Genetic diversity of Pericopsis mooniana from South Kalimantan based on Random Amplified Polymorphism DNA (RAPD) Markers

The genetic diversity and relationship of Pericopsis mooniana collected from Pulau Laut, South Kalimantan, was analyzed using RAPD markers. Currently, the natural distribution of P. mooniana in Pulau Laut no longer exists. Instead, PT Inhutani II, as the concession holder in the area, had collected the remaining P.mooniana and planted it in the seed orchard, arboretum, or around PT Inhutani’s mess/office. Forty-two samples from four locations: mess/residential house (3), seed orchard (33), arboretum (3), and PT Inhutani II Unit Stagen (3) were analyzed using seven RAPD primers. Our study showed that the total genetic diversity of all populations was low (He = 0.191 ± 0.013). P. mooniana collected from seed orchards had the highest diversity (He = 0.289 ± 0.021), while the lowest was from mess/residential houses (He = 0.134 ± 0.025). The genetic relationship data indicated the possibility that P. mooniana from mess/residential house, arboretum, and seed orchard may come from the same origin. These results can be used to support the development of ex-situ conservation plots to avoid inbreeding depression. At the same time, the genetic diversity will be helpful in its conservation and further utilization, such as establishing the plantations to reduce the pressure of the species in nature and provide valuable timber production in Indonesia.

Identification of molecular markers for type 2 Diabetes mellitus in Sidoarjo, Indonesia

T2DM can be triggered by two collaborating factors, namely genetics and the environment. This study aimed to identify genetic markers that can be used to detect the possibility of a person having T2D using the random amplified polymorphism DNA (RAPD) method. The study was carried out cross-sectional and involved 60 samples consisting of 30 positive T2D samples and 30 negative samples T2D. The primer used for PCR-RAPD was D20 (5'-ACCCGGTCAC-3’). The PCR-RAPD results were then analyzed using the scoring method and analyzed using the non-parametric Chi-Square test (cl: 95%). Among T2D, 576 bp band were confirmed to be markers in the patients.

Application of RAPD Markers on Sex Determination of Papaya (Carica papaya)

Molecular sex determination of five varieties of Indonesian papaya were investigated using RAPD (Random Amplified Polymorphism DNA) markers. Overall, 12 of 14 primers produced polymorphic bands on either several or all tested varieties. The OPC04 and RAPD2 markers could be used determined sex types on all varieties, whereas others primers are only on certain varieties. The Tangkai Ungu variety can be differentiate by markers: OPA11, OPA14, OPC14, RAPD2, RAPD3, and RAPD5; the Lokal Sumani can be determine using markers: OPA01, OPA11, OPA14, OPC01, OPC04, RAPD2, RAPD3, RAPD5, and RAPD6; the Merah Delima could be determined using OPC04, OPN09, RAPD2, and RAPD5; the Dampit could be determined using OPC01, OPC04, RAPD2, and RAPD6; whereas the Sicincing Panjang could be determined using OPA04, OPA11, OPA14, OPC04, RAPD2, and RAPD3.

Prevalence and Diversity of the Thermotolerant Bacterium Bacillus cytotoxicus among Dried Food Products

ABSTRACT Bacillus cytotoxicus, a member of the Bacillus cereus group, is a thermotolerant species originally reported from a lethal foodborne infection in France in 1998. The strain NVH391-98, isolated from this outbreak, produces cytotoxin K1, a potential cytotoxic enterotoxin. However, the habitat and diversity of B. cytotoxicus isolates so far have been poorly explored. The objective of this study was to assess the prevalence of this bacterium in different food products (mainly dried) and to estimate its diversity. Among the 210 samples analyzed, all potato flakes contained the bacterium at low concentrations (≤102 CFU/g). However, prepared and kept at room temperature for 2 days, the puree contained ca. 105 CFU/g B. cytotoxicus. Besides potato flakes, some samples of millet flour, salted potato chips, and soups also contained B. cytotoxicus. From these samples, 55 thermotolerant B. cytotoxicus isolates were obtained. When classified into six distinct random amplified polymorphism DNA patterns, they showed the existence of 11 distinct plasmid profiles. Although most isolates (including the reference strains NVH391-98 and NVH883-00) contained no detectable plasmid, some displayed one to three plasmids with sizes from ca. 8 to 90 kb. It also emerged from this study that a single food sample could contain B. cytotoxicus isolates with different genetic profiles. HIGHLIGHTS

ANALISIS KERAGAMAN GENETIK TIGA STRAIN NILA MERAH (Oreochromis sp) DENGAN ANOVA RAPD

Analysis Genetic Variation of Three Strains of Red Tilapia by Anova of RAPD. Study on the genetic variance of three strains of red tilapia (Oreochromis sp) had been conducted in the Biology Molecular Laboratory, Research Institute for Freshwater Aquaculture (RIFA) Bogor. Three different strains, Red NIFI from Thailand, Red Tilapia from Lido lake and Red Tilapia from Bogor’s farmer were analyzed in the study. Observation used Random Amplified Polymorphism DNA (RAPD) with OPA-03, OPA-04, OPC 14 and OPC-15 primers. The results showed that only OPA-03 primer was able to amplify numerous samples. Further analysis showed that the percentage of polimorphic range was between 16.67 – 38.89%, heterozygosity value 0.0378 – 0.1536 and genetic distance among strain 0.3051 – 0.6037.Keywords : RAPD, genetic, strain, nile tilapia, oreochromis ABSTRAK Penelitian mengenai variasi genetik tiga strain nila merah dari 3 lokasi yang berbeda telah dilakukan di Laboratorium Molekuler Biologi, Balai Riset Perikanan Budidaya Air Tawar (BRPBAT) Bogor. Strain yang diamati meliputi jenis nila Red NIFI dari Thailand, nila merah dari Danau Lido dan nila merah dari Petani Bogor. Penelitian menggunakan metode analisis Random Amplified Polymorphism DNA (RAPD), dengan menggunakan primer OPA-03, OPA-04, OPC-14 dan OPC-15. Hasil pengamatan menunjukkan hanya OPA-03 yang dapat menghasilkan amplifikasi dalam jumlah sampel yang memadai. Hasil analisis menunjukkan bahwa persentase polimorfik berkisar antara 20.00-40.00%, dengan nilai heterozigositas 0.0604–0.1516 dan jarak genetik antar strain 0.1770-0.4865. Kata kunci : RAPD, genetik, strain, ikan nila, oreochromis

APLIKASI TEKNIK RANDOM AMPLIFIED POLYMORPHISM DNA (PCR-RAPD) SEBAGAI PENANDA GENETIK PADA IKAN BETUTU (Oxyeleotris marmorata)

Ikan betutu merupakan ikan yang memiliki nilai ekonomis tinggi untuk konsumsi lokal dan komoditas ekspor. Dalam rangka pelestarian dan pengembangan budidaya ikan betutu, maka perlu dilakukan evaluasi keragaman genetik. Kegiatan ini bertujuan untuk mendapatkan informasi aplikasi teknik PCR-RAPD sebagai penanda genetik pada ikan betutu sebagai dasar untuk analisis keragaman genetik ikan Betutu. Dalam kegiatan ini primer yang digunakan adalah OPC-4 dan OPC-8. Sampel yang digunakan adalah sirip ikan betutu yang berasal dari tiga populasi yaitu Sumatera, Jawa, dan Kalimantan. Primer OPC-4 menghasilkan amplifikasi 14-21 band/pita DNA dengan ukuran 300-2.100 bp, sedangkan primer OPC-8 menghasilkan amplifikasi 14-15 band dengan ukuran 330-2.100 bp.