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KARAKTERISASI RESISTENSI GULMA Synedrella nodiflora TERHADAP HERBISIDA REFLEX MENGGUNAKAN GEN PPX2L SEBAGAI PENANDA MOLEKULER Dwiati, Murni; Susanto, Agus Hery
Prosiding Vol 3, No 1 (2012)
Publisher : Prosiding

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Fomesafen as an active substance of Reflex herbicide can inhibit PPOase, an enzyme playing important role in chlorophyl biosynthesis. Deletion of three bases at gene encoding PPOase, i.e. PPX2L, was reported as one of resistance mechanisms against PPOase inhibiting herbicides. Nevertheless, only a few studies on molecular characterization of Synedrella nodiflora resistance against Reflex were reported. Therefore, this study was aimed to (1) know the sequence of PPX2L gene isolated from resistant S. nodiflora against Reflex, (2) perform homology study of PPX2L gene from resistant S. nodiflora and various plant species in data base, and (3) know the sequence of PPX2L gene responsible to S. nodiflora resistance against Reflex. The PCR products of susceptible S. nodiflora showed three bands, in that of 500 bp is strongly assumed as PPX2L gene. Susceptible S. nodiflora is genetically different from susceptible A. tuberculatus, indicated by the absence of three base pairs at position 834, 835 and 836 in susceptible S. nodiflora, where in susceptible A. tuberculatus this position is occupied by CAG. Then, in both susceptible S. nodiflora and A. tuberculatus there is C at position 919 but T in resistant A. tuberculatus. At amino acid level this position is CCC (proline) in susceptible S. nodiflora, CTA (leucine) in susceptible A. tuberculatus and TTA (leucine) in resistant A. tuberculatus. Therefore, inspite of base alteration from C in susceptible A. tuberculatus to T in resistant A. tuberculatus, the amino acid formed remains constant, i.e. leucine. Significant difference is, however, observed in susceptible S. nodiflora because there is proline at the same posistion.

STUDI KEANEKARAGAMAN GENETIK TANAMAN KECIPIR (PSOPHOCARPUS TETRAGONOLOBUS (L.) DC): UPAYA MENUJU LABORATORIUM GENETIKA SEBAGAI PUSAT KAJIAN KETAHANAN PANGAN DAN BIOENERGI Amurwanto, Adi; Yuniaty, Alice; Susanto, Agus Hery; Sasongko, Nurtjahjo Dwi; Aziz, Saefuddin
Prosiding Vol 3, No 1 (2012)
Publisher : Prosiding

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Kecipir mempunyai potensi untuk dimanfaatkan sebagai bahan pangan segar maupun olahan bernilai gizi tinggi dan sebagai bahan dasar dalam industri biodiesel. Pemanfaatan kecipir yang belum optimal mendorong dilakukannya penelitian tentang keanekaragaman genetik tanaman kecipir sebagai langkah awal untuk mengembangkan potensi tanaman ini. Penelitian ini bertujuan untuk memperoleh data mengenai keanekaragaman genetik pada level molekuler kecipir polong panjang dan polong pendek dengan teknik RAPD. Dari 32 primer yang diskrining, 20 dipilih untuk analisis menggunakan Program GenAlEx 6.1. Hasilnya 156 buah fragmen dengan 140 diantaranya menunjukkan polimorfisme sehingga didapatkan polimorfisme total sebesar 89,74%. Polimorfisme dalam populasi kecipir polong pendek bernilai 64.10% dan polimorfisme dalam populasi kecipir polong panjang sebesar 51.28%. Kemiripan genetik Nei (bias) antara kecipir polong panjang dan kecipir polong pendek adalah 0,805 sementara jarak genetik antara keduanya adalah 0,218. Adapun kemiripan genetik tidak bias antara kedua populasi adalah 0,873, sementara jarak genetik tidak bias sebesar 0,136.

High Connectivity Among Synedrella nodiflora Populations in Java Island Based on Intergenic Spacer atpB-rbcL Susanto, Agus Hery; Nuryanto, Agus; Daryono, Budi Setiadi
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 1 (2018): April 2018
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v10i1.12038

Synedrella nodiflora (L.) Gaertn has taxonomically been the only species of genus Synedrella, which spreads over many tropical countries. In spite of its wide range of distribution, the genus remains monospecific. This leads to assumption of the very low genetic diversity among S. nodiflora populations worldwide. It may also be the case in Java Island, though rapid changes in ecosystem condition occurs. Here we report our study on S. nodiflora population genetics in Java Island using intergenic spacer (IGS) atpB âÂ rbcL as a molecular marker, since it has been well known as one of the most variable chloroplast genome regions in a wide range of plant species so far. As many as 58 individuals were collected randomly from ten different locations in the island. Based on IGS atpB â rbcL sequences of 860 bp length, only two haplotypes were observed. Both show only one polymorphic site (0.12%) and one transversion, where T is substituted by G at position 790, indicating that high connectivity among populations of S. nodiflora in Java Island is observed. This results in a low genetic differences among the populations, which at the same time provides a fact of nearly no variation among the IGS atpB â rbcL sequences.

Phylogeography and Genetic Diversity of Humpback Grouper Cromileptes altivelis based on Cytochrome C Oxidase I Susanto, Agus Hery; Nuryanto, Agus; Soedibja, Petrus Hary Tjahja
Jurnal Natur Indonesia Vol 14, No 1 (2011)
Publisher : Lembaga Penelitian dan Pengabdian kepada Masyarakat Universitas Riau

Humpback grouper is one of the most popular fish group in the international live trade in Asia-Pacific regions. The price for one kilogramlive of humpback grouper, especially in Spermonde Archipelago South of Sulawesi, is range from 350.000-400.000 IDR, whereas in theretail level in Hong Kong the price was about 92 US$. This condition leads to the reduction of nature population due to overexploitation.Population decreasing due to overexploitation may cause loss of genetic diversity within population and lead to reduce of potentialadaptive, population resistance, and productivity. Therefore, it is important to do some efforts to avoid adverse effect of overexploitationon humpback grouper population in Indonesia. One of the valuable efforts is providing genetic information such as phylogeography andgenetic diversity of humpback grouper Cromileptes altivelis. Analysis was based on 618 base pairs fragment of cytochrome c oxidase I genefrom 36 individuals (sequences) of Cromileptes altivelis collected at four different sites (e.g. Pulau Seribu, Jepara, Situbondo and SpermondeArchipelago). The results showed that humpback grouper population has a high haplotype and nucleotide diversity. However, high geneticdiversity and polymorphisms could not reveal population fragmentation (Φ stt = 0.000). It is suggested that high gene flow rather thanpopulation sub structuring was occurred. High level genetic diversity and polymorphisms are vital related to adaptive potential toenvironmental alteration.

Construction of Soil Metagenomic Library to Obtain Recombinant Clones with an Indigenous Lipase Activity Susanto, Agus Hery; Pramono, Hendro; Lestari, Puji
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 14, No 3 (2009): October 2009
Publisher : Universitas Atma Jaya Yogyakarta

Penelitian ini bertujuan untuk mengonstruksi perpustakaan metagenom tanah dari sekitar lokasi industri pengolahan minyak kelapa di Kabupaten Banyumas, Jawa Tengah, dalam upaya mendapatkan klon rekombinan dengan aktivitas lipase indigenuos. Penelitian dilakukan di Laboratorium Genetika, Fakultas Biologi, Universitas Jenderal Soedirman mulai bulan Mei hingga Desember 2006. Secara umum tahapan penelitian terdiri atas ekstraksi dan pemurnian DNA tanah, isolasi pUC19, pemotongan DNA tanah, pemotongan dan defosforilasi pUC19, ligasi fragmen-fragmen DNA tanah ke dalam pUC19 untuk menghasilkan molekul DNA rekombinan, dan transformasi sel inang E. coli JM109 menggunakan molekul DNA rekombinan yang diperoleh untuk mengonstruksi perpustakaan metagenom tanah. Pemotongan DNA tanah menghasilkan fragmen-fragmen yang sebagian besar berukuran lebih kurang 5 kb sehingga gen lipase dimungkinkan untuk dibawa di dalamnya. Transformasi sel inang E. coli JM109 memperlihatkan efisiensi 1.7 x 105 cfu/Î¼g plasmid. Di antara koloni-koloni yang diperoleh, terdapat 102 koloni berwarna putih, yang menunjukkan keberadaan molekul DNA rekombinan. Koloni putih ini dapat digunakan sebagai materi untuk skrining klon rekombinan dengan aktivitas lipase.

Variasi Biokimia Genetik Populasi Ikan Betutu (Oxyeleotris marmorata, BLKr.) di Waduk Penjalin Brebes Susanto, Agus Hery; Suryaningsih, Suhestri
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 11, No 3 (2006): October 2006
Publisher : Universitas Atma Jaya Yogyakarta

Penjalin water reservoir in Brebes Regency, Central Java, is one of the habitats of the sand goby. A study on its genetic diversity using approaches of isozyme analysis was needed to support domestication of the fish in this area. This study was aimed at the biochemical-genetic variation of sand goby population in Penjalin water reservoir based on esterase (EST), peroxidase (PER), malate dehydrogenase (MDH), aspartate amino-transferase (AAT), and acid phosphatase (ACP) polymorphisms. Visualization of the isozymes was carried out employing horizontal electrophoretic technique with potato starch gel and buffer system of L-histidin monohydrate. Of the five isozymes, ACP was not well-visualized in all samples tested while the remaining four showed no polymorphisms. It could be concluded that there is no biochemical-genetic variation of sand goby population in Penjalin water reservoir based on isozymes of EST, PER, MDH, and AAT.

GENETIC DIFFERENCE BETWEEN TWO PHENOTYPICALLY SIMILAR MEMBERS OF ASTERACEAE BY THE USE OF INTERGENIC SPACER ATPB â€“ RBCL Susanto, Agus Hery; Dwiati, Murni
Biosaintifika: Journal of Biology & Biology Education Vol 11, No 3 (2019): December 2019
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Two Asteraceae species, i.e. Synedrella nodiflora (L.) Gaertn and Eleutheranthea ruderalis (Swartz) Sch.-Bpi. are phenotypically similar with each other, although some differences in morphological and anatomical traits are apparently observable. Molecular comparison using particular marker is required to support a phenotype-based study that previously reported. Chloroplast DNA marker, . atpB ? rbcL IGS, was used to identify genetic difference between both species. Six samples of the respective species were collected randomly from some places in Banyumas Regency, Central Java, Indonesia. Amplification of the marker was performed employing a pair of universal primers. Sequence alignment on the PCR products showed that no difference in atpB ? rbcL IGS sequences, either within S. nodiflora or E. ruderalis samples was observed. On the other hands, several deletions and base substitution in both S. nodiflora and E. ruderalis were detected when alignment was made between both species. This result suggests that they reveal a convincing genetic difference. Inspite of no direct correlation between this genetic and some visible phenotypic differences, this finding provides preliminary scientific background on the phenotypic traits of both species, which are often difficult to find at a rapid observation.

Variasi Biokimia Genetik Populasi Ikan Betutu (Oxyeleotris marmorata, BLKr.) di Waduk Penjalin Brebes Agus Hery Susanto; Suhestri Suryaningsih
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 11, No 3 (2006): October 2006
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v11i3.2539

Penjalin water reservoir in Brebes Regency, Central Java, is one of the habitats of the sand goby. A study on its genetic diversity using approaches of isozyme analysis was needed to support domestication of the fish in this area. This study was aimed at the biochemical-genetic variation of sand goby population in Penjalin water reservoir based on esterase (EST), peroxidase (PER), malate dehydrogenase (MDH), aspartate amino-transferase (AAT), and acid phosphatase (ACP) polymorphisms. Visualization of the isozymes was carried out employing horizontal electrophoretic technique with potato starch gel and buffer system of L-histidin monohydrate. Of the five isozymes, ACP was not well-visualized in all samples tested while the remaining four showed no polymorphisms. It could be concluded that there is no biochemical-genetic variation of sand goby population in Penjalin water reservoir based on isozymes of EST, PER, MDH, and AAT.

Construction of Soil Metagenomic Library to Obtain Recombinant Clones with an Indigenous Lipase Activity Agus Hery Susanto; Hendro Pramono; Puji Lestari
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 14, No 3 (2009): October 2009
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v14i3.2577

Penelitian ini bertujuan untuk mengonstruksi perpustakaan metagenom tanah dari sekitar lokasi industri pengolahan minyak kelapa di Kabupaten Banyumas, Jawa Tengah, dalam upaya mendapatkan klon rekombinan dengan aktivitas lipase indigenuos. Penelitian dilakukan di Laboratorium Genetika, Fakultas Biologi, Universitas Jenderal Soedirman mulai bulan Mei hingga Desember 2006. Secara umum tahapan penelitian terdiri atas ekstraksi dan pemurnian DNA tanah, isolasi pUC19, pemotongan DNA tanah, pemotongan dan defosforilasi pUC19, ligasi fragmen-fragmen DNA tanah ke dalam pUC19 untuk menghasilkan molekul DNA rekombinan, dan transformasi sel inang E. coli JM109 menggunakan molekul DNA rekombinan yang diperoleh untuk mengonstruksi perpustakaan metagenom tanah. Pemotongan DNA tanah menghasilkan fragmen-fragmen yang sebagian besar berukuran lebih kurang 5 kb sehingga gen lipase dimungkinkan untuk dibawa di dalamnya. Transformasi sel inang E. coli JM109 memperlihatkan efisiensi 1.7 x 105 cfu/μg plasmid. Di antara koloni-koloni yang diperoleh, terdapat 102 koloni berwarna putih, yang menunjukkan keberadaan molekul DNA rekombinan. Koloni putih ini dapat digunakan sebagai materi untuk skrining klon rekombinan dengan aktivitas lipase.

Genetic Diversity Among Three Cultivars Of Peanut (Arachis hypogaea L.) Based On Rapd Markers Suryadi Suryadi; Alice Yuniaty; Agus Hery Susanto
BioEksakta : Jurnal Ilmiah Biologi Unsoed Vol 1 No 2 (2019): BioEksakta
Publisher : Fakultas Biologi Universitas Jenderal Soedirman

Peanut (Arachis hypogea) is a typical plant species of tropical regions that has high economic value. The plantation is widely spread over many areas and the production is being pushed to meet the increasing demand. Peanut breeding program is aimed to improve genetic quality, mainly with resepct of production and thus information on genetic diversity is necessary as a basis for consideration in breeding, management and sustainable utilization. One approach to analyse genetic diversity of peanut is by using molecular markers. Random Amplified Polymorphic DNA (RAPD) is a widely used molecular marker for genetic diversity analysis. Therefore, the aim of this study was to assess genetic diversity of peanut cultivars, i.e. Jerapah, Kancil, and Hypoma 2, based on RAPD markers. The study was conducted in a survey method, in which three individuals of each cultivar were analyzed using PCR-RAPD technique employing twelve primers, i.e. OPA-1, OPA-2, OPA-9, OPA-13, OPB-2, OPB-3, OPB-4, OPB-5, OPB-7, OPB-11, OPB-12 and OPJ-07. Data analysis based on morphological data is also included. Molecular analysis revealed that only 7.55% polymorphic band was obtained, while most of the bands were monomorphic, indicating very low variation among the cultivars. The phenogram that constructed based on literature showed that Kancil was closer to Jerapah cultivar, while RAPD-based dendogram showed that Hypoma 2 was closer to Kancil cultivar.

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