Fecal DNA Isolation and Degradation in Clam Cyclina sinensis: Noninvasive DNA Isolation for Conservation and Genetic Assessment

Abstract Background To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA.Results The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor.Conclusions The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

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Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment

BMC Biotechnology ◽

10.1186/s12896-019-0595-6 ◽

2019 ◽

Vol 19 (1) ◽

Author(s):

Min Zhang ◽

Min Wei ◽

Zhiguo Dong ◽

Haibao Duan ◽

Shuang Mao ◽

...

Keyword(s):

Dna Isolation ◽

Environmental Temperature ◽

Pcr Amplification ◽

Fecal Dna ◽

Soaking Time ◽

Cyclina Sinensis ◽

Genetic Assessment ◽

Noninvasive Dna ◽

Environmental Temperatures

Abstract Background To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA. Results The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor. Conclusions The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

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Dealing with hot rocky environments: Critical thermal maxima and locomotor performance in Leptodactylus lithonaetes (Anura: Leptodactylidae)

Herpetological Journal ◽

10.33256/hj29.3.155161 ◽

2019 ◽

pp. 155-161 ◽

Cited By ~ 1

Author(s):

Ivan Beltran

Keyword(s):

Environmental Temperature ◽

Extreme Temperature ◽

Effect Of Temperature ◽

Maximum Speed ◽

Locomotor Performance ◽

Extreme Temperatures ◽

Physiological Limits ◽

Fitness Consequences ◽

Thermal Maximum ◽

Environmental Temperatures

Environmental temperature has fitness consequences on ectotherm development, ecology and behaviour. Amphibians are especially vulnerable because thermoregulation often trades with appropriate water balance. Although substantial research has evaluated the effect of temperature in amphibian locomotion and physiological limits, there is little information about amphibians living under extreme temperature conditions. Leptodactylus lithonaetes is a frog allegedly specialised to forage and breed on dark granitic outcrops and associated puddles, which reach environmental temperatures well above 40 ˚C. Adults can select thermally favourable microhabitats during the day while tadpoles are constrained to rock puddles and associated temperature fluctuations; we thus established microhabitat temperatures and tested whether the critical thermal maximum (CTmax) of L. lithonaetes is higher in tadpoles compared to adults. In addition, we evaluated the effect of water temperature on locomotor performance of tadpoles. Contrary to our expectations, puddle temperatures were comparable and even lower than those temperatures measured in the microhabitats used by adults in the daytime. Nonetheless, the CTmax was 42.3 ˚C for tadpoles and 39.7 ˚C for adults. Regarding locomotor performance, maximum speed and maximum distance travelled by tadpoles peaked around 34 ˚C, approximately 1 ˚C below the maximum puddle temperatures registered in the puddles. In conclusion, L. lithonaetes tadpoles have a higher CTmax compared to adults, suggesting a longer exposure to extreme temperatures that lead to maintain their physiological performance at high temperatures. We suggest that these conditions are adaptations to face the strong selection forces driven by this granitic habitat.

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DMSO Improves the Ski-Slope Effect in Direct PCR

Applied Sciences ◽

10.3390/app11041943 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1943

Author(s):

Joo-Young Kim ◽

Ju Yeon Jung ◽

Da-Hye Kim ◽

Seohyun Moon ◽

Won-Hae Lee ◽

...

Keyword(s):

Dna Sequences ◽

Pcr Amplification ◽

Analytical Techniques ◽

Direct Pcr ◽

Dna Profile ◽

Novel Technologies ◽

Specific Amplification ◽

Polymerase Chain ◽

Dna Profiles

Analytical techniques such as DNA profiling are widely used in various fields, including forensic science, and novel technologies such as direct polymerase chain reaction (PCR) amplification are continuously being developed in order to acquire DNA profiles efficiently. However, non-specific amplification may occur depending on the quality of the crime scene evidence and amplification methods employed. In particular, the ski-slope effect observed in direct PCR amplification has led to inaccurate interpretations of the DNA profile results. In this study, we aimed to reduce the ski-slope effect by using dimethyl sulfoxide (DMSO) in direct PCR. We confirmed that DMSO (3.75%, v/v) increased the amplification yield of large-sized DNA sequences more than that of small-sized ones. Using 50 Korean buccal samples, we further demonstrated that DMSO reduced the ski-slope effect in direct PCR. These results suggest that the experimental method developed in this study is suitable for direct PCR and may help to successfully obtain DNA profiles from various types of evidence at crime scenes.

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The effects of environmental temperature and method of feeding on the performance and carcass composition of bacon pigs

Animal Science ◽

10.1017/s0003356100038472 ◽

1967 ◽

Vol 9 (2) ◽

pp. 209-218 ◽

Cited By ~ 14

Author(s):

D. W. Holme ◽

W. E. Coey

Keyword(s):

Environmental Temperature ◽

Average Daily Gain ◽

Carcass Composition ◽

Restricted Feeding ◽

Feed Conversion ◽

Feeding Method ◽

Feeding Regimes ◽

Higher Temperature ◽

Ad Libitum ◽

Environmental Temperatures

A trial designed to investigate the effects of two environmental temperatures, three feeding regimes and the interactions between them is described. A temperature of 72° F. was better than one of 54° F. for bacon pigs between 40 lb. and 200 lb. weight. The higher temperature resulted in faster growth, more efficient feed conversion and increased length of carcass. Other carcass characteristics were not significantly altered. Ad libitum feeding resulted in faster growth and fatter carcasses than restricted feeding, but did not have a significant effect on efficiency of feed conversion. When feed intake was restricted, feeding pigs once daily or twice daily resulted in similar performance and carcass composition.There was a significant interaction between environmental temperature and feeding method for average daily gain in that pigs fed ad libitum grew faster at the low temperature and pigs fed restricted amounts of feed grew faster at the high temperature. No other interaction reached significant levels.

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Sex identification based on AMEL gene PCR amplification from blue sheep (Pseudois nayaur) fecal DNA samples

Genetics and Molecular Research ◽

10.4238/2015.august.7.13 ◽

2015 ◽

Vol 14 (3) ◽

pp. 9045-9052 ◽

Cited By ~ 4

Author(s):

X. Liu ◽

Y.Y. Yang ◽

X.M. Wang ◽

Z.S. Liu ◽

Z.H. Wang ◽

...

Keyword(s):

Pcr Amplification ◽

Sex Identification ◽

Fecal Dna ◽

Blue Sheep ◽

Pseudois Nayaur

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The Optimization and Mathematical Modeling of Quality Attributes of Parboiled Rice Using a Response Surface Method

Journal of Food Quality ◽

10.1155/2017/5960743 ◽

2017 ◽

Vol 2017 ◽

pp. 1-13 ◽

Cited By ~ 4

Author(s):

Khurram Yousaf ◽

Chen Kunjie ◽

Chen Cairong ◽

Adnan Abbas ◽

Yuping Huang ◽

...

Keyword(s):

Response Surface ◽

Rice Variety ◽

Quality Parameters ◽

Cooking Time ◽

Soaking Time ◽

Parboiled Rice ◽

Surface Method ◽

Head Rice ◽

Soaking Temperature

The response surface methodology was used to optimize the hydrothermal processing conditions based on the rice quality parameters of the Rong Youhua Zhan rice variety (Indica). The effect of soaking temperature (29.77, 40, 55, 70, and 80.23°C), soaking time (67.55, 90, 120, 150, and 170.45 min), and steaming time (1.59, 5, 10, 15, and 18.41 min), each tested at five levels, on percentage of head rice yield (HRY), hardness, cooking time, lightness, and color were determined, with R2 values of 0.96, 0.94, 0.90, 0.88, and 0.94, respectively. HRY, hardness, cooking time, and color increased with process severity while lightness decreased, although HRY decreased after reaching a maximum. The predicted optimum soaking temperature, soaking time, and steaming time were 69.88°C, 150 min, and 6.73 min, respectively, and the predicted HRY, hardness, cooking time, lightness, and color under these conditions were 73.43%, 29.95 N, 32.14 min, 83.03 min, and 12.24 min, respectively, with a composite desirability of 0.9658. The parboiling industry could use the findings of the current study to obtain the desired quality of parboiled rice. This manuscript will be helpful for researchers working on commercializing parboiled rice processes in China as well as in other countries.

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Effect of Slice Weight and Soaking Time on the Physico-Chemical Properties of Cassava Flour (Manihotesculentus) used for Bakery Products

Asian Food Science Journal ◽

10.9734/afsj/2021/v20i630305 ◽

2021 ◽

pp. 10-24

Author(s):

C. R. Abah ◽

C. N. Ishiwu ◽

J. E. Obiegbuna ◽

E. F. Okpalanma ◽

C. S. Anarado

Keyword(s):

Chemical Properties ◽

Process Variables ◽

Soaking Time ◽

Cassava Flour ◽

Baked Goods ◽

Cassava Root ◽

Physico Chemical ◽

Physical And Chemical ◽

And Chemical Properties

Quality cassava(Manihotesculentus, Crantz) flour is often influenced by process variables such as slice weight and soaking time which may affect its nutritional quality. In this study, the effect of process variables (slice weight and soaking time) on quality of cassava flour was carried out. Cassava root was peeled, washed and cut into varied sizes (25.86 - 54.14 g) and soaked at varied time (7.03 - 40.97 h). The proximate composition, physical and chemical properties of the flour were carried out using standard methods. The result in our findings showed that slice weight and soaking time had significant increase (p<0.05) on the proximate and physico-chemical properties of the flour.The amylose and amylopectin content of the flour increased with increasing soaking time while the hydrogen cyanide content decreased with increase in soaking time. Overall, the quality cassava flour displayed desirable properties for its incorporation into baked goods.

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Method Comparison of DNA Isolation and Quantification for Fish and Seafood Authenticity Determination

SQUALEN Bulletin of Marine and Fisheries Postharvest and Biotechnology ◽

10.15578/squalen.v13i3.370 ◽

2018 ◽

Vol 13 (3) ◽

pp. 115

Author(s):

Dwiyitno Dwiyitno ◽

Stefan Hoffman ◽

Koen Parmentier ◽

Chris Van Keer

Keyword(s):

Polymerase Chain Reaction ◽

Dna Extraction ◽

Dna Isolation ◽

Blue Mussel ◽

Pcr Amplification ◽

Amplification Efficiency ◽

Chain Reaction ◽

Seafood Products ◽

Polymerase Chain ◽

Commercial Kit

Fish and seafood products has been commonly targeted for fraudulent activities. For that reason, authentication of fish and seafood products is important to protect consumers from fraudulent and adulteration practices, as well as to implement traceability regulation. From the viewpoint of food safety, authenticity is beneficial to protect public from serious food poisoning incidents, such as due to ingestion of toxic species. Since DNA based identification depends on the nucleic acid polymerase chain reaction (PCR), the quantity and quality/purity of DNA will contribute significantly to the species authentication. In the present study, different DNA extraction and purification methods (3 classical methods and one commercial kit) were compared to produce the better isolated DNA for PCR amplification. Additionally, different methods for the estimation of DNA concentration and purity which is essential for PCR amplification efficiency were also evaluated. The result showed that classical DNA extraction methods (based on TNES-Urea) yielded a higher amount of DNA (11.30-323.60 ng/g tissue) in comparison to commercial kit/Wizard Promega (5.70-83.45 ng/g tissue). Based on the purity of DNA extract (A260/280), classical DNA extraction method produced relatively similar on DNA quality to the commercial kit (1.79-2.12). Interestingly, all classical methods produced DNA with A260/280 ratio of more than 2.00 on the blue mussel, in contrast with commercial kit. The commercial kit also produced better quality of DNA compared to the classical methods, showing the higher efficiency in PCR amplification. NanoDrop is promising as cheap, robust and safe UV-spectrophotometer method for DNA quantification, as well as the purity evaluation.Keywords: seafood authenticity, DNA isolation, polymerase chain reaction, NanoDrop, Picogreen

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