scholarly journals Effective Molecular Identification of Ectomycorrhizal Fungi: Revisiting DNA Isolation Methods

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 218 ◽  
Author(s):  
Daniel Janowski ◽  
Robin Wilgan ◽  
Tomasz Leski ◽  
Leszek Karliński ◽  
Maria Rudawska
Keyword(s):  
Ectomycorrhizal Fungi ◽  
Dna Isolation ◽  
Morphological Identification ◽  
Root Tips ◽  
Ectomycorrhizal Symbiosis ◽  
Isolation Methods ◽  
Low Mass ◽  
Purification Methods ◽  
The Relationship ◽  
Dna Isolation Protocol

A better understanding of ectomycorrhizal symbiosis leads to numerous advancements in forest management and environmental protection. The morphological identification of the ectomycorrhizae often proves to be misleading. For this reason, in order to study the ectomycorrhizal fungi communities, a number of molecular methods that require the isolation of nucleic acids are being used. However, ectomycorrhizal root tips, low mass heterogenic material rich in inhibitors, are a recalcitrant substrate in DNA isolation. It is common for published studies to include some number of unidentified root tips in their results, in spite of diverse isolation protocols being available to researchers. This study aims to analyze the relationship between the collected fungal material and later isolation results, and to propose a DNA isolation protocol specifically optimized for ectomycorrhizal root tips. It was found that the taxonomic position can be used to predict the potential isolation efficiency, with Ascomycota being generally more difficult from which to isolate DNA. After a number of cell lysis and lysate purification methods were evaluated, the joined approach of mechanical and chemical lysis, followed by silica column purification, was found to provide the best results, even with recalcitrant material.

Conditional Outcomes in the Relationship between Pine and Ectomycorrhizal Fungi in Relation to Biotic and Abiotic Environment

Oikos ◽  
1997 ◽  
Vol 80 (1) ◽  
pp. 112 ◽  
Author(s):  
Heikki Setälä ◽  
Johanna Rissanen ◽  
Anna Mari Markkola ◽  
Heikki Setala
Keyword(s):  
Ectomycorrhizal Fungi ◽  
Abiotic Environment ◽  
Conditional Outcomes ◽  
The Relationship

A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria)

1992 ◽  
Vol 38 (1) ◽  
pp. 65-68 ◽  
Author(s):  
Ken F. Jarrell ◽  
David Faguy ◽  
Anne M. Hebert ◽  
Martin L. Kalmokoff
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Thermal Denaturation ◽  
Dna Isolation ◽  
Methanogenic Archaea ◽  
Restriction Enzymes ◽  
Mole Percent ◽  
High Molecular Weight Dna ◽  
Isolation Methods ◽  
General Method

High molecular weight DNA was readily isolated from all methanogens treated, as well as from thermophilic anaerobic eubacteria, by grinding cells frozen in liquid N2, prior to lysis with SDS. DNA can subsequently be purified by the usual phenol–chloroform extractions. The procedure yields DNA readily cut by restriction enzymes and suitable for oligonucleotide probing, as well as for mole percent G + C content determination by thermal denaturation. The method routinely yields DNA of high molecular weight and is an improvement over DNA isolation methods for many methanogens, which often involve an initial breakage of the cells in a French pressure cell. Key words: methanogens, archaebacteria, archaea, DNA isolation.

scholarly journals Preanalytical Conditions and DNA Isolation Methods Affect Telomere Length Quantification in Whole Blood

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0143889 ◽  
Author(s):  
Alexander Tolios ◽  
Daniel Teupser ◽  
Lesca M. Holdt
Keyword(s):  
Telomere Length ◽  
Whole Blood ◽  
Dna Isolation ◽  
Isolation Methods ◽  
Preanalytical Conditions

scholarly journals Biased nicking of mitochondrial DNA during extraction can be avoided by choice of isolation method

2021 ◽  
Author(s):  
Bruno Marçal Repolês ◽  
Choco Michael Gorospe ◽  
Phong Tran ◽  
Anna Karin Nilsson ◽  
Paulina H. Wanrooij
Keyword(s):  
Skeletal Muscle ◽  
Mitochondrial Dna ◽  
Dna Isolation ◽  
Isolation Procedure ◽  
Isolation Method ◽  
Strand Breaks ◽  
Careful Choice ◽  
Isolation Methods ◽  
Solid Tissues ◽  
Long Range Pcr

AbstractThe integrity of mitochondrial DNA (mtDNA) isolated from solid tissues is critical for analyses such as long-range PCR. We show that a commonly-used DNA isolation procedure preferentially introduces strand breaks into the mtDNA extracted from the skeletal muscle of aged mice, while mtDNA from adult animals is less affected. We present a comparison of mtDNA isolation methods and identify one that avoids this biased loss of muscle mtDNA integrity. Our results highlight the importance of a careful choice of mtDNA isolation method and serve as a resource to researchers planning analysis of mtDNA isolated from solid tissues.

scholarly journals Comparison of Economically Favourable and Further Development Friendly DNA Isolation Methods from Microbial Cultures

2020 ◽  
Vol 10 (01) ◽  
pp. 1-13
Author(s):  
Barbara Bánkuti ◽  
Zoltán Tudós ◽  
Susan Szathmary ◽  
László Stipkovits ◽  
Zsófia Sipos-Kozma ◽  
...  
Keyword(s):  
Dna Isolation ◽  
Microbial Cultures ◽  
Isolation Methods ◽  
Further Development

scholarly journals Chromosome-level de novo assembly of Coprinopsis cinerea A43mut B43mut pab1-1 #326 and genetic variant identification of mutants using Nanopore MinION sequencing

2020 ◽  
Author(s):  
Yichun Xie ◽  
Yiyi Zhong ◽  
Jinhui Chang ◽  
Hoi Shan Kwan
Keyword(s):  
Genome Assembly ◽  
Dna Isolation ◽  
Variant Calling ◽  
Genomic Analysis ◽  
Single Nucleotide ◽  
Sequencing Platform ◽  
Genomic Dna Isolation ◽  
Long Reads ◽  
Dna Isolation Protocol ◽  
Chromosome Level

AbstractThe homokaryotic Coprinopsis cinerea strain A43mut B43mut pab1-1 #326 is a widely used experimental model for developmental studies in mushroom-forming fungi. It can grow on defined artificial media and complete the whole lifecycle within two weeks. The mutations in mating type factors A and B result in the special feature of clamp formation and fruiting without mating. This feature allows investigations and manipulations with a homokaryotic genetic background. Current genome assembly of strain #326 was based on short-read sequencing data and was highly fragmented, leading to the bias in gene annotation and downstream analyses. Here, we report a chromosome-level genome assembly of strain #326. Oxford Nanopore Technology (ONT) MinION sequencing was used to get long reads. Illumina short reads was used to polish the sequences. A combined assembly yield 13 chromosomes and a mitochondrial genome as individual scaffolds. The assembly has 15,250 annotated genes with a high synteny with the C. cinerea strain Okayama-7 #130. This assembly has great improvement on contiguity and annotations. It is a suitable reference for further genomic studies, especially for the genetic, genomic and transcriptomic analyses in ONT long reads. Single nucleotide variants and structural variants in six mutagenized and cisplatin-screened mutants could be identified and validated. A 66 bp deletion in Ras GTPase-activating protein (RasGAP) was found in all mutants. To make a better use of ONT sequencing platform, we modified a high-molecular-weight genomic DNA isolation protocol based on magnetic beads for filamentous fungi. This study showed the use of MinION to construct a fungal reference genome and to perform downstream studies in an individual laboratory. An experimental workflow was proposed, from DNA isolation and whole genome sequencing, to genome assembly and variant calling. Our results provided solutions and parameters for fungal genomic analysis on MinION sequencing platform.HighlightA chromosome-level genome assembly of C. cinerea #326A fast and efficient high-molecular-weight fungal genomic DNA isolation protocolStructural variant and single nucleotide variant calling using Nanopore readsA series of solutions and reference parameters for fungal genomic analysis on MinION

scholarly journals KARAKTERISTIK AKAR BEREKTOMIKORIZA PADA Shorea pinanga, Pinus merkusii DAN Gnetum gnemon

PERENNIAL ◽  
2010 ◽  
Vol 6 (1) ◽  
pp. 11
Author(s):  
Melya Riniarti ◽  
Irdika Mansur ◽  
Arum Sekar Wulandari ◽  
Cecep Kusmana
Keyword(s):  
Key Words ◽  
Ectomycorrhizal Fungi ◽  
Host Plants ◽  
Clamp Connection ◽  
The Other ◽  
Branching Pattern ◽  
Root Tips ◽  
Hartig Net ◽  
Gnetum Gnemon ◽  
Pinus Merkusii

Morphology and anatomy characteristics often used to identify ectomycorrhizal fungi. We used three Scleroderma spp. (Scleroderma columnare, S. dictyosporum), and S. sinnamariense) and inoculated to Shorea pinanga, Pinus merkusii, and Gnetum gnemon. After 6,8, and 10 months, each root tips were collected to determined hyphae colour, branching pattern, clamp-connection, hartig net and mantle. This result revealed that S. sinnamariense did not form association with S. pinanga and P. merkusii but form association with G. gnemon. On the other hand, S. columnare and S. dictyosporum could form association with all the host plants. S. columnare and S. dictyosporum formed white hyphae while S. sinnamariense formed yellow hyphae with monopodial branching pattern. The depth of hartig net and mantle was increased by timed. Key words: ectomycorrhizal fungi, hartig net, mantle, Scleroderma

Blood Collection and Cell-Free DNA Isolation Methods Influence the Sensitivity of Liquid Biopsy Analysis for Colorectal Cancer Detection

2018 ◽  
Vol 25 (3) ◽  
pp. 915-923 ◽  
Author(s):  
Barbara Kinga Barták ◽  
Alexandra Kalmár ◽  
Orsolya Galamb ◽  
Barnabás Wichmann ◽  
Zsófia Brigitta Nagy ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Detection ◽  
Liquid Biopsy ◽  
Dna Isolation ◽  
Blood Collection ◽  
Cell Free Dna ◽  
Free Dna ◽  
Isolation Methods

scholarly journals Continuous Microfluidic Purification of DNA Using Magnetophoresis

Micromachines ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 187
Author(s):  
Ying Xu ◽  
Zhen Zhang ◽  
Zhen Su ◽  
Xiaoxiang Zhou ◽  
Xiaoming Han ◽  
...  
Keyword(s):  
Dna Isolation ◽  
Fluid Velocity ◽  
Microfluidic System ◽  
Recovery Efficiency ◽  
Ndfeb Magnet ◽  
Chain Reaction ◽  
Dna Recovery ◽  
Fluid Velocities ◽  
Polymerase Chain ◽  
The Relationship

Automatic microfluidic purification of nucleic acid is predictable to reduce the input of original samples and improve the throughput of library preparation for sequencing. Here, we propose a novel microfluidic system using an external NdFeB magnet to isolate DNA from the polymerase chain reaction (PCR) mixture. The DNA was purified and isolated when the DNA-carrying beads transported to the interface of multi-laminar flow under the influence of magnetic field. Prior to the DNA recovery experiments, COMSOL simulations were carried out to study the relationship between trajectory of beads and magnet positions as well as fluid velocities. Afterwards, the experiments to study the influence of varying velocities and input of samples on the DNA recovery were conducted. Compared to experimental results, the relative error of the final position of beads is less than 10%. The recovery efficiency decreases with increase of input or fluid velocity, and the maximum DNA recovery efficiency is 98.4% with input of l00 ng DNA at fluid velocity of 1.373 mm/s. The results show that simulations significantly reduce the time for parameter adjustment in experiments. In addition, this platform uses a basic two-layer chip to realize automatic DNA isolation without any other liquid switch value or magnet controller.

scholarly journals Use of Real-Time Quantitative PCR to Compare DNA Isolation Methods

1998 ◽  
Vol 44 (10) ◽  
pp. 2201-2204 ◽  
Author(s):  
Jacques B de Kok ◽  
Jan C M Hendriks ◽  
Wouter W van Solinge ◽  
Hans L Willems ◽  
Ewald J Mensink ◽  
...  
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Dna Isolation ◽  
Real Time Quantitative Pcr ◽  
Isolation Methods
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