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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Jurnal Natur Indonesia Biosaintifika: Journal of Biology & Biology Education The Journal of Society and Media BioEksakta : Jurnal Ilmiah Biologi Unsoed Molekul: Jurnal Ilmiah Kimia Biosaintifika: Journal of Biology & Biology Education
Agus Nuryanto
Faculty of Biology, Universitas Jenderal Soedirman, Indonesia
Religion Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Environmental Science Immunology & microbiology Languange, Linguistic, Communication & Media Materials Science & Nanotechnology Social Sciences Veterinary

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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

Abstract

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 –  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 – 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 – rbcL sequences.
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.
Molecular Characteristics of Batanghari, Tambago, Orange, and Mandiangin Giant Gourami Strains Nuryanto, Agus; Pulungsari, Anatasia Endang
Biosaintifika: Journal of Biology & Biology Education Vol 9, No 3 (2017): December 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.v9i3.12097

Abstract

Morphological variations among geographic and can be identified as different species. However, a lot of studies proved that morphological variations are also common in conspecific individuals. Therefore, precise identification using additional characters is vital, such as using a molecular marker. Here, we characterized Batanghari, Tambago, Orange, and Mandiangin gourami strains using the cytochrome b gene to evaluate their taxonomic status. Partial sequences of cytochrome b gene were sequenced for 40 individuals. Taxonomic status was checked for giant gourami sequences available in GenBank. Kimura 2-Parameter genetic distances were calculated in MEGA6 software. Haplotype and nucleotide diversity within population and ?st-value among populations were estimated in Arlequin software. Phylogenetic relationship was reconstructed using the neighbor-joining method in MEGA6 software based on Kimura 2-parameter model with 1000 pseudobootstraps. Taxonomic identification results in 99% sequences homology to Osphronemus goramy sequences (accession number KU984978.1 and AY763768.1), means that all strains belong to single species. Low genetic distances, medium haplotype and low-level nucleotide diversity were observed among strains. Pairwise ?st-comparison indicates no genetic differences among Sumatera strain, whereas strong genetic structures observed between Sumatera and Mandiangin strains. The phylogenetic tree showed that Mandiangin formed separate subclades from other strains with bootstraps value of 100%. This finding has important implication for breeding sciences and efforts.
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.
Phylogenetic Relationships among Ornamental Achanturid Fish from Ujunggenteng and Taman Manalusu, West Java Nabila, Afra; Nuryanto, Agus; Prabowo, Romanus Edy; Bhagawati, Dian; Kusbiyanto, Kusbiyanto
Biosaintifika: Journal of Biology & Biology Education Vol 11, No 3 (2019): Article-in-Press
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.v11i3.20671

Abstract

Acanthuridae is a marine fish family with some members are known as ornamental species. Previous studies has been reported the diversity of Acanthuridae. However, there was no study on the phylogenetic relationship of the Acanthuridae from Ujunggenteng and Taman Manalusu southern coast of West Java. The purpose of this study was to provide information about the phylogenetic relationship among ornamental fishes under the Acanthuridae family of Ujunggenteng Beach Sukabumi and Taman Manalusu Beach Garut, West Java. The phylogenetic tree was reconstructed based on morphological characters using maximum parsimony algorithm in software PAUP with 1000 pseudoreplicates and with Halichoeres marginatus selected as an outgroup species. The phylogenetic tree had a consistency index of 0.6429. The value means that the tree was highly reliable due to its low homoplasy. Acanthuridae formed a monophyletic clade compared to the outgroup species by having seven synapomorphic characters. Acanthurid clade was divided into two subclades at generic levels by nine derived characters; three apomorphic characters in Acanthurus and six apomorphic characters in Naso. The tree indicates that Naso brevirostris and Naso lituratus represents basal group, while all species within genus Acanthurus are the most advanced species.  This study is the first to provide the data about the evolutionary relationship of ornamental acanthurid fish from the southern coast of West Java. Data on closely related species is one of the essential scientific basis on making policies regarding the sustainable use of those closely related species.
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

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (146.477 KB) | DOI: 10.31258/jnat.14.1.47-51

Abstract

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.
KRITIK BUDAYA AKADEMIK DI PENDIDIKAN TINGGI Nuryanto, Agus
The Journal of Society and Media Vol 1, No 1 (2017): education in Society & media
Publisher : Department of Social Science, Faculty of Social Science &Law, Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jsm.v1n1.p35-42

Abstract

AbstrakPendidikan menjadi arena politis dan tidak netral. Karena dari rahim pendidikan akan lahir manusia-manusia idealis atau pragmatis, humanis atau dehumanis, toleran atau intoleran, berintegritas atau krisis integritas, individualis atau sosialis. Pendidikan memiliki peran yang sangat signifikan dalam melahirkan dan membentuk pribadi-pribadi tertentu. Semuanya tergantung pada dasar filosofi dan nilai di atas mana institusi pendidikan dibangun serta praksis pendidikan apa yang dikembangkan. Iklim sosial yang dibangun di kampus, merupakan bagian dari kurikulum tersembunyi (hidden curriculum) yang juga berkontribusi dalam membentuk kepribadian sivitas akademika. Saat ini yang tengah terjadi adalah pertarungan kepentingan antar ideologi dalam pendidikan tinggi, yaitu kontestasi antara pendidikan tinggi yang berbasiskan pada nilai-nilai akademik (academic values) yang cenderung etis-utopis dan yang berbasiskan pada nilai-nilai korporasi (corporate values) yang cenderung praktis-pragmatis. Tarik menarik kepentingan ideologi dalam pendidikan sesungguhnya merupakan tarik menarik kepentingan antara idealisme dan pragmatisme.   Seharusnya pendidikan tinggi menjadi bagian dari institusi sosial yang ikut mendorong terbentuknya masyarakat etis-demokratis. Ketika pendidikan tinggi kehilangan nalar kritisnya maka ia tidak mampu menjadi pencerah bagi masyarakat, atau menjadi agent of social change. Tetapi sebaliknya, pendidikan tinggi semakin jauh dari realitas masyarakat.Kata kunci: kritik, perguruan tinggi, budaya akademikAbstractEducation becomes political arena and it is not neutral. Because of education womb will create idealistic or pragmatic people, humanist or dehumanis, tolerant or intolerant, integrity or the critical integrity, and individualist or socialist. Education has a very significant role in the birth and form certain individuals. All of it depends on the basic philosophy and values on which educational institutions are built and what educational praxis developed. A social climate that is built on the campus, is part of the hidden curriculum which also contribute in shaping the personality of academic society. Current phenomenon shows that there is a conflict of interests between ideology in higher education, the contestation between higher education based on academic values (academic values) that tend ethical-utopian and based on the values of the corporation (corporate values) which tends practically. Ideology of interests in education is real conflict of the interests between idealism and pragmatism. Higher education is supposed to be part of the social institutions that contributed to the formation of ethical-democratic society. When higher education loses its critical reason, it was not able to be a lightening for the community, or become agents of social change. But on the contrary, higher education is getting away from the reality in particular society.Keywords: critic, higher education, academic culture
MOLECULAR BARCODING REVEAL THE EXISTENCE OF MOLE CRABS EMERITA EMERITUS IN NORTH COAST OF CENTRAL JAVA Bhagawati, Dian; Winarni, Elly Tuti; Nuryanto, Agus
Biosaintifika: Journal of Biology & Biology Education Vol 12, No 1 (2020): April 2020
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 (392.708 KB) | DOI: 10.15294/biosaintifika.v12i1.20497

Abstract

The existence of mole crabs had been reported from the southern coast of Central Java. However, no mole crab data was available from the northern coast Central Java.  This study aimed to figure out the existence of mole crabs in the northern coast of Central Java as revealed from the cytochrome c oxidase 1 (COI) barcoding. Mole crabs samples collected in Sendang Sikucing Beach Kendal. Taxonomic status of the samples was inferred from sequences similarity test using basic local alignment search tool to conspecific sequence deposited in GenBank. Pairwise genetic distances were calculated based on the Kimura 2-parameter model. A phylogenetic tree had reconstructed in molecular evolution genetic analysis (MEGA) software based on neighbor-joining algorithm. Branching reliability was obtained from 1000 bootstraps replication while branching polarity was obtained from the out-group comparison. The mole crab samples from the northern coast of Central Java had unambiguously identified as Emerita emeritus based on high sequences similarities (98.27%-99.70%), low genetic distances (0.002-0.005), and their monophyly with Emerita emeritus (KR047035) in GenBank. Pairwise analysis among each possibility pair of samples had genetic distances ranged between 0.000 and 0.005, indicated that all sample belong to single species. The data provide the first record of the existence of Emerita emeritus in the northern coast of Central Java. Our data on the existence of E. emeritus in the northern coast of Central Java is among essentials information as a scientific basis in creating policy for the management of sustainable use of the mole crabs in the areas.
Morphological Variation of Blue Panchax (Aplocheilus panchax) Lives in Different Habitat Assessed Using Truss Morphometric Mustikasari, Diah; Suryaningsih, Suhestri; Nuryanto, Agus
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.v12i3.26593

Abstract

Blue panchax (Aplocheilus panchax Hamilton, 1822) lives in broad ranges of habitat from open waters to closed waters, including at ex-tin mining pits in Bangka Island, Indonesia. Variable habitats might cause morphological variations due to different ecological factors. This study aimed to assess the morphological variation of blue panchax collected from different habitats using truss morphometric characters. Fish samples (70 individuals) were collected from abandoned ex-tin mining pits of different ages and a river in Bangka Island. Twenty-nine truss characters were analyzed using the Kruskal-Wallis test and post hoc with Dunn’s test . The results showed that almost all of the body parts of blue panchax found in ex-tin mining pits and rivers were significantly different (p-value < 0.05), except some truss characters of caudal peduncle. The post hoc of Dunn’s test showed a positive correlation between habitats and truss characters (adj. sig < 0.05). Some truss characters of killifish were different between ex-tin mining pits with different ages chronosequence, and some other characters were different between pits and river.  This study provides the first data about the morphological variation of blue panchax in ex-tin mining pits of different ages. The data is valuable as a scientific basis of further utilization of ex-tin mining pits in the areas.
Co-Authors Abdalla Mohammed, Mohammed AGUS HERY SUSANTO Ali Suman Andareswari, Novi BUDI SETIADI DARYONO Diah Mustikasari Dwi Nugroho Wibowo Elly Tuti Winarni Endang Hilmi Fathurahman, Fabian Rizky Ghifari, Muhammad Iqbal Hendro Pramono Kusbiyanto Kusbiyanto, Kusbiyanto Mahmoud, Hanan Hassan Alsheikh Moh. Husein Sastranegara Nabila, Afra Nael Huda Qonita Norman Arie Prayogo, Norman Arie Petrus Hary Tjahja Soedibja Pulungsari, Anastasia Endang Pulungsari, Anatasia Endang Purnama Sukardi Purry, Dyah Rofiqoh, Aswi Andriasari Romanus Edy Prabowo Rosita, Rita Eka Suryaningsih, Suhestri Syakuri, Hamdan Tuti Winarni, Elly