A comparison of silver staining protocols for detecting DNA in polyester-backed polyacrylamide gel

Shanlian, Qiu; Chen, Jichen; Lin, Si S.; Lin, Xi Zhang

doi:10.1590/s1517-83822012000200029

Cited by 11 publications

(4 citation statements)

References 15 publications

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“…(Tsang et al 1986). The bands were visualized by staining with silver nitrate (Qiu et al 2012), using DNA ladder, where the range of the molecular weight marker used ranged between 50 and 500 bp. The gels were photographed with a CANON ELPH180 IS camera and the determination of the allelic size was carried out by the ImageJ program (Abràmoff…”

Section: Materials Y Methodsmentioning

confidence: 99%

Genetic diversity in a population of creole maize (Zea mays L.) evaluated by microsatellite markers in Puerto Libertador, Córdoba

Pérez

Martínez

Vanegas

2018

Rev. U.D.C.A Act. & Div. Cient.

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Cavadía Martínez, T.; Herrera Vanegas, Y.: Genetic diversity of creole maize GENETIC DIVERSITY IN A POPULATION OF CREOLE MAIZE (Zea mays L.) EVALUATED BY MICROSATELLITE MARKERS IN PUERTO LIBERTADOR, CORDOBA DIVERSIDAD GENÉTICA EN UNA POBLACIÓN DE MAÍZ CRIOLLO (Zea mays L.) EVALUADA MEDIANTE MARCADORES MICROSATÉLITES EN PUERTO LIBERTADOR, CÓRDOBAABSTRACT Maize a plant of Mesoamerican origin, has evolved in different microenvironments, generating the great diversity of maize that exists in the world. In order to determine the genetic diversity of a population of Creole maize, twelve microsatellite markers were evaluated in 30 accessions, in Puerto Libertador, Córdoba. The DNA of each accession was extracted using the PROMEGA kit, the markers were amplified by the PCR technique and the amplicons were run on polyacrylamide gels, the gels were digitalized and the molecular sizes were determined by an exponential model. Results showed a total of 66 alleles and an average of alleles of 5.5, the expected heterozygosity was 0.655, the values of the polymorphic information content (PIC) ranged from 0.352 to 0.838, with an average of 0.592 and the Hardy-Weinberg equilibrium showed imbalance (p <0.05). This work revealed that the studied accessions of Creole maize showed a high degree of polymorphism, high genetic variability and microsatellite markers were the appropriate for the evaluation of genetic diversity. This information shows to be useful for the conservation and protection of the genetic diversity of the studied Creole Maize.

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Section: Materials Y Methodsmentioning

confidence: 99%

Genetic diversity in a population of creole maize (Zea mays L.) evaluated by microsatellite markers in Puerto Libertador, Córdoba

Pérez

Martínez

Vanegas

2018

Rev. U.D.C.A Act. & Div. Cient.

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“…The electrophoresis stage ran between 3-5 hours depending on the microsatellite size at constant 15 W and fluctuating voltage from 300 to 400 V. The sample subjected to electrophoresis consisted of amplified DNA and loading buffer (bromophenol blue 2% w/v dissolved in MiliQ water). The markers were visualized by exposing the gel to white light after staining with silver nitrate (Qiu et al ., 2012). An allelic ladder was used to determine the size of the alleles, and allele assignment involved fitting a linear regression curve developed from migration distances of known-size fragments.…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity of domestic pigs in Tierralta (Colombia) using microsatellites

Pérez

Qca

Cavadía

et al. 2015

Rev Colomb Cienc Pecu

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SummaryBackground: according to several authors, domestic pigs come from different wild boar populations with varied geographic distribution and are grouped in the genus Sus. Pig domestication occurred gradually. The first animals were small and gathered in small numbers. Several civilizations domesticated this animal as an important source of protein. Tierralta, in Córdoba province, has a large population of domestic pigs, which are a mixture of creole and other breeds. The genetic characterization of populations is used to check the status of genetic diversity, a conclusive element in determining breeding strategies and genetic conservation programs. PCR is the most commonly used technique for studying highly polymorphic markers, such as microsatellites or SSRs. The use of microsatellites is a powerful tool in genetic studies. They have been used for characterization studies of genetic diversity, genetic relationships between populations, paternity testing, inbreeding and genetic bottlenecks. Objective: the purpose of this study was to determine the genetic diversity of domestic pigs in Tierralta (Córdoba, Colombia) using 20 microsatellites. Methods: fifty four samples were studied. Twenty microsatellites recommended by the FAO/ISAG for swine biodiversity studies were used. Results: all the microsatellites were polymorphic, and were detected between 3 (SW911) and 14 (TNFB) alleles (the average number was 6.9 alleles) and a total of 138 alleles were detected. Average expected heterozygosity was 0.5259 and the observed heterozygosity was 0.5120. PIC values ranged from 0.3212 to 0.7980 for loci SW2410 and IFNG, respectively. Conclusions: the results suggest that the analyzed population represents a group with high genetic diversity.

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“…DGGE was run using 1× TAE buffer at 120 V and 60 °C for 10 h using DCode TM Universal Mutation Detection System (Bio-rad, USA). Silver staining method was applied to stain the DGGE gel (Qiu et al, 2012). The consistency of DGGE banding pattern was confirmed by replication of the second DGGE of PCR products.…”

Section: Polymerase Chain Reaction-denaturing Gradient Gel Electropho...mentioning

confidence: 99%

Changes in microbial community structure and diversity during decomposition of oil palm empty fruit bunches at different decomposition sites in humid tropical oil palm plantation

2022

ANRES

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Importance of the work: Environmental conditions during the decomposition of organic matter play an important role in the structure and diversity of microbial communities. Objectives: To compare changes in the microbial community structure and diversity during decomposition of oil palm empty fruit bunch (OPEFB) under the oil palm canopy and on open land. Materials & Methods: A polymerase chain reaction-denaturing gradient gel electrophoresis technique was used to compare microbial community structures at two different decomposition sites during 6 mth, 12 mth and 24 mth. The physico-chemical parameters-temperature, relative humidity, pH, total organic carbon (TOC) and total nitrogen-in OPEFB during decomposition were determined to analyze differences in the decomposition rates of OPEFB. Results: Different stacking location sites (under the oil palm canopy and on open land) of OPEFB affected the microbial community structure and diversity. The bacterial and fungal diversity indices were significantly higher in OPEFB decomposed on open land (H = 2.979 and D = 0.941 for bacteria; H = 1.969 and D = 0.828 for fungi) than under the oil palm canopy (H = 2.483 and D = 0.902 for bacteria; H = 1.866 and D = 0.776 for fungi), but the richness indices for bacteria was significantly higher on open land (S = 6.026) than under the oil palm canopy (S = 4.201) and that for fungi was significantly lower on open land (S = 2.512) than under the oil palm canopy (S = 2.914).The significant decrease in TOC and texture of OPEFB decomposed under the canopy revealed that the decomposition rate of OPEFB for this site was faster than that on open land. Main finding: Changes in the microbial community structure and diversity were closely correlated to changes in temperature, relative humidity, pH and TOC. These findings could contribute to the improvement of OPEFB waste management in oil palm plantations.

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A comparison of silver staining protocols for detecting DNA in polyester-backed polyacrylamide gel

Cited by 11 publications

References 15 publications

Genetic diversity in a population of creole maize (Zea mays L.) evaluated by microsatellite markers in Puerto Libertador, Córdoba

Genetic diversity in a population of creole maize (Zea mays L.) evaluated by microsatellite markers in Puerto Libertador, Córdoba

Genetic diversity of domestic pigs in Tierralta (Colombia) using microsatellites

Changes in microbial community structure and diversity during decomposition of oil palm empty fruit bunches at different decomposition sites in humid tropical oil palm plantation

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