence ofC. albicanswhich we demonstrated using aCaenorhabditis elegansinfection model.IMPORTANCESuccessful human colonizers have evolved mechanisms to bypass immune surveillance. Infiltration of PMNs to the site of infection led to the generation of a low oxygen niche. Exposure to low oxygen levels induced fungal cell wall masking, which in turn hindered pathogen sensing and antifungal responses by PMNs. The cell wall masking effect was prolonged by increasing lactate amounts produced by neutrophil metabolism under oxygen deprivation. In an invertebrate infection model,C. albicanswas able to kill infectedC. elegansnematodes within 2 days under low oxygen conditions, whereas the majority of uninfected controls and infected worms under normoxic conditions survived. These results suggest thatC. albicansbenefited from low oxygen niches to increase virulence. The interplay ofC. albicanswith innate immune cells under these conditions contributed to the overall outcome of infection. Adaption to low oxygen levels was in addition beneficial forC. albicansby reducing susceptibility to selected antifungal drugs. Hence, immunomodulation of host cells under low oxygen conditions could provide a valuable approach to improve current antifungal therapies.

scholarly journals Determination of Virus Abundance in Marine Sediments

2001 ◽  
Vol 67 (3) ◽  
pp. 1384-1387 ◽  
Author(s):  
R. Danovaro ◽  
A. Dell'Anno ◽  
A. Trucco ◽  
M. Serresi ◽  
S. Vanucci
Keyword(s):  
Electron Microscopy ◽  
Marine Sediments ◽  
Extracellular Dna ◽  
Epifluorescence Microscopy ◽  
Masking Effect ◽  
Sediment Storage ◽  
Virus Particles ◽  
Transmission Electron ◽  
Virus Abundance

ABSTRACT In this study, we optimized procedures to enumerate viruses from marine sediments by epifluorescence microscopy using SYBR Green I as a stain. The highest virus yields from the bulk of the sediments were obtained by utilizing pyrophosphate and 3 min of sonication. The efficiency of extraction benthic viruses by pyrophosphate-ultrasound treatment was about 60% of the extractable virus particles. Samples treated with nucleases had increased virus counts, suggesting a masking effect of extracellular DNA. No significant differences were observed between virus counts obtained by epifluorescence microscopy and transmission electron microscopy. Both formaldehyde and glutaraldehyde gave significant reductions of virus counts after only 24 h of sediment storage, but no further loss occurred after 7 days.

scholarly journals Extracellular DNA in Single- and Multiple-Species Unsaturated Biofilms

2005 ◽  
Vol 71 (9) ◽  
pp. 5404-5410 ◽  
Author(s):  
R. E. Steinberger ◽  
P. A. Holden
Keyword(s):  
Dna Analysis ◽  
Rhodococcus Erythropolis ◽  
Extracellular Dna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Single Strain ◽  
Principle Components Analysis ◽  
Total Dna ◽  
Multiple Species ◽  
Cellular Dna

ABSTRACT The extracellular polymeric substances (EPS) of bacterial biofilms form a hydrated barrier between cells and their external environment. Better characterization of EPS could be useful in understanding biofilm physiology. The EPS are chemically complex, changing with both bacterial strain and culture conditions. Previously, we reported that Pseudomonas aeruginosa unsaturated biofilm EPS contains large amounts of extracellular DNA (eDNA) (R. E. Steinberger, A. R. Allen, H. G. Hansma, and P. A. Holden, Microb. Ecol. 43:416-423, 2002). Here, we investigated the compositional similarity of eDNA to cellular DNA, the relative quantity of eDNA, and the terminal restriction fragment length polymorphism (TRFLP) community profile of eDNA in multiple-species biofilms. By randomly amplified polymorphic DNA analysis, cellular DNA and eDNA appear identical for P. aeruginosa biofilms. Significantly more eDNA was produced in P. aeruginosa and Pseudomonas putida biofilms than in Rhodococcus erythropolis or Variovorax paradoxus biofilms. While the amount of eDNA in dual-species biofilms was of the same order of magnitude as that of of single-species biofilms, the amounts were not predictable from single-strain measurements. By the Shannon diversity index and principle components analysis of TRFLP profiles generated from 16S rRNA genes, eDNA of four-species biofilms differed significantly from either cellular or total DNA of the same biofilm. However, total DNA- and cellular DNA-based TRFLP analyses of this biofilm community yielded identical results. We conclude that extracellular DNA production in unsaturated biofilms is species dependent and that the phylogenetic information contained in this DNA pool is quantifiable and distinct from either total or cellular DNA.

scholarly journals Extracellular DNA can preserve the genetic signatures of present and past viral infection events in deep hypersaline anoxic basins

2014 ◽  
Vol 281 (1780) ◽  
pp. 20133299 ◽  
Author(s):  
C. Corinaldesi ◽  
M. Tangherlini ◽  
G. M. Luna ◽  
A. Dell'Anno
Keyword(s):  
Viral Infections ◽  
Extracellular Dna ◽  
Rdna Sequences ◽  
Anoxic Basins ◽  
16S Rdna Sequences ◽  
Dna Pools ◽  
Dna Pool ◽  
Genetic Signatures ◽  
Microbial Dna ◽  
The Impact

Deep hypersaline anoxic basins (DHABs) of the Mediterranean Sea are among the most extreme ecosystems on Earth and host abundant, active and diversified prokaryotic assemblages. However, factors influencing biodiversity and ecosystem functioning are still largely unknown. We investigated, for the first time, the impact of viruses on the prokaryotic assemblages and dynamics of extracellular DNA pool in the sediments of La Medee, the largest DHAB found on Earth. We also compared, in La Medee and L'Atalante sediments, the diversity of prokaryotic 16S rDNA sequences contained in the extracellular DNA released by virus-induced prokaryotic mortality. We found that DHAB sediments are hot-spots of viral infections, which largely contribute to the release of high amounts of extracellular DNA. DNase activities in DHAB sediments were much higher than other extracellular enzymatic activities, suggesting that extracellular DNA released from killed prokaryotes can be the most suitable trophic resource for benthic prokaryotes. Preserved extracellular DNA pools, which contained novel and diversified gene sequences, were very similar between the DHABs but dissimilar from the respective microbial DNA pools. We conclude that the strong viral impact in DHAB sediments influences the genetic composition of extracellular DNA, which can preserve the signatures of present and past infections.

Targeting Platelets Containing Electro-encapsulated lloprost to Balloon Injured Aorta in Rats

1995 ◽  
Vol 73 (03) ◽  
pp. 535-542 ◽  
Author(s):  
N Crawford ◽  
A Chajara ◽  
G Pfliegler ◽  
B EI Gamal ◽  
L Brewer ◽  
...  
Keyword(s):  
Time Course ◽  
Therapeutic Potential ◽  
Simple Procedure ◽  
Rat Aorta ◽  
Balloon Injury ◽  
Post Injury ◽  
Antiproliferative Effects ◽  
Platelet Deposition ◽  
Total Dna ◽  
Novel Drug

SummaryDrugs can be electro-encapsulated within platelets and targeted to damaged blood vessels by exploiting the platelet’s natural haemostatic properties to adhere to collagen and other vessel wall constituents revealed by injury. A rat aorta balloon angioplasty model has been used to study the effect on platelet deposition of giving iloprost loaded platelets i.v. during the balloon injury. After labelling the circulating platelets with 111-Indium before balloon injury, time course studies showed maximum platelet deposition on the injured aorta occurred at about 1 h post-injury and the deposition remained stable over the next 2-3 h. When iloprost-loaded platelets were given i.v. during injury and the circulating platelet pool labelled with 111-Indium 30 min later, platelet deposition, measured at 2 h postinjury, was substantially and significantly reduced compared with control platelet treatment. Some antiproliferative effects of iloprost-loaded platelets given i.v. during injury have also been observed. Whereas the incorporation of [3H]-thymidine into aorta intima-media DNA at 3 days post injury was 62-fold higher in balloon injured rats than in control sham operated rats, thymidine incorporation into intima/media of rats which had received iloprost loaded platelets during injury was reduced as compared with rats subjected only to the injury procedure. The reduction was only of near significance, however, but at 14 days after injury the total DNA content of the aorta intima/media of rats given iloprost loaded platelets during injury was significantly reduced. Although iloprost loaded platelets can clearly inhibit excessive platelet deposition, other encapsulated agents may have greater anti-proliferative effects. These studies have shown that drug loaded platelets can be targeted to injured arteries, where they may be retained as depots for local release. We believe this novel drug delivery protocol may have therapeutic potential in reducing the incidence of occlusion and restenosis after angioplasty and thrombolysis treatment. Electro-encapsulation of drugs into platelets is a simple procedure and, using autologous and fully biocompatible and biodegradable platelets as delivery vehicles, might overcome some of the immunological and toxicological problems which have been encountered with other delivery vectors such as liposomes, microbeads, synthetic microcapsules and antibodies.

MASKING EFFECT OF NON-PREDICTABLE ENERGY OF IMAGE REGIONS

2017 ◽  
Vol 76 (8) ◽  
pp. 685-708 ◽  
Author(s):  
O. I. Ieremeiev ◽  
N. N. Ponomarenko ◽  
V. V. Lukin ◽  
J. T. Astola ◽  
Karen O. Egiazarian
Keyword(s):  
Masking Effect

Antimicrobial Activity of Iron-Halide Complexes Against Gram-Positive and Gram-Negative Bacteria

2020 ◽  
Author(s):  
Nusrat Abedin ◽  
Abdullah Hamed A Alshehri ◽  
Ali M A Almughrbi ◽  
Olivia Moore ◽  
Sheikh Alyza ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Antimicrobial Resistance ◽  
Extracellular Dna ◽  
Antibiofilm Activity ◽  
Gram Negative Bacteria ◽  
Bacterial Strains ◽  
Gram Positive ◽  
Gram Negative ◽  
Antimicrobial Substances ◽  
Mammalian Cell Lines

Antimicrobial resistance (AMR) has become one of the more serious threats to the global health. The emergence of bacteria resistant to antimicrobial substances decreases the potencies of current antibiotics. Consequently, there is an urgent and growing need for the developing of new classes of antibiotics. Three prepared novel iron complexes have a broad-spectrum antimicrobial activity with minimum bactericidal concentration (MBC) values ranging from 3.5 to 10 mM and 3.5 to 40 mM against Gram-positive and Gram-negative bacteria with antimicrobial resistance phenotype, respectively. Time-kill studies and quantification of the extracellular DNA confirmed the bacteriolytic mode of action of the iron-halide compounds. Additionally, the novel complexes showed significant antibiofilm activity against the tested pathogenic bacterial strains at concentrations lower than the MBC. The cytotoxic effect of the complexes on different mammalian cell lines show sub-cytotoxic values at concentrations lower than the minimum bactericidal concentrations.

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