scholarly journals ALLELE FREQUENCY, HETEROZIGOSITY, AND ALLELE MIGRATION IN JAVANESE AND MADURESE POPULATION IN MALANG AND MADURA, EAST JAVA INDONESIA

2017 ◽  
Vol 17 (1) ◽  
pp. 43
Author(s):  
Nikmatul Iza
Keyword(s):  
Allele Frequency ◽  
Dna Extraction ◽  
Pcr Amplification ◽  
Polyacrylamide Gel ◽  
Salting Out ◽  
Blood Samples ◽  
Band Profile ◽  
Program Software

FREKUENSI ALEL, HETEROZIGOSITAS DAN MIGRASI ALEL PADA POPULASI ETNIS JAWA DAN MADURA DI MALANG DAN MADURA,  JAWA TIMUR, INDONESA ABSTRAKPenelitian ini bertujuan untuk menentukan frekuensi alel, heterozigositas, dan migrasi alel pada populasi etnis Jawa dan Madura berdasarkan penanda 13 CODIS. Metode yang digunakan dalam penelitian ini adalah (1) Pengambilan sampel darah dari 5 populasi yang terdiri dari 3 populasi etnis jawa dan 2 populasi etnis Madura; (2) Isolasi DNA dari sampel darah dilakukan dengan menggunakan metode salting out; (3) Amplifikasi PCR dengan menggunakan 13 CODIS  yang terdiri dari TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 dan divisualisasi dengan elektroforesis gel polyacrylamid 8%; serta (4) Profil pita dianalisis dengan program QuantityOne dan variasi pola pita DNA dianalisis dengan menggunakan program software GENEPOP package versi 4.2 yang akan digunakan untuk menentukan frekuensi alel, heterozigositas, dan migrasi alel. Hasil penelitian menunjukkan bahwa (1) Pada populasi etnis Jawa frekuensi alel yang memiliki keragaman tertinggi terdapat pada lokus D21S11 dengan jumlah alel sebanyak enam, lokus VWA dengan jumlah alel sebanyak lima, dan lokus FGA, TH01, D13S317, D16S539 dengan jumlah alel sebanyak empat yang digunakan sebagai penanda. Populasi etnis Madura memiliki frekuensi alel dengan keragaman tertinggi terdapat pada lokus TH01, D13S317, dan D21S11 dengan jumlah alel sebanyak lima dan lokus FGA dengan jumlah alel sebanyak empat. (2) Nilai heterozigositas populasi etnis Madura I (90.38%) dan populasi etnis Madura II (86.54%) lebih tinggi dibandingkan dengan populasi etnis Jawa I (67.69%), populasi etnis Jawa II (83.03%), maupun populasi etnis Jawa III (70.77%) dan (3) Migrasi alel pada populasi etnis Jawa sebesar 0.085% dan pada populasi etnis Madura sebesar 0.081%.Kata kunci: Frekuensi Alel, Heterozigositas, Migrasi Alel, 13 CODIS, Etnis Jawa dan Madura ALLELE FREQUENCY, HETEROZIGOSITY, AND ALLELE MIGRATION IN JAVANESE AND MADURESE POPULATION IN MALANG AND MADURA, EAST JAVA INDONESIA ABSTRACTThe aim of this study is to determine the frequency of alleles, heterozygosity, and allele migration in Javanese and Madurese population use 13 CODIS. The methods used in this study were (1) blood samples from five population consist three population of Javanese ethnic and two population of Madurese ethnic, (2) DNA extraction from blood samples by salting out method, (3) PCR amplification use 13 CODIS were TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 and visualized by 8% polyacrylamide gel (4) The band profile was analyzed by using QuantityOne software and variations in the pattern of DNA bands were analyzed by using GENEPOP software version 4.2 package to determine the frequency of alleles, heterozygosity, and allele migration. The results showed that (1) The population of Javanese allele frequency that has the highest diversity found in the locus D21S11 with a number of alleles of six, locus VWA by the number of alleles of five, and the locus FGA, TH01, D13S317, and D16S539 with a number of alleles of four  which is used as a marker. The populations of Madurese allele frequency that has the highest diversity found in the locus TH01, D13S317, and D21S11 with a number of alleles of five and locus FGA with a number of alleles of four, (2) Value of heterozygosity populations of Madurese I (90.38 %) and populations of Madurese II (86.54%) was higher than the population of Javanese I (67.69%), the population of Javanese II (83.03%), as well as the population of Javanese III (70.77%) and (3) There has been a migration of alleles in population Javanese of 0.085% and population Madurese of 0.081%.Keywords: Allele Frequency, Heterozigosity, Allele Migration, 13 CODIS,       Javanese and Madurese ethnic.

scholarly journals DNA Isolation: A Method for Improving the Efficiency of DNA Extraction From Clotted Blood Samples

2021 ◽  
Vol 1 (2) ◽  
pp. 44-47
Author(s):  
Bobby Rianto Adi Putra
Keyword(s):  
Dna Extraction ◽  
Ball Bearing ◽  
Dna Isolation ◽  
Genome Research ◽  
Salting Out ◽  
Blood Samples ◽  
Blood Clots ◽  
Safe Technique ◽  
Yield And Purity

In generally, the genome research of high DNA extraction from clotted blood produced a low quality. The aim of this study is to develop a simple and safe technique to dispering the blood clots by the ball bearing metal shots. The yield and purity of DNA obtained by three steps were significantly different (P < 0.0001), with a higher yield in the modified salting-out method. The salting-out method is simple, efficient and economical for DNA isolation from old clotted blood samples.

scholarly journals Improving DNA extraction quality by the salting‐out method to prepare blood samples for real‐time PCR. (LB124)

2014 ◽  
Vol 28 (S1) ◽  
Author(s):  
Natalia Araujo ◽  
Bruno Carmona ◽  
Glaucia Regina Nogueira ◽  
Marcor Ferreira Minicucci ◽  
Sandro Conde
Keyword(s):  
Real Time ◽  
Dna Extraction ◽  
Real Time Pcr ◽  
Salting Out ◽  
Blood Samples

A rapid salting out method for DNA extraction from buccal swabs

2012 ◽  
Vol 31 (12) ◽  
pp. 1370-1374
Author(s):  
Wei-feng ZHU ◽  
Da-ya LUO ◽  
Shuo TU ◽  
Xia-li ZHANG ◽  
Ke-min JIE ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Salting Out ◽  
Buccal Swabs

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

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

scholarly journals The Fellowship of the Ring Test: DNAqua-Net WG2 initiative to compare diatom metabarcoding protocols used in routine freshwater biomonitoring for standardisation

2021 ◽  
Vol 4 ◽  
Author(s):  
Valentin Vasselon ◽  
Éva Ács ◽  
Salomé Almeida ◽  
Karl Andree ◽  
Laure Apothéloz-Perret-Gentil ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Aquatic Ecosystems ◽  
Quality Index ◽  
Ecological Status ◽  
Pcr Amplification ◽  
Ring Test ◽  
Dna Metabarcoding ◽  
Ecological Status Assessment ◽  
Status Assessment

During the past decade genetic approaches have been developed to monitor biodiversity in aquatic ecosystems. These enable access to taxonomic and genetic information from biological communities using DNA from environmental samples (e.g. water, biofilm, soil) and methods based on high-throughput sequencing technologies, such as DNA metabarcoding. Within the context of the Water Framework Directive (WFD), such approaches could be applied to assess Biological Quality Elements (BQE). These are used as indicators of the ecological status of aquatic ecosystems as part of national monitoring programs of the european network of 110,000 surface water monitoring sites with 79.5% rivers and 11% lake sites (Charles et al. 2020). A high-throughput method has the potential to increase our spatio-temporal monitoring capacity and to accelerate the transfer of information to water managers with the aim to increase protection of aquatic ecosystems. Good progress has been made with developing DNA metabarcoding approaches for benthic diatom assemblages. Technological innovation and protocol optimization have allowed robust taxonomic (species) and genetic (OTU, ESV) information to be obtained from which diatom quality indices can be calculated to infer ecological status to rivers and lakes. Diatom DNA metabarcoding has been successfully applied for biomonitoring at the scale of national river monitoring networks in several countries around the world and can now be considered technically ready for routine application (e.g. Apothéloz-Perret-Gentil et al. 2017, Bailet et al. 2019, Mortágua et al. 2019, Vasselon et al. 2019, Kelly et al. 2020, Pérez-Burillo et al. 2020, Pissaridou et al. 2021). However, protocols and methods used by each laboratory still vary between and within countries, limiting their operational transferability and the ability to compare results. Thus, routine use of DNA metabarcoding for diatom biomonitoring requires standardization of all steps of the metabarcoding procedure, from the sampling to the final ecological status assessment in order to define good practices and standards. Following previous initiatives which resulted in a CEN technical report for biofilm sampling and preservation (CEN 2018), a set of experiments was initiated during the DNAqua-Net WG2 diatom workshop (Cyprus, 2019) to focus on DNA extraction and PCR amplification steps in order to evaluate: i) the transferability and reproducibility of a protocol between different laboratories; ii) the variability introduced by different protocols currently applied by the scientific community. 19 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using i) the same fixed protocol and ii) their own protocol. Experiments were performed by each participant on a set of standardized DNA and biofilm samples (river, lake, mock community). In order to specifically test the variability of DNA extraction and PCR amplification steps, all other steps of the metabarcoding process were fixed and the preparation of the Miseq sequencing was performed by only one laboratory. The variability within and between participants will be evaluated on DNA extracts quantity, taxonomic (genus, species) and genetic richness, community structure comparison and diatom quality index scores (IPS). We will also evaluate the variability introduced by different DNA extraction and PCR amplification protocols on diatom quality index scores and the final ecological status assessment. The results from this collaborative work will not serve to define “one protocol to rule them all”, but will provide valuable information to define guidelines and minimum requirements that should be considered when performing diatom metabarcoding for biomonitoring.

scholarly journals Short Communication: Molecular characterization and blood hematology profile of dogs infected by Ehrlichia canis in Yogyakarta, Indonesia

2020 ◽  
Vol 21 (7) ◽  
Author(s):  
Yustinus oswin primajuni Wuhan ◽  
Aris Haryanto ◽  
Ida Tjahajati
Keyword(s):  
Molecular Characterization ◽  
Microscopic Examination ◽  
Short Communication ◽  
Pcr Amplification ◽  
Ehrlichia Canis ◽  
Infected Blood ◽  
Blood Samples ◽  
Glta Gene ◽  
Vector Borne ◽  
Positive Results

Abstract. Wuhan YOP, Haryanto A, Tjahajati I. 2020. Short Communication: Molecular characterization and blood hematology profile of dogs infected by Ehrlichia canis in Yogyakarta, Indonesia. Biodiversitas 21: 3242-3248. Ehrlichia canis is Gram-negative intracellular obligate bacteria that cause ehrlichiosis, a companion vector-borne disease is a potentially fatal disease that attacks dogs. The purpose of this study was to molecular characterize and determine the features of Ehrlichia-infected blood based on the amplification of the gltA gene in Ehrlichia infected dogs from Yogyakarta, Indonesia. Blood samples were collected from 51 dog patients from the Prof. Dr. Soeparwi Animal Hospital, animal clinics, and pet shops based on the anamnesis, clinical sign, and physical examination, followed by microscopic examination, routine hematology, PCR amplification, and DNA sequencing were carried out on the blood samples. Based on positive PCR amplification and blood hematology profile examination ehrlichiosis-positive in dogs showed that thrombocytopenia case was 82.3%, anemia was 70.5%, eosinopenia was 70.5%, neutropenia was 29.4%, monocytopenia was 23%, leukopenia was 17% and lymphopenia was 11.7%. Morulae of Ehrlichia sp.was not found in microscopic examination. Molecularly, detected of E. canis using the gltA gene showed that 34% of samples were positive results. Then 5 of positive Ehrlichia samples were DNA sequenced, they showed a high homology of 100% with Hat Yai isolates (KU765199.1). There was no genetic diversity between E. canis samples in Yogyakarta.

scholarly journals Molecular detection and occurrence of equine theileriosis in Arabian horses in Al-Najaf province/Iraq

2020 ◽  
Vol 57 (3) ◽  
pp. e166996
Author(s):  
Hayder Mohammad Al-Rammahi ◽  
Abdulameer Abed Hatem ◽  
Asaad Chasib Al-Atabi
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Extraction ◽  
Molecular Detection ◽  
Molecular Technique ◽  
Chain Reaction ◽  
Blood Samples ◽  
Equine Piroplasmosis ◽  
Polymerase Chain

This study was designed to detect equine piroplasmosis using the molecular technique in Al-Najaf province during the season that showed an increment in tick activities. Blood samples were collected from 110 horses with more than two signs of piroplasmosis. After DNA extraction, the product was examined by a polymerase chain reaction to amplify 18SrRNA. The results showed that the overall percentage of equine theileriosis was 38.18%. According to gender, the percentage of infection was 43.48% and 29.27% in females and males, respectively. Significant variations appeared between infected horses according to age, and the percentage of infection was 50% and 35.22% in less than 2 years and more than 2 years age, respectively. Moreover, the percentage of infection was 62.5% and 19.35% in animals with and without acariasis, respectively. Significant variations were also seen in equine theileriosis according to geographical areas, and the higher percentage was reported in Hera district (60.87%), while the lowest percentage was in the center of Al-Najaf (21.43%). This difference may be due to different distribution of vector of disease (tick), which may be the availability of the suitable weather that helped in the multiplication of the intermediate vectors. In conclusion, this study proved the variations in the occurrences of equine piroplasmosis according to gender, age, and geographical areas.

Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces

2008 ◽  
Vol 72 (2) ◽  
pp. 124-132 ◽  
Author(s):  
Jordan M. Nechvatal ◽  
Jeffrey L. Ram ◽  
Marc D. Basson ◽  
Phanramphoei Namprachan ◽  
Stephanie R. Niec ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Pcr Amplification ◽  
Human Feces ◽  
Fecal Collection

scholarly journals A Comprehensive Comparison of DNA Extraction Using Fresh and Stored Bloods in Molecular Hematology Diagnostic Study

2018 ◽  
Vol 17 (3) ◽  
pp. 424-432
Author(s):  
Siti Nazihahasma Hassan ◽  
Suharni Mohamad ◽  
Rosline Hassan ◽  
Selamah Ghazali ◽  
Wan Suriana Wan Ab Rahman
Keyword(s):  
Medical Science ◽  
Pcr Amplification ◽  
Diagnostic Study ◽  
Fresh Blood ◽  
Blood Samples ◽  
Acceptable Alternative ◽  
Significant Difference ◽  
Comprehensive Comparison ◽  
One Year ◽  
Stored Blood

Objective: Blood is the main source of DNA in molecular biology. It provides a high DNA quality and quantity. In this study, we compare the quality and quantity of DNA isolated from stored blood that has been kept at -40°C for one-year to that of fresh blood.Materials and Methods: Twelve fresh and stored blood samples were randomly selected for this study. Nucleo Spin® Blood L kit was used to isolate the DNA from the samples. The integrity and intensity of DNA were examined through 1.6% agarose gel precast with SYBR® safe DNA stain. The DNA samples were further examined through PCR amplification and Sanger sequencing.Results: There was no significant difference in quality and quantity of isolated DNA from fresh blood and stored blood samples. The high intensity of an intact DNA band as well as the success in PCR amplification and sequencing are indicators of high DNA quality.Conclusion: Proper storage of patients’left-over whole blood sample at -40°C offers an acceptable alternative for DNA resources in molecular study.Bangladesh Journal of Medical Science Vol.17(3) 2018 p.424-432

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