• Title/Summary/Keyword: nucleic acid extraction

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Diagnosis of Potato Leafroll Virus with Digoxigenin-labeled cRNA Probes (Digoxigenin으로 표지된 cRNA 프로브를 이용한 감자잎말림바이러스(PLRV)의 짐단)

  • 서효원;함영일;오승은;신관용;최장경
    • Korean Journal Plant Pathology
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    • v.14 no.6
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    • pp.636-641
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    • 1998
  • Digoxigenin (DIG) was used to prepare nucleic acid probe for the detection of RNA of potato leafroll virus (PLRV) in the potato leaf extracts. The 0.6 kb coat protein (CP) gene cDNA of PLRV in plasmid pSPT 18 vector was labeled with digoxigenin by in vitro run-off transcription and then used for cRNA probe. In the several buffers tested for increase the total RNA extraction efficiency AMES buffer was the most suitable for this detection method. The RNA extracts from potato leaves shown symptoms of PLRV were dot blotted onto nylon membrane and hybridized with labeled RNA probes. After hybridization, labeled RNA bound to PLRV RNA on membrane was detected with anti-digoxigenin alkaline phosphatase. 5-bromo-4-chloro-3-indolyl-phosphate/nitroblue tetrazolium (NBT) salt and CSPD were used as substrate for colorimetric and film exposure detection, respectively. These detection methods were very sensitive allowing for detection of 1/32 diluted total RNA extract from 100 mg leaf tissue.

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Optimal Fuzzy Sliding-Mode Control for Microcontroller-based Microfluidic Manipulation in Biochip System

  • Chung, Yung-Chiang;Wen, Bor-Jiunn
    • 제어로봇시스템학회:학술대회논문집
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    • 2004.08a
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    • pp.196-201
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    • 2004
  • In biometric and biomedical applications, a special transporting mechanism must be designed for the ${\mu}$TAS (micro total analysis system) to move samples and reagents through the microchannels that connect the unit procedure components in the system. An important issue for this miniaturization and integration is microfluid management technique, i.e., microfluid transportation, metering, and mixing. In view of this, this study presents an optimal fuzzy sliding-mode control (OFSMC) design based on the 8051 microprocessor and implementation of a complete microfluidic manipulated system implementation of biochip system with a pneumatic pumping actuator, a feedback-signal photodiodes and flowmeter. The new microfluid management technique successfully improved the efficiency of molecular biology reaction by increasing the velocity of the target nucleic acid molecules, which increases the effective collision into the probe molecules as the target molecules flow back and forth. Therefore, this hybridization chip was able to increase hybridization signal 6-fold and reduce non-specific target-probe binding and background noises within 30 minutes, as compared to conventional hybridization methods, which may take from 4 hours to overnight. In addition, the new technique was also used in DNA extraction. When serum existed in the fluid, the extraction efficiency of immobilized beads with solution flowing back and forth was 88-fold higher than that of free-beads.

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Optimization of Proteolytic Enzyme Treatment for the Production of Spirulina Extract (단백질 분해 효소를 이용한 스피루리나 추출물 제조 공정 최적화)

  • In, Man-Jin
    • Journal of the Korea Academia-Industrial cooperation Society
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    • v.9 no.2
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    • pp.550-555
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    • 2008
  • An efficient production method of spirulina extract was developed by enzymatic treatment using proteolytic enzymes. The suitable dosage of Tunicase, a cell lytic enzyme, was used to be 2.0% (w/w). To maximize solid recovery and spirulina extraction (SE) index, which indicates nucleic acid-related substances content, the dosage of Alcalase, commercially available pretense, was found to be 1.0% (w/w). By simultaneous treatments using optimal dosages of Tunicase and Alcalase, the highest SE index and solid recovery were obtained. The SE index and solid recovery of simultaneous treatments were notably enhanced by 100% ($11.4%\;{\rightarrow}\;22.8%$) and 56% ($45.2%\;{\rightarrow}\;70.7%$), respectively, than those of the non-treated extracts.

DNA Extraction from Protozoan Oocysts/Cysts in Feces for Diagnostic PCR

  • Hawash, Yousry
    • Parasites, Hosts and Diseases
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    • v.52 no.3
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    • pp.263-271
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    • 2014
  • PCR detection of intestinal protozoa is often restrained by a poor DNA recovery or by inhibitors present in feces. The need for an extraction protocol that can overcome these obstacles is therefore clear. $QIAamp^{(R)}$ DNA Stool Mini Kit (Qiagen) was evaluated for its ability to recover DNA from oocysts/cysts directly from feces. Twenty-five Giardia-positive, 15 Cryptosporidium-positive, 15 Entamoeba histolytica-positive, and 45 protozoa-free samples were processed as control by microscopy and immunoassay tests. DNA extracts were amplified using 3 sets of published primers. Following the manufacturer's protocol, the kit showed sensitivity and specificity of 100% towards Giardia and Entamoeba. However, for Cryptosporidium, the sensitivity and specificity were 60% (9/15) and 100%, respectively. A series of optimization experiments involving various steps of the kit's protocol were conducted using Cryptosporidium-positive samples. The best DNA recoveries were gained by raising the lysis temperature to the boiling point for 10 min and the incubation time of the InhibitEX tablet to 5 min. Also, using a pre-cooled ethanol for nucleic acid precipitation and small elution volume ($50-100{\mu}l$) were valuable. The sensitivity of the amended protocol to Cryptosporidium was raised to 100%. Cryptosporidium DNA was successfully amplified by either the first or the second primer set. When applied on parasite-free feces spiked with variable oocysts/cysts counts, ${\approx}2$ oocysts/cysts were theoretically enough for detection by PCR. To conclude, the Qiagen kit with the amended protocol was proved to be suitable for protozoan DNA extraction directly from feces and support PCR diagnosis.

Limits of Direct PCR Amplification from Seaweeds Using Arbitrary and ITS Primers (해조류로부터 Arbitrary 및 ITS Primer들을 사용한 직접 PCR 유전자 증폭반응의 한계)

  • 김용국;진형주;박선미;진덕희;홍용기
    • Journal of Life Science
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    • v.9 no.1
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    • pp.15-21
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    • 1999
  • The random amplified ploymorphic DNAs (RAPD) assay is a simple and useful tool in identification of appropriate genetic markers, that requires no knowledge of target DNA sequence. RAPD products were generated directly from seaweed tissues, without prior nucleic acid extraction, of Porphyra yezoensis, Ulva pertusa and Undaria pinnatifida. The nuclear rDNA internal transcribed spacer (ITS) fragment however was not amplified directly from the seaweed tissues. Using DNA extracted by the LiCl method, both the ITS and RAPD's have been amplified by the polymerase chain reaction. RAPD of P yezoensis, thallus (n) and conchocelis (2n) produced lots of different polymorphic bands (36-50$\%$) depending on the arbitrary primers used. Difference was also observed between direct tissues amplification and DNA extracts amplification (53-57$\%$). Thus it is important to use the same ploidy of tissue for DNA extraction and as a RAPD template.

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Production of Spirulina Extract by Enzymatic Hydrolysis (효소 가수분해 방법을 이용한 스피루리나 추출물의 제조)

  • In, Man-Jin;Gwon, Su-Yeon;Chae, Hee-Jeong;Kim, Dong-Chung;Kim, Dong-Ho
    • Applied Biological Chemistry
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    • v.50 no.4
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    • pp.304-307
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    • 2007
  • An efficient production method of spirulina extract was developed by enzymatic treatment using cell lytic and proteolytic enzymes. The suitable dosage of Tunicase, a cell lytic enzyme, was found to be 2.0% (w/w). Proteolytic enzymes were screened to obtain high solid recovery and spirulina extraction (SE) index, which indicates nucleic acid-related substances content. Among the seven tested proteases, Esperase was selected and optimal dosage of this enzyme was 2.0% (w/w). The solid recovery and SE index of simultaneous treatment and co-treatment using optimal dosages of Tunicase and Esperase were greatly similar, respectively. However, co-treatment had the effect of shortening total hydrolysis time. The SE index and solid recovery of co-treatment were significantly enhanced by 75% $(11.4{\rightarrow}20.0)$ and 45% $(45.2%{\rightarrow}65.3%)$, respectively, than those of the non-treated extracts.

A Study on The Content of Liver Protein, Nucleic Acids, and Guanine Deaminase Activity of Mouse During Acute Starvation (급성(急性) 기아(饑餓)마우스의 간단백질(肝蛋白質), 핵산(核酸) 및 Guanine Deaminase 활성(活性)에 관(關)한 연구(硏究))

  • Park, Seung-Hee;Kim, Seung-Won
    • Journal of Nutrition and Health
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    • v.1 no.2
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    • pp.107-115
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    • 1968
  • Number of aspects, not only nutritional but social as well as political involved in human starvation pose nowadays global problems. In order to help establish the minimum nutritional requirements in the daily life of a man and to free people as well from either undernourishment, malnutrition or even starvation many workers have devoted themselves so far on the research programs to know what and how number of metabolic events take place in animals in vivo. It is the purpose of the present paper to examine in effect to what extent both of the protein and nucleic acids (DNA & RNA) together with an enzyme, guanine deaminase, which converts guanine into xanthine and in turn ends up to uric acid as an end product, undergo changes, quantitatively during acute starvation, using the mouse as an experimental animal. The mouse was strictly inhibited from taking foods except drinking water ad libitum and was sacriflced 24, 48, and 72 hours following starvation thus acutely induced. The animals consisted of two experimental groups, one control and another starvation groups, each being consisted of 6-24 mice of whose body weights ranged in the vicinity of 10 g. The animals were sacriflced by a blow on the head, followed by immediate excision of their livers into ice-cold distilled water, washing adherent blood and other contaminant tissues. The liver was minced foramin, by an all-glass homogenizer immersing it in an ice-bath, followed by subsequent fractionatin of the homogenate (10% W/V in 0.25M sucrose solution made up with 0.05M phosphate buffer of pH 7.4). For the liver protein and guanine deaminase assay, the 10% homogenate was centrifuged at 600 x g for 10 minutes to eliminate the nuclear fraction; and for the estimation of DNA and RNA, the homogenate was prepared by the addition of 10% trichloroacetic acid in order to free the homogenate from the acid-soluble fraction, the remaining residue being delipidate by the addition of alcohol and dried in vacuo for later KOH (IN) hydrolysis. The changes in body and liver wegihts during acute starvation were checked gravimetrically. Protein contents in the liver were monitored by the method of Lowry et al; and guanine deaminase activities were followed by the assay of liberated ammonia from the substrate utilizing the Caraway's colorimetry. The extraction of both DNA and RNA was performed by the Schmidt-Thannhauser's method, which was followed by Marmur's method of purification for DNA and by Chargaff's method of purification for RNA. The determinations of both DNA and RNA were carried out by the diphenylamine reaction for the former and by the orcinol reaction for the latter. The following resume was the results of the present work. 1. It was observed that the body as well as liver weights fall abruptly during starvation, and that the loss of body weight showed no statistical correlation with the decreases in the content of liver protein. 2. The content of liver protein and activity of liver guanine deaminase activity as well decline dramatically, and the specific activities of the enzyme (activity/protein), however, decreased gradually as starvation proceeded. 3. Both of the nucleic acids, DNA and RNA, showed decrements in the liver of mouse during acute starvation; the latter, however, being more striking in the decline as compared to the former. 4. The decreases in the liver protein content as resulted from the acute starvation had no statistically significant correlation with the decrements of DNA in the same tissue, but had regressed with a significant statistical correlation with the fall of RNA in the tissue. 5. The decrease in the activity of guanine deaminase in the liver of mouse during acute starvation was functionally more proportional to the decrease in RNA than DNA, and moreover correlated with the changes in the content of the liver protein. 6. The possible mechanisms involved during in this acute starvation as bring the decreases in the contents of DNA, protein, and guanine deaminase were discussed briefly.

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Effect of Succinylation on Functional Properties of Aspergillus fumiagtus Cell Protein (숙시닐화가 Aspergillus fumiagtus 균체단백질의 기능적 특성에 미치는 영향)

  • Choi, Jong-Duck;Kim, Jeong-Gyun;Cho, Sung-Hwan
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.21 no.5
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    • pp.573-579
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    • 1992
  • The influence of succinylation on several functional properties of fungal protein (Aspergillus fumigatus) was investigated. Fungal protein was succinylated to 20.7 and 85.3% by addition of 2.5 and 10% succinic anhydride, respectively. Succinylated fungal protein decreased the absorbance at 260nm, nucleic acid and carbohydrate, but increased the proteinous nitrogen and protein extraction in fungal protein. Succinylation had an enhancing effect on the functional properties as much as the degree of it was increased. Oil retention of succinylated fungal protein was higher about from two to five times than those of milk casein. Nitrogen solubility of succinylated fungal protein was increased to 32 and 51% than that of milk casein and soy flour. Emulsifying activity and stability were increased in proportion to the succinylated degree of fungal protein. As the result of succinylation increase more than 80%, emulsifying activity increased about 8.4 times. In conclusion, succinylated fungal protein improved functional properties, compared with nonsuccinylated fungal protein, milk casein and soy flour.

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A Simple Method for Extraction of High Molecular Weight DNA fromPorphyra Tenera (Rhodophyta) Using Diatomaceous Earth

  • Kim, Tae-Hoon;Hwang, Mi-Sook;Song, Ju-Dong;Oh, Min-Hyuk;Moon, Yong-Hwan;Chung, Ik-Kyo;Rhew, Tae-Hyoung;Lee, Choon-Hwan
    • ALGAE
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    • v.21 no.2
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    • pp.261-266
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    • 2006
  • The innate soluble polysaccharides and phenolic compounds of marine macroalgae are serious contaminants which interfere with experimental procedures such as restriction enzyme digestion, polymerase chain reaction (PCR) and other enzymatic reactions using extracted DNA samples. The viscous polysaccharides are co-precipitated with DNA samples by isopropanol or ethanol precipitation in conventional experiment. To overcome the problem, a method for the isolation of high molecular weight DNA from Porphyra tenera is developed with the application of diatomaceous earth column. The isolated DNAs by this method were about 50-100 kb in size and could be digested well with restriction enzymes. The nuclease activity seemed to be minimal, and high reproducibility in the arbitrary primed PCR for RAPD analyses was a distinctive feature. These results suggest that this method is very efficient in isolating nucleic acid from macroalgae including Porphyra.

Convenient Nucleic Acid Detection for Tomato spotted wilt virus: Virion Captured/RT-PCR (VC/RT-PCR) (Tomato spotted wilt virus를 위한 간편한 식물바이러스 핵산진단법: Virion Captured/RT-PCR (VC/RT-PCR))

  • Cho Jeom-Deog;Kim Jeong-Soo;Kim Hyun-Ran;Chung Bong-Nam;Ryu Ki-Hyun
    • Research in Plant Disease
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    • v.12 no.2
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    • pp.139-143
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    • 2006
  • Virion captured reverse transcription polymerase chain reaction (VC/RT-PCR) could detect plant virus quickly and accurately. In the VC/RT-PCR, no antibody is needed unlike immuno-captured RT-PCR (IC/RT-PCR) which had been improved method of RT-PCR for plant viruses, and virus nucleic acids can be obtained easily within 30minutes by property of polypropylene PCR tube which is hold and immobilized viral particles on its surface. For the virion capture of Tomato spotted wilt virus (TSWV), the extraction buffer was tested. The optimum macerating buffer for TSWV was 0.01M potassium phosphate buffer, pH 7.0, containing 0.5% sodium sulfite. The viral crude sap was incubated for 30 min at $4^{\circ}C$. The virions in the PCR tubes were washed two times with 0.01M PBS containing 0.05% Tween-20. The washed virions were treated at $95^{\circ}C$ immediately for 1 min containing RNase free water and chilled quickly in the ice. Disclosed virions' RNAs by heat treatment were used for RT-PCR. Dilution end point of $10^{-5}$ from plant's crude sap infected with TSWV showed relatively higher detection sensitivity for VC/RT-PCR. During multiple detection using two or more primers, interference was arisen by interactions between primer-primer and plant species. The result of multiplex RT-PCR was influenced by combinations of primers and the kind of plant, and the optimum extraction buffer for the multiplex detection by VC/RT-PCR should be developed.