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All Journal Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Biosaintifika: Journal of Biology & Biology Education
Hendro Pramono
Faculty Of Biology, Universitas Jenderal Soedirman, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology

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Molecular Identification of Fish Larvae from East Plawangan of Segara Anakan, Cilacap, Central Java, Indonesia Nuryanto, Agus; Pramono, Hendro; Sastranegara, Moh Husein
Biosaintifika: Journal of Biology & Biology Education Vol 9, No 1 (2017): April 2017
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.v9i1.9191

Abstract

Correct identification of fish larvae from East Plawangan is very difficult to be done due to undefined of their morphology, while correct name is an important information for management of that area as spawning and nersery ground. Therefore, so far no scientific report on what species that utilize East Plawangan as their spawning and nursery ground. Cytochrome c oxidase 1 gene provide a precise tool for correct larvae identification. This study aims to test the accuracy of the cytochrome c oxidase 1 gene on fish larvae identification. The COI gene were amplified and sequenced. The homology of sequences were checked using Basic Local Alignment Search Tool (BLAST). Genetic distances were calculated with the help of MEGA 6 software. Taxonomic tree was reconstructed using neighbor-joining and maximum parsimony methods with 1000 bootstraps repeats. A sum of 24 morphotypes were identified, indicating high diversity of fish that utilize East Plawangan as their spawning and nursery ground. BLAST result showed that seven morphotypes were convincingly identified into species level, while three remaining morphotypes could only be identified at generic level. Taxonomic tree shows clear discrimination among morphotypes. This proved that cytochrome c oxidase 1 gene showed high accuracy on larval species discrimination.
Genetic Variation in Cytochrome b-Hinf1 and -Alu1 Gene Correlated to Body Size in Soang Gourami (Osphronemus goramy) from Single Spawning Kusbiyanto, Kusbiyanto; Soedibja, Petrus Hary Tjahja; Nuryanto, Agus; Qonita, Nael Huda; Pramono, Hendro
Biosaintifika: Journal of Biology & Biology Education Vol 9, No 2 (2017): August 2017
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.v9i2.9301

Abstract

Soang gourami fingerling shows variable body sizes eventhough resulted from single spawning. Differences in body sizes among individuals is assumed to be correlated to their genetic component which can be studied using cytochrome b gene PCR-RFLP marker. This study aimed to determine specific PCR-RFLP marker among different sizes of soang gourami collected from single spawning. Genomic DNA was isolated using Chelex method. Cytochrome b gene were amplified and digested using four restriction enzymes. Specific markers were analyzed descriptivelly based on DNA band pattern appear in agarose gel. The result showed that PCR-RFLP markers of Cytochrome b-HinfI of 315 bp, and 210 bp, and also Cytochrome b-AluI of 334 bp and 189 bp are specific markers for large individuals, whereas small individuals are characterized by having Cytochrome b- HinfI 366 bp, and 159 bp and Cytochrome b-AluI 525 bp fragments. It is observed that genetic variation of Cytochrome b-HinfI and -AluI markers are possitively correlated to body size in soang gourami fingerling. Therefore, both cytochrome b-HinfI and -AluI gene can be reffered as specific markers to differentiate among different sizes of soang gourami strain fingerling from single spawning. This result proved that genetic divergences among individuals can be related with certain quantitative characters, such size related. Therefore our study can contribute on fisheries development, especially by providing new technique for fingerling selection to obtain high quality fingerling and also provide new insight the application of molecular technique in fisheries.
Antibacterial Activity of Streptomyces SAE4034 Isolated from Segara Anakan Mangrove Rhizosphere against Antibiotic Resistant Bacteria Ryandini, Dini; Pramono, Hendro; Sukanto, Sukanto
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.v10i1.12896

Abstract

Actinomycetes SAE4034 isolates was isolated from Rhizophora apiculata rhizosphere mud showed some antibacterial properties. The antibacterial ability of this isolate has not been tested on antibiotic resistant bacterial pathogens. However, there was no research has been reported regarding actinomycetes from Segara Anakan mangrove area resulting compounds inhibit the growth of antibiotics-resistant bacteria. Therefore, it is important to investigate its capability against antibiotics resistant bacteria or multi drug resistant bacteria (MDR bacteria). The research aimed to know the ability of actinomycetes SAE4034 in inhibit MDR bacteria and to identify the species profiles. The research methods included isolate characterization involving morphology, physiology/enzymatic and molecular properties. MDR bacterial inhibition assay, antibacterial compound extraction and antibacterial compound test using thin layer chromatography (TLC) method, observation of morphological and biochemical properties, DNA isolation, amplification and analysis of 16SrRNA sequence, and phylogeny tree analysis. The methods of this study included MDR anti-bacterial assay and antibacterial compound test. Subsequent step was isolate characterization including observation of morphological and physiological / enzymatic properties, and 16S rRNA gene sequence. The results showed that culture extract was able to inhibit the growth of MDR bacteria i.e. Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus sp., but no inhibition to Enterobacter cloacae. The bioactive compound showed 4 spots with Rf values of 0.36; 0.45; 0.54; and 0.6. Based on morphology, physiology / enzymatic and 16S rRNA gene sequences characteristics, actinomycetes SAE4034 isolate is Streptomyces sp. This research showed new Streptomyces strain that serves as a source of MDR antibacterial compounds and useful in development of antibiotic for combating infectious diseases caused by MDR bacteria
Potential of Chemolitotrophic Bacteria From Gold Mining Area in Sulfur Oxidation Process Fitriyani, Nur Lu'lu; Irianto, Agus; Pramono, Hendro
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 3 (2018): December 2018
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (251.663 KB) | DOI: 10.15294/biosaintifika.v10i3.12544

Abstract

Gold in nature is covered by rocks which contain sulfide minerals such as pyrite, chalcopyrite, arsenopyrite, and others sulfide minerals. Chemolithotrophic bacteria have the ability to oxidize the sulfur compounds and can be used in the process of releasing gold from carrier rocks which contain sulfide minerals. This research aimed to explore and identify the chemolithotrophic bacteria from gold mining areas as well as determine their potential for sulfur oxidation. The methods used in this study were exploring the potential of bacteria in sulfur oxidation and describing the variety of bacteria that were isolated from gold mining areas by 16s rRNA identification. The results showed that there were six isolates from isolation with Starkey solid medium, i.e. Bl-1, B1-2, B1-3, B1-4, B1-5 and B1-6 that were similar to Paenibacillus sp., Enterobacter ludwigiis train E8-13, uncultured Burkholderia sp., Uncultured bacterium clone N4.5, Bacillus subtilis strain CICC 10023, and Bacterium enrichment culture clone 02 respectively. The B1-3 isolate showed the highest increase of sulfate compound in the medium (8.04 % at 649.55 ppm). This indigenous bacteria will be able to be used to release gold from rock which contains sulfide minerals and reduce the use of hazardous chemicals commonly used in gold mining.
Barcoding of Fin Clip Samples Revealed High Exploitation of Plectropomus leopardus in Spermonde Archipelago Nuryanto, Agus; Pramono, Hendro; Kusbiyanto, Kusbiyanto; Ghifari, Muhammad Iqbal; Andareswari, Novi
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 3 (2018): December 2018
Publisher : Department of Biology, Faculty of Mathematics and Sciences, Semarang State University . Ro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (290.053 KB) | DOI: 10.15294/biosaintifika.v10i3.16142

Abstract

Spermonde Archipelago in South Sulawesi is among groupers sources in Indonesia for International Marine Live Trade. It was not much known which species are mostly exploited in those areas during the study because only fin clip samples could be obtained. Here we performed DNA forensic analysis to groupers fin clips collected from Spermonde Archipelago using barcode marker to know what species were exploited and which ones was the most exploited species. A total of 110 fin clip samples were obtained during the field trips. Sequencing of the cytochrome c oxidase 1 gene was successful for only 36 samples. Species determination was based on sequences similarity to conspecific sequence available in barcoding of life database (BOLD). BOLD similarity test placed the 36 fin clip samples into four different species, namely Cromileptes altivelis, Epinephelus ongus, Plectropomus leopardus, and Plectropomus maculatus. The K-2P taxonomic tree showed clear separation among species which was supported by high K2P genetic distances among species. Most of fin clips were identified as Plectropomus leopardus indicates that this species was the most exploited in Spermonde Archipelago. This proved that molecular identification not only can be used to biodiversity study in certain area but also in forensic analysis of a threatened wildlife. This study has important contribution for conservation effort of those groupers species, especially P. leopradus and provides new approach for taxonomist and conservation managers to identify samples, especially when only incomplete specimens are available.
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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (350.658 KB) | DOI: 10.24002/biota.v14i3.2577

Abstract

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.
Bifidobacterium longum, a Predominant Bifidobacterium in Early-life Infant Potentially Used as Probiotic Kusharyati, Dyah Fitri; Rovik, Anwar; Ryandini, Dini; Pramono, Hendro
Biosaintifika: Journal of Biology & Biology Education Vol 12, No 3 (2020): December 2020
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.v12i3.25895

Abstract

In early life, Bifidobacteria are reported as dominant bacteria in the human digestive tract. Bifidobacterium is potential as a probiotic. The probiotic property of Bifidobacterium is strain-specific. This study aimed to identify the Bifidobacterium (isolated from less than one-month-old healthy infant stool that potentially used as probiotic) based on the 16S rRNA gene and determining their similarities among Bifidobacteria. The probiotic-potentially Bifidobacterium was re-characterized by performing a Gram’s staining and catalase test. The DNA extraction process was followed by the 16S rRNA amplification using 27F-1492R primers. Sequence similarity was checked by using the BLAST program in the GenBank. The phylogenetic tree was constructed by using a neighbor-joining (NJ) method within the MEGA version 7.0 package. The 16S rRNA gene was presented at 1,500 bp length. Bifidobacterium strains have a 91.14-94.26 % sequence similarity to B. longum subsp. longum strain CCUG30698 which is considered as insufficient for species and genus identifications. However, those isolates could be assigned in a phylogenetic position. This present study suggested the B. longum as the dominant strain of Bifidobacterium in the gut of early-life infants which has potential as a probiotic and is considered as an ideal probiotic for human consumption. This study is useful as basic information for other related research, as well as its application in industrial or community service fields.
Barcoding of Fin Clip Samples Revealed High Exploitation of Plectropomus leopardus in Spermonde Archipelago Agus Nuryanto; Hendro Pramono; Kusbiyanto Kusbiyanto; Muhammad Iqbal Ghifari; Novi Andareswari
Biosaintifika: Journal of Biology & Biology Education Vol 10, No 3 (2018): December 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.v10i3.16142

Abstract

Spermonde Archipelago in South Sulawesi is among groupers sources in Indonesia for International Marine Live Trade. It was not much known which species are mostly exploited in those areas during the study because only fin clip samples could be obtained. Here we performed DNA forensic analysis to groupers fin clips collected from Spermonde Archipelago using barcode marker to know what species were exploited and which ones was the most exploited species. A total of 110 fin clip samples were obtained during the field trips. Sequencing of the cytochrome c oxidase 1 gene was successful for only 36 samples. Species determination was based on sequences similarity to conspecific sequence available in barcoding of life database (BOLD). BOLD similarity test placed the 36 fin clip samples into four different species, namely Cromileptes altivelis, Epinephelus ongus, Plectropomus leopardus, and Plectropomus maculatus. The K-2P taxonomic tree showed clear separation among species which was supported by high K2P genetic distances among species. Most of fin clips were identified as Plectropomus leopardus indicates that this species was the most exploited in Spermonde Archipelago. This proved that molecular identification not only can be used to biodiversity study in certain area but also in forensic analysis of a threatened wildlife. This study has important contribution for conservation effort of those groupers species, especially P. leopradus and provides new approach for taxonomist and conservation managers to identify samples, especially when only incomplete specimens are available.
Genetic Variation in Cytochrome b-Hinf1 and -Alu1 Gene Correlated to Body Size in Soang Gourami (Osphronemus goramy) from Single Spawning Agus Nuryanto; Nael Huda Qonita; Hendro Pramono; Kusbiyanto Kusbiyanto; Petrus Hary Tjahja Soedibja
Biosaintifika: Journal of Biology & Biology Education Vol 9, No 2 (2017): August 2017
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.v9i2.9301

Abstract

Soang gourami fingerling shows variable body sizes eventhough resulted from single spawning. Differences in body sizes among individuals is assumed to be correlated to their genetic component which can be studied using cytochrome b gene PCR-RFLP marker. This study aimed to determine specific PCR-RFLP marker among different sizes of soang gourami collected from single spawning. Genomic DNA was isolated using Chelex method. Cytochrome b gene were amplified and digested using four restriction enzymes. Specific markers were analyzed descriptivelly based on DNA band pattern appear in agarose gel. The result showed that PCR-RFLP markers of Cytochrome b-HinfI of 315 bp, and 210 bp, and also Cytochrome b-AluI of 334 bp and 189 bp are specific markers for large individuals, whereas small individuals are characterized by having Cytochrome b- HinfI 366 bp, and 159 bp and Cytochrome b-AluI 525 bp fragments. It is observed that genetic variation of Cytochrome b-HinfI and -AluI markers are possitively correlated to body size in soang gourami fingerling. Therefore, both cytochrome b-HinfI and -AluI gene can be reffered as specific markers to differentiate among different sizes of soang gourami strain fingerling from single spawning. This result proved that genetic divergences among individuals can be related with certain quantitative characters, such size related. Therefore our study can contribute on fisheries development, especially by providing new technique for fingerling selection to obtain high quality fingerling and also provide new insight the application of molecular technique in fisheries. 
Molecular Identification of Fish Larvae from East Plawangan of Segara Anakan, Cilacap, Central Java, Indonesia Agus Nuryanto; Hendro Pramono; Moh Husein Sastranegara
Biosaintifika: Journal of Biology & Biology Education Vol 9, No 1 (2017): April 2017
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.v9i1.9191

Abstract

Correct identification of fish larvae from East Plawangan is very difficult to be done due to undefined of their morphology, while correct name is an important information for management of that area as spawning and nersery ground. Therefore, so far no scientific report on what species that utilize East Plawangan as their spawning and nursery ground. Cytochrome c oxidase 1 gene provide a precise tool for correct larvae identification. This study aims to test the accuracy of the cytochrome c oxidase 1 gene on fish larvae identification. The COI gene were amplified and sequenced. The homology of sequences were checked using Basic Local Alignment Search Tool (BLAST). Genetic distances were calculated with the help of MEGA 6 software. Taxonomic tree was reconstructed using neighbor-joining and maximum parsimony methods with 1000 bootstraps repeats. A sum of 24 morphotypes were identified, indicating high diversity of fish that utilize East Plawangan as their spawning and nursery ground. BLAST result showed that seven morphotypes were convincingly identified into species level, while three remaining morphotypes could only be identified at generic level. Taxonomic tree shows clear discrimination among morphotypes. This proved that cytochrome c oxidase 1 gene showed high accuracy on larval species discrimination.
Co-Authors A.A. Ketut Agung Cahyawan W AGUS HERY SUSANTO Agus Irianto Agus Nuryanto Agus Nuryanto Andareswari, Novi Dini Ryandini Dyah Fitri Kusharyati Fitriyani, Nur Lu'lu Ghifari, Muhammad Iqbal Kusbiyanto Kusbiyanto Kusbiyanto Kusbiyanto, Kusbiyanto Moh Husein Sastranegara Moh. Husein Sastranegara Muhammad Iqbal Ghifari Nael Huda Qonita Nael Huda Qonita Novi Andareswari Petrus Hary Tjahja Soedibja Petrus Hary Tjahja Soedibja Rovik, Anwar Sukanto Sukanto