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Method for analyzing plankton community DNA polymorphism

A DNA polymorphism, plankton technology, applied in biochemical equipment and methods, microbial determination/inspection, etc., can solve the problems of unclear morphological classification characteristics, limited human cognition, small individuals, etc., and achieve the programmed technical route , Comparative analysis of standardized and easy-to-operate effects

Inactive Publication Date: 2008-07-09
INST OF AQUATIC LIFE ACAD SINICA
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, due to the bottleneck constraints of small size and indistinct morphological classification characteristics, human understanding of them is greatly limited, and some of them cannot even be identified by morphological characteristics.

Method used

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  • Method for analyzing plankton community DNA polymorphism
  • Method for analyzing plankton community DNA polymorphism
  • Method for analyzing plankton community DNA polymorphism

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0023]1. Sample Collection A

[0024] Use plexiglass water sampling devices to collect equal volumes of surface and bottom water from 6 sampling points of the Songhua River (Hongqidukou, Shaokou, Songyuan, Zhaoyuan, Harbin, and Jiamusi). After the water samples are fully mixed, use GF / C membrane filter 500mL water sample.

[0025] 2. DNA Extraction of Plankton Community B

[0026] Cut the filtered GF / C filter membrane under sterile conditions (about 1×1mm fragments), and immerse in 3mL lysis buffer (0.5% SDS, 10mM Tris-Cl, 100mM EDTA, 0.1mg / mL proteinase K) in a centrifuge tube, lyse in a water bath at 55°C for 10 h. After centrifugation at 10000r / min for 5min (20°C), transfer the supernatant to a new centrifuge tube, and centrifuge again under the same conditions to obtain the supernatant, which is extracted three times with an equal volume of phenol→phenol:chloroform (1:1)→chloroform. Pre-cooled absolute ethanol (containing 0.3M NaCl) was precipitated at -20°C for 3h. ...

Embodiment 2

[0036] 1. Sample Collection A

[0037] Use plexiglass water collectors to collect equal volumes of surface and bottom water from four indoor ecological simulation boxes (1×1×1m) and mix them. After the water samples are fully mixed, filter 250 mL of water samples with GF / C membranes.

[0038] 2. DNA Extraction of Plankton Community B

[0039] Cut the filtered GF / C filter membrane under sterile conditions (about 1×1mm fragments), and immerse in 3mL lysis buffer (0.5% SDS, 10mM Tris-Cl, 100mM EDTA, 0.1mg / mL proteinase K) in a centrifuge tube, lyse in a water bath at 55°C for 10 h. After centrifugation at 10000r / min for 5min (20°C), transfer the supernatant to a new centrifuge tube, and centrifuge again under the same conditions to obtain the supernatant, which is extracted three times with an equal volume of phenol→phenol:chloroform (1:1)→chloroform. Pre-cooled absolute ethanol (containing 0.3M NaCl) was precipitated at -20°C for 3h. After centrifugation at 13000r / min for 10...

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Abstract

The invention discloses a process of analyzing DNA polymorphism of plankton coenosis, which comprises firstly collecting sample, secondly extracting plankton coenosis DNA, thirdly augmenting the analysis of DNA polymorphism randomly, fourthly carrying out PCR augmentation of ribosome RNA gene of plankton coenosis and degeneration gradient gel electrophoresis analysis, fifthly quantitatively analyzing atlas through utilizing Quantity One software to calculate the similarity of DNA polymorphism of plankton coenosis of each sample. The invention has the characteristics of technical route routinization and comparison and analysis standardization, also has simple operation, and can fast and effectively analyze in parallel a plurality of samples, which overcomes the affect by personal factors, increases comparability among different space-time researches, and provides reliable premise for searching for bio-ecology mechanism.

Description

technical field [0001] The present invention relates to the research on the microbial community structure in the field of metagenomics, and more specifically to a method for analyzing the DNA polymorphism of the plankton community, that is, analyzing the DNA polymorphism of the plankton community by RAPD and PCR-DGGE to reflect its community structure and its space-time Variety. Background technique [0002] Biodiversity is the diversity and variability of the system composed of organisms and their environment. It is essentially a highly comprehensive resource form with multiple values, and is the material basis for human survival and social development. It plays an important role in maintaining the stability of the ecosystem, improving the productivity of the ecosystem, and realizing the sustainable development of the ecosystem. Therefore, biodiversity has been widely concerned and studied since human civilization. Among them, the study of species diversity based on morph...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68
Inventor 余育和颜庆云冯伟松
Owner INST OF AQUATIC LIFE ACAD SINICA
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