scholarly journals Environmental (e)RNA advances the reliability of eDNA by predicting its age

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nathaniel T. Marshall ◽  
Henry A. Vanderploeg ◽  
Subba Rao Chaganti
Keyword(s):  
Nucleic Acids ◽  
Conservation Biology ◽  
Genetic Material ◽  
Detection Limits ◽  
Environmental Dna ◽  
Accurate Estimation ◽  
Biodiversity Management ◽  
High Concentrations ◽  
Detection And Quantification ◽  
Genomic Material

AbstractEnvironmental DNA (eDNA) analysis has advanced conservation biology and biodiversity management. However, accurate estimation of age and origin of eDNA is complicated by particle transport and the presence of legacy genetic material, which can obscure accurate interpretation of eDNA detection and quantification. To understand the state of genomic material within the environment, we investigated the degradation relationships between (a) size of fragments (long vs short), (b) genomic origins (mitochondrial vs nuclear), (c) nucleic acids (eDNA vs eRNA), and (d) RNA types (messenger (m)RNA vs ribosomal (r)RNA) from non-indigenous Dreissena mussels. Initial concentrations of eRNA followed expected transcriptional trends, with rRNAs found at > 1000 × that of eDNA, and a mitosis-associated mRNA falling below detection limits within 24 h. Furthermore, the ratio of eRNA:eDNA significantly decreased throughout degradation, potentially providing an estimate for the age of genomic material. Thus, eRNA quantification can increase detection due to the high concentrations of rRNAs. Furthermore, it may improve interpretation of positive detections through the eRNA:eDNA ratio and/or by detecting low abundant mitosis-associated mRNAs that degrade within ~ 24 h.

scholarly journals Transcription of 4′-thioDNA templates to natural RNA in vitro and in mammalian cells

2015 ◽  
Vol 51 (37) ◽  
pp. 7887-7890 ◽  
Author(s):  
Hideto Maruyama ◽  
Kazuhiro Furukawa ◽  
Hiroyuki Kamiya ◽  
Noriaki Minakawa ◽  
Akira Matsuda
Keyword(s):  
Nucleic Acids ◽  
Mammalian Cells ◽  
Genetic Material ◽  
Rna Polymerases ◽  
Chemically Modified ◽  
Biological Studies ◽  
Modified Nucleic Acids

Synthetic chemically modified nucleic acids, which are compatible with DNA/RNA polymerases, have great potential as a genetic material for synthetic biological studies.

scholarly journals Effects of preservation strategies on environmental DNA detection and quantification using ddPCR

2021 ◽  
Author(s):  
Quentin Mauvisseau ◽  
David Halfmaerten ◽  
Sabrina Neyrinck ◽  
Alfred Burian ◽  
Rein Brys
Keyword(s):  
Dna Detection ◽  
Environmental Dna ◽  
Detection And Quantification

scholarly journals Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mizuki Ogata ◽  
Reiji Masuda ◽  
Hiroya Harino ◽  
Masayuki K. Sakata ◽  
Makoto Hatakeyama ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Oil Spills ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Target Species ◽  
Tank Experiment ◽  
Polycyclic Aromatic ◽  
Flow Through ◽  
High Concentrations ◽  
One Year

AbstractEnvironmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

DNA-based in situ hybridisation assay for the detection and quantification of parvovirus B19 nucleic acids

2006 ◽  
Vol 36 ◽  
pp. S34
Author(s):  
M. Zerbini ◽  
F. Bonvicini ◽  
C. Filippone ◽  
E. Manaresi ◽  
G.A. Gentilomi ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Parvovirus B19 ◽  
In Situ Hybridisation ◽  
Detection And Quantification

scholarly journals Electric chips for rapid detection and quantification of nucleic acids

2004 ◽  
Vol 19 (6) ◽  
pp. 537-546 ◽  
Author(s):  
M Gabig-Ciminska ◽  
A Holmgren ◽  
H Andresen ◽  
K Bundvig Barken ◽  
M Wümpelmann ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Rapid Detection ◽  
Detection And Quantification

The isolation of nucleic acids from woody tissue using dimethyl sulfoxide

1972 ◽  
Vol 50 (5) ◽  
pp. 1085-1090 ◽  
Author(s):  
L. V. Gusta ◽  
V. C. Runeckles
Keyword(s):  
Nucleic Acids ◽  
Experimental Evidence ◽  
Dimethyl Sulfoxide ◽  
Ribonuclease Activity ◽  
Woody Tissue ◽  
Bark Tissue ◽  
High Concentrations ◽  
High Degree

A procedure is described for the isolation of nucleic acids from apple bark tissue using dimethyl sulfoxide. Nucleic acids isolated by this method are high in yield, and exhibit a high degree of purity as evidenced by their spectra. Experimental evidence is given to show that extraction of the tissue with dimethyl sulfoxide before the extraction of nucleic acids removes protein and pigments. Little or no ribonuclease activity could be detected in apple bark tissue after extraction with dimethyl sulfoxide. Ribonuclease activity was shown to be strongly inhibited by high concentrations of dimethyl sulfoxide.

scholarly journals Estimation accuracy of species abundance based on environmental DNA with relation to its production source, state, and assay methodology suggested by meta-analyses

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Hiroki Yamanaka
Keyword(s):  
Meta Analysis ◽  
Empirical Studies ◽  
Species Abundance ◽  
Environmental Dna ◽  
Efficient Estimation ◽  
Estimation Accuracy ◽  
Accurate Estimation ◽  
Abundance Estimation ◽  
Natural Environments ◽  
Promising Tool

Environmental DNA (eDNA) analysis is a promising tool for non-disruptive and cost-efficient estimation of species abundance. However, its practical applicability in natural environments is limited because it is unclear whether eDNA concentrations actually represent species abundance in the field. Although the importance of accounting for eDNA dynamics, such as transport and degradation, has been discussed, the influences of eDNA characteristics, including production source and state, and methodology, including collection and quantification strategy and abundance metrics, on the accuracy of eDNA-based abundance estimation were entirely overlooked. We conducted a meta-analysis using 56 previous eDNA literature and investigated the relationships between the accuracy (R2) of eDNA-based abundance estimation and eDNA characteristics and methodology. Our meta-regression analysis found that R2 values were significantly lower for crustaceans than fish, suggesting that less frequent eDNA production owing to their external morphology and physiology may impede accurate estimation of their abundance via eDNA. Moreover, R2 values were positively associated with filter pore size, indicating that selective collection of larger-sized eDNA, which is typically fresher, could improve the estimation accuracy of species abundance. Furthermore, R2 values were significantly lower for natural than laboratory conditions, while there was no difference in the estimation accuracy among natural environments. Our findings shed a new light on the importance of what characteristics of eDNA should be targeted for more accurate estimation of species abundance. Further empirical studies are required to validate our findings and fully elucidate the relationship between eDNA characteristics and eDNA-based abundance estimation.

scholarly journals Сationic liposomes as delivery systems for nucleic acids

2020 ◽  
Vol 15 (1) ◽  
pp. 7-27
Author(s):  
A. A. Mikheev ◽  
E. V. Shmendel ◽  
E. S. Zhestovskaya ◽  
G. V. Nazarov ◽  
M. A. Maslov
Keyword(s):  
Gene Therapy ◽  
Nucleic Acids ◽  
Serum Proteins ◽  
Transfection Efficiency ◽  
Biological Fluids ◽  
Genetic Material ◽  
Cationic Liposomes ◽  
Delivery Systems ◽  
Cationic Lipids

Objectives. Gene therapy is based on the introduction of genetic material into cells, tissues, or organs for the treatment of hereditary or acquired diseases. A key factor in the success of gene therapy is the development of delivery systems that can efficiently transfer genetic material to the place of their therapeutic action without causing any associated side effects. Over the past 10 years, significant effort has been directed toward creating more efficient and biocompatible vectors capable of transferring nucleic acids (NAs) into cells without inducing an immune response. Cationic liposomes are among the most versatile tools for delivering NAs into cells; however, the use of liposomes for gene therapy is limited by their low specificity. This is due to the presence of various biological barriers to the complex of liposomes with NA, including instability in biological fluids, interaction with serum proteins, plasma and nuclear membranes, and endosomal degradation. This review summarizes the results of research in recent years on the development of cationic liposomes that are effective in vitro and in vivo. Particular attention is paid to the individual structural elements of cationic liposomes that determine the transfection efficiency and cytotoxicity. The purpose of this review was to provide a theoretical justification of the most promising choice of cationic liposomes for the delivery of NAs into eukaryotic cells and study the effect of the composition of cationic lipids (CLs) on the transfection efficiency in vitro.Results. As a result of the analysis of the related literature, it can be argued that one of the most promising delivery systems of NAs is CL based on cholesterol and spermine with the addition of a helper lipid DOPE. In addition, it was found that varying the composition of cationic liposomes, the ratio of CL to NA, or the size and zeta potential of liposomes has a significant effect on the transfection efficiency.Conclusions. Further studies in this direction should include optimization of the conditions for obtaining cationic liposomes, taking into account the physicochemical properties and established laws. It is necessary to identify mechanisms that increase the efficiency of NA delivery in vitro by searching for optimal structures of cationic liposomes, determining the ratio of lipoplex components, and studying the delivery efficiency and properties of multicomponent liposomes.

scholarly journals BIOLOGICAL ACTIVITY OF YERSINIA PSEUDOTUBERCULOSIS TOXINS

2016 ◽  
pp. 10-19
Author(s):  
N. A. Terentieva ◽  
N. F. Timchenko ◽  
V. A. Golotin ◽  
V. A. Rasskazov
Keyword(s):  
Nucleic Acids ◽  
Sea Urchin ◽  
Yersinia Pseudotuberculosis ◽  
Protein Biosynthesis ◽  
Sea Urchin Embryos ◽  
Dna And Rna ◽  
Embryo Cells ◽  
Protein Toxins ◽  
Rna Biosynthesis ◽  
High Concentrations

Aim. Study of effect of heat-labile (HLT) and thermostable (HST) lethal toxins of Yersinia pseudotuberculosis on the development of embryos of sea urchin Strongylocentrotus intermedius, processes of biosynthesis of nucleic acids and protein in embryo cells and activity of nucleoside-kinases of sea urchin. Materials and methods. Y. pseudotuberculosis strains 2517 (pYV-) and 512 (pYV48MD, pYV82MD) were used for isolation of HLT and HST. Gametes and embryos of sea urchin S. intermedius were used to carry out the experiments and isolate nucleoside-kinases. Results. Both of the studied toxins of Y. pseudotuberculosis possessed spermiotoxic effect and reduced fertilizing ability of sea urchin spermies. HLT LD50 was 1 (ig/ml, and HST - 2 pg/ml. Toxins affected the development of embryos of sea urchin resulting in severe morphologic damages, cessation of the development of embryos at early stages of embryogenesis, destruction of cells and death of embryos. Wherein, damaging effect of HLT was observed at lower concentrations compared with HST. HLT inhibited DNA and RNA biosynthesis at concentrations of 1-2 pg/ml. HST did not affect biosynthesis of nucleic acids even at high concentrations, but inhibited protein biosynthesis in sea urchin embryos. HLT did not reduce the level of inclusion of labeled amino acids into embryo cells. HLT had inhibiting effect on the activity of thymidine- and uridine-kinase of sea urchin, whereas HST did not affect these enzymes. Conclusion. Both of Y. pseudotuberculosis protein toxins affect the development of sea urchin embryos, however, mechanisms of action of HLT and HST on embryos and processes occurring in them differ.

Sign in / Sign up

Export Citation Format

Share Document