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Molecular Phylogeny of Giant Clams Based on Mitochondrial DNA Cytochrome C Oxidase I Gene AGUS NURYANTO; DEDY DURYADI; DEDI SOEDHARMA; DIETMAR BLOHM
HAYATI Journal of Biosciences Vol. 14 No. 4 (2007): December 2007
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (37.454 KB) | DOI: 10.4308/hjb.14.4.162

Abstract

There is an uncertainty for the relationships among giant clam species of Tridacninae, in particular among species belongs to subgenus Chametrachea i.e. Tridacna crocea, T. maxima, and T. squamosa based on different genetic markers. This study examined the relationships among three species within subgenus Chametrachea compared to the previous studies. Neighbour Joining, Maximum Parsimony and Maximum Likelihood tree were constructed based on 455 bp of the mitochondrial DNA cytochrome c oxidase I gene from T. crocea, T. squamosa, T. maxima, T. gigas, and several sequences derived from Genbank for the outgroups. The results showed that giant clams formed a monophyletic group. Within Tridacna group, T. crocea was more closely related to T. squamosa than to T. maxima and they formed a monophyletic group. T. crocea and T. squamosa were sister taxa and sister group to T. maxima and T. gigas. Close affinity between T. crocea and T. squamosa was also supported by high similarity on nucleotide level (94.30%) and concordant with the results of the previous studies using mitochondrial 16S rRNA and nuclear 18S rRNA. Key words: phylogenetic relationships, Chametrachea, cytochrome c oxidase I
KRITIK BUDAYA AKADEMIK DI PENDIDIKAN TINGGI Agus Nuryanto
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
MORFOLOGI KEPITING Albunea symmysta (ALBUNEIDAE:CRUSTACEAE) DARI PANTAI PARANGKUSUMO YOGYAKARTA Dyah Purry; Dian Bhagawati; Agus Nuryanto
BioEksakta : Jurnal Ilmiah Biologi Unsoed Vol 2 No 1 (2020): BioEksakta
Publisher : Fakultas Biologi Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (410.431 KB) | DOI: 10.20884/1.bioe.2020.2.1.1842

Abstract

Familia Albuneidae terdiri atas Sembilan Genus dan salah satunya yaitu Albunea. Distribusi Albunea di Indonesia telah dilaporkan oleh beberapa peneliti terdahulu, diantaranya terdapat di pesisir Cilacap, Kebumen, Yogyakarta, Aceh, dan Bengkulu. Berdasarkan hasil survei pendahuluan yang dilakukan di Pantai Parangkusumo Yogyakarta telah ditemukan kepiting yang memiliki morfologi hampir sama dengan dengan spesies Albunea symmysta yang pernah ditemukan sebelumnya di lokasi yang berbeda. Atas dasar hal tersebut maka telah dilakukan kajian untuk mengetahui kepastian nama spesiesnya. Penelitian ini bertujuan untuk mengidentifikasi kepiting Albunea yang dimiliki oleh yang berasal dari pantai Parangkusumo Yogyakarta serta untuk mengetahui semua karakter performa dan meristik milik kepiting Albunea yang berasal dari pantai Parangkusumo. Metode penelitian yang digunakan adalah survei dan pengambilan sampel secara purposive random sampling. Sampel dari pantai Parangkusumo diambil sebanyak dua kali dengan interval waktu dua minggu, pengambilan sampel dilakukan hingga memperoleh jumlah sampel sebanyak 60 ekor. Identifikasi dilakukan berdasarkan karakter morfologi, yang meliputi performa, morfometri dan meristik. Analisis data dilakukan secara deskriptif untuk performa dan meristik, sedangkan morfometrik dengan uji T. Berdasarkan pengamatan performa morfologi, meristik, hasil penelitian yang didapat yaitu kepiting Albunea yang diperoleh dari Parangkusumo Yogyakarta adalah spesies Albunea symmysta yang memiliki karakter karapas dengan bentuk hampir empat persegi panjang, memiliki antenula yang sangat panjang, karapas dengan permukaan rata, memiliki dactylus pertama subchelate, memiliki 9-12 buah duri anterolateral dan memiliki tujuh buah segmen flagella antena
Genetic Variability in the Indonesian Giant Clam (Tridacna crocea and Tridacna maxima) Populations: Implication for Mariculture and Restocking Program Agus Nuryanto; Dedy Duryadi
Majalah Ilmiah Biologi BIOSFERA: A Scientific Journal Vol 24, No 2 (2007)
Publisher : Fakultas Biologi | Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.mib.2007.24.2.154

Abstract

Tridacna crocea and T. maxima are relatively abundant in the Indonesian coral reef. These two species are, however, under high presure due to exploitation for food, industry, and aquarium trade.  It is, therefore, necessary to understand their biology, such as genetic variability within and between populations, before utilizing them for strain improvement and restocking, prior to the extinction of the populations of T. crocea and T. maxima.  Here we amplified a length of 456 bp of the mitochondrial DNA cytochrome c oxidase I gene from Tridacna crocea and of 484 bp from T. maxima to asses the genetic variability within and between populations of both species.  The results showed that both species have high genetic diversity and polymorphism within each local population. This provides a sufficient basis for selection of improved strain of T. crocea and T. maxima for mariculture. However, if the genetic variation led to genetic differentiation among populations due to the result of evolutionary adaptation, mixing genetically different populations may result in the break up of co-adaptation gene complexes.  This might result in the loss of the physiological capacities of the parental populations.
Variasi Sekuens Gen Mitokondrial Sitokrom C Oksidase I dari Siput Lola (Trochus niloticus) Agus Nuryanto; Dedy Duryadi Solihin
Majalah Ilmiah Biologi BIOSFERA: A Scientific Journal Vol 23, No 1 (2006)
Publisher : Fakultas Biologi | Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.mib.2006.23.1.143

Abstract

A study on sequence variation in the mitochondrial DNA of Trochus niloticus has been conducted. Polymerase chain reactions (PCR) technique was applied to amplify cytochrome c oxidase I gene of 533 bp and ABI 310 aotomatic DNA sequencer was used to sequence the PCR product.  This study was aimed to know the genetic variation of T. niloticus and the suitability of partial sequence of cytochrome c oxidase I gene as a molecular marker in the genetic study.  The results showed that from two T. niloticus specimens, 12 polymorphic sites were detected yielding 2 haplotypes. This indicated a highly genetic variation in thecytochrome c oxidase I (COI) gene of T niloticus.  In addition, cytochrome c oxidase I gene was proved to be a suitable marker for the genetics studies of various species of organisms.
Molecular Identification of Color Variants of Procambarus clarkii Using the COI Gene for Taxonomic Validation Bhagawati, Dian; Husein Sastranegara, Muhammad; Agus Nuryanto; Anastasia Endang Pulungsari; Elly Tuti Winarni; Atang; Hanan Hassan Alsheikh Mahmoud
Advance Sustainable Science Engineering and Technology Vol. 7 No. 2 (2025): February-April
Publisher : Science and Technology Research Centre Universitas PGRI Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26877/hcaz9264

Abstract

This study addresses taxonomic uncertainty surrounding color variants of Procambarus clarkii in aquaculture and conservation contexts. We investigated whether commercially significant color morphs represent distinct subspecies or phenotypic variations of a single species. Using the cytochrome c oxidase subunit I (COI) gene as a molecular marker, we analyzed four color morphs (blue, white, orange, and brown) from aquaculture facilities in Banyumas Regency. DNA extraction, PCR amplification, and sequencing were performed on 20 specimens. Results showed high sequence homology (98.7-99.8%) across all variants, confirming they belong to a single species. Genetic distance analysis revealed minimal divergence (0.2-1.3%), insufficient for subspecies classification. Phylogenetic reconstruction demonstrated specimens clustered by genetic similarity rather than color or geographic origin, indicating coloration results from genetic mutations rather than environmental adaptations. This COI-based approach provides a molecular framework for taxonomic classification of P. clarkii varieties, with implications for breeding programs, variety certification, and management of this economically important yet potentially invasive species.