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All Journal Jurnal Biologi Udayana ILMU KELAUTAN: Indonesian Journal of Marine Sciences Biotropika Current Biochemistry Journal of Innovation and Applied Technology The Journal of Pure and Applied Chemistry Research Jurnal Kelautan Tropis Jurnal Sumberdaya Akuatik Indopasifik JFMR (Journal of Fisheries and Marine Research) Indonesian Journal of Chemistry Jurnal Perikanan Universitas Gadjah Mada Jurnal Iktiologi Indonesia (Indonesian Journal of Ichthyology) Musamus Fisheries and Marine Journal Tomini Journal of Aquatic Science Bioscientist : Jurnal Ilmiah Biologi Nekton ACROPORA: Jurnal Ilmu Kelautan dan Perikanan Papua
Dailami, Muhammad
Aquaculture Study Program, Faculty Of Fisheries And Marine Science, Brawijaya University, Veteran Street, Malang 65145, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Environmental Science Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Social Sciences

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Analisis Pola Pertumbuhan dan Pendekatan DNA Barcoding untuk Identifikasi Turbo stenogyrus P. Fischer, 1873 (Mollusca: Gastropoda) Dandi Saleky; Simon P.O Leatemia; Thomas F. Pattiasina; Isma Isma; Rosa D. Pangaribuan; Marius A. Welliken; Edy H.P. Melmambessy; Muhammad Dailami
Biotropika: Journal of Tropical Biology Vol 8, No 2 (2020)
Publisher : University of Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2020.008.02.03

Abstract

Pengelolaan dan pelestarian keanekaragaman hayati berawal dari pengetahuan tentang ketersediaan sumberdaya, identifikasi, dan sistematika spesies. Banyaknya spesies Turbinidae dengan berbagai bentuk morfologi dan transformasi bentuk menjadikan identifikasi dengan gen COI sangat penting dalam mempercepat pengungkapan identitas spesies. Penelitian ini dilakukan dengan tujuan menganalisis pola pertumbuhan dan mengidentifikasi gastopoda Turbinidae dengan pendekatan DNA barcode. Hasil identifikasi berdasarkan karakter morfologi menunjukkan bahwa genus Turbo yang diamati adalah dari spesies Turbo stenogyrus. Analisis pola pertumbuhan menunjukkan bahwa pola pertumbuhan T. stenogyrus adalah allometrik negatif. Amplifikasi DNA dengan gen COI menghasilkan panjang sekuen DNA 650 bp dengan hasil identifikasi sesuai dengan pengamatan morfologi yaitu Turbo stenogyrus. Berdasarkan analisis filogenetik dan jarak genetik, sekuen DNA yang dianalisis membentuk clade yang sama dengan spesies Turbo stenogyrus dengan jarak genetik terdekat 4,2%. Analisis genetik melalui gen COI sangat baik dan memberi kemudahan dalam identifikasi spesies gastropoda
Phylogenetic Analysis of Cytochrome Oxidase I from Buduk Toads Duttaphrynus melanostictus and Phrynoidis asper from Bogor Muhammad Dailami; I Made Artika; Mirza Dikari Kusrini; Dodi Safari
Current Biochemistry Vol. 3 No. 2 (2016)
Publisher : IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Indonesia have high diversity of Amphibians. Amphibians have an important role in ecosystem and produce many bioactive peptides. However, the genetic information of amphibians from Indonesia is very limited, especially Duttaphrynus melanostictus and Phrynoidis asper. The aims of this study are to determine the nucleotide sequence of cytochrome oxidase I (COI) from D. melanostictus and P. asper, to analyze their genetic diversity and their phylogenetic relationship. A total 668 base pairs of COI gene fragment were successfully amplified and their nucleotide sequence determined. P. asper (5 haplotypes) samples group have high haplotype diversity compared to D. melanostictus (1 haplotype). The results of Basic Local Alignment Search Tools (BLAST) to the NCBI and BOLD database, showed 99 % - 100 % identity to sequence of D. melanostictus. For the sequence of P. asper showed 99.23 % identity to sequence P. asper in BOLD database. There was no sequence of COI gene of P. asper in NCBI database. Genetic relationship among species in family Bufonidae, indicated that D. melanostictus has closer relation to P. asper than to another species, inspite of their pharapyletic characteristic. For intern species relationship of D. melanostictus, the data showed that D. melanostictus from Bogor have closer relationship to D. melanostictus from India than D. melanostictus from China.
Improvement Of Teaching Material And Capacity Building On Laboratory Of Aquaculture, Fish Disease Division, Faculty Of Fisheries And Marine Science, Universitas Brawijaya Maftuch Maftuch; Sri Andayani; Yenny Risjani; Muhammad Musa; Asus Maizar Suryanto Hertika; Febriyani Eka Supriatin; Muhammad Dailami
Journal of Innovation and Applied Technology Vol 6, No 2 (2020)
Publisher : Lembaga Penelitian dan Pengabdian Kepada Masyarakat Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jiat.2020.006.02.15

Abstract

The laboratory is one of the effective learning places for students to develop scientific knowledge and skills. FPIK has 6 laboratories and 4 UPTs that can be used by students and lecturers. In practice, there are still limitations in this laboratory, including the malfunction of the equipment in the laboratory, due to damage to the equipment and the lack of mastery in operating the tools. This community service is intended to help solve problems that exist in the Aquaculture Laboratory of the Fish Disease Division of FPIK UB by increasing the capacity of human resources and laboratories in testing services. The form of service activities carried out includes organizing online workshops on fish hematology and histology testing, making learning videos for practicum analysis of fish hematology, developing collaboration networks with other laboratories, adding laboratory testing instruments and packages and cooperation in scientific publications.
Analysis and Prediction of some Histone-derived Antimicrobial Peptides from Toads Duttaphrynus melanostictus and Phyrinoidis asper Muhammad Dailami; I Made Artika; Mirza Dikari Kusrini
The Journal of Pure and Applied Chemistry Research Vol 5, No 2 (2016)
Publisher : Chemistry Department, The University of Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1579.558 KB) | DOI: 10.21776/ub.jpacr.2016.005.02.231

Abstract

Antimicrobial peptides in skin secretions of toads is a promising methods to combat a wide spectrum of bacteria. Histone H2A is a type of DNA-binding protein that acts as a precursor for several antimicrobial peptides. In toads (family Bufonidae) buforin I and buforin II are examples of antimicrobial peptides that derived from histone H2A. This study investigated the genetic diversity and phylogenetic analysis and in silico prediction of antimicrobial peptides derived from histone H2A of Duttaphrynus melanostictus and Phyrinoidis asper, which were collected from Bogor Agricultural University’s campus area. A new set of primers (Buf_fwd and Buf_rev) were designed by using PrimerBLAST, to amplify 393 nucleotides of the histone H2A gene that codes 131 amino acids. Haplotype diversity of both species are very low. Phylogenetic analysis shows the sample D. melanostictus and P. asper are separated to each other in two different clades. Several short predicted peptides from histone H2A show a potential as an antimicrobial peptides based on in silico prediction. Psychochemical characteristics and 3D structure of potent antimicrobial peptides are described.
DNA barcoding pada invertebrata laut Agus Mohammad Hikam; Nurul Jadid Mubarakati; Muhammad Dailami; Abdul Hamid A. Toha
Jurnal Biologi Udayana Vol 25 No 1 (2021): JURNAL BIOLOGI UDAYANA
Publisher : Program Studi Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Udayana

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24843/JBIOUNUD.2021.v25.i01.p06

Abstract

A large number of species of marine invertebrates that have similar morphology cause misidentification very possible. Molecular species identification is important in taxonomy study accurately. This study aims to determine the identity of Aquatic Papua marine invertebrates with DNA barcoding technique using markers COI gene (Cytochrome c oxidase I). The study identified 29 individuals of marine invertebrates, which came from sea cucumbers (6 samples), lobsters (6 samples), octopus (6 samples), chitons (5 samples), and sea urchins (6 samples). Molecular identification methods consist of DNA isolation, PCR COI gene fragments, sequencing, and DNA sequence analysis using bioinformatics software. The results showed that the sea cucumber came from the Bohadschia marmorata species, the lobster came from the Panulirus versicolor species, the octopus came from the Octopus cyanea species, the chiton came from the Ischnochitonaustralis species, and the sea urchins came from the Tripneustesgratilla species. The similarity of samples and references are in the range of 84.58 to 100.00%. The disparity index, genetic distance, and phylogenetic tree supported this result.
Cryptic Species from Biodiversity Hotspot: Estimation of Decapoda on Dead Coral Head Pocillopora in Raja Ampat Papua Eka Maya Kurniasih; Andrianus Sembiring; Ni Putu Dian Pertiwi; Aji Wahyu Anggoro; Ni Kadek Dita Cahyani; Muhammad Dailami; Ambariyanto Ambariyanto; Diah Permata Wijayanti; Christopher P. Meyer
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 25, No 1 (2020): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (404.259 KB) | DOI: 10.14710/ik.ijms.25.1.1-6

Abstract

Cryptic organisms that live within the interstices of reef habitats contribute significantly to coral reef biodiversity. One example of this cryptic biodiversity is the high abundance of decapods in dead coral heads that associated with various biota. However, this diversity poorly studied especially species identification and species richness. This study aims to estimate the decapods diversity in Raja Ampat, Papua, using Pocillopora dead coral head method as semi-quantitative sampling approach. Raja Ampat in Papua is chosen because it situated in the center of Coral Triangle marine hotspot. Data were collected from 10 dead coral heads of genus Pocillopora from 10-meter depth near the islands of Kri and Misool. This study observed a total of 205 individuals Decapoda from Kri Island and 672 Individual from Misool Islands. Species richness observation (Chao1 and ACE) of the total samples reports only 11 families of decapoda detected in this study. Rarefaction curve reach an asymptote after all after all ten dead coral were analyzed; indicating that additional sample collection would not change estimates of diversity found in this study. The Shannon-Wiener index diversity on the Kri Island showed lower diversity value (2.09) compared to Misool Island (2.18). In the future, this research can be used as a basis for understanding the diversity of coral reefs as well as for management and conservation of coral reef ecosystems.
Pola Pertumbuhan dan Identifikasi Genetik Turbo setosus Gmelin, 1791 [Turbinidae, Gastropoda] Dandi Saleky; Febriyani Eka Supriyatin; Muhammad Dailami
Jurnal Kelautan Tropis Vol 23, No 3 (2020): JURNAL KELAUTAN TROPIS
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jkt.v23i3.7514

Abstract

Morphological dan genetic identification is an essential part of biology and ecological study. Environmental degradation, physical and chemical facto in water, and utilization of gastropod by society will give impact in distribution pattern, population size, morphology and genetic characteristic of the snail. This research aims to analyze the growth pattern and molecular aspect of Turbo setosus. The variable that examined is total weight and length, and cytochrome oxidase subunit one gene sequence. The growth factor of T. setosus is negative allometric, which means weight growth is slower than the length growth. The total length of cytochrome oxidase subunit 1 of these samples were 650 base pairs. Based on the DNA barcoding analysis, the sequence is 96.92% identic with the sequence of T. setosus in GenBank. The phylogenetic tree was reconstructed with neighbour-joining methods and 1000 replication bootstrap, show the clade grouping based on the similarity and genetic distance of the species. The sequence data is vital for species identification fast and accurately.    Identifikasi morfologi dan genetik menjadi bagian penting dari setiap studi biologi maupun ekologi, degradasi lingkungan, faktor fisik-kimia lingkungan dan pemanfaatan gastropoda secara terus menerus akan mempengaruhi penyebaran, penurunan populasi, karakteristik morfologi dan juga karakter molekuler spesies. Penelitian ini bertujuan untuk menganalisis pola pertumbuhan dan karakter molekuler Turbo setosus. Variabel yang diukur adalah berat total dan panjang total serta identifikasi molekuler dengan menggunakan gen sitokrom oksidase I. Pola pertumbuhan T. setosus adalah allometrik negatif yang berarti pertambahan berat lebih lambat dari pertambahan panjang. Hasil identifikasi dengan DNA barcoding diperoleh spesies T. setosus dengan panjang sekuen DNA 650 bp. Rekonstruksi filogenetik dengan metode Neighbor-Joining boostrap 1000x memperlihatkan pengelompokan sekuen berdasarkan kimiripan dan jarak genetik antar spesies. penting dalam identifikasi spesies secara cepat, tepat dan akurat.
Konservasi Genetik Ikan Kakap Putih (Lates calcarifer, Bloch, 1790) Melalui Pendekatan DNA Barcoding dan Analisis Filogenetik di Sungai Kumbe Merauke Papua Dandi Saleky; Muhammad Dailami
Jurnal Kelautan Tropis Vol 24, No 2 (2021): JURNAL KELAUTAN TROPIS
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jkt.v24i2.10760

Abstract

Genetic data is very important as the basis for fisheries management and conservation related to connectivity between regions and population structure. White snapper Fish is one of the fish that has high economic value which is utilized either by its meat or by its swim bladder. This research was aimed to identify the species of white snapper fish were collected from the Kumbe River, Merauke Regency, Papua using the Cytochrome Oxidase I gene. The results shows that this sample is a species of Lates calcarifer, Bloch, 1790 with 100% similarity. The haplotype of white snapper fish from Merauke has similarities with the haplotype from Australia, Malaysia and China, this indicating that there is gene flow and connectivity among those locations. The phylogenetic tree explains the grouping of species based on genetic distance and the level of DNA Sequences similarities. Molecular approach can be used in the management and conservation of fish with high economic value.
Genetic analisys of cytochrome oxidase sub unit 1 gene fragment from Cirrhilabrus cf. ryukyuensis (Labridae) from Cenderawasih Bay and Raja Ampat Muhammad Dailami; Darma Santi; . Murtihapsari; Hermawaty Abubakar; Abdul Hamid A. Toha
Jurnal Iktiologi Indonesia Vol 18 No 3 (2018): October 2018
Publisher : Masyarakat Iktiologi Indonesia (Indonesian Ichthyological Society)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32491/jii.v18i3.347

Abstract

Cirrhilabrus cf. ryukyuensis from Cenderawasih Bay and Raja Ampat have different colormorphs with Cirrhilabrus ryukyuensis. This study was conducted to determine the phylogenetic relationship, evolution and genetic diversity of Cirrhilabrus cf. ryukyuensis based on Cytochrome oxidase sub unit 1 (COI) gene. Mitochondrial DNA extracted by using chelex 10%. FISH-BCH and BCL primers were used to amplify COI gene fragment and sequencing. Data analysis conducted by using software Sequencher 4.1 and MEGA 5. COI genes from six samples of C. cf rykyuensis from Cenderawasih Bay and Raja Ampat have total 613 base pairs. The average compositions of nucleotides are T 32.8%, C 26.3%, A 23.2% and G 17.7%. There is six positions of polymorphism that caused by transition. Conversion of nucleotides to amino acid sequence resulted in 204 amino acid with the same sequence. The phylogenetic tree from six sample showed that all in one clade, but different clade from Cirrhilabrus cyanopleura from GenBank Abstrak Cirrhilabrus cf. ryukyuensis asal Teluk Cenderawasih dan Raja Ampat secara morfologi memiliki perbedaan warna dengan Cirrhilabrus ryukyuensis. Penelitian ini bertujuan menentukan hubungan filogenetik, evolusi, dan keragaman genetik Cirrhilabrus cf. ryukyuensis berdasarkan gen Sitokrom Oksidase sub Unit I (COI). Genom DNA mitokondria diekstrak menggunakan larutan chelex 10%. Primer FISH-BCH dan BCL digunakan untuk mengamplifikasi fragmen Gen COI dan sekuensing. Analisis data dilakukan dengan menggunakan perangkat lunak Sequencher 4.1 dan MEGA 5. Gen COI dari enam sampel C. cf. rykyuensis asal Teluk Cenderawasih dan Raja Ampat, memiliki panjang basa men-capai 613 bp. Komposisi rata-rata nukleotida T 32,8%, C 26,3%, A 23,2% dan G 17,7%. Terdapat enam posisi poli-morfisme yang kesemuanya disebabkan oleh mutasi transition. Hasil penerjemahan nukleotida, diperoleh asam amino dengan panjang 204 asam amino dengan urutan yang sama. Pohon filogenetik menunjukkan keenam sampel berada dalam satu clade yang sama dan berbeda dari clade Cirrhilabrus cyanopleura data Gene Bank.
Sizing and scarring of whale shark (Rhincodon typus Smith, 1828) in the Cenderawasih Bay National Park Yusup A Jentewo; Roni Bawole; Tresia S Tururaja; Mudjirahayu Mudjirahayu; Zeth Parinding; Hendrikus R Siga; Muhammad Dailami; Abdul Hamid A Toha
Jurnal Iktiologi Indonesia Vol 21 No 3 (2021): October 2021
Publisher : Masyarakat Iktiologi Indonesia (Indonesian Ichthyological Society)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32491/jii.v21i3.587

Abstract

This study aims to determine the total length and scar condition of the body of whale sharks (Rhincodon typus) in Cendrawasih Bay National Park (TNTC), Papua-Indonesia. Photo-identification was used to identify individuals of the whale shark R. typus based on spot patterns behind the last gill slit of each individual. Photo-identification was also used to determine the scar of the whale shark. The total length of whale sharks were estimated based on the length of a snorkeller (assumed to be 1.6 m) swimming alongside the whale shark. We identified 21 individuals of R. typus. Of these 21 individuals, 14 were new sightings and seven were re-sightings that have been recorded in the previous photo collection database. R. typus ranged in size from 2 to 5 m total length (average 3.78 m, ±0,86, N= 21). Based on their size, all individuals of whale shark were categorized as juvenile. 52% of R. typus identified had scars and 38 % were not and 10% were unknown. The majority of whale sharks had amputation (12 individuals) and abrasion (7 individuals) scars. Scars occurred most often on the caudal fin and dorsal fin, five and four individuals respectively. This information is useful for understanding potential threats and designing better management programmes for R. typus conservation in TNTC. Abstrak Penelitian ini bertujuan untuk menganalisis panjang total dan kondisi luka hiu paus (Rhincodon typus) di Taman Nasional Teluk Cendrawasih (TNTC), Papua-Indonesia. Identifikasi foto digunakan untuk menentukan identitas individu hiu paus berdasarkan pola bintik di balik celah insang terakhir masing-masing individu. Identifikasi juga menggunakan foto berdasarkan luka hiu paus. Panjang tubuh total hiu paus diperkirakan berdasarkan panjang seorang perenang snorkel (diasumsikan 1,6 m) yang berenang bersama hiu paus. Kami mengidentifikasi 21 individu hiu paus, 14 individu diantaranya adalah hiu paus baru, sedangkan tujuh individu lainnya merupakan hiu paus yang pernah tercatat dalam database koleksi foto sebelumnya. Hiu paus berukuran panjang total 2 sampai 5 m (rata-rata 3,78 m, ± 0,86, N = 21). Berdasarkan ukurannya, semua individu hiu paus termasuk dalam kategori yuwana. Sebanyak 52% dari hiu paus yang diidentifikasi memiliki luka, 38% tidak memiliki luka dan 10% tidak teridentifikasi. Mayoritas hiu paus memiliki bekas luka potong (12 individu) dan luka lecet (tujuh individu). Lokasi luka paling sering terjadi pada sirip ekor dan sirip punggung, masing-masing lima dan empat individu. Informasi ini berguna untuk memahami potensi ancaman dan untuk merancang program pengelolaan yang lebih baik untuk konservasi R. typus di TNTC.
Co-Authors Abdul Hamid A. Toha Abraham Welliam Manumpil Agus Mohammad Hikam Aji Wahyu Anggoro Ambariyanto Ambariyanto Andrianus Sembiring Aradea Bujana Kusuma Asus Maizar Suryanto H Aulia Rahmawati Buana Insan Kamil Christopher P. Meyer Condro Puspo Nugroho Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Dandi Saleky Darma Santi Dean Rama Prayoga Delvira Riska Ananta Dewa Gede Raka Wiadnya Diah Permata Wijayanti Dodi Safari Dyah Kinasih Wuragil EDY H.P. MELMAMBESSY Eka Maya Kurniasih Elsa Syafi’ul Umma Febriyani Eka Supriatin Febriyani Eka Supriyatin Fitri Nur Azizah Hardoko Hardoko Hardoko Hardoko Hariati, Anik Martinah Heder Djamaludin Hendrikus R Siga Hermawaty Abubakar I MADE ARTIKA Indria Graha Hayuningtyas Isma Isma Jemmy Manan Lalu Panji Imam Agamawan Maftuch Maftuch Marius Agustinus Welliken Mirza Dikari Kusrini Mohammad Sholeh Uluwwi Mudjirahayu Mudjirahayu Muhammad Fakhri Muhammad Musa Murtihapsari, Murtihapsari Nasrullah Bai Arifin Ni Kadek Dita Cahyani Ni Putu Dian Pertiwi Novaldo Yuri Muhammad Nurul Jadid Mubarokati Putri Nur Azizah Reny Sianturi Roni Bawole Rosa D. Pangaribuan Simon P.O Leatemia Sri Andayani Supriatin, Febriyani Eka Surya Dewa Ramadhan Thomas F. Pattiasina Tresia S Tururaja Tristany Brighton Jorghi Vivi Nurhadianty Vivi Nurhadianty, Vivi Yenny Risjani Yuni Widyawati Yuni Widyawati Yusup A Jentewo Zeth Parinding